{"entity": "publications", "timestamp": "2026-08-12T17:48:36.223Z", "year": "2013", "links": {"self": {"href": "https://publications.scilifelab.se/publications/2013.json"}, "display": {"href": "https://publications.scilifelab.se/publications/2013"}}, "publications_count": 319, "full": true, "publications": [{"entity": "publication", "iuid": "b695a1f42a0f4417b066ba2e33a3d879", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b695a1f42a0f4417b066ba2e33a3d879.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b695a1f42a0f4417b066ba2e33a3d879"}}, "title": "Structure-activity relationships of synthetic cordycepin analogues as experimental therapeutics for African trypanosomiasis.", "authors": [{"family": "Vodnala", "given": "Suman K", "initials": "SK"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Yeheskieli", "given": "Esther", "initials": "E"}, {"family": "Sj\u00f6berg", "given": "Birger", "initials": "B"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Olivera", "given": "Gabriela C", "initials": "GC"}, {"family": "Eze", "given": "Anthonius A", "initials": "AA"}, {"family": "de Koning", "given": "Harry P", "initials": "HP"}, {"family": "Hammarstr\u00f6m", "given": "Lars G J", "initials": "LG"}, {"family": "Rottenberg", "given": "Martin E", "initials": "ME"}], "type": "journal article", "published": "2013-12-27", "journal": {"volume": "56", "issn": "1520-4804", "issue": "24", "pages": "9861-9873", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": "Novel methods for treatment of African trypanosomiasis, caused by infection with Trypanosoma brucei are needed. Cordycepin (3'-deoxyadenosine, 1a) is a powerful trypanocidal compound in vitro but is ineffective in vivo because of rapid metabolic degradation by adenosine deaminase (ADA). We elucidated the structural moieties of cordycepin required for trypanocidal activity and designed analogues that retained trypanotoxicity while gaining resistance to ADA-mediated metabolism. 2-Fluorocordycepin (2-fluoro-3'-deoxyadenosine, 1b) was identified as a selective, potent, and ADA-resistant trypanocidal compound that cured T. brucei infection in mice. Compound 1b is transported through the high affinity TbAT1/P2 adenosine transporter and is a substrate of T. b. brucei adenosine kinase. 1b has good preclinical properties suitable for an oral drug, albeit a relatively short plasma half-life. We present a rapid and efficient synthesis of 2-halogenated cordycepins, also useful synthons for the development of additional novel C2-substituted 3'-deoxyadenosine analogues to be evaluated in development of experimental therapeutics.", "doi": "10.1021/jm401530a", "pmid": "24283924", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": "Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)\r\nADME of Therapeutics (UDOPP)", "created": "2017-05-04T14:56:48.005Z", "modified": "2025-10-17T13:04:30.196Z"}, {"entity": "publication", "iuid": "1e4ae076b4fa47ce8bcfb0847b5c7ba4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e4ae076b4fa47ce8bcfb0847b5c7ba4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e4ae076b4fa47ce8bcfb0847b5c7ba4"}}, "title": "Association of STAT4 polymorphism with severe renal insufficiency in lupus nephritis.", "authors": [{"family": "Bolin", "given": "Karin", "initials": "K"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Zickert", "given": "Agneta", "initials": "A"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}], "type": "clinical trial", "published": "2013-12-27", "journal": {"volume": "8", "issn": "1932-6203", "issue": "12", "pages": "e84450", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Lupus nephritis is a cause of significant morbidity in systemic lupus erythematosus (SLE) and its genetic background has not been completely clarified. The aim of this investigation was to analyze single nucleotide polymorphisms (SNPs) for association with lupus nephritis, its severe form proliferative nephritis and renal outcome, in two Swedish cohorts. Cohort I (n = 567 SLE cases, n = 512 controls) was previously genotyped for 5676 SNPs and cohort II (n = 145 SLE cases, n = 619 controls) was genotyped for SNPs in STAT4, IRF5, TNIP1 and BLK. Case-control and case-only association analyses for patients with lupus nephritis, proliferative nephritis and severe renal insufficiency were performed. In the case-control analysis of cohort I, four highly linked SNPs in STAT4 were associated with lupus nephritis with genome wide significance with p = 3.7 \u00d7 10(-9), OR 2.20 for the best SNP rs11889341. Strong signals of association between IRF5 and an HLA-DR3 SNP marker were also detected in the lupus nephritis case versus healthy control analysis (p <0.0001). An additional six genes showed an association with lupus nephritis with p <0.001 (PMS2, TNIP1, CARD11, ITGAM, BLK and IRAK1). In the case-only meta-analysis of the two cohorts, the STAT4 SNP rs7582694 was associated with severe renal insufficiency with p = 1.6 \u00d7 10(-3) and OR 2.22. We conclude that genetic variations in STAT4 predispose to lupus nephritis and a worse outcome with severe renal insufficiency.", "doi": "10.1371/journal.pone.0084450", "pmid": "24386384", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-14730"}, {"db": "pmc", "key": "PMC3873995"}], "notes": [], "created": "2017-05-04T15:01:27.367Z", "modified": "2021-07-07T15:11:02.307Z"}, {"entity": "publication", "iuid": "e2c12498a4ee40849faac3f32a0dfe51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2c12498a4ee40849faac3f32a0dfe51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2c12498a4ee40849faac3f32a0dfe51"}}, "title": "Profiling post-centrifugation delay of serum and plasma with antibody bead arrays.", "authors": [{"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Tybring", "given": "Gunnel", "initials": "G"}, {"family": "Divers", "given": "Mark", "initials": "M"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "clinical trial", "published": "2013-12-16", "journal": {"volume": "95", "issn": "1876-7737", "issue": null, "pages": "46-54", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "Several biobanking initiatives have emerged to create extensive collections of specimen for biomedical studies and various analytical platforms. An affinity proteomic analysis with antibody suspension bead arrays was conducted to investigate the influence of the pre-analytical time and temperature conditions on blood derived samples. Serum and EDTA plasma prepared from 16 individuals was centrifuged and aliquots were kept either at 4\u00b0C or in ambient temperature for 1h and up to 36h prior to first storage. Multiplexed protein profiles of post-centrifugation delay were generated in 384 biotinylated samples using 373 antibodies that targeted 343 unique proteins. Very few profiles were observed as significantly altered by the studied temperature and time intervals. Single binder and sandwich assays revealed decreasing levels of caldesmon 1 (CALD1) related to EDTA standard tubes and prolonged post-centrifugation delay of 36h. Indications from changes in CALD1 levels require further confirmation in independent material, but the current data suggests that samples should preferentially be frozen during the day of collection when to be profiled with antibody arrays selected for this study.\r\n\r\nAffinity-based profiling of serum and plasma by microarray assays can provide unique opportunities for the discovery of biomarkers. It is though often not known how differences in sample handling after collection influence the downstream analysis. By profiling three types of blood preparations for alterations in protein profiles with respect to time and temperature post centrifugation, we addressed an important component in the analysis and of such specimen. We believe that this analysis adds valuable information to be considered when biobanking blood derived samples. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.", "doi": "10.1016/j.jprot.2013.04.020", "pmid": "23631827", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1874-3919(13)00209-1"}], "notes": [], "created": "2017-05-04T14:55:37.485Z", "modified": "2021-07-08T13:44:33.695Z"}, {"entity": "publication", "iuid": "d757e4ec2c9645bf9b2e900d4b22d853", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d757e4ec2c9645bf9b2e900d4b22d853.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d757e4ec2c9645bf9b2e900d4b22d853"}}, "title": "Automated quality control system for LC-SRM setups.", "authors": [{"family": "Teleman", "given": "Johan", "initials": "J"}, {"family": "Waldemarson", "given": "Sofia", "initials": "S"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2013-12-16", "journal": {"volume": "95", "issn": "1876-7737", "issue": null, "pages": "77-83", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "Selected reaction monitoring (SRM) is emerging as a standard tool for high-throughput protein quantification. For reliable and reproducible SRM protein quantification it is essential that system performance is stable. We present here a quality control workflow that is based on repeated analysis of a standard sample to allow insight into the stability of the key properties of a SRM setup. This is supported by automated software to monitor system performance and display information like signal intensities and retention time stability over time, and alert upon deviations from expected metrics. Utilising the software to evaluate 407 repeated injections of a standard sample during half a year, outliers in relative peptide signal intensities and relative peptide fragment ratios are identified, indicating the need for instrument maintenance. We therefore believe that the software could be a vital and powerful tool for any lab regularly performing SRM, increasing the reliability and quality of the SRM platform.\n\nSelected reaction monitoring (SRM) mass spectrometry is becoming established as a standard technique for accurate protein quantification. However, to achieve the required quantification reproducibility of the liquid chromatography (LC)-SRM setup, system performance needs to be monitored over time. Here we introduce a workflow with associated software to enable automated monitoring of LC-SRM setups. We believe that usage of the presented concepts will further strengthen the role of SRM as a reliable tool for protein quantification. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.", "doi": "10.1016/j.jprot.2013.03.029", "pmid": "23584149", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S1874-3919(13)00176-0"}], "notes": [], "created": "2017-05-04T14:56:24.885Z", "modified": "2020-01-21T13:53:20.898Z"}, {"entity": "publication", "iuid": "efeedfd96084458ca410cc81b55165ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/efeedfd96084458ca410cc81b55165ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/efeedfd96084458ca410cc81b55165ec"}}, "title": "Combining genetic mapping with genome-wide expression in experimental autoimmune encephalomyelitis highlights a gene network enriched for T cell functions and candidate genes regulating autoimmunity.", "authors": [{"family": "Thessen Hedreul", "given": "Melanie", "initials": "M"}, {"family": "M\u00f6ller", "given": "Steffen", "initials": "S"}, {"family": "Stridh", "given": "Pernilla", "initials": "P"}, {"family": "Gupta", "given": "Yask", "initials": "Y"}, {"family": "Gillett", "given": "Alan", "initials": "A"}, {"family": "Daniel Beyeen", "given": "Amennai", "initials": "A"}, {"family": "\u00d6ckinger", "given": "Johan", "initials": "J"}, {"family": "Flytzani", "given": "Sevasti", "initials": "S"}, {"family": "Diez", "given": "Margarita", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}], "type": "journal article", "published": "2013-12-15", "journal": {"volume": "22", "issn": "1460-2083", "issue": "24", "pages": "4952-4966", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "The experimental autoimmune encephalomyelitis (EAE) is an autoimmune disease of the central nervous system commonly used to study multiple sclerosis (MS). We combined clinical EAE phenotypes with genome-wide expression profiling in spleens from 150 backcross rats between susceptible DA and resistant PVG rat strains during the chronic EAE phase. This enabled correlation of transcripts with genotypes, other transcripts and clinical EAE phenotypes and implicated potential genetic causes and pathways in EAE. We detected 2285 expression quantitative trait loci (eQTLs). Sixty out of 599 cis-eQTLs overlapped well-known EAE QTLs and constitute positional candidate genes, including Ifit1 (Eae7), Atg7 (Eae20-22), Klrc3 (eEae22) and Mfsd4 (Eae17). A trans-eQTL that overlaps Eae23a regulated a large number of small RNAs and implicates a master regulator of transcription. We defined several disease-correlated networks enriched for pathways involved in cell-mediated immunity. They include C-type lectins, G protein coupled receptors, mitogen-activated protein kinases, transmembrane proteins, suppressors of transcription (Jundp2 and Nr1d1) and STAT transcription factors (Stat4) involved in interferon signaling. The most significant network was enriched for T cell functions, similar to genetic findings in MS, and revealed both established and novel gene interactions. Transcripts in the network have been associated with T cell proliferation and differentiation, the TCR signaling and regulation of regulatory T cells. A number of network genes and their family members have been associated with MS and/or other autoimmune diseases. Combining disease and genome-wide expression phenotypes provides a link between disease risk genes and distinct molecular pathways that are dysregulated during chronic autoimmune inflammation.", "doi": "10.1093/hmg/ddt343", "pmid": "23900079", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "ddt343"}, {"db": "pmc", "key": "PMC3836475"}], "notes": [], "created": "2017-05-04T15:03:15.069Z", "modified": "2021-07-06T15:16:00.395Z"}, {"entity": "publication", "iuid": "c6dbbaf52b434306af5050f32ed8bf8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6dbbaf52b434306af5050f32ed8bf8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6dbbaf52b434306af5050f32ed8bf8d"}}, "title": "Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B.", "authors": [{"family": "Karlsson", "given": "Elinor K", "initials": "EK"}, {"family": "Sigurdsson", "given": "Snaevar", "initials": "S"}, {"family": "Ivansson", "given": "Emma", "initials": "E"}, {"family": "Thomas", "given": "Rachael", "initials": "R"}, {"family": "Elvers", "given": "Ingegerd", "initials": "I"}, {"family": "Wright", "given": "Jason", "initials": "J"}, {"family": "Howald", "given": "Cedric", "initials": "C"}, {"family": "Tonomura", "given": "Noriko", "initials": "N"}, {"family": "Perloski", "given": "Michele", "initials": "M"}, {"family": "Swofford", "given": "Ross", "initials": "R"}, {"family": "Biagi", "given": "Tara", "initials": "T"}, {"family": "Fryc", "given": "Sarah", "initials": "S"}, {"family": "Anderson", "given": "Nathan", "initials": "N"}, {"family": "Courtay-Cahen", "given": "Celine", "initials": "C"}, {"family": "Youell", "given": "Lisa", "initials": "L"}, {"family": "Ricketts", "given": "Sally L", "initials": "SL"}, {"family": "Mandlebaum", "given": "Sarah", "initials": "S"}, {"family": "Rivera", "given": "Patricio", "initials": "P"}, {"family": "von Euler", "given": "Henrik", "initials": "H"}, {"family": "Kisseberth", "given": "William C", "initials": "WC"}, {"family": "London", "given": "Cheryl A", "initials": "CA"}, {"family": "Lander", "given": "Eric S", "initials": "ES"}, {"family": "Couto", "given": "Guillermo", "initials": "G"}, {"family": "Comstock", "given": "Kenine", "initials": "K"}, {"family": "Starkey", "given": "Mike P", "initials": "MP"}, {"family": "Modiano", "given": "Jaime F", "initials": "JF"}, {"family": "Breen", "given": "Matthew", "initials": "M"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2013-12-12", "journal": {"volume": "14", "issn": "1474-760X", "issue": "12", "pages": "R132", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "Canine osteosarcoma is clinically nearly identical to the human disease, but is common and highly heritable, making genetic dissection feasible.\r\n\r\nThrough genome-wide association analyses in three breeds (greyhounds, Rottweilers, and Irish wolfhounds), we identify 33 inherited risk loci explaining 55% to 85% of phenotype variance in each breed. The greyhound locus exhibiting the strongest association, located 150 kilobases upstream of the genes CDKN2A/B, is also the most rearranged locus in canine osteosarcoma tumors. The top germline candidate variant is found at a >90% frequency in Rottweilers and Irish wolfhounds, and alters an evolutionarily constrained element that we show has strong enhancer activity in human osteosarcoma cells. In all three breeds, osteosarcoma-associated loci and regions of reduced heterozygosity are enriched for genes in pathways connected to bone differentiation and growth. Several pathways, including one of genes regulated by miR124, are also enriched for somatic copy-number changes in tumors.\r\n\r\nMapping a complex cancer in multiple dog breeds reveals a polygenic spectrum of germline risk factors pointing to specific pathways as drivers of disease.", "doi": "10.1186/gb-2013-14-12-r132", "pmid": "24330828", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "gb-2013-14-12-r132"}, {"db": "pmc", "key": "PMC4053774"}, {"db": "GEO", "key": "GSE52147"}], "notes": [], "created": "2017-05-04T14:57:55.409Z", "modified": "2021-06-16T10:19:26.628Z"}, {"entity": "publication", "iuid": "c43ed1589593433d9bbce84df56b6c35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c43ed1589593433d9bbce84df56b6c35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c43ed1589593433d9bbce84df56b6c35"}}, "title": "Chemical probes to study ADP-ribosylation: synthesis and biochemical evaluation of inhibitors of the human ADP-ribosyltransferase ARTD3/PARP3.", "authors": [{"family": "Lindgren", "given": "Anders E G", "initials": "AE"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Ekblad", "given": "Torun", "initials": "T"}, {"family": "Spjut", "given": "Sara", "initials": "S"}, {"family": "Thorsell", "given": "Ann-Gerd", "initials": "AG"}, {"family": "Andersson", "given": "C David", "initials": "CD"}, {"family": "Nhan", "given": "Ton Tong", "initials": "TT"}, {"family": "Hellsten", "given": "Victor", "initials": "V"}, {"family": "Weigelt", "given": "Johan", "initials": "J"}, {"family": "Linusson", "given": "Anna", "initials": "A"}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2013-12-12", "journal": {"volume": "56", "issn": "1520-4804", "issue": "23", "pages": "9556-9568", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": "The racemic 3-(4-oxo-3,4-dihydroquinazolin-2-yl)-N-[1-(pyridin-2-yl)ethyl]propanamide, 1, has previously been identified as a potent but unselective inhibitor of diphtheria toxin-like ADP-ribosyltransferase 3 (ARTD3). Herein we describe synthesis and evaluation of 55 compounds in this class. It was found that the stereochemistry is of great importance for both selectivity and potency and that substituents on the phenyl ring resulted in poor solubility. Certain variations at the meso position were tolerated and caused a large shift in the binding pose. Changes to the ethylene linker that connects the quinazolinone to the amide were also investigated but proved detrimental to binding. By combination of synthetic organic chemistry and structure-based design, two selective inhibitors of ARTD3 were discovered.", "doi": "10.1021/jm401394u", "pmid": "24188023", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "PDB", "key": "4L6Z"}, {"db": "PDB", "key": "4L70"}, {"db": "PDB", "key": "4L7L"}, {"db": "PDB", "key": "4L7N"}, {"db": "PDB", "key": "4L7O"}, {"db": "PDB", "key": "4L7P"}, {"db": "PDB", "key": "4L7R"}, {"db": "PDB", "key": "4L7U"}], "notes": [], "created": "2017-05-04T15:03:47.893Z", "modified": "2017-09-06T11:42:09.315Z"}, {"entity": "publication", "iuid": "1d3d7629f89949b7a615689e384b642a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d3d7629f89949b7a615689e384b642a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d3d7629f89949b7a615689e384b642a"}}, "title": "Linkage analysis in familial non-Lynch syndrome colorectal cancer families from Sweden.", "authors": [{"family": "Kontham", "given": "Vinaykumar", "initials": "V"}, {"family": "von Holst", "given": "Susanna", "initials": "S"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "clinical trial", "published": "2013-12-11", "journal": {"volume": "8", "issn": "1932-6203", "issue": "12", "pages": "e83936", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Family history is a major risk factor for colorectal cancer and many families segregate the disease as a seemingly monogenic trait. A minority of familial colorectal cancer could be explained by known monogenic genes and genetic loci. Familial polyposis and Lynch syndrome are two syndromes where the predisposing genes are known but numerous families have been tested without finding the predisposing gene. We performed a genome wide linkage analysis in 121 colorectal families with an increased risk of colorectal cancer. The families were ascertained from the department of clinical genetics at the Karolinska University Hospital in Stockholm, Sweden and were considered negative for Familial Polyposis and Lynch syndrome. In total 600 subjects were genotyped using single nucleotide polymorphism array chips. Parametric- and non-parametric linkage analyses were computed using MERLIN in all and subsets of families. No statistically significant result was seen, however, there were suggestive positive HLODs above two in parametric linkage analysis. This was observed in a recessive model for high-risk families, at locus 9q31.1 (HLOD=2.2, rs1338121) and for moderate-risk families, at locus Xp22.33 (LOD=2.2 and HLOD=2.5, rs2306737). Using families with early-onset, recessive analysis suggested one locus on 4p16.3 (LOD=2.2, rs920683) and one on 17p13.2 (LOD/HLOD=2.0, rs884250). No NPL score above two was seen for any of the families. Our linkage study provided additional support for the previously suggested region on chromosome 9 and suggested additional loci to be involved in colorectal cancer risk. Sequencing of genes in the regions will be done in future studies.", "doi": "10.1371/journal.pone.0083936", "pmid": "24349560", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-40988"}, {"db": "pmc", "key": "PMC3859667"}], "notes": [], "created": "2017-05-04T14:56:27.482Z", "modified": "2020-01-21T13:56:16.717Z"}, {"entity": "publication", "iuid": "bc874f0af2d147b9bf8a435cf8fd65c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc874f0af2d147b9bf8a435cf8fd65c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc874f0af2d147b9bf8a435cf8fd65c2"}}, "title": "Utilizing twins as controls for non-twin case-materials in genome wide association studies.", "authors": [{"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Ortega-Alonso", "given": "Alfredo", "initials": "A"}, {"family": "Havulinna", "given": "Aki", "initials": "A"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}], "type": "journal article", "published": "2013-12-10", "journal": {"volume": "8", "issn": "1932-6203", "issue": "12", "pages": "e83101", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Twin registries around the globe have collected DNA samples from large numbers of monozygotic and dizygotic twins. The twin sample collections are frequently used as controls in disease-specific studies together with non-twins. This approach is unbiased under the hypothesis that twins and singletons are comparable in terms of allele frequencies; i.e. there are no genetic variants associated with being a twin per se. To test this hypothesis we performed a genome-wide association study comparing the allele frequency of 572,352 single nucleotide polymorphisms (SNPs) in 1,413 monozygotic (MZ) and 5,451 dizygotic (DZ) twins with 3,720 healthy singletons. Twins and singletons have been genotyped using the same platform. SNPs showing association with being a twin at P-value < 1 \u00d7 10(-5) were selected for replication analysis in 1,492 twins (463 MZ and 1,029 DZ) and 1,880 singletons from Finland. No SNPs reached genome-wide significance (P-value < 5 \u00d7 10(-8)) in the main analysis combining MZ and DZ twins. In a secondary analysis including only DZ twins two SNPs (rs2033541 close to ADAMTSL1 and rs4149283 close to ABCA1)\u00a0were genome-wide significant after meta-analysis with the Finnish population. The estimated proportion of variance on the liability scale explained by all SNPs was 0.08 (P-value=0.003) when MZ and DZ were considered together and smaller for MZ (0.06, P-value=0.10) compared to DZ (0.09, P-value=0.003) when analyzed separately. In conclusion, twins and singletons can be used in genetic studies together with general population samples without introducing large bias. Further research is needed to explore genetic variances associated with DZ twinning.", "doi": "10.1371/journal.pone.0083101", "pmid": "24340086", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-27564"}, {"db": "pmc", "key": "PMC3858365"}], "notes": [], "created": "2017-05-04T14:58:14.943Z", "modified": "2020-01-21T13:56:08.751Z"}, {"entity": "publication", "iuid": "27830c7f05394bbeaadc407a6b1ce591", "links": {"self": {"href": "https://publications.scilifelab.se/publication/27830c7f05394bbeaadc407a6b1ce591.json"}, "display": {"href": "https://publications.scilifelab.se/publication/27830c7f05394bbeaadc407a6b1ce591"}}, "title": "Statistical molecular design: a tool to follow up hits from small-molecule screening.", "authors": [{"family": "Lindgren", "given": "Anders E G", "initials": "AE"}, {"family": "Larsson", "given": "Andreas", "initials": "A"}, {"family": "Linusson", "given": "Anna", "initials": "A"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2013-12-07", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "1056", "issue": null, "pages": "169-188", "issn-l": "1064-3745"}, "abstract": "In high-throughput screening (HTS) a robust assay is used to interrogate a large collection of small organic molecules in order to find compounds, hits, with a desired biological activity. The hits are then further explored by an iterative process where new compounds are designed, purchased, or synthesized, followed by an evaluation in one or more assays. Statistical molecular design (SMD) is a useful method to select a balanced, varied, and information-rich compound collection based on hits from HTS in order to create a foundation for development of optimized compounds with improved properties. In this chapter, we describe the use of SMD to explore a hit obtained from small-molecule screening.", "doi": "10.1007/978-1-62703-592-7_17", "pmid": "24306873", "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2019-11-11T10:02:23.491Z", "modified": "2025-10-17T13:04:30.224Z"}, {"entity": "publication", "iuid": "7fb2788e0424442a8beda206a5ba52a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7fb2788e0424442a8beda206a5ba52a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7fb2788e0424442a8beda206a5ba52a1"}}, "title": "Urinary prognostic biomarkers and classification of IgA nephropathy by high resolution mass spectrometry coupled with liquid chromatography.", "authors": [{"family": "Kalantari", "given": "Shiva", "initials": "S"}, {"family": "Rutishauser", "given": "Dorothea", "initials": "D"}, {"family": "Samavat", "given": "Shiva", "initials": "S"}, {"family": "Nafar", "given": "Mohsen", "initials": "M"}, {"family": "Mahmudieh", "given": "Leyla", "initials": "L"}, {"family": "Rezaei-Tavirani", "given": "Mostafa", "initials": "M"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2013-12-05", "journal": {"volume": "8", "issn": "1932-6203", "issue": "12", "pages": "e80830", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "IgA nephropathy is the most common cause of primary glomerulonephritis. There are different pathologic biopsy-based scoring systems in use, but there is no consensus among nephrologists yet regarding the best classification method. Our aim was to test urine proteomics as a non-invasive method for classification of IgA nephropathy. This aim was pursued by discovering novel prognostic protein biomarkers in urine, and linking them to pathogenesis of the disease through known signaling and metabolic pathways. 13 urine samples of the patients with biopsy-proven IgA nephropathy were analyzed via two proteomics approaches: nanoflow LC-MS/MS and GeLC-MS/MS. The results of label-free quantification were subjected to multivariate statistical analysis, which could classify patients into two groups, broadly corresponding to the primary and advance stages. The proteome classification correlated well with biopsy-based scoring systems, especially endocapillary hypercellularity score of the Oxford's classification. Differentially excreted candidate proteins were found as potential prognostic biomarkers: afamin, leucine-rich alpha-2-glycoprotein, ceruloplasmin, alpha-1-microgolbulin, hemopexin, apolipoprotein A-I, complement C3, vitamin D-binding protein, beta-2-microglobulin, and retinol-binding protein 4. Pathway analysis suggested impairment of Extra Cellular Matrix (ECM)-Receptor Interaction pathways as well as activation of complement and coagulation pathway in progression of IgA nephropathy.", "doi": "10.1371/journal.pone.0080830", "pmid": "24339887", "labels": {"Advanced Mass Spectrometry Proteomics": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-33465"}, {"db": "pmc", "key": "PMC3855054"}], "notes": [], "created": "2017-05-04T15:02:44.272Z", "modified": "2021-07-08T08:58:46.799Z"}, {"entity": "publication", "iuid": "4e0d648beb724ac882611eb7ebb736ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e0d648beb724ac882611eb7ebb736ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e0d648beb724ac882611eb7ebb736ef"}}, "title": "Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment.", "authors": [{"family": "Berglund", "given": "Eva C", "initials": "EC"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Hayat", "given": "Shahina", "initials": "S"}, {"family": "\u00d6vern\u00e4s", "given": "Elin", "initials": "E"}, {"family": "Henriksson", "given": "Niklas", "initials": "N"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Wahlberg", "given": "Per", "initials": "P"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2013-12-05", "journal": {"volume": "14", "issn": "1471-2164", "issue": null, "pages": "856", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Target enrichment and resequencing is a widely used approach for identification of cancer genes and genetic variants associated with diseases. Although cost effective compared to whole genome sequencing, analysis of many samples constitutes a significant cost, which could be reduced by pooling samples before capture. Another limitation to the number of cancer samples that can be analyzed is often the amount of available tumor DNA. We evaluated the performance of whole genome amplified DNA and the power to detect subclonal somatic single nucleotide variants in non-indexed pools of cancer samples using the HaloPlex technology for target enrichment and next generation sequencing.\n\nWe captured a set of 1528 putative somatic single nucleotide variants and germline SNPs, which were identified by whole genome sequencing, with the HaloPlex technology and sequenced to a depth of 792-1752. We found that the allele fractions of the analyzed variants are well preserved during whole genome amplification and that capture specificity or variant calling is not affected. We detected a large majority of the known single nucleotide variants present uniquely in one sample with allele fractions as low as 0.1 in non-indexed pools of up to ten samples. We also identified and experimentally validated six novel variants in the samples included in the pools.\n\nOur work demonstrates that whole genome amplified DNA can be used for target enrichment equally well as genomic DNA and that accurate variant detection is possible in non-indexed pools of cancer samples. These findings show that analysis of a large number of samples is feasible at low cost, even when only small amounts of DNA is available, and thereby significantly increases the chances of indentifying recurrent mutations in cancer samples.", "doi": "10.1186/1471-2164-14-856", "pmid": "24314227", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-14-856"}, {"db": "pmc", "key": "PMC4046713"}], "notes": [], "created": "2017-05-04T14:57:49.698Z", "modified": "2021-07-07T15:11:02.446Z"}, {"entity": "publication", "iuid": "cb0392808b7d462a8d5675af3413c62d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb0392808b7d462a8d5675af3413c62d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb0392808b7d462a8d5675af3413c62d"}}, "title": "The resveratrol tetramer (-)-hopeaphenol inhibits type III secretion in the gram-negative pathogens Yersinia pseudotuberculosis and Pseudomonas aeruginosa.", "authors": [{"family": "Zetterstr\u00f6m", "given": "Caroline E", "initials": "CE"}, {"family": "Hasselgren", "given": "Jenny", "initials": "J"}, {"family": "Salin", "given": "Olli", "initials": "O"}, {"family": "Davis", "given": "Rohan A", "initials": "RA"}, {"family": "Quinn", "given": "Ronald J", "initials": "RJ"}, {"family": "Sundin", "given": "Charlotta", "initials": "C"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2013-12-04", "journal": {"volume": "8", "issn": "1932-6203", "issue": "12", "pages": "e81969", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Society faces huge challenges, as a large number of bacteria have developed resistance towards many or all of the antibiotics currently available. Novel strategies that can help solve this problem are urgently needed. One such strategy is to target bacterial virulence, the ability to cause disease e.g., by inhibition of type III secretion systems (T3SSs) utilized by many clinically relevant gram-negative pathogens. Many of the antibiotics used today originate from natural sources. In contrast, most virulence-blocking compounds towards the T3SS identified so far are small organic molecules. A recent high-throughput screening of a prefractionated natural product library identified the resveratrol tetramer (-)-hopeaphenol as an inhibitor of the T3SS in Yersinia pseudotuberculosis. In this study we have investigated the virulence blocking properties of (-)-hopeaphenol in three different gram-negative bacteria. (-)-Hopeaphenol was found to have micromolar activity towards the T3SSs in Yersinia pseudotuberculosis and Pseudomonas aeruginosa in cell-based infection models. In addition (-)-hopeaphenol reduced cell entry and subsequent intracellular growth of Chlamydia trachomatis.", "doi": "10.1371/journal.pone.0081969", "pmid": "24324737", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-13-39735"}, {"db": "pmc", "key": "PMC3853165"}], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:40.324Z", "modified": "2025-10-17T13:04:30.235Z"}, {"entity": "publication", "iuid": "5777fcc31a434305bb0a6ce50470d2fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5777fcc31a434305bb0a6ce50470d2fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5777fcc31a434305bb0a6ce50470d2fa"}}, "title": "Integrated molecular portrait of non-small cell lung cancers.", "authors": [{"family": "Lazar", "given": "Vladimir", "initials": "V"}, {"family": "Suo", "given": "Chen", "initials": "C"}, {"family": "Orear", "given": "Cedric", "initials": "C"}, {"family": "van den Oord", "given": "Joost", "initials": "J"}, {"family": "Balogh", "given": "Zsofia", "initials": "Z"}, {"family": "Guegan", "given": "Justine", "initials": "J"}, {"family": "Job", "given": "Bastien", "initials": "B"}, {"family": "Meurice", "given": "Guillaume", "initials": "G"}, {"family": "Ripoche", "given": "Hugues", "initials": "H"}, {"family": "Calza", "given": "Stefano", "initials": "S"}, {"family": "Hasmats", "given": "Johanna", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Lacroix", "given": "Ludovic", "initials": "L"}, {"family": "Vielh", "given": "Philippe", "initials": "P"}, {"family": "Dufour", "given": "Fabienne", "initials": "F"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Napieralski", "given": "Rudolf", "initials": "R"}, {"family": "Eggermont", "given": "Alexander", "initials": "A"}, {"family": "Schmitt", "given": "Manfred", "initials": "M"}, {"family": "Cadranel", "given": "Jacques", "initials": "J"}, {"family": "Besse", "given": "Benjamin", "initials": "B"}, {"family": "Girard", "given": "Philippe", "initials": "P"}, {"family": "Blackhall", "given": "Fiona", "initials": "F"}, {"family": "Validire", "given": "Pierre", "initials": "P"}, {"family": "Soria", "given": "Jean-Charles", "initials": "JC"}, {"family": "Dessen", "given": "Philippe", "initials": "P"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}], "type": "journal article", "published": "2013-12-03", "journal": {"volume": "6", "issn": "1755-8794", "issue": null, "pages": "53", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "Non-small cell lung cancer (NSCLC), a leading cause of cancer deaths, represents a heterogeneous group of neoplasms, mostly comprising squamous cell carcinoma (SCC), adenocarcinoma (AC) and large-cell carcinoma (LCC). The objectives of this study were to utilize integrated genomic data including copy-number alteration, mRNA, microRNA expression and candidate-gene full sequencing data to characterize the molecular distinctions between AC and SCC.\n\nComparative genomic hybridization followed by mutational analysis, gene expression and miRNA microarray profiling were performed on 123 paired tumor and non-tumor tissue samples from patients with NSCLC.\n\nAt DNA, mRNA and miRNA levels we could identify molecular markers that discriminated significantly between the various histopathological entities of NSCLC. We identified 34 genomic clusters using aCGH data; several genes exhibited a different profile of aberrations between AC and SCC, including PIK3CA, SOX2, THPO, TP63, PDGFB genes. Gene expression profiling analysis identified SPP1, CTHRC1 and GREM1 as potential biomarkers for early diagnosis of the cancer, and SPINK1 and BMP7 to distinguish between AC and SCC in small biopsies or in blood samples. Using integrated genomics approach we found in recurrently altered regions a list of three potential driver genes, MRPS22, NDRG1 and RNF7, which were consistently over-expressed in amplified regions, had wide-spread correlation with an average of ~800 genes throughout the genome and highly associated with histological types. Using a network enrichment analysis, the targets of these potential drivers were seen to be involved in DNA replication, cell cycle, mismatch repair, p53 signalling pathway and other lung cancer related signalling pathways, and many immunological pathways. Furthermore, we also identified one potential driver miRNA hsa-miR-944.\n\nIntegrated molecular characterization of AC and SCC helped identify clinically relevant markers and potential drivers, which are recurrent and stable changes at DNA level that have functional implications at RNA level and have strong association with histological subtypes.", "doi": "10.1186/1755-8794-6-53", "pmid": "24299561", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1755-8794-6-53"}, {"db": "pmc", "key": "PMC4222074"}], "notes": [], "created": "2017-05-04T14:57:50.305Z", "modified": "2021-07-08T13:26:08.184Z"}, {"entity": "publication", "iuid": "a46ef766eefd45899dc259fcca9ece5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a46ef766eefd45899dc259fcca9ece5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a46ef766eefd45899dc259fcca9ece5e"}}, "title": "A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis.", "authors": [{"family": "Weidinger", "given": "Stephan", "initials": "S"}, {"family": "Willis-Owen", "given": "Saffron A G", "initials": "SA"}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y"}, {"family": "Baurecht", "given": "Hansj\u00f6rg", "initials": "H"}, {"family": "Morar", "given": "Nilesh", "initials": "N"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Edser", "given": "Pauline", "initials": "P"}, {"family": "Street", "given": "Teresa", "initials": "T"}, {"family": "Rodriguez", "given": "Elke", "initials": "E"}, {"family": "O'Regan", "given": "Grainne M", "initials": "GM"}, {"family": "Beattie", "given": "Paula", "initials": "P"}, {"family": "F\u00f6lster-Holst", "given": "Regina", "initials": "R"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Novak", "given": "Natalija", "initials": "N"}, {"family": "Fahy", "given": "Caoimhe M", "initials": "CM"}, {"family": "Winge", "given": "M\u00e5rten C G", "initials": "MC"}, {"family": "Kabesch", "given": "Michael", "initials": "M"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Heath", "given": "Simon", "initials": "S"}, {"family": "S\u00f6derh\u00e4ll", "given": "Cilla", "initials": "C"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Bradley", "given": "Maria", "initials": "M"}, {"family": "Lieden", "given": "Agne", "initials": "A"}, {"family": "Nordenskjold", "given": "Magnus", "initials": "M"}, {"family": "Harper", "given": "John I", "initials": "JI"}, {"family": "McLean", "given": "W H Irwin", "initials": "WH"}, {"family": "Brown", "given": "Sara J", "initials": "SJ"}, {"family": "Cookson", "given": "William O C", "initials": "WO"}, {"family": "Lathrop", "given": "G Mark", "initials": "GM"}, {"family": "Irvine", "given": "Alan D", "initials": "AD"}, {"family": "Moffatt", "given": "Miriam F", "initials": "MF"}], "type": "journal article", "published": "2013-12-01", "journal": {"volume": "22", "issn": "1460-2083", "issue": "23", "pages": "4841-4856", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Atopic dermatitis (AD) is the most common dermatological disease of childhood. Many children with AD have asthma and AD shares regions of genetic linkage with psoriasis, another chronic inflammatory skin disease. We present here a genome-wide association study (GWAS) of childhood-onset AD in 1563 European cases with known asthma status and 4054 European controls. Using Illumina genotyping followed by imputation, we generated 268 034 consensus genotypes and in excess of 2 million single nucleotide polymorphisms (SNPs) for analysis. Association signals were assessed for replication in a second panel of 2286 European cases and 3160 European controls. Four loci achieved genome-wide significance for AD and replicated consistently across all cohorts. These included the epidermal differentiation complex (EDC) on chromosome 1, the genomic region proximal to LRRC32 on chromosome 11, the RAD50/IL13 locus on chromosome 5 and the major histocompatibility complex (MHC) on chromosome 6; reflecting action of classical HLA alleles. We observed variation in the contribution towards co-morbid asthma for these regions of association. We further explored the genetic relationship between AD, asthma and psoriasis by examining previously identified susceptibility SNPs for these diseases. We found considerable overlap between AD and psoriasis together with variable coincidence between allergic rhinitis (AR) and asthma. Our results indicate that the pathogenesis of AD incorporates immune and epidermal barrier defects with combinations of specific and overlapping effects at individual loci.", "doi": "10.1093/hmg/ddt317", "pmid": "23886662", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "ddt317"}, {"db": "pmc", "key": "PMC3820131"}], "notes": [], "created": "2017-05-04T15:03:35.911Z", "modified": "2017-05-30T12:45:43.082Z"}, {"entity": "publication", "iuid": "946ff156ff6d4f3da475a7dd36b2ec55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/946ff156ff6d4f3da475a7dd36b2ec55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/946ff156ff6d4f3da475a7dd36b2ec55"}}, "title": "Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803.", "authors": [{"family": "Anfelt", "given": "Josefine", "initials": "J"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "79", "issn": "1098-5336", "issue": "23", "pages": "7419-7427", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "Cyanobacteria are emerging as promising hosts for production of advanced biofuels such as n-butanol and alkanes. However, cyanobacteria suffer from the same product inhibition problems as those that plague other microbial biofuel hosts. High concentrations of butanol severely reduce growth, and even small amounts can negatively affect metabolic processes. An understanding of how cyanobacteria are affected by their biofuel product can enable identification of engineering strategies for improving their tolerance. Here we used transcriptome sequencing (RNA-Seq) to assess the transcriptome response of Synechocystis sp. strain PCC 6803 to two concentrations of exogenous n-butanol. Approximately 80 transcripts were differentially expressed at 40 mg/liter butanol, and 280 transcripts were different at 1 g/liter butanol. Our results suggest a compromised cell membrane, impaired photosynthetic electron transport, and reduced biosynthesis. Accumulation of intracellular reactive oxygen species (ROS) scaled with butanol concentration. Using the physiology and transcriptomics data, we selected several genes for overexpression in an attempt to improve butanol tolerance. We found that overexpression of several proteins, notably, the small heat shock protein HspA, improved tolerance to butanol. Transcriptomics-guided engineering created more solvent-tolerant cyanobacteria strains that could be the foundation for a more productive biofuel host.", "doi": "10.1128/AEM.02694-13", "pmid": "24056459", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "AEM.02694-13"}, {"db": "pmc", "key": "PMC3837751"}], "notes": [], "created": "2017-05-04T14:57:48.179Z", "modified": "2021-07-08T13:44:33.438Z"}, {"entity": "publication", "iuid": "2aebfba2d6f7437a881e7bd5a0c8b561", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2aebfba2d6f7437a881e7bd5a0c8b561.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2aebfba2d6f7437a881e7bd5a0c8b561"}}, "title": "The association between plasma homocysteine and coronary heart disease is modified by the MTHFR 677C>T polymorphism.", "authors": [{"family": "Mehlig", "given": "K", "initials": "K"}, {"family": "Leander", "given": "K", "initials": "K"}, {"family": "de Faire", "given": "U", "initials": "U"}, {"family": "Nyberg", "given": "F", "initials": "F"}, {"family": "Berg", "given": "C", "initials": "C"}, {"family": "Rosengren", "given": "A", "initials": "A"}, {"family": "Bj\u00f6rck", "given": "L", "initials": "L"}, {"family": "Zetterberg", "given": "H", "initials": "H"}, {"family": "Blennow", "given": "K", "initials": "K"}, {"family": "Tognon", "given": "G", "initials": "G"}, {"family": "Tor\u00e9n", "given": "K", "initials": "K"}, {"family": "Strandhagen", "given": "E", "initials": "E"}, {"family": "Lissner", "given": "L", "initials": "L"}, {"family": "Thelle", "given": "D", "initials": "D"}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "99", "issn": "1468-201X", "issue": "23", "pages": "1761-1765", "title": "Heart", "issn-l": "1355-6037"}, "abstract": "An elevated level of total plasma homocysteine (tHcy) has been associated with risk of coronary heart disease (CHD). The level of tHcy is affected by lifestyle, in addition to genetic predisposition. The methylene tetrahydrofolate reductase (MTHFR) 677C>T polymorphism (rs1801133) is among the strongest genetic predictors of tHcy. We examined whether the association between tHcy and CHD is modified by the MTHFR 677C>T polymorphism.\n\nData from two case-control studies of first-time myocardial infarction (MI), Stockholm Heart Epidemiology Programme (SHEEP), and for MI and unstable angina, INTERGENE, were analysed in parallel.\n\nTHcy was determined in a total of 1150 cases and 1753 controls.\n\nNone.\n\nThe outcome comprised first-time MI and unstable angina, subsumed as CHD. Logistic regression was used to investigate the association between tHcy and CHD, and its modification by genotype.\n\nHigh tHcy was confirmed to be a risk factor for CHD in both studies. In SHEEP, the association between tHcy and MI was observed in MTHFR 677 C-homozygotes (OR=1.4, 95% CI 1.2 to 1.6, for a difference by 1 SD of log tHcy) and in heterozygotes (OR=1.3, 95% CI 1.1 to 1.6) but not in T-homozygotes, independent of smoking, physical activity and obesity. An effect modification of similar magnitude was observed but not statistically significant in the smaller INTERGENE study, and confirmed in a meta-analysis of both studies.\n\nTwo Swedish case-control studies showed that the association between elevated tHcy and CHD was confined to carriers of the MTHFR 677 C-allele, which could have implications for the efficiency of tHcy-lowering treatment.", "doi": "10.1136/heartjnl-2013-304460", "pmid": "24014284", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "heartjnl-2013-304460"}], "notes": [], "created": "2017-05-04T15:03:35.602Z", "modified": "2017-05-30T12:45:38.356Z"}, {"entity": "publication", "iuid": "87e3d2bb0d5442fe9c4911cc26f86f2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87e3d2bb0d5442fe9c4911cc26f86f2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87e3d2bb0d5442fe9c4911cc26f86f2f"}}, "title": "Selectivity analysis of single binder assays used in plasma protein profiling.", "authors": [{"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Johansson", "given": "Henrik", "initials": "H"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Nygren", "given": "Per-\u00c5ke", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "23-24", "pages": "3406-3410", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "The increasing availability of antibodies toward human proteins enables broad explorations of the proteomic landscape in cells, tissues, and body fluids. This includes assays with antibody suspension bead arrays that generate protein profiles of plasma samples by flow cytometer analysis. However, antibody selectivity is context dependent so it is necessary to corroborate on-target detection over off-target binding. To address this, we describe a concept to directly verify interactions from antibody-coupled beads by analysis of their eluates by Western blots and MS. We demonstrate selective antibody binding in complex samples with antibodies toward a set of chosen proteins with different abundance in plasma and serum, and illustrate the need to adjust sample and bead concentrations accordingly. The presented approach will serve as an important tool for resolving differential protein profiles from antibody arrays within plasma biomarker discoveries.", "doi": "10.1002/pmic.201300030", "pmid": "24151238", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC4265267"}], "notes": [], "created": "2017-05-04T14:55:38.987Z", "modified": "2021-07-08T13:44:33.385Z"}, {"entity": "publication", "iuid": "c4b3d70c6f7544148e5ab0eb59554e42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4b3d70c6f7544148e5ab0eb59554e42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4b3d70c6f7544148e5ab0eb59554e42"}}, "title": "Protein expansion is primarily due to indels in intrinsically disordered regions.", "authors": [{"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Sagit", "given": "Rauan", "initials": "R"}, {"family": "Sachenkova", "given": "Oxana", "initials": "O"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "30", "issn": "1537-1719", "issue": "12", "pages": "2645-2653", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Proteins evolve not only through point mutations but also by insertion and deletion events, which affect the length of the protein. It is well known that such indel events most frequently occur in surface-exposed loops. However, detailed analysis of indel events in distantly related and fast-evolving proteins is hampered by the difficulty involved in correctly aligning such sequences. Here, we circumvent this problem by first only analyzing homologous proteins based on length variation rather than pairwise alignments. Using this approach, we find a surprisingly strong relationship between difference in length and difference in the number of intrinsically disordered residues, where up to three quarters of the length variation can be explained by changes in the number of intrinsically disordered residues. Further, we find that disorder is common in both insertions and deletions. A more detailed analysis reveals that indel events do not induce disorder but rather that already disordered regions accrue indels, suggesting that there is a lowered selective pressure for indels to occur within intrinsically disordered regions.", "doi": "10.1093/molbev/mst157", "pmid": "24037790", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "mst157"}], "notes": [], "created": "2017-05-04T14:56:25.405Z", "modified": "2020-01-21T13:53:20.855Z"}, {"entity": "publication", "iuid": "fe1fc2c14bcd46d5bfcb3010f2a515fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe1fc2c14bcd46d5bfcb3010f2a515fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe1fc2c14bcd46d5bfcb3010f2a515fe"}}, "title": "High expression of glycolytic and pigment proteins is associated with worse clinical outcome in stage III melanoma.", "authors": [{"family": "Falkenius", "given": "Johan", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Johansson", "given": "Hemming", "initials": "H"}, {"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "Frostvik-Stolt", "given": "Marianne", "initials": "M"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Egyhazi Brage", "given": "Suzanne", "initials": "S"}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "23", "issn": "1473-5636", "issue": "6", "pages": "452-460", "title": "Melanoma Res.", "issn-l": "0960-8931"}, "abstract": "There are insufficient numbers of prognostic factors available for prediction of clinical outcome in patients with stage III malignant cutaneous melanoma, even when known adverse pathological risk factors, such as macrometastasis, number of lymph node metastases, and ulceration are taken into consideration. The aim of this study was therefore to identify additional prognostic factors to better predict patients with a high risk of relapse, thus enabling us to better determine the need for adjuvant treatment in stage III disease. An RNA oligonucleotide microarray study was performed on first regional lymph node metastases in 42 patients with stage III melanoma: 23 patients with short-term survival (\u2264 13 months) and 19 with long-term survival (\u2265 60 months), to identify genes associated with clinical outcome. Candidate genes were validated by real-time PCR and immunohistochemical analysis. Several gene ontology (GO) categories were highly significantly differentially expressed including glycolysis (GO: 0006096; P<0.001) and the pigment biosynthetic process (GO: 0046148; P<0.001), in which overexpression was associated with short-disease-specific survival. Three overexpressed glycolytic genes, GAPDHS, GAPDH, and PKM2, and two pigment-related genes, TYRP1 and OCA2, were selected for validation. A significant difference in GAPDHS protein expression between short- and long-term survivors (P=0.021) and a trend for PKM2 (P=0.093) was observed in univariate analysis. Positive expression of at least two of four proteins (GAPDHS, GAPDH, PKM2, TYRP1) in immunohistochemical analysis was found to be an independent adverse prognostic factor for disease-specific survival (P=0.011). Our results indicate that this prognostic panel in combination with established risk factors may contribute to an improved prediction of patients with a high risk of relapse.", "doi": "10.1097/CMR.0000000000000027", "pmid": "24128789", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:03.917Z", "modified": "2021-07-08T13:26:08.445Z"}, {"entity": "publication", "iuid": "7f49476863204a018c8ee67c73b87ef9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f49476863204a018c8ee67c73b87ef9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f49476863204a018c8ee67c73b87ef9"}}, "title": "Genetic variation at the IGF1 locus shows association with post-stroke outcome and to circulating IGF1.", "authors": [{"family": "Aberg", "given": "N David", "initials": "ND"}, {"family": "Olsson", "given": "Sandra", "initials": "S"}, {"family": "Aberg", "given": "Daniel", "initials": "D"}, {"family": "Jood", "given": "Katarina", "initials": "K"}, {"family": "Stanne", "given": "Tara M", "initials": "TM"}, {"family": "Nilsson", "given": "Michael", "initials": "M"}, {"family": "Blomstrand", "given": "Christian", "initials": "C"}, {"family": "Svensson", "given": "Johan", "initials": "J"}, {"family": "Isgaard", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Jern", "given": "Christina", "initials": "C"}], "type": "comparative study", "published": "2013-12-00", "journal": {"volume": "169", "issn": "1479-683X", "issue": "6", "pages": "759-765", "title": "Eur. J. Endocrinol.", "issn-l": "0804-4643"}, "abstract": "In humans, serum IGF1 (s-IGF1) is associated with outcome after ischemic stroke (IS). Therefore variation at the IGF1 locus could also associate with both IS and s-IGF1. We investigated whether genetic variation at the IGF1 locus is associated with i) s-IGF1, ii) IS occurrence, iii) IS severity, and iv) post-stroke outcome.\n\nPatients (n=844; 66% males, mean age 56 years) and community controls (n=668) were included from the Sahlgrenska Academy Study on Ischemic Stroke (SAHLSIS). Post-stroke outcome was evaluated with the modified Rankin Scale at 3 and 24 months after index stroke, and baseline stroke severity with the Scandinavian Stroke Scale. s-IGF1 was determined in patients and after random selection in 40 of the controls.\n\nEleven single nucleotide polymorphisms (SNPs) were selected in the IGF1 gene. In healthy controls the major allele of rs7136446 was associated with higher s-IGF1, whereas in patients no such association was found. No SNP was associated with IS, nor with stroke severity. After multivariate correction for presence of diabetes, smoking, and hypertension, the major allele of rs7136446 was associated with favorable functional outcome 24-months post-stroke (odds ratio 1.46; 95% CI 1.09-1.96).\n\nVariation in rs7136446 of the IGF1 gene associates with post-stroke outcome in relatively young IS patients. Also, rs7136446 associates with s-IGF1 in controls but not in IS, which indicates that IS perturbs a normal genetic impact on s-IGF1 levels.", "doi": "10.1530/EJE-13-0486", "pmid": "24005314", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "EJE-13-0486"}], "notes": [], "created": "2017-05-04T15:01:17.356Z", "modified": "2021-07-07T13:53:12.874Z"}, {"entity": "publication", "iuid": "286e1b55573747cd98907f413c45d288", "links": {"self": {"href": "https://publications.scilifelab.se/publication/286e1b55573747cd98907f413c45d288.json"}, "display": {"href": "https://publications.scilifelab.se/publication/286e1b55573747cd98907f413c45d288"}}, "title": "Evaluation of real-time immunohistochemistry and interaction map as an alternative objective assessment of HER2 expression in human breast cancer tissue.", "authors": [{"family": "Gedda", "given": "Lars", "initials": "L"}, {"family": "Bj\u00f6rkelund", "given": "Hanna", "initials": "H"}, {"family": "Lebel", "given": "Lena", "initials": "L"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Dubois", "given": "Louise", "initials": "L"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Penagos", "given": "Nelly", "initials": "N"}, {"family": "Malmqvist", "given": "Magnus", "initials": "M"}, {"family": "Andersson", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "21", "issn": "1533-4058", "issue": "6", "pages": "497-505", "title": "Appl. Immunohistochem. Mol. Morphol.", "issn-l": null}, "abstract": "Immunohistochemical study (IHC) is a critical tool in the clinical diagnosis of breast cancer. One common assessment is the expression level of the HER2 receptor in breast cancer tissue samples with the aim of stratifying patients for applicability of the therapeutic antibody Herceptin. In this study, we aimed to investigate whether a novel assay, real-time IHC combined with Interaction Map analysis, offers the possibility of objective assessment of HER2 expression. Interaction Map presents real-time interaction data as a collection of peaks on a surface, and it was performed on 20 patient tissue samples previously scored for HER2 expression. The result shows that the relative weight of the peaks in the maps contains novel information that could discriminate between high and low HER2 expression in an operator-independent manner (P<0.001). We conclude that the real-time IHC assay has a promising potential to complement conventional IHC and may improve the precision in the future clinical diagnostics of breast cancer.", "doi": "10.1097/PAI.0b013e318281162d", "pmid": "23455178", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:54.413Z", "modified": "2017-05-30T12:52:30.643Z"}, {"entity": "publication", "iuid": "488ee7f3752e40e88f157740054a9687", "links": {"self": {"href": "https://publications.scilifelab.se/publication/488ee7f3752e40e88f157740054a9687.json"}, "display": {"href": "https://publications.scilifelab.se/publication/488ee7f3752e40e88f157740054a9687"}}, "title": "Distinct loci in the CHRNA5/CHRNA3/CHRNB4 gene cluster are associated with onset of regular smoking.", "authors": [{"family": "Stephens", "given": "Sarah H", "initials": "SH"}, {"family": "Hartz", "given": "Sarah M", "initials": "SM"}, {"family": "Hoft", "given": "Nicole R", "initials": "NR"}, {"family": "Saccone", "given": "Nancy L", "initials": "NL"}, {"family": "Corley", "given": "Robin C", "initials": "RC"}, {"family": "Hewitt", "given": "John K", "initials": "JK"}, {"family": "Hopfer", "given": "Christian J", "initials": "CJ"}, {"family": "Breslau", "given": "Naomi", "initials": "N"}, {"family": "Coon", "given": "Hilary", "initials": "H"}, {"family": "Chen", "given": "Xiangning", "initials": "X"}, {"family": "Ducci", "given": "Francesca", "initials": "F"}, {"family": "Dueker", "given": "Nicole", "initials": "N"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Frank", "given": "Josef", "initials": "J"}, {"family": "Han", "given": "Younghun", "initials": "Y"}, {"family": "Hansel", "given": "Nadia N", "initials": "NN"}, {"family": "Jiang", "given": "Chenhui", "initials": "C"}, {"family": "Korhonen", "given": "Tellervo", "initials": "T"}, {"family": "Lind", "given": "Penelope A", "initials": "PA"}, {"family": "Liu", "given": "Jason", "initials": "J"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Michel", "given": "Martha", "initials": "M"}, {"family": "Shaffer", "given": "John R", "initials": "JR"}, {"family": "Short", "given": "Susan E", "initials": "SE"}, {"family": "Sun", "given": "Juzhong", "initials": "J"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Thompson", "given": "John R", "initials": "JR"}, {"family": "Vogelzangs", "given": "Nicole", "initials": "N"}, {"family": "Vink", "given": "Jacqueline M", "initials": "JM"}, {"family": "Wenzlaff", "given": "Angela", "initials": "A"}, {"family": "Wheeler", "given": "William", "initials": "W"}, {"family": "Yang", "given": "Bao-Zhu", "initials": "BZ"}, {"family": "Aggen", "given": "Steven H", "initials": "SH"}, {"family": "Balmforth", "given": "Anthony J", "initials": "AJ"}, {"family": "Baumeister", "given": "Sebastian E", "initials": "SE"}, {"family": "Beaty", "given": "Terri H", "initials": "TH"}, {"family": "Benjamin", "given": "Daniel J", "initials": "DJ"}, {"family": "Bergen", "given": "Andrew W", "initials": "AW"}, {"family": "Broms", "given": "Ulla", "initials": "U"}, {"family": "Cesarini", "given": "David", "initials": "D"}, {"family": "Chatterjee", "given": "Nilanjan", "initials": "N"}, {"family": "Chen", "given": "Jingchun", "initials": "J"}, {"family": "Cheng", "given": "Yu-Ching", "initials": "YC"}, {"family": "Cichon", "given": "Sven", "initials": "S"}, {"family": "Couper", "given": "David", "initials": "D"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "Dick", "given": "Danielle", "initials": "D"}, {"family": "Foroud", "given": "Tatiana", "initials": "T"}, {"family": "Furberg", "given": "Helena", "initials": "H"}, {"family": "Giegling", "given": "Ina", "initials": "I"}, {"family": "Gillespie", "given": "Nathan A", "initials": "NA"}, {"family": "Gu", "given": "Fangyi", "initials": "F"}, {"family": "Hall", "given": "Alistair S", "initials": "AS"}, {"family": "H\u00e4llfors", "given": "Jenni", "initials": "J"}, {"family": "Han", "given": "Shizhong", "initials": "S"}, {"family": "Hartmann", "given": "Annette M", "initials": "AM"}, {"family": "Heikkil\u00e4", "given": "Kauko", "initials": "K"}, {"family": "Hickie", "given": "Ian B", "initials": "IB"}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ"}, {"family": "Jousilahti", "given": "Pekka", "initials": "P"}, {"family": "Kaakinen", "given": "Marika", "initials": "M"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Koellinger", "given": "Philipp D", "initials": "PD"}, {"family": "Kittner", "given": "Stephen", "initials": "S"}, {"family": "Konte", "given": "Bettina", "initials": "B"}, {"family": "Landi", "given": "Maria-Teresa", "initials": "MT"}, {"family": "Laatikainen", "given": "Tiina", "initials": "T"}, {"family": "Leppert", "given": "Mark", "initials": "M"}, {"family": "Levy", "given": "Steven M", "initials": "SM"}, {"family": "Mathias", "given": "Rasika A", "initials": "RA"}, {"family": "McNeil", "given": "Daniel W", "initials": "DW"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Murray", "given": "Tanda", "initials": "T"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Par\u00e9", "given": "Peter D", "initials": "PD"}, {"family": "Pergadia", "given": "Michele", "initials": "M"}, {"family": "Ruczinski", "given": "Ingo", "initials": "I"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Barnes", "given": "Kathleen C", "initials": "KC"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Caporaso", "given": "Neil", "initials": "N"}, {"family": "Edenberg", "given": "Howard J", "initials": "HJ"}, {"family": "Francks", "given": "Clyde", "initials": "C"}, {"family": "Gelernter", "given": "Joel", "initials": "J"}, {"family": "Grabe", "given": "Hans J\u00f6rgen", "initials": "HJ"}, {"family": "Hops", "given": "Hyman", "initials": "H"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Johannesson", "given": "Magnus", "initials": "M"}, {"family": "Kendler", "given": "Kenneth S", "initials": "KS"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Marazita", "given": "Mary L", "initials": "ML"}, {"family": "Marchini", "given": "Jonathan", "initials": "J"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Rietschel", "given": "Marcella", "initials": "M"}, {"family": "Rujescu", "given": "Dan", "initials": "D"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Schwartz", "given": "Ann G", "initials": "AG"}, {"family": "Shete", "given": "Sanjay", "initials": "S"}, {"family": "Spitz", "given": "Margaret", "initials": "M"}, {"family": "Swan", "given": "Gary E", "initials": "GE"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Veijola", "given": "Juha", "initials": "J"}, {"family": "Wei", "given": "Qingyi", "initials": "Q"}, {"family": "Amos", "given": "Chris", "initials": "C"}, {"family": "Cannon", "given": "Dale S", "initials": "DS"}, {"family": "Grucza", "given": "Richard", "initials": "R"}, {"family": "Hatsukami", "given": "Dorothy", "initials": "D"}, {"family": "Heath", "given": "Andrew", "initials": "A"}, {"family": "Johnson", "given": "Eric O", "initials": "EO"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Madden", "given": "Pamela", "initials": "P"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Stevens", "given": "Victoria L", "initials": "VL"}, {"family": "Weiss", "given": "Robert B", "initials": "RB"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Bierut", "given": "Laura J", "initials": "LJ"}, {"family": "Ehringer", "given": "Marissa A", "initials": "MA"}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "37", "issn": "1098-2272", "issue": "8", "pages": "846-859", "title": "Genet. Epidemiol.", "issn-l": "0741-0395"}, "abstract": "Neuronal nicotinic acetylcholine receptor (nAChR) genes (CHRNA5/CHRNA3/CHRNB4) have been reproducibly associated with nicotine dependence, smoking behaviors, and lung cancer risk. Of the few reports that have focused on early smoking behaviors, association results have been mixed. This meta-analysis examines early smoking phenotypes and SNPs in the gene cluster to determine: (1) whether the most robust association signal in this region (rs16969968) for other smoking behaviors is also associated with early behaviors, and/or (2) if additional statistically independent signals are important in early smoking. We focused on two phenotypes: age of tobacco initiation (AOI) and age of first regular tobacco use (AOS). This study included 56,034 subjects (41 groups) spanning nine countries and evaluated five SNPs including rs1948, rs16969968, rs578776, rs588765, and rs684513. Each dataset was analyzed using a centrally generated script. Meta-analyses were conducted from summary statistics. AOS yielded significant associations with SNPs rs578776 (beta = 0.02, P = 0.004), rs1948 (beta = 0.023, P = 0.018), and rs684513 (beta = 0.032, P = 0.017), indicating protective effects. There were no significant associations for the AOI phenotype. Importantly, rs16969968, the most replicated signal in this region for nicotine dependence, cigarettes per day, and cotinine levels, was not associated with AOI (P = 0.59) or AOS (P = 0.92). These results provide important insight into the complexity of smoking behavior phenotypes, and suggest that association signals in the CHRNA5/A3/B4 gene cluster affecting early smoking behaviors may be different from those affecting the mature nicotine dependence phenotype.", "doi": "10.1002/gepi.21760", "pmid": "24186853", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC3947535"}, {"db": "mid", "key": "NIHMS538239"}], "notes": [], "created": "2017-05-04T14:57:55.075Z", "modified": "2020-01-21T13:56:02.100Z"}, {"entity": "publication", "iuid": "ab50afb774244a2e9807d20362a79c94", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab50afb774244a2e9807d20362a79c94.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab50afb774244a2e9807d20362a79c94"}}, "title": "DNA damage leads to progressive replicative decline but extends the life span of long-lived mutant animals.", "authors": [{"family": "Lans", "given": "H", "initials": "H"}, {"family": "Lindvall", "given": "J M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Thijssen", "given": "K", "initials": "K"}, {"family": "Karambelas", "given": "A E", "initials": "AE"}, {"family": "Cupac", "given": "D", "initials": "D"}, {"family": "Fensg\u00e5rd", "given": "O", "initials": "O"}, {"family": "Jansen", "given": "G", "initials": "G"}, {"family": "Hoeijmakers", "given": "J H J", "initials": "JH"}, {"family": "Nilsen", "given": "H", "initials": "H"}, {"family": "Vermeulen", "given": "W", "initials": "W"}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "20", "issn": "1476-5403", "issue": "12", "pages": "1709-1718", "title": "Cell Death Differ.", "issn-l": "1350-9047"}, "abstract": "Human-nucleotide-excision repair (NER) deficiency leads to different developmental and segmental progeroid symptoms of which the pathogenesis is only partially understood. To understand the biological impact of accumulating spontaneous DNA damage, we studied the phenotypic consequences of DNA-repair deficiency in Caenorhabditis elegans. We find that DNA damage accumulation does not decrease the adult life span of post-mitotic tissue. Surprisingly, loss of functional ERCC-1/XPF even further extends the life span of long-lived daf-2 mutants, likely through an adaptive activation of stress signaling. Contrariwise, NER deficiency leads to a striking transgenerational decline in replicative capacity and viability of proliferating cells. DNA damage accumulation induces severe, stochastic impairment of development and growth, which is most pronounced in NER mutants that are also impaired in their response to ionizing radiation and inter-strand crosslinks. These results suggest that multiple DNA-repair pathways can protect against replicative decline and indicate that there might be a direct link between the severity of symptoms and the level of DNA-repair deficiency in patients.", "doi": "10.1038/cdd.2013.126", "pmid": "24013725", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "cdd2013126"}, {"db": "pmc", "key": "PMC3824592"}], "notes": [], "created": "2017-05-04T15:03:14.767Z", "modified": "2021-07-05T12:48:15.934Z"}, {"entity": "publication", "iuid": "a6b0b408e07c4c90b513a8d6b54e9ce6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6b0b408e07c4c90b513a8d6b54e9ce6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6b0b408e07c4c90b513a8d6b54e9ce6"}}, "title": "Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade.", "authors": [{"family": "Zaremba-Niedzwiedzka", "given": "Katarzyna", "initials": "K"}, {"family": "Viklund", "given": "Johan", "initials": "J"}, {"family": "Zhao", "given": "Weizhou", "initials": "W"}, {"family": "Ast", "given": "Jennifer", "initials": "J"}, {"family": "Sczyrba", "given": "Alexander", "initials": "A"}, {"family": "Woyke", "given": "Tanja", "initials": "T"}, {"family": "McMahon", "given": "Katherina", "initials": "K"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Stepanauskas", "given": "Ramunas", "initials": "R"}, {"family": "Andersson", "given": "Siv G E", "initials": "SG"}], "type": "journal article", "published": "2013-11-28", "journal": {"volume": "14", "issn": "1474-760X", "issue": "11", "pages": "R130", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt- and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet.\n\nWe isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules.\n\nWe conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.", "doi": "10.1186/gb-2013-14-11-r130", "pmid": "24286338", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "gb-2013-14-11-r130"}, {"db": "pmc", "key": "PMC4053759"}], "notes": [], "created": "2017-05-04T14:57:56.022Z", "modified": "2020-01-21T13:56:04.303Z"}, {"entity": "publication", "iuid": "8f37c309a6f64a31b226eebe05a10d7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f37c309a6f64a31b226eebe05a10d7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f37c309a6f64a31b226eebe05a10d7c"}}, "title": "Identification of candidate serum proteins for classifying well-differentiated small intestinal neuroendocrine tumors.", "authors": [{"family": "Darmanis", "given": "Spyros", "initials": "S"}, {"family": "Cui", "given": "Tao", "initials": "T"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Li", "given": "Su-Chen", "initials": "S"}, {"family": "\u00d6berg", "given": "Kjell", "initials": "K"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Giandomenico", "given": "Valeria", "initials": "V"}], "type": "journal article", "published": "2013-11-25", "journal": {"volume": "8", "issn": "1932-6203", "issue": "11", "pages": "e81712", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Patients with well-differentiated small intestine neuroendocrine tumors (WD-SI-NETs) are most often diagnosed at a metastatic stage of disease, which reduces possibilities for a curative treatment. Thus new approaches for earlier detection and improved monitoring of the disease are required.\r\n\r\nSuspension bead arrays targeting 124 unique proteins with antibodies from the Human Protein Atlas were used to profile biotinylated serum samples. Discoveries from a cohort of 77 individuals were followed up in a cohort of 132 individuals both including healthy controls as well as patients with untreated primary WD-SI-NETs, lymph node metastases and liver metastases.\r\n\r\nA set of 20 antibodies suggested promising proteins for further verification based on technically verified statistical significance. Proceeding, we assessed the classification performance in an independent cohort of patient serum, achieving, classification accuracy of up to 85% with different subsets of antibodies in respective pairwise group comparisons. The protein profiles of nine targets, namely IGFBP2, IGF1, SHKBP1, ETS1, IL1\u03b1, STX2, MAML3, EGR3 and XIAP were verified as significant contributors to tumor classification.\r\n\r\nWe propose new potential protein biomarker candidates for classifying WD-SI-NETs at different stage of disease. Further evaluation of these proteins in larger sample sets and with alternative approaches is needed in order to further improve our understanding of their functional relation to WD-SI-NETs and their eventual use in diagnostics.", "doi": "10.1371/journal.pone.0081712", "pmid": "24282616", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-13-03665"}, {"db": "pmc", "key": "PMC3839889"}], "notes": [], "created": "2017-05-04T14:55:38.382Z", "modified": "2021-07-08T12:07:34.174Z"}, {"entity": "publication", "iuid": "cf9a1e018f4a47939792c0af142bb446", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf9a1e018f4a47939792c0af142bb446.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf9a1e018f4a47939792c0af142bb446"}}, "title": "Germline genetic contributions to risk for esophageal adenocarcinoma, Barrett's esophagus, and gastroesophageal reflux.", "authors": [{"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Levine", "given": "David M", "initials": "DM"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Bresso", "given": "Francesca", "initials": "F"}, {"family": "Onstad", "given": "Lynn E", "initials": "LE"}, {"family": "Schmidt", "given": "Peter T", "initials": "PT"}, {"family": "T\u00f6rnblom", "given": "Hans", "initials": "H"}, {"family": "Nordenstedt", "given": "Helena", "initials": "H"}, {"family": "Romero", "given": "Yvonne", "initials": "Y"}, {"family": "Mayo Clinic Esophageal Adenocarcinoma and Barrett\u2019s Esophagus Registry Consortium", "given": "", "initials": ""}, {"family": "Chow", "given": "Wong-Ho", "initials": "W"}, {"family": "Murray", "given": "Liam J", "initials": "LJ"}, {"family": "Gammon", "given": "Marilie D", "initials": "MD"}, {"family": "Liu", "given": "Geoffrey", "initials": "G"}, {"family": "Bernstein", "given": "Leslie", "initials": "L"}, {"family": "Casson", "given": "Alan G", "initials": "AG"}, {"family": "Risch", "given": "Harvey A", "initials": "HA"}, {"family": "Shaheen", "given": "Nicholas J", "initials": "NJ"}, {"family": "Bird", "given": "Nigel C", "initials": "NC"}, {"family": "Reid", "given": "Brian J", "initials": "BJ"}, {"family": "Corley", "given": "Douglas A", "initials": "DA"}, {"family": "Hardie", "given": "Laura J", "initials": "LJ"}, {"family": "Ye", "given": "Weimin", "initials": "W"}, {"family": "Wu", "given": "Anna H", "initials": "AH"}, {"family": "Zucchelli", "given": "Marco", "initials": "M"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Hysi", "given": "Pirro", "initials": "P"}, {"family": "Vaughan", "given": "Thomas L", "initials": "TL"}, {"family": "Whiteman", "given": "David C", "initials": "DC"}, {"family": "MacGregor", "given": "Stuart", "initials": "S"}, {"family": "BEACON study investigators", "given": "", "initials": ""}], "type": "journal article", "published": "2013-11-20", "journal": {"volume": "105", "issn": "1460-2105", "issue": "22", "pages": "1711-1718", "title": "J. Natl. Cancer Inst.", "issn-l": "0027-8874"}, "abstract": "Esophageal adenocarcinoma (EA) is an increasingly common cancer with poor survival. Barrett's esophagus (BE) is the main precursor to EA, and every year 0.12% to 0.5% of BE patients progress to EA. BE typically arises on a background of chronic gastroesophageal reflux (GERD), one of the risk factors for EA.\r\n\r\nWe used genome-wide association data to investigate the genetic architecture underlying GERD, BE, and EA. We applied a method to estimate the variance explained (array heritability, h(2)g) and the genetic correlation (rg) between GERD, BE, and EA by considering all single nucleotide polymorphisms (SNPs) simultaneously. We also estimated the polygenic overlap between GERD, BE, and EA using a prediction approach. All tests were two-sided, except in the case of variance-explained estimation where one-sided tests were used.\r\n\r\nWe estimated a statistically significant genetic variance explained for BE (h(2)g = 35%; standard error [SE] = 6%; one-sided P = 1 \u00d7 10(-9)) and for EA (h(2)g = 25 %; SE = 5%; one-sided P = 2 \u00d7 10(-7)). The genetic correlation between BE and EA was found to be high (rg = 1.0; SE = 0.37). We also estimated a statistically significant polygenic overlap between BE and EA (one-sided P = 1 \u00d7 10(-6)), which suggests, together with the high genetic correlation, that shared genes underlie the development of BE and EA. Conversely, no statistically significant results were obtained for GERD.\r\n\r\nWe have demonstrated that risk to BE and EA is influenced by many germline genetic variants of small effect and that shared polygenic effects contribute to risk of these two diseases.", "doi": "10.1093/jnci/djt303", "pmid": "24168968", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "djt303"}, {"db": "pmc", "key": "PMC3833931"}], "notes": [], "created": "2017-05-04T14:58:02.681Z", "modified": "2020-01-21T13:56:08.558Z"}, {"entity": "publication", "iuid": "424de8c4b51a4760b5bb0e7234c425c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/424de8c4b51a4760b5bb0e7234c425c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/424de8c4b51a4760b5bb0e7234c425c6"}}, "title": "Rule-based models of the interplay between genetic and environmental factors in childhood allergy.", "authors": [{"family": "Bornel\u00f6v", "given": "Susanne", "initials": "S"}, {"family": "S\u00e4\u00e4f", "given": "Annika", "initials": "A"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Torabi Moghadam", "given": "Behrooz", "initials": "B"}, {"family": "Pulkkinen", "given": "Ville", "initials": "V"}, {"family": "Acevedo", "given": "Nathalie", "initials": "N"}, {"family": "Orsmark Pietras", "given": "Christina", "initials": "C"}, {"family": "Ege", "given": "Markus", "initials": "M"}, {"family": "Braun-Fahrl\u00e4nder", "given": "Charlotte", "initials": "C"}, {"family": "Riedler", "given": "Josef", "initials": "J"}, {"family": "Doekes", "given": "Gert", "initials": "G"}, {"family": "Kabesch", "given": "Michael", "initials": "M"}, {"family": "van Hage", "given": "Marianne", "initials": "M"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}, {"family": "S\u00f6derh\u00e4ll", "given": "Cilla", "initials": "C"}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2013-11-19", "journal": {"volume": "8", "issn": "1932-6203", "issue": "11", "pages": "e80080", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Both genetic and environmental factors are important for the development of allergic diseases. However, a detailed understanding of how such factors act together is lacking. To elucidate the interplay between genetic and environmental factors in allergic diseases, we used a novel bioinformatics approach that combines feature selection and machine learning. In two materials, PARSIFAL (a European cross-sectional study of 3113 children) and BAMSE (a Swedish birth-cohort including 2033 children), genetic variants as well as environmental and lifestyle factors were evaluated for their contribution to allergic phenotypes. Monte Carlo feature selection and rule based models were used to identify and rank rules describing how combinations of genetic and environmental factors affect the risk of allergic diseases. Novel interactions between genes were suggested and replicated, such as between ORMDL3 and RORA, where certain genotype combinations gave odds ratios for current asthma of 2.1 (95% CI 1.2-3.6) and 3.2 (95% CI 2.0-5.0) in the BAMSE and PARSIFAL children, respectively. Several combinations of environmental factors appeared to be important for the development of allergic disease in children. For example, use of baby formula and antibiotics early in life was associated with an odds ratio of 7.4 (95% CI 4.5-12.0) of developing asthma. Furthermore, genetic variants together with environmental factors seemed to play a role for allergic diseases, such as the use of antibiotics early in life and COL29A1 variants for asthma, and farm living and NPSR1 variants for allergic eczema. Overall, combinations of environmental and life style factors appeared more frequently in the models than combinations solely involving genes. In conclusion, a new bioinformatics approach is described for analyzing complex data, including extensive genetic and environmental information. Interactions identified with this approach could provide useful hints for further in-depth studies of etiological mechanisms and may also strengthen the basis for risk assessment and prevention.", "doi": "10.1371/journal.pone.0080080", "pmid": "24260339", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-20229"}, {"db": "pmc", "key": "PMC3833974"}], "notes": [], "created": "2017-05-04T15:03:37.151Z", "modified": "2017-05-30T14:52:55.534Z"}, {"entity": "publication", "iuid": "8cd7a8a94b4c44cbaceaf3096806f0cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cd7a8a94b4c44cbaceaf3096806f0cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cd7a8a94b4c44cbaceaf3096806f0cf"}}, "title": "De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).", "authors": [{"family": "Norman", "given": "Anita J", "initials": "AJ"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2013-11-18", "journal": {"volume": "8", "issn": "1932-6203", "issue": "11", "pages": "e81012", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Information about relatedness between individuals in wild populations is advantageous when studying evolutionary, behavioural and ecological processes. Genomic data can be used to determine relatedness between individuals either when no prior knowledge exists or to confirm suspected relatedness. Here we present a set of 96 SNPs suitable for inferring relatedness for brown bears (Ursus arctos) within Scandinavia. We sequenced reduced representation libraries from nine individuals throughout the geographic range. With consensus reads containing putative SNPs, we applied strict filtering criteria with the aim of finding only high-quality, highly-informative SNPs. We tested 150 putative SNPs of which 96% were validated on a panel of 68 individuals. Ninety-six of the validated SNPs with the highest minor allele frequency were selected. The final SNP panel includes four mitochondrial markers, two monomorphic Y-chromosome sex-determination markers, three X-chromosome SNPs and 87 autosomal SNPs. From our validation sample panel, we identified two previously known parent-offspring dyads with reasonable accuracy. This panel of SNPs is a promising tool for inferring relatedness in the brown bear population in Scandinavia.", "doi": "10.1371/journal.pone.0081012", "pmid": "24260529", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-25655"}, {"db": "pmc", "key": "PMC3832409"}], "notes": [], "created": "2017-05-04T14:58:16.158Z", "modified": "2020-01-21T13:56:03.649Z"}, {"entity": "publication", "iuid": "6fdc95562b3e43dd8b114345f285b393", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6fdc95562b3e43dd8b114345f285b393.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6fdc95562b3e43dd8b114345f285b393"}}, "title": "miR-128 regulates non-myocyte hyperplasia, deposition of extracellular matrix and Islet1 expression during newt cardiac regeneration.", "authors": [{"family": "Witman", "given": "Nevin", "initials": "N"}, {"family": "Heigwer", "given": "Jana", "initials": "J"}, {"family": "Thaler", "given": "Barbara", "initials": "B"}, {"family": "Lui", "given": "Weng-Onn", "initials": "WO"}, {"family": "Morrison", "given": "Jamie Ian", "initials": "JI"}], "type": "journal article", "published": "2013-11-15", "journal": {"volume": "383", "issn": "1095-564X", "issue": "2", "pages": "253-263", "title": "Dev. Biol.", "issn-l": "0012-1606"}, "abstract": "Cardiovascular disease is a global scourge to society, with novel therapeutic approaches required in order to alleviate the suffering caused by sustained cardiac damage. MicroRNAs (miRNAs) are being touted as one such approach in the fight against heart disease, acting as possible post-transcriptional molecular triggers responsible for invoking cardiac regeneration. To further ones understanding of miRNAs and cardiac regeneration, it is prudent to learn from organisms that can intrinsically regenerate their hearts following injury. Using the red-spotted newt, an adult chordate capable of cardiac regeneration, we decided to delve deeper into the role miRNAs play during this process. RNA isolated from regenerating newt heart samples, was used in a microarray screen, to identify significantly expressed candidate miRNAs during newt cardiac regeneration. We performed quantitative qPCR analysis on several conserved miRNAs and found one in particular, miR-128, to be significantly elevated when cardiac hyperplasia is at its peak following injury. In-situ hybridisation techniques revealed a localised expression pattern for miR-128 in the cardiomyocytes and non-cardiomyocytes in close proximity to the regeneration zone and in vivo knockdown studies revealed a regulatory role for miR-128 in proliferating non-cardiomyocyte populations and extracellular matrix deposition. Finally, 3'UTR reporter assays revealed Islet1 as a biological target for miR-128, which was confirmed further through in vivo Islet1 transcriptional and translational expression analysis in regenerating newt hearts. From these studies we conclude that miR-128 regulates both cardiac hyperplasia and Islet1 expression during newt heart regeneration and that this information could be translated into future mammalian cardiac studies.", "doi": "10.1016/j.ydbio.2013.09.011", "pmid": "24055866", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0012-1606(13)00485-5"}], "notes": [], "created": "2017-05-04T14:57:51.585Z", "modified": "2020-01-21T13:56:02.925Z"}, {"entity": "publication", "iuid": "1ce5c99db9a6499388a5f8a45c816b5b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ce5c99db9a6499388a5f8a45c816b5b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ce5c99db9a6499388a5f8a45c816b5b"}}, "title": "Substrate specificity and oligomerization of human GMP synthetase.", "authors": [{"family": "Welin", "given": "Martin", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Lari", "initials": "L"}, {"family": "Johansson", "given": "Andreas", "initials": "A"}, {"family": "Flodin", "given": "Susanne", "initials": "S"}, {"family": "Nyman", "given": "Tomas", "initials": "T"}, {"family": "Tr\u00e9saugues", "given": "Lionel", "initials": "L"}, {"family": "Hammarstr\u00f6m", "given": "Martin", "initials": "M"}, {"family": "Gr\u00e4slund", "given": "Susanne", "initials": "S"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2013-11-15", "journal": {"volume": "425", "issn": "1089-8638", "issue": "22", "pages": "4323-4333", "title": "J. Mol. Biol.", "issn-l": "0022-2836"}, "abstract": "Guanine monophosphate (GMP) synthetase is a bifunctional two-domain enzyme. The N-terminal glutaminase domain generates ammonia from glutamine and the C-terminal synthetase domain aminates xanthine monophosphate (XMP) to form GMP. Mammalian GMP synthetases (GMPSs) contain a 130-residue-long insert in the synthetase domain in comparison to bacterial proteins. We report here the structure of a eukaryotic GMPS. Substrate XMP was bound in the crystal structure of the human GMPS enzyme. XMP is bound to the synthetase domain and covered by a LID motif. The enzyme forms a dimer in the crystal structure with subunit orientations entirely different from the bacterial counterparts. The inserted sub-domain is shown to be involved in substrate binding and dimerization. Furthermore, the structural basis for XMP recognition is revealed as well as a potential allosteric site. Enzymes in the nucleotide metabolism typically display an increased activity in proliferating cells due to the increased need for nucleotides. Many drugs used as immunosuppressants and for treatment of cancer and viral diseases are indeed nucleobase- and nucleoside-based compounds, which are acting on or are activated by enzymes in this pathway. The information obtained from the crystal structure of human GMPS might therefore aid in understanding interactions of nucleoside-based drugs with GMPS and in structure-based design of GMPS-specific inhibitors.", "doi": "10.1016/j.jmb.2013.06.032", "pmid": "23816837", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "S0022-2836(13)00427-0"}, {"db": "PDB", "key": "2VXO"}], "notes": [], "created": "2017-05-04T15:03:48.503Z", "modified": "2017-09-06T11:42:09.003Z"}, {"entity": "publication", "iuid": "0e3e7d2669db4343813208ec913c4d7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e3e7d2669db4343813208ec913c4d7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e3e7d2669db4343813208ec913c4d7c"}}, "title": "Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner.", "authors": [{"family": "\u00c5hsberg", "given": "Josefine", "initials": "J"}, {"family": "Ungerb\u00e4ck", "given": "Jonas", "initials": "J"}, {"family": "Strid", "given": "Tobias", "initials": "T", "orcid": "0000-0002-2166-5170", "researcher": {"href": "https://publications.scilifelab.se/researcher/8294f89150574803a12bc1944714d12b.json"}}, {"family": "Welinder", "given": "Eva", "initials": "E"}, {"family": "Stjernberg", "given": "Jenny", "initials": "J"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Sigvardsson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2013-11-15", "journal": {"volume": "288", "issn": "1083-351X", "issue": "46", "pages": "33449-33461", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Transcription factor doses are of importance for normal and malignant B-lymphocyte development; however, the understanding of underlying mechanisms and functional consequences of reduced transcription factor levels is limited. We have analyzed progenitor and B-lineage compartments in mice carrying heterozygote mutations in the E2a, Ebf1, or Pax5 gene. Although lymphoid progenitors from Ebf1 or Pax5 heterozygote mice were specified and lineage-restricted in a manner comparable with Wt progenitors, this process was severely impaired in E2a heterozygote mutant mice. This defect was not significantly enhanced upon combined deletion of E2a with Ebf1 or Pax5. Analysis of the pre-B-cell compartment in Ebf1 heterozygote mice revealed a reduction in cell numbers. These cells expressed Pax5 and other B-lineage-associated genes, and global gene expression analysis suggested that the reduction of the pre-B-cell compartment was a result of impaired pre-B-cell expansion. This idea was supported by a reduction in IL2R\u03b1-expressing late pre-B-cells as well as by cell cycle analysis and by the finding that the complexity of the VDJ rearrangement patterns was comparable in Wt and Ebf1(+/-) pre-B-cells, although the number of progenitors was reduced. Heterozygote deletion of Ebf1 resulted in impaired response to IL7 in vitro and reduced expression levels of pre-BCR on the cell surface, providing possible explanations for the observed stage-specific reduction in cellular expansion. Thus, transcription factor doses are critical for specification as well as expansion of B-lymphoid progenitors, providing increased insight into the molecular regulation of B-cell development.", "doi": "10.1074/jbc.M113.506261", "pmid": "24078629", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0021-9258(19)54468-4"}, {"db": "pmc", "key": "PMC3829190"}], "notes": [], "created": "2017-05-04T14:56:24.274Z", "modified": "2021-07-06T15:17:27.838Z"}, {"entity": "publication", "iuid": "c1caa61eb6a045a3b3bb6d3d1a71bb72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1caa61eb6a045a3b3bb6d3d1a71bb72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1caa61eb6a045a3b3bb6d3d1a71bb72"}}, "title": "Discovery of an allosteric inhibitor binding site in 3-Oxo-acyl-ACP reductase from Pseudomonas aeruginosa.", "authors": [{"family": "Cukier", "given": "Cyprian D", "initials": "CD"}, {"family": "Hope", "given": "Anthony G", "initials": "AG"}, {"family": "Elamin", "given": "Ayssar A", "initials": "AA"}, {"family": "Moynie", "given": "Lucile", "initials": "L"}, {"family": "Schnell", "given": "Robert", "initials": "R"}, {"family": "Schach", "given": "Susanne", "initials": "S"}, {"family": "Kneuper", "given": "Holger", "initials": "H"}, {"family": "Singh", "given": "Mahavir", "initials": "M"}, {"family": "Naismith", "given": "James H", "initials": "JH"}, {"family": "Lindqvist", "given": "Ylva", "initials": "Y"}, {"family": "Gray", "given": "David W", "initials": "DW"}, {"family": "Schneider", "given": "Gunter", "initials": "G"}], "type": "journal article", "published": "2013-11-15", "journal": {"volume": "8", "issn": "1554-8937", "issue": "11", "pages": "2518-2527", "title": "ACS Chem. Biol.", "issn-l": "1554-8929"}, "abstract": "3-Oxo-acyl-acyl carrier protein (ACP) reductase (FabG) plays a key role in the bacterial fatty acid synthesis II system in pathogenic microorganisms, which has been recognized as a potential drug target. FabG catalyzes reduction of a 3-oxo-acyl-ACP intermediate during the elongation cycle of fatty acid biosynthesis. Here, we report gene deletion experiments that support the essentiality of this gene in P. aeruginosa and the identification of a number of small molecule FabG inhibitors with IC50 values in the nanomolar to low micromolar range and good physicochemical properties. Structural characterization of 16 FabG-inhibitor complexes by X-ray crystallography revealed that the compounds bind at a novel allosteric site located at the FabG subunit-subunit interface. Inhibitor binding relies primarily on hydrophobic interactions, but specific hydrogen bonds are also observed. Importantly, the binding cavity is formed upon complex formation and therefore would not be recognized by virtual screening approaches. The structure analysis further reveals that the inhibitors act by inducing conformational changes that propagate to the active site, resulting in a displacement of the catalytic triad and the inability to bind NADPH.", "doi": "10.1021/cb4005063", "pmid": "24015914", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pmc", "key": "PMC3833349"}], "notes": [], "created": "2017-05-04T15:03:46.688Z", "modified": "2017-09-06T11:42:09.295Z"}, {"entity": "publication", "iuid": "e2d39a0589534e9cbe4380eb83850135", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2d39a0589534e9cbe4380eb83850135.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2d39a0589534e9cbe4380eb83850135"}}, "title": "Polymer\u2013Pendant Interactions in Poly(pyrrol-3-ylhydroquinone): A Solution for the Use of Conducting Polymers at Stable Conditions", "authors": [{"family": "Karlsson", "given": "Christoffer", "initials": "C"}, {"family": "Huang", "given": "Hao", "initials": "H"}, {"family": "Str\u00f8mme", "given": "Maria", "initials": "M"}, {"family": "Gogoll", "given": "Adolf", "initials": "A"}, {"family": "Sj\u00f6din", "given": "Martin", "initials": "M"}], "type": "journal-article", "published": "2013-11-14", "journal": {"volume": "117", "issn": "1932-7447", "issue": "45", "pages": "23558-23567", "title": "J. Phys. Chem. C", "issn-l": null}, "abstract": null, "doi": "10.1021/jp408567h", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T11:01:06.711Z", "modified": "2025-10-17T13:04:00.837Z"}, {"entity": "publication", "iuid": "ff05473b33024d5c9f21023b2d66771d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff05473b33024d5c9f21023b2d66771d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff05473b33024d5c9f21023b2d66771d"}}, "title": "Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.", "authors": [{"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Nyberg", "given": "Linnea", "initials": "L"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2013-11-13", "journal": {"volume": "13", "issn": "1472-6750", "issue": null, "pages": "99", "title": "BMC Biotechnol.", "issn-l": "1472-6750"}, "abstract": "The starting material for RNA sequencing (RNA-seq) studies is usually total RNA or polyA+ RNA. Both forms of RNA represent heterogeneous pools of RNA molecules at different levels of maturation and processing. Such heterogeneity, in addition to the biases associated with polyA+ purification steps, may influence the analysis, sensitivity and the interpretation of RNA-seq data. We hypothesize that subcellular fractions of RNA may provide a more accurate picture of gene expression.\n\nWe present results for sequencing of cytoplasmic and nuclear RNA after cellular fractionation of tissue samples. In comparison with conventional polyA+ RNA, the cytoplasmic RNA contains a significantly higher fraction of exonic sequence, providing increased sensitivity in expression analysis and splice junction detection, and in improved de novo assembly of RNA-seq data. Conversely, the nuclear fraction shows an enrichment of unprocessed RNA compared with total RNA-seq, making it suitable for analysis of nascent transcripts and RNA processing dynamics.\n\nOur results show that cellular fractionation is a more rapid and cost effective approach than conventional polyA+ enrichment when studying mature RNAs. Thus, RNA-seq of separated cytosolic and nuclear RNA can significantly improve the analysis of complex transcriptomes from mammalian tissues.", "doi": "10.1186/1472-6750-13-99", "pmid": "24225116", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1472-6750-13-99"}, {"db": "pmc", "key": "PMC3833653"}], "notes": [], "created": "2017-05-04T14:57:49.079Z", "modified": "2021-07-08T12:52:24.453Z"}, {"entity": "publication", "iuid": "3e542af66758413d8305a824c4580c52", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e542af66758413d8305a824c4580c52.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e542af66758413d8305a824c4580c52"}}, "title": "Disturbance induced decoupling between host genetics and composition of the associated microbiome.", "authors": [{"family": "Wegner", "given": "Karl Mathias", "initials": "KM"}, {"family": "Volkenborn", "given": "Nils", "initials": "N"}, {"family": "Peter", "given": "Hannes", "initials": "H"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2013-11-09", "journal": {"volume": "13", "issn": "1471-2180", "issue": null, "pages": "252", "title": "BMC Microbiol.", "issn-l": "1471-2180"}, "abstract": "Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity however remains underexplored and unexplained, although environmental conditions and host genetics have been implicated. We used 454 next generation 16S rRNA amplicon sequencing of individually tagged PCR reactions to explore the diversity of bacterial communities in gill tissue of the invasive Pacific oyster Crassostrea gigas stemming from genetically differentiated beds under ambient outdoor conditions and after a multifaceted disturbance treatment imposing stress on the host.\n\nWhile the gill associated microbial communities in oysters were dominated by few abundant taxa (i.e. Sphingomonas, Mycoplasma) the distribution of rare bacterial groups correlated to relatedness between the hosts under ambient conditions. Exposing the host to disturbance broke apart this relationship by removing rare phylotypes thereby reducing overall microbial diversity. Shifts in the microbiome composition in response to stress did not result in a net increase in genera known to contain potentially pathogenic strains.\n\nThe decrease in microbial diversity and the disassociation between population genetic structure of the hosts and their associated microbiome suggest that disturbance (i.e. stress) may play a significant role for the assembly of the natural microbiome. Such community shifts may in turn also feed back on the course of disease and the occurrence of mass mortality events in oyster populations.", "doi": "10.1186/1471-2180-13-252", "pmid": "24206899", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2180-13-252"}, {"db": "pmc", "key": "PMC3840651"}], "notes": [], "created": "2017-05-04T14:57:50.614Z", "modified": "2020-01-21T13:56:01.793Z"}, {"entity": "publication", "iuid": "f61ae0b4ae3247e08413933bcabfd54c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f61ae0b4ae3247e08413933bcabfd54c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f61ae0b4ae3247e08413933bcabfd54c"}}, "title": "ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer.", "authors": [{"family": "Bysani", "given": "Madhusudhan", "initials": "M"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Bornel\u00f6v", "given": "Susanne", "initials": "S"}, {"family": "Zatloukal", "given": "Kurt", "initials": "K"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "journal article", "published": "2013-11-08", "journal": {"volume": "6", "issn": "1755-8794", "issue": null, "pages": "50", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "Steatohepatitis occurs in alcoholic liver disease and may progress to liver cirrhosis and hepatocellular carcinoma. Its molecular pathogenesis is to a large degree unknown. Histone modifications play a key role in transcriptional regulations as marks for silencing and activation of gene expression and as marks for functional elements. Many transcription factors (TFs) are crucial for the control of the genes involved in metabolism, and abnormality in their function may lead to disease.\n\nWe performed ChIP-seq of the histone modifications H3K4me1, H3K4me3 and H3K27ac and a candidate transcription factor (USF1) in liver tissue from patients with steatohepatitis and normal livers and correlated results to mRNA-expression and genotypes.\n\nWe found several regions that are differentially enriched for histone modifications between disease and normal tissue, and qRT-PCR results indicated that the expression of the tested genes strongly correlated with differential enrichment of histone modifications but is independent of USF1 enrichment. By gene ontology analysis of differentially modified genes we found many disease associated genes, some of which had previously been implicated in the etiology of steatohepatitis. Importantly, the genes associated to the strongest histone peaks in the patient were over-represented in cancer specific pathways suggesting that the tissue was on a path to develop to cancer, a common complication to the disease. We also found several novel SNPs and GWAS catalogue SNPs that are candidates to be functional and therefore needs further study.\n\nIn summary we find that analysis of chromatin features in tissue samples provides insight into disease mechanisms.", "doi": "10.1186/1755-8794-6-50", "pmid": "24206787", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1755-8794-6-50"}, {"db": "pmc", "key": "PMC3831757"}, {"db": "SRA", "key": "SRA066400"}], "notes": [], "created": "2017-05-04T15:01:15.314Z", "modified": "2020-01-21T13:56:06.351Z"}, {"entity": "publication", "iuid": "f5d0e962ca7849b3aab152e12b610925", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5d0e962ca7849b3aab152e12b610925.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5d0e962ca7849b3aab152e12b610925"}}, "title": "Inference of the genetic architecture underlying BMI and height with the use of 20,240 sibling pairs.", "authors": [{"family": "Hemani", "given": "Gibran", "initials": "G"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Vinkhuyzen", "given": "Anna", "initials": "A"}, {"family": "Powell", "given": "Joseph E", "initials": "JE"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "J"}, {"family": "Abdellaoui", "given": "Abdel", "initials": "A"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Valdes", "given": "Ana M", "initials": "AM"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Madden", "given": "Pamela A", "initials": "PA"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Henders", "given": "Anjali K", "initials": "AK"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}], "type": "journal article", "published": "2013-11-07", "journal": {"volume": "93", "issn": "1537-6605", "issue": "5", "pages": "865-875", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Evidence that complex traits are highly polygenic has been presented by population-based genome-wide association studies (GWASs) through the identification of many significant variants, as well as by family-based de novo sequencing studies indicating that several traits have a large mutational target size. Here, using a third study design, we show results consistent with extreme polygenicity for body mass index (BMI) and height. On a sample of 20,240 siblings (from 9,570 nuclear families), we used a within-family method to obtain narrow-sense heritability estimates of 0.42 (SE = 0.17, p = 0.01) and 0.69 (SE = 0.14, p = 6\u00a0\u00d7 10(-)(7)) for BMI and height, respectively, after adjusting for covariates. The genomic inflation factors from locus-specific linkage analysis were 1.69 (SE = 0.21, p = 0.04) for BMI and 2.18 (SE = 0.21, p = 2\u00a0\u00d7 10(-10)) for height. This inflation is free of confounding and congruent with polygenicity, consistent with observations of ever-increasing genomic-inflation factors from GWASs with large sample sizes, implying that those signals are due to true genetic signals across the genome rather than population stratification. We also demonstrate that the distribution of the observed test statistics is consistent with both rare and common variants underlying a polygenic architecture and that previous reports of linkage signals in complex traits are probably a consequence of polygenic architecture rather than the segregation of variants with large effects. The convergent empirical evidence from GWASs, de novo studies, and within-family segregation implies that family-based sequencing studies for complex traits require very large sample sizes because the effects of causal variants are small on average.", "doi": "10.1016/j.ajhg.2013.10.005", "pmid": "24183453", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9297(13)00462-X"}, {"db": "pmc", "key": "PMC3965855"}], "notes": [], "created": "2017-05-04T14:57:47.556Z", "modified": "2020-01-21T13:56:08.575Z"}, {"entity": "publication", "iuid": "5a8e5648af424a1daf3ce96a387a87de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a8e5648af424a1daf3ce96a387a87de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a8e5648af424a1daf3ce96a387a87de"}}, "title": "Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data.", "authors": [{"family": "Ahsan", "given": "Muhammad", "initials": "M"}, {"family": "Li", "given": "Xidan", "initials": "X"}, {"family": "Lundberg", "given": "Andreas E", "initials": "AE"}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Carlborg", "given": "Orjan", "initials": "O"}, {"family": "Marklund", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2013-11-05", "journal": {"volume": "4", "issn": "1664-8021", "issue": null, "pages": "226", "title": "Front Genet", "issn-l": "1664-8021"}, "abstract": "Mapping of chromosomal regions harboring genetic polymorphisms that regulate complex traits is usually followed by a search for the causative mutations underlying the observed effects. This is often a challenging task even after fine mapping, as millions of base pairs including many genes will typically need to be investigated. Thus to trace the causative mutation(s) there is a great need for efficient bioinformatic strategies. Here, we searched for genes and mutations regulating growth in the Virginia chicken lines - an experimental population comprising two lines that have been divergently selected for body weight at 56 days for more than 50 generations. Several quantitative trait loci (QTL) have been mapped in an F2 intercross between the lines, and the regions have subsequently been replicated and fine mapped using an Advanced Intercross Line. We have further analyzed the QTL regions where the largest genetic divergence between the High-Weight selected (HWS) and Low-Weight selected (LWS) lines was observed. Such regions, covering about 37% of the actual QTL regions, were identified by comparing the allele frequencies of the HWS and LWS lines using both individual 60K SNP chip genotyping of birds and analysis of read proportions from genome resequencing of DNA pools. Based on a combination of criteria including significance of the QTL, allele frequency difference of identified mutations between the selected lines, gene information on relevance for growth, and the predicted functional effects of identified mutations we propose here a subset of candidate mutations of highest priority for further evaluation in functional studies. The candidate mutations were identified within the GCG, IGFBP2, GRB14, CRIM1, FGF16, VEGFR-2, ALG11, EDN1, SNX6, and BIRC7 genes. We believe that the proposed method of combining different types of genomic information increases the probability that the genes underlying the observed QTL effects are represented among the candidate mutations identified.", "doi": "10.3389/fgene.2013.00226", "pmid": "24204379", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pmc", "key": "PMC3817360"}], "notes": [], "created": "2017-05-04T15:02:24.397Z", "modified": "2020-01-21T13:56:02.483Z"}, {"entity": "publication", "iuid": "9e71b1a3eb5349e9ac0dc76875ccf830", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e71b1a3eb5349e9ac0dc76875ccf830.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e71b1a3eb5349e9ac0dc76875ccf830"}}, "title": "In vitro and in vivo evaluation of osteoporosis therapeutic peptide PTH 1-34 loaded pegylated chitosan nanoparticles.", "authors": [{"family": "Narayanan", "given": "Deepa", "initials": "D"}, {"family": "Anitha", "given": "A", "initials": "A"}, {"family": "Jayakumar", "given": "R", "initials": "R"}, {"family": "Chennazhi", "given": "K P", "initials": "KP"}], "type": "journal article", "published": "2013-11-04", "journal": {"volume": "10", "issn": "1543-8392", "issue": "11", "pages": "4159-4167", "title": "Mol. Pharm.", "issn-l": "1543-8384"}, "abstract": "Oral formulation of human parathyroid hormone 1-34 (PTH 1-34) is an alternative patient compliant route in treating osteoporosis. PTH 1-34 loaded chitosan nanoparticles were PEGylated (PEG-CS-PTH NPs) and characterized by DLS, SEM, TEM and FTIR. PEG-CS-PTH NP aggregates of 200-250 nm which in turn comprised 20 nm individual nanoparticles were observed in SEM and TEM images respectively. The PEG-CS-PTH NP with 40% encapsulation efficiency was subjected to an in vitro release in simulated rat body fluids. PEG-CS-PTH NP treated human primary osteoblast cells, upon PTH 1-34 receptor activation, produced second messenger-cAMP, which downstream stimulated intracellular calcium uptake, production of bone specific alkaline phosphatase, osteocalcin etc., which substantiates the anabolic effect of the peptide. PEG-CS-PTH NPs showed an oral bioavailability of 100-160 pg/mL PTH 1-34 throughout 48 h, which is remarkable compared to the bare PTH 1-34 and CS-PTH NPs. The NIR image of gastrointestinal transit of ICG conjugated PEG-CS-PTH NPs supports this significant finding.", "doi": "10.1021/mp400184v", "pmid": "24006937", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:20.077Z", "modified": "2020-01-21T13:56:04.092Z"}, {"entity": "publication", "iuid": "1956081d2c194ceb9123bdd54fd2a414", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1956081d2c194ceb9123bdd54fd2a414.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1956081d2c194ceb9123bdd54fd2a414"}}, "title": "Combined in vitro-in vivo approach to assess the hepatobiliary disposition of a novel oral thrombin inhibitor.", "authors": [{"family": "Matsson", "given": "Elin M", "initials": "EM"}, {"family": "Eriksson", "given": "Ulf G", "initials": "UG"}, {"family": "Palm", "given": "Johan E", "initials": "JE"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Karlgren", "given": "Maria", "initials": "M"}, {"family": "Lazorova", "given": "Lucia", "initials": "L"}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Marie", "initials": "M"}, {"family": "Ekdahl", "given": "Anja", "initials": "A"}, {"family": "Dun\u00e9r", "given": "Kristina", "initials": "K"}, {"family": "Knutson", "given": "Lars", "initials": "L"}, {"family": "Johansson", "given": "Susanne", "initials": "S"}, {"family": "Sch\u00fctzer", "given": "Kajs-Marie", "initials": "K"}, {"family": "Lennern\u00e4s", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2013-11-04", "journal": {"volume": "10", "issn": "1543-8392", "issue": "11", "pages": "4252-4262", "title": "Mol. Pharm.", "issn-l": "1543-8384"}, "abstract": "Two clinical trials and a large set of in vitro transporter experiments were performed to investigate if the hepatobiliary disposition of the direct thrombin inhibitor prodrug AZD0837 is the mechanism for the drug-drug interaction with ketoconazole observed in a previous clinical study. In Study 1, [(3)H]AZD0837 was administered to healthy male volunteers (n = 8) to quantify and identify the metabolites excreted in bile. Bile was sampled directly from the jejunum by duodenal aspiration via an oro-enteric tube. In Study 2, the effect of ketoconazole on the plasma and bile pharmacokinetics of AZD0837, the intermediate metabolite (AR-H069927), and the active form (AR-H067637) was investigated (n = 17). Co-administration with ketoconazole elevated the plasma exposure to AZD0837 and the active form approximately 2-fold compared to placebo, which may be explained by inhibited CYP3A4 metabolism and reduced biliary clearance, respectively. High concentrations of the active form was measured in bile with a bile-to-plasma AUC ratio of approximately 75, indicating involvement of transporter-mediated excretion of the compound. AZD0837 and its metabolites were further investigated as substrates of hepatic uptake and efflux transporters in vitro. Studies in MDCK-MDR1 cell monolayers and P-glycoprotein (P-gp) expressing membrane vesicles identified AZD0837, the intermediate, and the active form as substrates of P-gp. The active form was also identified as a substrate of the multidrug and toxin extrusion 1 (MATE1) transporter and the organic cation transporter 1 (OCT1), in HEK cells transfected with the respective transporter. Ketoconazole was shown to inhibit all of these three transporters; in particular, inhibition of P-gp and MATE1 occurred in a clinically relevant concentration range. In conclusion, the hepatobiliary transport pathways of AZD0837 and its metabolites were identified in vitro and in vivo. Inhibition of the canalicular transporters P-gp and MATE1 may lead to enhanced plasma exposure to the active form, which could, at least in part, explain the clinical interaction with ketoconazole.", "doi": "10.1021/mp400341t", "pmid": "24079718", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": "Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)\r\nADME of Therapeutics (UDOPP)", "created": "2017-05-04T14:56:48.902Z", "modified": "2025-10-17T13:04:30.265Z"}, {"entity": "publication", "iuid": "a892d5f80fc540f693889b0cb504cfbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a892d5f80fc540f693889b0cb504cfbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a892d5f80fc540f693889b0cb504cfbe"}}, "title": "7,8- and 5,8-Linoleate diol synthases support the heterolytic scission of oxygen-oxygen bonds by different amide residues.", "authors": [{"family": "Hoffmann", "given": "Inga", "initials": "I"}, {"family": "Oliw", "given": "Ernst H", "initials": "EH"}], "type": "journal article", "published": "2013-11-01", "journal": {"volume": "539", "issn": "1096-0384", "issue": "1", "pages": "87-91", "title": "Arch. Biochem. Biophys.", "issn-l": "0003-9861"}, "abstract": "Linoleate diol synthases (LDS) are fungal dioxygenase-cytochrome P450 fusion enzymes. They oxidize 18:2n-6 sequentially to 8R-hydroperoxylinoleic acid (8R-HPODE) and 7S,8S- or 5S,8R-dihydroxylinoleic acids (DiHODE) by intramolecular oxygen transfer. The P450 domains contain a conserved sequence, Ala-Asn-Gln-Xaa-Gln, presumably located in the I-helices. The Asn938Leu replacement of 7,8-LDS of Gaeumannomyces graminis virtually abolished and the Asn938Asp and Asn938Gln replacements reduced the hydroperoxide isomerase activity. Gln941Leu and Gln941Glu substitutions had little effects. Replacements of the homologous Asn(887) and Gln(890) residues of 5,8-LDS of Aspergillus fumigatus yielded the opposite results. Asn887Leu and Asn887Gln of 5,8-LDS retained 5,8-DiHODE as the main metabolite with an increased formation of 6,8- and 8,11-DiHODE, whereas Gln890Leu almost abolished the 5,8-LDS activity. Replacement of Gln(890) with Glu also retained 5,8-DiHODE as the main product, but shifted oxygenation from C-5 to C-7 and C-11 and to formation of epoxyalcohols by homolytic scission of 8R-HPODE. P450 hydroxylases usually contain an \"acid-alcohol\" pair in the I-helices for the heterolytic scission of O2 and formation of compound I (Por(+) Fe(IV)=O) and water. The function of the acid-alcohol pair appears to be replaced by two different amide residues, Asn(938) of 7,8-LDS and Gln(890) of 5,8-LDS, for heterolysis of 8R-HPODE to generate compound I.", "doi": "10.1016/j.abb.2013.09.010", "pmid": "24060467", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0003-9861(13)00286-5"}], "notes": [], "created": "2017-05-04T15:02:18.533Z", "modified": "2020-01-21T13:56:04.386Z"}, {"entity": "publication", "iuid": "58e76170cfb442e4bd07dfbecc1442a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58e76170cfb442e4bd07dfbecc1442a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58e76170cfb442e4bd07dfbecc1442a9"}}, "title": "Wobble decoding by the Escherichia coli selenocysteine insertion machinery.", "authors": [{"family": "Xu", "given": "Jianqiang", "initials": "J"}, {"family": "Croitoru", "given": "Victor", "initials": "V"}, {"family": "Rutishauser", "given": "Dorothea", "initials": "D"}, {"family": "Cheng", "given": "Qing", "initials": "Q"}, {"family": "Arn\u00e9r", "given": "Elias S J", "initials": "ES"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "41", "issn": "1362-4962", "issue": "21", "pages": "9800-9811", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Selenoprotein expression in Escherichia coli redefines specific single UGA codons from translational termination to selenocysteine (Sec) insertion. This process requires the presence of a Sec Insertion Sequence (SECIS) in the mRNA, which forms a secondary structure that binds a unique Sec-specific elongation factor that catalyzes Sec insertion at the predefined UGA instead of release factor 2-mediated termination. During overproduction of recombinant selenoproteins, this process nonetheless typically results in expression of UGA-truncated products together with the production of recombinant selenoproteins. Here, we found that premature termination can be fully avoided through a SECIS-dependent Sec-mediated suppression of UGG, thereby yielding either tryptophan or Sec insertion without detectable premature truncation. The yield of recombinant selenoprotein produced with this method approached that obtained with a classical UGA codon for Sec insertion. Sec-mediated suppression of UGG thus provides a novel method for selenoprotein production, as here demonstrated with rat thioredoxin reductase. The results also reveal that the E. coli selenoprotein synthesis machinery has the inherent capability to promote wobble decoding.", "doi": "10.1093/nar/gkt764", "pmid": "23982514", "labels": {"Advanced Mass Spectrometry Proteomics": null}, "xrefs": [{"db": "pii", "key": "gkt764"}, {"db": "pmc", "key": "PMC3834832"}], "notes": [], "created": "2017-05-04T15:02:43.970Z", "modified": "2017-05-30T12:33:38.162Z"}, {"entity": "publication", "iuid": "4ef4aaece11743eca976ff9c1e0d76a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ef4aaece11743eca976ff9c1e0d76a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ef4aaece11743eca976ff9c1e0d76a7"}}, "title": "Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sj\u00f6gren's syndrome.", "authors": [{"family": "Lessard", "given": "Christopher J", "initials": "CJ"}, {"family": "Li", "given": "He", "initials": "H"}, {"family": "Adrianto", "given": "Indra", "initials": "I"}, {"family": "Ice", "given": "John A", "initials": "JA"}, {"family": "Rasmussen", "given": "Astrid", "initials": "A"}, {"family": "Grundahl", "given": "Kiely M", "initials": "KM"}, {"family": "Kelly", "given": "Jennifer A", "initials": "JA"}, {"family": "Dozmorov", "given": "Mikhail G", "initials": "MG"}, {"family": "Miceli-Richard", "given": "Corinne", "initials": "C"}, {"family": "Bowman", "given": "Simon", "initials": "S"}, {"family": "Lester", "given": "Sue", "initials": "S"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Brun", "given": "Johan G", "initials": "JG"}, {"family": "G\u00f8ransson", "given": "Lasse G", "initials": "LG"}, {"family": "Harboe", "given": "Erna", "initials": "E"}, {"family": "Guthridge", "given": "Joel M", "initials": "JM"}, {"family": "Kaufman", "given": "Kenneth M", "initials": "KM"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Jazebi", "given": "Helmi", "initials": "H"}, {"family": "Cunninghame Graham", "given": "Deborah S", "initials": "DS"}, {"family": "Grandits", "given": "Martha E", "initials": "ME"}, {"family": "Nazmul-Hossain", "given": "Abu N M", "initials": "AN"}, {"family": "Patel", "given": "Ketan", "initials": "K"}, {"family": "Adler", "given": "Adam J", "initials": "AJ"}, {"family": "Maier-Moore", "given": "Jacen S", "initials": "JS"}, {"family": "Farris", "given": "A Darise", "initials": "AD"}, {"family": "Brennan", "given": "Michael T", "initials": "MT"}, {"family": "Lessard", "given": "James A", "initials": "JA"}, {"family": "Chodosh", "given": "James", "initials": "J"}, {"family": "Gopalakrishnan", "given": "Rajaram", "initials": "R"}, {"family": "Hefner", "given": "Kimberly S", "initials": "KS"}, {"family": "Houston", "given": "Glen D", "initials": "GD"}, {"family": "Huang", "given": "Andrew J W", "initials": "AJ"}, {"family": "Hughes", "given": "Pamela J", "initials": "PJ"}, {"family": "Lewis", "given": "David M", "initials": "DM"}, {"family": "Radfar", "given": "Lida", "initials": "L"}, {"family": "Rohrer", "given": "Michael D", "initials": "MD"}, {"family": "Stone", "given": "Donald U", "initials": "DU"}, {"family": "Wren", "given": "Jonathan D", "initials": "JD"}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ"}, {"family": "Gaffney", "given": "Patrick M", "initials": "PM"}, {"family": "James", "given": "Judith A", "initials": "JA"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Illei", "given": "Gabor G", "initials": "GG"}, {"family": "Witte", "given": "Torsten", "initials": "T"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Rischmueller", "given": "Maureen", "initials": "M"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Ng", "given": "Wan-Fai", "initials": "WF"}, {"family": "UK Primary Sj\u00f6gren's Syndrome Registry", "given": null, "initials": null}, {"family": "Mariette", "given": "Xavier", "initials": "X"}, {"family": "Anaya", "given": "Juan-Manuel", "initials": "JM"}, {"family": "Rhodus", "given": "Nelson L", "initials": "NL"}, {"family": "Segal", "given": "Barbara M", "initials": "BM"}, {"family": "Scofield", "given": "R Hal", "initials": "RH"}, {"family": "Montgomery", "given": "Courtney G", "initials": "CG"}, {"family": "Harley", "given": "John B", "initials": "JB"}, {"family": "Sivils", "given": "Kathy L", "initials": "KL"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "45", "issn": "1546-1718", "issue": "11", "pages": "1284-1292", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Sj\u00f6gren's syndrome is a common autoimmune disease (affecting \u223c0.7% of European Americans) that typically presents as keratoconjunctivitis sicca and xerostomia. Here we report results of a large-scale association study of Sj\u00f6gren's syndrome. In addition to strong association within the human leukocyte antigen (HLA) region at 6p21 (Pmeta = 7.65 \u00d7 10(-114)), we establish associations with IRF5-TNPO3 (Pmeta = 2.73 \u00d7 10(-19)), STAT4 (Pmeta = 6.80 \u00d7 10(-15)), IL12A (Pmeta = 1.17 \u00d7 10(-10)), FAM167A-BLK (Pmeta = 4.97 \u00d7 10(-10)), DDX6-CXCR5 (Pmeta = 1.10 \u00d7 10(-8)) and TNIP1 (Pmeta = 3.30 \u00d7 10(-8)). We also observed suggestive associations (Pmeta < 5 \u00d7 10(-5)) with variants in 29 other regions, including TNFAIP3, PTTG1, PRDM1, DGKQ, FCGR2A, IRAK1BP1, ITSN2 and PHIP, among others. These results highlight the importance of genes that are involved in both innate and adaptive immunity in Sj\u00f6gren's syndrome.", "doi": "10.1038/ng.2792", "pmid": "24097067", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.2792"}, {"db": "pmc", "key": "PMC3867192"}, {"db": "mid", "key": "EMS54762"}], "notes": [], "created": "2017-05-04T15:01:23.896Z", "modified": "2020-01-21T13:56:02.242Z"}, {"entity": "publication", "iuid": "fdcdc8ea93584bc7be93efd313fc2982", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdcdc8ea93584bc7be93efd313fc2982.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdcdc8ea93584bc7be93efd313fc2982"}}, "title": "Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.", "authors": [{"family": "'t Hoen", "given": "Peter A C", "initials": "PA"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Alml\u00f6f", "given": "Jonas", "initials": "J"}, {"family": "Sammeth", "given": "Michael", "initials": "M"}, {"family": "Pulyakhina", "given": "Irina", "initials": "I"}, {"family": "Anvar", "given": "Seyed Yahya", "initials": "SY"}, {"family": "Laros", "given": "Jeroen F J", "initials": "JF"}, {"family": "Buermans", "given": "Henk P J", "initials": "HP"}, {"family": "Karlberg", "given": "Olof", "initials": "O"}, {"family": "Br\u00e4nnvall", "given": "Mathias", "initials": "M"}, {"family": "GEUVADIS Consortium", "given": null, "initials": null}, {"family": "den Dunnen", "given": "Johan T", "initials": "JT"}, {"family": "van Ommen", "given": "Gert-Jan B", "initials": "GJ"}, {"family": "Gut", "given": "Ivo G", "initials": "IG"}, {"family": "Guig\u00f3", "given": "Roderic", "initials": "R"}, {"family": "Estivill", "given": "Xavier", "initials": "X"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Dermitzakis", "given": "Emmanouil T", "initials": "ET"}, {"family": "Lappalainen", "given": "Tuuli", "initials": "T"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "31", "issn": "1546-1696", "issue": "11", "pages": "1015-1022", "title": "Nat. Biotechnol.", "issn-l": "1087-0156"}, "abstract": "RNA sequencing is an increasingly popular technology for genome-wide analysis of transcript sequence and abundance. However, understanding of the sources of technical and interlaboratory variation is still limited. To address this, the GEUVADIS consortium sequenced mRNAs and small RNAs of lymphoblastoid cell lines of 465 individuals in seven sequencing centers, with a large number of replicates. The variation between laboratories appeared to be considerably smaller than the already limited biological variation. Laboratory effects were mainly seen in differences in insert size and GC content and could be adequately corrected for. In small-RNA sequencing, the microRNA (miRNA) content differed widely between samples owing to competitive sequencing of rRNA fragments. This did not affect relative quantification of miRNAs. We conclude that distributing RNA sequencing among different laboratories is feasible, given proper standardization and randomization procedures. We provide a set of quality measures and guidelines for assessing technical biases in RNA-seq data.", "doi": "10.1038/nbt.2702", "pmid": "24037425", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "nbt.2702"}], "notes": [], "created": "2017-05-04T15:01:22.129Z", "modified": "2021-07-07T15:11:02.814Z"}, {"entity": "publication", "iuid": "3f85e6a78e4446b18a32b9417514858d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f85e6a78e4446b18a32b9417514858d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f85e6a78e4446b18a32b9417514858d"}}, "title": "Metal-mediated crystallization of the xylose transporter XylE from Escherichia coli in three different crystal forms.", "authors": [{"family": "Quistgaard", "given": "Esben M", "initials": "EM"}, {"family": "L\u00f6w", "given": "Christian", "initials": "C"}, {"family": "Moberg", "given": "Per", "initials": "P"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "184", "issn": "1095-8657", "issue": "2", "pages": "375-378", "title": "J. Struct. Biol.", "issn-l": "1047-8477"}, "abstract": "XylE is a major facilitator (MFS) xylose transporter, which is homologous to the mammalian glucose transporters (GLUT family). We have previously reported the structure of XylE in fully inward open and partially occluded inward open conformations in space groups P61 and C2, respectively. Here we present the crystallization of a third crystal form, P212121 (~4 \u00c5 resolution), also representing an inward facing conformation, and analyze all three forms in terms of crystallization conditions and packing. The crystallization conditions were generally very similar with only slight changes needed to favor one form over another, e.g. the presence of lanthanide ions greatly favors C2 over P212121 under otherwise identical conditions. Cadmium was essential for crystallization of all three forms, which indeed all contain a Cd(2+) ion in a crystal packing interface, though surprisingly in different positions. Cadmium was also found to bind to XylE in solution. The diffraction data were highly anisotropic for all forms, reflecting a lack of ordered crystal contacts along one or two of the cell axes. The best diffracting directions thus consistently correlate with the presence of ordered contacts, most of which are metal-mediated. The data presented here highlight the utility of metal ions in membrane protein crystallization and suggest that metal site engineering may be a productive path towards obtaining additional crystal forms of XylE and other membrane proteins.", "doi": "10.1016/j.jsb.2013.09.009", "pmid": "24060988", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "S1047-8477(13)00239-6"}], "notes": [], "created": "2017-05-04T15:03:48.801Z", "modified": "2017-09-06T11:42:09.053Z"}, {"entity": "publication", "iuid": "5eec2eb4880c440a81bb8c33a7186826", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5eec2eb4880c440a81bb8c33a7186826.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5eec2eb4880c440a81bb8c33a7186826"}}, "title": "Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi.", "authors": [{"family": "Meerupati", "given": "Tejashwari", "initials": "T"}, {"family": "Andersson", "given": "Karl-Magnus", "initials": "KM"}, {"family": "Friman", "given": "Eva", "initials": "E"}, {"family": "Kumar", "given": "Dharmendra", "initials": "D"}, {"family": "Tunlid", "given": "Anders", "initials": "A"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "9", "issn": "1553-7404", "issue": "11", "pages": "e1003909", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity in the Orbiliomycetes suggested that this mechanism was present early in the evolution of the filamentous ascomycetes.", "doi": "10.1371/journal.pgen.1003909", "pmid": "24244185", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-13-01003"}, {"db": "pmc", "key": "PMC3828140"}], "notes": [], "created": "2017-05-04T14:56:27.183Z", "modified": "2020-01-21T13:53:20.545Z"}, {"entity": "publication", "iuid": "29c8265f35684c9b9aa061f8bba87c57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29c8265f35684c9b9aa061f8bba87c57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29c8265f35684c9b9aa061f8bba87c57"}}, "title": "Genome-wide DNA methylation assay reveals novel candidate biomarker genes in cervical cancer.", "authors": [{"family": "Farkas", "given": "Sanja A", "initials": "SA"}, {"family": "Milutin-Ga\u0161perov", "given": "Nina", "initials": "N"}, {"family": "Grce", "given": "Magdalena", "initials": "M"}, {"family": "Nilsson", "given": "Torbj\u00f6rn K", "initials": "TK"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "8", "issn": "1559-2308", "issue": "11", "pages": "1213-1225", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "The oncogenic human papilloma viruses (HPVs) are associated with precancerous cervical lesions and development of cervical cancer. The DNA methylation signatures of the host genome in normal, precancerous and cervical cancer tissue may indicate tissue-specific perturbation in carcinogenesis. The aim of this study was to identify new candidate genes that are differentially methylated in squamous cell carcinoma compared with DNA samples from cervical intraepithelial neoplasia grade 3 (CIN3) and normal cervical scrapes. The Illumina Infinium HumanMethylation450 BeadChip method identifies genome-wide DNA methylation changes in CpG islands, CpG shores and shelves. Our findings showed an extensive differential methylation signature in cervical cancer compared with the CIN3 or normal cervical tissues. The identified candidate biomarker genes for cervical cancer represent several types of mechanisms in the cellular machinery that are epigenetically deregulated by hypermethylation, such as membrane receptors, intracellular signaling and gene transcription. The results also confirm extensive hypomethylation of genes in the immune system in cancer tissues. These insights into the functional role of DNA methylome alterations in cervical cancer could be clinically applicable in diagnostics and prognostics, and may guide the development of new epigenetic therapies.", "doi": "10.4161/epi.26346", "pmid": "24030264", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "26346"}], "notes": [], "created": "2017-05-04T15:01:17.049Z", "modified": "2020-01-21T13:56:01.204Z"}, {"entity": "publication", "iuid": "e587e6e01c2f47bda5c8997ebe8be351", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e587e6e01c2f47bda5c8997ebe8be351.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e587e6e01c2f47bda5c8997ebe8be351"}}, "title": "Discovery and refinement of loci associated with lipid levels.", "authors": [{"family": "Global Lipids Genetics Consortium", "given": "None", "initials": "N"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Schmidt", "given": "Ellen M", "initials": "EM"}, {"family": "Sengupta", "given": "Sebanti", "initials": "S"}, {"family": "Peloso", "given": "Gina M", "initials": "GM"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Chen", "given": "Jin", "initials": "J"}, {"family": "Buchkovich", "given": "Martin L", "initials": "ML"}, {"family": "Mora", "given": "Samia", "initials": "S"}, {"family": "Beckmann", "given": "Jacques S", "initials": "JS"}, {"family": "Bragg-Gresham", "given": "Jennifer L", "initials": "JL"}, {"family": "Chang", "given": "Hsing-Yi", "initials": "H"}, {"family": "Demirkan", "given": "Ay\u015fe", "initials": "A"}, {"family": "Den Hertog", "given": "Heleen M", "initials": "HM"}, {"family": "Do", "given": "Ron", "initials": "R"}, {"family": "Donnelly", "given": "Louise A", "initials": "LA"}, {"family": "Ehret", "given": "Georg B", "initials": "GB"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Ferreira", "given": "Teresa", "initials": "T"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Fontanillas", "given": "Pierre", "initials": "P"}, {"family": "Fraser", "given": "Ross M", "initials": "RM"}, {"family": "Freitag", "given": "Daniel F", "initials": "DF"}, {"family": "Gurdasani", "given": "Deepti", "initials": "D"}, {"family": "Heikkil\u00e4", "given": "Kauko", "initials": "K"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Kaakinen", "given": "Marika", "initials": "M"}, {"family": "Kettunen", "given": "Johannes", "initials": "J"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Li", "given": "Xiaohui", "initials": "X"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "L"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "Palmer", "given": "Cameron D", "initials": "CD"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Petersen", "given": "Ann-Kristin", "initials": "A"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Saxena", "given": "Richa", "initials": "R"}, {"family": "Service", "given": "Susan K", "initials": "SK"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Sidore", "given": "Carlo", "initials": "C"}, {"family": "Song", "given": "Ci", "initials": "C"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Van den Herik", "given": "Evita G", "initials": "EG"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Volcik", "given": "Kelly A", "initials": "KA"}, {"family": "Waite", "given": "Lindsay L", "initials": "LL"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Zhang", "given": 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"initials": "LS"}, {"family": "Arveiler", "given": "Dominique", "initials": "D"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Bennett", "given": "Franklyn", "initials": "F"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Boehm", "given": "Bernhard O", "initials": "BO"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Bovet", "given": "Pascal", "initials": "P"}, {"family": "Burnier", "given": "Michel", "initials": "M"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Chakravarti", "given": "Aravinda", "initials": "A"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Cooper", "given": "Richard S", "initials": "RS"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Feranil", "given": "Alan B", "initials": "AB"}, {"family": "Ferri\u00e8res", "given": "Jean", "initials": "J"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Freimer", "given": "Nelson B", "initials": "NB"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Groop", "given": "Leif C", "initials": "LC"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hingorani", "given": "Aroon", "initials": "A"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Hsiung", "given": "Chao Agnes", "initials": "CA"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Hunt", "given": "Steven C", "initials": "SC"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Iribarren", "given": "Carlos", "initials": "C"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Kes\u00e4niemi", "given": "Antero", "initials": "A"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Koudstaal", "given": "Peter J", "initials": "PJ"}, {"family": "Krauss", "given": "Ronald M", "initials": "RM"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Kyvik", "given": "Kirsten O", "initials": "KO"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "McKenzie", "given": "Colin A", "initials": "CA"}, {"family": "Meneton", "given": "Pierre", "initials": "P"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Moilanen", "given": "Leena", "initials": "L"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Nj\u00f8lstad", "given": "Inger", "initials": "I"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Price", "given": "Jackie F", "initials": "JF"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Quertermous", "given": "Thomas", "initials": "T"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Sanghera", "given": "Dharambir K", "initials": "DK"}, {"family": "Saramies", "given": "Jouko", "initials": "J"}, {"family": "Schwarz", "given": "Peter E H", "initials": "PEH"}, {"family": "Sheu", "given": "Wayne H-H", "initials": "WH"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Tayo", "given": "Bamidele O", "initials": "BO"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Uusitupa", "given": "Matti", "initials": "M"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BHR"}, {"family": "Ordovas", "given": "Jose M", "initials": "JM"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Sandhu", "given": "Manjinder S", "initials": "MS"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "45", "issn": "1546-1718", "issue": "11", "pages": "1274-1283", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Levels of low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides and total cholesterol are heritable, modifiable risk factors for coronary artery disease. To identify new loci and refine known loci influencing these lipids, we examined 188,577 individuals using genome-wide and custom genotyping arrays. We identify and annotate 157 loci associated with lipid levels at P < 5 \u00d7 10(-8), including 62 loci not previously associated with lipid levels in humans. Using dense genotyping in individuals of European, East Asian, South Asian and African ancestry, we narrow association signals in 12 loci. We find that loci associated with blood lipid levels are often associated with cardiovascular and metabolic traits, including coronary artery disease, type 2 diabetes, blood pressure, waist-hip ratio and body mass index. Our results demonstrate the value of using genetic data from individuals of diverse ancestry and provide insights into the biological mechanisms regulating blood lipids to guide future genetic, biological and therapeutic research.", "doi": "10.1038/ng.2797", "pmid": "24097068", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ng.2797"}, {"db": "pmc", "key": "PMC3838666"}, {"db": "mid", "key": "NIHMS524703"}], "notes": [], "created": "2017-05-04T14:58:07.437Z", "modified": "2020-01-21T13:56:08.815Z"}, {"entity": "publication", "iuid": "e9c9a297dc294e8a9b7a9be667c54458", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9c9a297dc294e8a9b7a9be667c54458.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9c9a297dc294e8a9b7a9be667c54458"}}, "title": "Comparative drug pair screening across multiple glioblastoma cell lines reveals novel drug-drug interactions.", "authors": [{"family": "Schmidt", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Kling", "given": "Teresia", "initials": "T"}, {"family": "Monsefi", "given": "Naser", "initials": "N"}, {"family": "Olsson", "given": "Maja", "initials": "M"}, {"family": "Hansson", "given": "Caroline", "initials": "C", "orcid": "0000-0001-6738-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f707f6560ae4e948196bf0f5abfa36f.json"}}, {"family": "Baskaran", "given": "Sathishkumar", "initials": "S"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M", "orcid": "0000-0002-3857-1437", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2b5f5d0486a4422b93a626a2cd1583f.json"}}, {"family": "Westermark", "given": "Bengt", "initials": "B", "orcid": "0000-0001-7153-5545", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbaf3a1cdd7d48e5ba9e147bfb5055b6.json"}}, {"family": "Forsberg Nilsson", "given": "Karin", "initials": "K"}, {"family": "Uhrbom", "given": "Lene", "initials": "L", "orcid": "0000-0001-8595-5698", "researcher": {"href": "https://publications.scilifelab.se/researcher/67bb8672ad514a9bb5f86c8d6b494269.json"}}, {"family": "Karlsson-Lindahl", "given": "Linda", "initials": "L"}, {"family": "Gerlee", "given": "Philip", "initials": "P"}, {"family": "Nelander", "given": "Sven", "initials": "S", "orcid": "0000-0003-1758-1262", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d684fc3b26d4741b850790ba0571c96.json"}}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "15", "issn": "1523-5866", "issue": "11", "pages": "1469-1478", "title": "Neuro-oncology", "issn-l": "1522-8517"}, "abstract": "Glioblastoma multiforme (GBM) is the most aggressive brain tumor in adults, and despite state-of-the-art treatment, survival remains poor and novel therapeutics are sorely needed. The aim of the present study was to identify new synergistic drug pairs for GBM. In addition, we aimed to explore differences in drug-drug interactions across multiple GBM-derived cell cultures and predict such differences by use of transcriptional biomarkers.\r\n\r\nWe performed a screen in which we quantified drug-drug interactions for 465 drug pairs in each of the 5 GBM cell lines U87MG, U343MG, U373MG, A172, and T98G. Selected interactions were further tested using isobole-based analysis and validated in 5 glioma-initiating cell cultures. Furthermore, drug interactions were predicted using microarray-based transcriptional profiling in combination with statistical modeling.\r\n\r\nOf the 5 \u00d7 465 drug pairs, we could define a subset of drug pairs with strong interaction in both standard cell lines and glioma-initiating cell cultures. In particular, a subset of pairs involving the pharmaceutical compounds rimcazole, sertraline, pterostilbene, and gefitinib showed a strong interaction in a majority of the cell cultures tested. Statistical modeling of microarray and interaction data using sparse canonical correlation analysis revealed several predictive biomarkers, which we propose could be of importance in regulating drug pair responses.\r\n\r\nWe identify novel candidate drug pairs for GBM and suggest possibilities to prospectively use transcriptional biomarkers to predict drug interactions in individual cases.", "doi": "10.1093/neuonc/not111", "pmid": "24101737", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "not111"}, {"db": "pmc", "key": "PMC3813417"}], "notes": "Biochemical and Cellular Screening", "created": "2017-05-04T14:57:02.204Z", "modified": "2025-10-23T08:55:35.813Z"}, {"entity": "publication", "iuid": "30b8dffde0b64a4fb0ffe52a1e453302", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30b8dffde0b64a4fb0ffe52a1e453302.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30b8dffde0b64a4fb0ffe52a1e453302"}}, "title": "Common variants associated with plasma triglycerides and risk for coronary artery disease.", "authors": [{"family": "Do", "given": "Ron", "initials": "R"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Schmidt", "given": "Ellen M", "initials": "EM"}, {"family": "Sengupta", "given": "Sebanti", "initials": "S"}, {"family": "Gao", "given": "Chi", "initials": "C"}, {"family": "Peloso", "given": "Gina M", "initials": "GM"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Chen", "given": "Jin", "initials": "J"}, {"family": "Buchkovich", "given": "Martin L", "initials": "ML"}, {"family": "Mora", "given": "Samia", "initials": "S"}, {"family": "Beckmann", "given": "Jacques S", "initials": "JS"}, {"family": "Bragg-Gresham", "given": "Jennifer L", "initials": "JL"}, {"family": "Chang", "given": "Hsing-Yi", "initials": "HY"}, {"family": "Demirkan", "given": "Ay\u015fe", "initials": "A"}, {"family": "Den Hertog", "given": "Heleen M", "initials": "HM"}, {"family": "Donnelly", "given": "Louise A", "initials": "LA"}, {"family": "Ehret", "given": "Georg B", "initials": "GB"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Ferreira", "given": "Teresa", "initials": "T"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Fontanillas", "given": "Pierre", "initials": "P"}, {"family": "Fraser", "given": "Ross M", "initials": "RM"}, {"family": "Freitag", "given": "Daniel F", "initials": "DF"}, {"family": "Gurdasani", "given": "Deepti", "initials": "D"}, {"family": "Heikkil\u00e4", "given": "Kauko", "initials": "K"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}, {"family": "Isaacs", "given": "Aaron", 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"initials": "P"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Moilanen", "given": "Leena", "initials": "L"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Nj\u00f8lstad", "given": "Inger", "initials": "I"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Price", "given": "Jackie F", "initials": "JF"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Quertermous", "given": "Thomas", "initials": "T"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Sanghera", "given": "Dharambir K", "initials": "DK"}, {"family": "Saramies", "given": "Jouko", "initials": "J"}, {"family": "Schwarz", "given": "Peter E H", "initials": "PE"}, {"family": "Sheu", "given": "Wayne H-H", "initials": "WH"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Tayo", "given": "Bamidele O", "initials": "BO"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Uusitupa", "given": "Matti", "initials": "M"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BH"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Ordovas", "given": "Jose M", "initials": "JM"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Palmer", "given": "Colin N A", "initials": "CN"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Sandhu", "given": "Manjinder S", "initials": "MS"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Abecasis", "given": "Goncalo R", "initials": "GR"}, {"family": "Daly", "given": "Mark J", "initials": "MJ"}, {"family": "Neale", "given": "Benjamin M", "initials": "BM"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "45", "issn": "1546-1718", "issue": "11", "pages": "1345-1352", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Triglycerides are transported in plasma by specific triglyceride-rich lipoproteins; in epidemiological studies, increased triglyceride levels correlate with higher risk for coronary artery disease (CAD). However, it is unclear whether this association reflects causal processes. We used 185 common variants recently mapped for plasma lipids (P < 5 \u00d7 10(-8) for each) to examine the role of triglycerides in risk for CAD. First, we highlight loci associated with both low-density lipoprotein cholesterol (LDL-C) and triglyceride levels, and we show that the direction and magnitude of the associations with both traits are factors in determining CAD risk. Second, we consider loci with only a strong association with triglycerides and show that these loci are also associated with CAD. Finally, in a model accounting for effects on LDL-C and/or high-density lipoprotein cholesterol (HDL-C) levels, the strength of a polymorphism's effect on triglyceride levels is correlated with the magnitude of its effect on CAD risk. These results suggest that triglyceride-rich lipoproteins causally influence risk for CAD.", "doi": "10.1038/ng.2795", "pmid": "24097064", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ng.2795"}, {"db": "pmc", "key": "PMC3904346"}, {"db": "mid", "key": "NIHMS524704"}], "notes": [], "created": "2017-05-04T14:58:07.053Z", "modified": "2020-01-21T13:56:01.359Z"}, {"entity": "publication", "iuid": "2a7cc31b9e5c4010a13eeec2c183d3af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a7cc31b9e5c4010a13eeec2c183d3af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a7cc31b9e5c4010a13eeec2c183d3af"}}, "title": "Association of genes in the NF-\u03baB pathway with antibody-positive primary Sj\u00f6gren's syndrome.", "authors": [{"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Wang", "given": "Chuan", "initials": "C"}, {"family": "Vasaitis", "given": "Lilian", "initials": "L"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Theander", "given": "Elke", "initials": "E"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Jazebi", "given": "Helmi", "initials": "H"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Reksten", "given": "Tove Ragna", "initials": "TR"}, {"family": "Brun", "given": "Johan G", "initials": "JG"}, {"family": "Jonsson", "given": "Malin V", "initials": "MV"}, {"family": "Johnsen", "given": "Svein J", "initials": "SJ"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Bowman", "given": "Simon", "initials": "S"}, {"family": "Ng", "given": "Wan-Fai", "initials": "WF"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "UK Primary Sj\u00f6gren\u2019s Syndrome Registry", "given": null, "initials": null}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "78", "issn": "1365-3083", "issue": "5", "pages": "447-454", "title": "Scand. J. Immunol.", "issn-l": "0300-9475"}, "abstract": "Primary Sj\u00f6gren's syndrome (SS) is a systemic autoimmune inflammatory disease characterized by focal lymphocytic infiltrates in the lachrymal and salivary glands and autoantibodies against the SSA/Ro and SSB/La antigens. Experimental studies have shown an activation of NF-\u03baB in primary SS. NF-\u03baB activation results in inflammation and autoimmunity and is regulated by inhibitory and activating proteins. Genetic studies have shown an association between multiple autoimmune diseases and TNFAIP3 (A20) and TNIP1 (ABIN1), both repressors of NF-\u03baB and of IKBKE (IKK\u03b5), which is an NF-\u03baB activator. The aim of this study was to analyse single nucleotide polymorphisms (SNPs) in the IKBKE, NFKB1, TNIP1 and TNFAIP3 genes for association with primary SS. A total of 12 SNPs were genotyped in 1105 patients from Scandinavia (Sweden and Norway, n = 684) and the UK (n = 421) and 4460 controls (Scandinavia, n = 1662, UK, n = 2798). When patients were stratified for the presence of anti-SSA and/or anti-SSB antibodies (n = 868), case-control meta-analysis found an association between antibody-positive primary SS and two SNPs in TNIP1 (P = 3.4 \u00d7 10(-5) , OR = 1.33, 95%CI: 1.16-1.52 for rs3792783 and P = 1.3 \u00d7 10(-3) , OR = 1.21, 95%CI: 1.08-1.36 for rs7708392). A TNIP1 risk haplotype was associated with antibody-positive primary SS (P = 5.7 \u00d7 10(-3) , OR = 1.47, 95%CI: 1.12-1.92). There were no significant associations with IKBKE, NFKB1 or TNFAIP3 in the meta-analysis of the Scandinavian and UK cohorts. We conclude that polymorphisms in TNIP1 are associated with antibody-positive primary SS.", "doi": "10.1111/sji.12101", "pmid": "23944604", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:30.803Z", "modified": "2021-07-07T15:11:02.362Z"}, {"entity": "publication", "iuid": "9bc18320f3eb4b8c84a460c382604ee3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bc18320f3eb4b8c84a460c382604ee3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bc18320f3eb4b8c84a460c382604ee3"}}, "title": "Antibodies biotinylated using a synthetic Z-domain from protein A provide stringent in situ protein detection.", "authors": [{"family": "Andersson", "given": "Sandra", "initials": "S"}, {"family": "Konrad", "given": "Anna", "initials": "A"}, {"family": "Ashok", "given": "Nikhil", "initials": "N"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Asplund", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2013-11-00", "journal": {"volume": "61", "issn": "1551-5044", "issue": "11", "pages": "773-784", "title": "J. Histochem. Cytochem.", "issn-l": "0022-1554"}, "abstract": "Antibody-based protein profiling on a global scale using immunohistochemistry constitutes an emerging strategy for mapping of the human proteome, which is crucial for an increased understanding of biological processes in the cell. Immunohistochemistry is often performed indirectly using secondary antibodies for detection, with the benefit of signal amplification. Direct immunohistochemistry instead brings the advantage of multiplexing; however, it requires labeling of the primary antibody. Many antibody-labeling kits do not specifically target IgG and may therefore cause labeling of stabilizing proteins present in the antibody solution. A new conjugation method has been developed that utilizes a modified Z-domain of protein A (ZBPA) to specifically target the Fc part of antibodies. The aim of the present study was to compare the ZBPA conjugation method and a commercially available labeling kit, Lightning-Link, for in situ protein detection. Fourteen antibodies were biotinylated with each method and stained using immunohistochemistry. For all antibodies tested, ZBPA biotinylation resulted in distinct immunoreactivity without off-target staining, regardless of the presence of stabilizing proteins in the buffer, whereas the majority of the Lightning-Link biotinylated antibodies displayed a characteristic pattern of nonspecific staining. We conclude that biotinylated ZBPA domain provides a stringent method for antibody biotinylation, advantageous for in situ protein detection in tissues.", "doi": "10.1369/0022155413502360", "pmid": "23920108", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "0022155413502360"}, {"db": "pmc", "key": "PMC3808578"}], "notes": [], "created": "2017-05-04T14:55:59.857Z", "modified": "2017-05-30T12:55:44.005Z"}, {"entity": "publication", "iuid": "892f7083f3cc432d9a2d0efb261333d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/892f7083f3cc432d9a2d0efb261333d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/892f7083f3cc432d9a2d0efb261333d3"}}, "title": "In situ Protein Detection for Companion Diagnostics.", "authors": [{"family": "Gremel", "given": "Gabriela", "initials": "G"}, {"family": "Grannas", "given": "Karin", "initials": "K"}, {"family": "Sutton", "given": "Lesley Ann", "initials": "LA"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Zieba", "given": "Agata", "initials": "A"}], "type": "journal article", "published": "2013-10-31", "journal": {"volume": "3", "issn": "2234-943X", "issue": null, "pages": "271", "title": "Front Oncol", "issn-l": "2234-943X"}, "abstract": "The emergence of targeted therapies for cancer has created a need for the development of companion diagnostic tests. Assays developed in recent years are aimed at determining both the effectiveness and safety of specific drugs for a defined group of patients, thus, enabling the more efficient design of clinical trials and also supporting physicians when making treatment-related decisions. Immunohistochemistry (IHC) is a widely accepted method for protein expression analyses in human tissues. Immunohistochemical assays, used to localize and quantitate relative protein expression levels within a morphological context, are frequently used as companion diagnostics during clinical trials and also following drug approval. Herein, we describe established immunochemistry-based methods and their application in routine diagnostics. We also explore the possibility of using IHC to detect specific protein mutations in addition to DNA-based tests. Finally, we review alternative protein binders and proximity ligation assays and discuss their potential to facilitate the development of novel, targeted therapies against cancer.", "doi": "10.3389/fonc.2013.00271", "pmid": "24199171", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pmc", "key": "PMC3814083"}], "notes": [], "created": "2017-05-04T14:55:57.752Z", "modified": "2017-05-31T07:54:59.926Z"}, {"entity": "publication", "iuid": "85f6c19f555c4c98970dbe95b129cc87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85f6c19f555c4c98970dbe95b129cc87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85f6c19f555c4c98970dbe95b129cc87"}}, "title": "Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress.", "authors": [{"family": "Butler", "given": "\u00c8ile", "initials": "\u00c8"}, {"family": "Alsterfjord", "given": "Magnus", "initials": "M"}, {"family": "Olofsson", "given": "Tobias C", "initials": "TC"}, {"family": "Karlsson", "given": "Christofer", "initials": "C"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "V\u00e1squez", "given": "Alejandra", "initials": "A"}], "type": "journal article", "published": "2013-10-22", "journal": {"volume": "13", "issn": "1471-2180", "issue": null, "pages": "235", "title": "BMC Microbiol.", "issn-l": "1471-2180"}, "abstract": "Lactic acid bacteria (LAB) has been considered a beneficial bacterial group, found as part of the microbiota of diverse hosts, including humans and various animals. However, the mechanisms of how hosts and LAB interact are still poorly understood. Previous work demonstrates that 13 species of Lactobacillus and Bifidobacterium from the honey crop in bees function symbiotically with the honeybee. They protect each other, their hosts, and the surrounding environment against severe bee pathogens, bacteria, and yeasts. Therefore, we hypothesized that these LAB under stress, i.e. in their natural niche in the honey crop, are likely to produce bioactive substances with antimicrobial activity.\n\nThe genomic analysis of the LAB demonstrated varying genome sizes ranging from 1.5 to 2.2 mega-base pairs (Mbps) which points out a clear difference within the protein gene content, as well as specialized functions in the honeybee microbiota and their adaptation to their host. We demonstrate a clear variation between the secreted proteins of the symbiotic LAB when subjected to microbial stressors. We have identified that 10 of the 13 LAB produced extra-cellular proteins of known or unknown function in which some are arranged in interesting putative operons that may be involved in antimicrobial action, host interaction, or biofilm formation. The most common known extra-cellular proteins secreted were enzymes, DNA chaperones, S-layer proteins, bacteriocins, and lysozymes. A new bacteriocin may have been identified in one of the LAB symbionts while many proteins with unknown functions were produced which must be investigated further.\n\nThe 13 LAB symbionts likely play different roles in their natural environment defending their niche and their host and participating in the honeybee's food production. These roles are partly played through producing extracellular proteins on exposure to microbial stressors widely found in natural occurring flowers. Many of these secreted proteins may have a putative antimicrobial function. In the future, understanding these processes in this complicated environment may lead to novel applications of honey crop LAB proteins.", "doi": "10.1186/1471-2180-13-235", "pmid": "24148670", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2180-13-235"}, {"db": "pmc", "key": "PMC4015849"}, {"db": "GENBANK", "key": "KC776061"}, {"db": "GENBANK", "key": "KC776062"}, {"db": "GENBANK", "key": "KC776063"}, {"db": "GENBANK", "key": "KC776064"}, {"db": "GENBANK", "key": "KC776065"}, {"db": "GENBANK", "key": "KC776066"}, {"db": "GENBANK", "key": "KC776067"}, {"db": "GENBANK", "key": "KC776068"}, {"db": "GENBANK", "key": "KC776069"}, {"db": "GENBANK", "key": "KC776070"}, {"db": "GENBANK", "key": "KC776071"}, {"db": "GENBANK", "key": "KC776073"}, {"db": "GENBANK", "key": "KC776074"}, {"db": "GENBANK", "key": "KC776075"}, {"db": "GENBANK", "key": "KC776076"}, {"db": "GENBANK", "key": "KC776077"}, {"db": "GENBANK", "key": "KC776078"}, {"db": "GENBANK", "key": "KC776079"}, {"db": "GENBANK", "key": "KC776080"}, {"db": "GENBANK", "key": "KC776081"}, {"db": "GENBANK", "key": "KC776082"}, {"db": "GENBANK", "key": "KC776083"}, {"db": "GENBANK", "key": "KC776084"}, {"db": "GENBANK", "key": "KC776085"}, {"db": "GENBANK", "key": "KC776086"}, {"db": "GENBANK", "key": "KC776087"}, {"db": "GENBANK", "key": "KC776088"}, {"db": "GENBANK", "key": "KC776089"}, {"db": "GENBANK", "key": "KC776090"}, {"db": "GENBANK", "key": "KC776091"}, {"db": "GENBANK", "key": "KC776092"}, {"db": "GENBANK", "key": "KC776093"}, {"db": "GENBANK", "key": "KC776094"}, {"db": "GENBANK", "key": "KC776095"}, {"db": "GENBANK", "key": "KC776096"}, {"db": "GENBANK", "key": "KC776097"}, {"db": "GENBANK", "key": "KC776098"}, {"db": "GENBANK", "key": "KC776099"}, {"db": "GENBANK", "key": "KC776100"}, {"db": "GENBANK", "key": "KC776101"}, {"db": "GENBANK", "key": "KC776102"}, {"db": "GENBANK", "key": "KC776103"}, {"db": "GENBANK", "key": "KC776104"}, {"db": "GENBANK", "key": "KC776105"}, {"db": "GENBANK", "key": "KC776106"}, {"db": "GENBANK", "key": "KC776107"}, {"db": "GENBANK", "key": "KC776108"}, {"db": "GENBANK", "key": "KC776109"}, {"db": "GENBANK", "key": "KC776110"}, {"db": "GENBANK", "key": "KC776111"}, {"db": "GENBANK", "key": "KC789963"}, {"db": "GENBANK", "key": "KC789964"}, {"db": "GENBANK", "key": "KC789965"}, {"db": "GENBANK", "key": "KC789966"}, {"db": "GENBANK", "key": "KC789967"}, {"db": "GENBANK", "key": "KC789968"}, {"db": "GENBANK", "key": "KC789969"}, {"db": "GENBANK", "key": "KC789970"}, {"db": "GENBANK", "key": "KC789971"}, {"db": "GENBANK", "key": "KC789972"}, {"db": "GENBANK", "key": "KC789973"}, {"db": "GENBANK", "key": "KC789974"}, {"db": "GENBANK", "key": "KC789975"}, {"db": "GENBANK", "key": "KC789976"}, {"db": "GENBANK", "key": "KC789977"}, {"db": "GENBANK", "key": "KC789978"}, {"db": "GENBANK", "key": "KC789979"}, {"db": "GENBANK", "key": "KC789980"}, {"db": "GENBANK", "key": "KC789981"}, {"db": "GENBANK", "key": "KC789982"}, {"db": "GENBANK", "key": "KC789983"}, {"db": "GENBANK", "key": "KC789984"}, {"db": "GENBANK", "key": "KC789985"}, {"db": "GENBANK", "key": "KC789986"}, {"db": "GENBANK", "key": "KC789987"}, {"db": "GENBANK", "key": "KC789988"}, {"db": "GENBANK", "key": "KC789989"}, {"db": "GENBANK", "key": "KC789990"}, {"db": "GENBANK", "key": "KC789991"}, {"db": "GENBANK", "key": "KC789992"}, {"db": "GENBANK", "key": "KC789993"}, {"db": "GENBANK", "key": "KC789994"}, {"db": "GENBANK", "key": "KC789995"}, {"db": "GENBANK", "key": "KC789996"}, {"db": "GENBANK", "key": "KC789997"}, {"db": "GENBANK", "key": "KC789998"}, {"db": "GENBANK", "key": "KC789999"}, {"db": "GENBANK", "key": "KC790000"}, {"db": "GENBANK", "key": "KC790001"}, {"db": "GENBANK", "key": "KC790002"}, {"db": "GENBANK", "key": "KC790003"}, {"db": "GENBANK", "key": "KC790004"}, {"db": "GENBANK", "key": "KC790005"}, {"db": "GENBANK", "key": "KC790006"}, {"db": "GENBANK", "key": "KC790007"}, {"db": "GENBANK", "key": "KC790008"}, {"db": "GENBANK", "key": "KC790009"}, {"db": "GENBANK", "key": "KC790010"}, {"db": "GENBANK", "key": "KC790011"}, {"db": "GENBANK", "key": "KC790012"}, {"db": "GENBANK", "key": "KC790013"}, {"db": "GENBANK", "key": "KC790014"}, {"db": "GENBANK", "key": "KC790015"}, {"db": "GENBANK", "key": "KC790016"}, {"db": "GENBANK", "key": "KC790017"}, {"db": "GENBANK", "key": "KC790018"}, {"db": "GENBANK", "key": "KC801035"}], "notes": [], "created": "2017-05-04T14:56:21.844Z", "modified": "2020-01-21T13:53:20.622Z"}, {"entity": "publication", "iuid": "02d4edc9fa77447d8b1c217f69c866b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02d4edc9fa77447d8b1c217f69c866b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02d4edc9fa77447d8b1c217f69c866b7"}}, "title": "Nanobody mediated crystallization of an archeal mechanosensitive channel.", "authors": [{"family": "L\u00f6w", "given": "Christian", "initials": "C"}, {"family": "Yau", "given": "Yin Hoe", "initials": "YH"}, {"family": "Pardon", "given": "Els", "initials": "E"}, {"family": "Jegersch\u00f6ld", "given": "Caroline", "initials": "C"}, {"family": "W\u00e5hlin", "given": "Lisa", "initials": "L"}, {"family": "Quistgaard", "given": "Esben M", "initials": "EM"}, {"family": "Moberg", "given": "Per", "initials": "P"}, {"family": "Geifman-Shochat", "given": "Susana", "initials": "S"}, {"family": "Steyaert", "given": "Jan", "initials": "J"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2013-10-21", "journal": {"volume": "8", "issn": "1932-6203", "issue": "10", "pages": "e77984", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Mechanosensitive channels (MS) are integral membrane proteins and allow bacteria to survive sudden changes in external osmolarity due to transient opening of their pores. The efflux of cytoplasmic osmolytes reduces the membrane tension and prevents membrane rupture. Therefore these channels serve as emergency valves when experiencing significant environmental stress. The preparation of high quality crystals of integral membrane proteins is a major bottleneck for structure determination by X-ray crystallography. Crystallization chaperones based on various protein scaffolds have emerged as promising tool to increase the crystallization probability of a selected target protein. So far archeal mechanosensitive channels of small conductance have resisted crystallization in our hands. To structurally analyse these channels, we selected nanobodies against an archeal MS channel after immunization of a llama with recombinant expressed, detergent solubilized and purified protein. Here we present the characterization of 23 different binders regarding their interaction with the channel protein using analytical gel filtration, western blotting and surface plasmon resonance. Selected nanobodies bound the target with affinities in the pico- to nanomolar range and some binders had a profound effect on the crystallization of the MS channel. Together with previous data we show that nanobodies are a versatile and valuable tool in structural biology by widening the crystallization space for highly challenging proteins, protein complexes and integral membrane proteins.", "doi": "10.1371/journal.pone.0077984", "pmid": "24205053", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-33201"}, {"db": "pmc", "key": "PMC3804602"}], "notes": [], "created": "2017-05-04T15:03:50.036Z", "modified": "2017-09-06T11:42:08.932Z"}, {"entity": "publication", "iuid": "8bdc034874724611ab7e81f7f3a523c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8bdc034874724611ab7e81f7f3a523c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8bdc034874724611ab7e81f7f3a523c3"}}, "title": "Eleven candidate susceptibility genes for common familial colorectal cancer.", "authors": [{"family": "Gylfe", "given": "Alexandra E", "initials": "AE"}, {"family": "Katainen", "given": "Riku", "initials": "R"}, {"family": "Kondelin", "given": "Johanna", "initials": "J"}, {"family": "Tanskanen", "given": "Tomas", "initials": "T"}, {"family": "Cajuso", "given": "Tatiana", "initials": "T"}, {"family": "H\u00e4nninen", "given": "Ulrika", "initials": "U"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}, {"family": "Taipale", "given": "Minna", "initials": "M"}, {"family": "Renkonen-Sinisalo", "given": "Laura", "initials": "L"}, {"family": "J\u00e4rvinen", "given": "Heikki", "initials": "H"}, {"family": "Mecklin", "given": "Jukka-Pekka", "initials": "JP"}, {"family": "Kilpivaara", "given": "Outi", "initials": "O"}, {"family": "Pitk\u00e4nen", "given": "Esa", "initials": "E"}, {"family": "Vahteristo", "given": "Pia", "initials": "P"}, {"family": "Tuupanen", "given": "Sari", "initials": "S"}, {"family": "Karhu", "given": "Auli", "initials": "A"}, {"family": "Aaltonen", "given": "Lauri A", "initials": "LA"}], "type": "journal article", "published": "2013-10-17", "journal": {"volume": "9", "issn": "1553-7404", "issue": "10", "pages": "e1003876", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Hereditary factors are presumed to play a role in one third of colorectal cancer (CRC) cases. However, in the majority of familial CRC cases the genetic basis of predisposition remains unexplained. This is particularly true for families with few affected individuals. To identify susceptibility genes for this common phenotype, we examined familial cases derived from a consecutive series of 1514 Finnish CRC patients. Ninety-six familial CRC patients with no previous diagnosis of a hereditary CRC syndrome were included in the analysis. Eighty-six patients had one affected first-degree relative, and ten patients had two or more. Exome sequencing was utilized to search for genes harboring putative loss-of-function variants, because such alterations are likely candidates for disease-causing mutations. Eleven genes with rare truncating variants in two or three familial CRC cases were identified: UACA, SFXN4, TWSG1, PSPH, NUDT7, ZNF490, PRSS37, CCDC18, PRADC1, MRPL3, and AKR1C4. Loss of heterozygosity was examined in all respective cancer samples, and was detected in seven occasions involving four of the candidate genes. In all seven occasions the wild-type allele was lost (P = 0.0078) providing additional evidence that these eleven genes are likely to include true culprits. The study provides a set of candidate predisposition genes which may explain a subset of common familial CRC. Additional genetic validation in other populations is required to provide firm evidence for causality, as well as to characterize the natural history of the respective phenotypes.", "doi": "10.1371/journal.pgen.1003876", "pmid": "24146633", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-13-01401"}, {"db": "pmc", "key": "PMC3798264"}], "notes": [], "created": "2017-05-04T14:57:06.590Z", "modified": "2017-05-30T14:30:18.659Z"}, {"entity": "publication", "iuid": "21a96555ec1b4b9faeb9d22a4c6c6c25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21a96555ec1b4b9faeb9d22a4c6c6c25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21a96555ec1b4b9faeb9d22a4c6c6c25"}}, "title": "Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker.", "authors": [{"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Worah", "given": "Kuntal", "initials": "K"}, {"family": "Wang", "given": "Shugui", "initials": "S"}, {"family": "Hibberd", "given": "Martin Lloyd", "initials": "ML"}, {"family": "Sj\u00f6vall", "given": "Henrik", "initials": "H"}, {"family": "Pettersson", "given": "Sven", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Lundin", "given": "Samuel B", "initials": "SB"}], "type": "journal article", "published": "2013-10-11", "journal": {"volume": "6", "issn": "1755-8794", "issue": null, "pages": "41", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "The majority of gastric cancer cases are believed to be caused by chronic infection with the bacterium Helicobacter pylori, and atrophic corpus gastritis is a predisposing condition to gastric cancer development. We aimed to increase understanding of the molecular details of atrophy by performing a global transcriptome analysis of stomach tissue.\n\nBiopsies from patients with different stages of H. pylori infection were taken from both the antrum and corpus mucosa and analyzed on microarrays. The stages included patients without current H. pylori infection, H. pylori-infected without corpus atrophy and patients with current or past H. pylori-infection with corpus-predominant atrophic gastritis.\n\nUsing clustering and integrated analysis, we found firm evidence for antralization of the corpus mucosa of atrophy patients. This antralization harbored gain of gastrin expression, as well as loss of expression of corpus-related genes, such as genes associated with acid production, energy metabolism and blood clotting. The analyses provided detailed molecular evidence for simultaneous intestinal metaplasia (IM) and spasmolytic polypeptide expressing metaplasia (SPEM) in atrophic corpus tissue. Finally, acidic mammalian chitinase, a chitin-degrading enzyme produced by chief cells, was shown to be strongly down-regulated in corpus atrophy.\n\nTranscriptome analysis revealed several gene groups which are related to development of corpus atrophy, some of which were increased also in H. pylori-infected non-atrophic patients. Furthermore, loss of acidic chitinase expression is a promising marker for corpus atrophy.", "doi": "10.1186/1755-8794-6-41", "pmid": "24119614", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1755-8794-6-41"}, {"db": "pmc", "key": "PMC4015281"}], "notes": [], "created": "2017-05-04T14:56:21.543Z", "modified": "2021-07-05T13:05:37.549Z"}, {"entity": "publication", "iuid": "da203131eb704581a609bf3f880db815", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da203131eb704581a609bf3f880db815.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da203131eb704581a609bf3f880db815"}}, "title": "Divergent structure-activity relationships of structurally similar acetylcholinesterase inhibitors.", "authors": [{"family": "Andersson", "given": "C David", "initials": "CD"}, {"family": "Forsgren", "given": "Nina", "initials": "N"}, {"family": "Akfur", "given": "Christine", "initials": "C"}, {"family": "Allgardsson", "given": "Anders", "initials": "A"}, {"family": "Berg", "given": "Lotta", "initials": "L"}, {"family": "Engdahl", "given": "Cecilia", "initials": "C"}, {"family": "Qian", "given": "Weixing", "initials": "W"}, {"family": "Ekstr\u00f6m", "given": "Fredrik", "initials": "F"}, {"family": "Linusson", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2013-10-10", "journal": {"volume": "56", "issn": "1520-4804", "issue": "19", "pages": "7615-7624", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": "The molecular interactions between the enzyme acetylcholinesterase (AChE) and two compound classes consisting of N-[2-(diethylamino)ethyl]benzenesulfonamides and N-[2-(diethylamino)ethyl]benzenemethanesulfonamides have been investigated using organic synthesis, enzymatic assays, X-ray crystallography, and thermodynamic profiling. The inhibitors' aromatic properties were varied to establish structure-activity relationships (SAR) between the inhibitors and the peripheral anionic site (PAS) of AChE. The two structurally similar compound classes proved to have distinctly divergent SARs in terms of their inhibition capacity of AChE. Eight X-ray structures revealed that the two sets have different conformations in PAS. Furthermore, thermodynamic profiles of the binding between compounds and AChE revealed class-dependent differences of the entropy/enthalpy contributions to the free energy of binding. Further development of the entropy-favored compound class resulted in the synthesis of the most potent inhibitor and an extension beyond the established SARs. The divergent SARs will be utilized to develop reversible inhibitors of AChE into reactivators of nerve agent-inhibited AChE.", "doi": "10.1021/jm400990p", "pmid": "23984975", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:40.023Z", "modified": "2025-10-17T13:04:30.280Z"}, {"entity": "publication", "iuid": "c522f5cf12954e2ca97ffac12e5e0bfb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c522f5cf12954e2ca97ffac12e5e0bfb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c522f5cf12954e2ca97ffac12e5e0bfb"}}, "title": "Chemical fragmentation for massively parallel sequencing library preparation.", "authors": [{"family": "Gyarmati", "given": "P", "initials": "P"}, {"family": "Song", "given": "Y", "initials": "Y"}, {"family": "H\u00e4llman", "given": "J", "initials": "J"}, {"family": "K\u00e4ller", "given": "M", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}], "type": "journal article", "published": "2013-10-10", "journal": {"volume": "168", "issn": "1873-4863", "issue": "1", "pages": "95-100", "title": "J. Biotechnol.", "issn-l": "0168-1656"}, "abstract": "Fragmentation is essential in most library preparation protocols for use with massively parallel sequencing systems. Complexes that generate hydroxyl radicals, such as iron-EDTA, can be used to introduce random DNA cleavage. Here we describe a chemical fragmentation method that can be incorporated into library preparation protocols for next-generation sequencing workflows. This protocol has been validated by whole genome, amplicon and exome sequencing. Chemical fragmentation is a cost-effective alternative to current fragmentation methods that has no observable sequence bias and requires no instrumentation.", "doi": "10.1016/j.jbiotec.2013.08.020", "pmid": "23994687", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0168-1656(13)00365-9"}], "notes": [], "created": "2017-05-04T14:57:59.697Z", "modified": "2021-07-07T15:22:42.796Z"}, {"entity": "publication", "iuid": "dc5fe3e123854fb6b55ca080222083e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc5fe3e123854fb6b55ca080222083e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc5fe3e123854fb6b55ca080222083e0"}}, "title": "Molecular characterization of the \u03b1-subunit of Na\u207a/K\u207a ATPase from the euryhaline barnacle Balanus improvisus reveals multiple genes and differential expression of alternative splice variants.", "authors": [{"family": "Lind", "given": "Ulrika", "initials": "U"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Wrange", "given": "Anna-Lisa", "initials": "AL"}, {"family": "Sundell", "given": "Kristina S", "initials": "KS"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Havenhand", "given": "Jonathan", "initials": "J"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2013-10-09", "journal": {"volume": "8", "issn": "1932-6203", "issue": "10", "pages": "e77069", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The euryhaline bay barnacle Balanus improvisus has one of the broadest salinity tolerances of any barnacle species. It is able to complete its life cycle in salinities close to freshwater (3 PSU) up to fully marine conditions (35 PSU) and is regarded as one of few truly brackish-water species. Na\u207a/K\u207a ATPase (NAK) has been shown to be important for osmoregulation when marine organisms are challenged by changing salinities, and we therefore cloned and examined the expression of different NAKs from B. improvisus. We found two main gene variants, NAK1 and NAK2, which were approximately 70% identical at the protein level. The NAK1 mRNA existed in a long and short variant with the encoded proteins differing only by 27 N-terminal amino acids. This N-terminal stretch was coded for by a separate exon, and the two variants of NAK1 mRNAs appeared to be created by alternative splicing. We furthermore showed that the two NAK1 isoforms were differentially expressed in different life stages and in various tissues of adult barnacle, i.e the long isoform was predominant in cyprids and in adult cirri. In barnacle cyprid larvae that were exposed to a combination of different salinities and pCO2 levels, the expression of the long NAK1 mRNA increased relative to the short in low salinities. We suggest that the alternatively spliced long variant of the Nak1 protein might be of importance for osmoregulation in B. improvisus in low salinity conditions.", "doi": "10.1371/journal.pone.0077069", "pmid": "24130836", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-40484"}, {"db": "pmc", "key": "PMC3793950"}, {"db": "GENBANK", "key": "KC357568"}, {"db": "GENBANK", "key": "KC357569"}, {"db": "GENBANK", "key": "KC357570"}], "notes": [], "created": "2017-05-04T14:56:27.783Z", "modified": "2020-01-21T13:53:20.916Z"}, {"entity": "publication", "iuid": "686aa4bcce6a41fba7fb74f8e6951f2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/686aa4bcce6a41fba7fb74f8e6951f2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/686aa4bcce6a41fba7fb74f8e6951f2f"}}, "title": "Brain proteomics supports the role of glutamate metabolism and suggests other metabolic alterations in protein l-isoaspartyl methyltransferase (PIMT)-knockout mice.", "authors": [{"family": "Yang", "given": "Hongqian", "initials": "H"}, {"family": "Lowenson", "given": "Jonathan D", "initials": "JD"}, {"family": "Clarke", "given": "Steven", "initials": "S"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2013-10-04", "journal": {"volume": "12", "issn": "1535-3907", "issue": "10", "pages": "4566-4576", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Protein l-isoaspartyl methyltransferase (PIMT) repairs the isoaspartyl residues (isoAsp) that originate from asparagine deamidation and aspartic acid (Asp) isomerization to Asp residues. Deletion of the gene encoding PIMT in mice (Pcmt1) leads to isoAsp accumulation in all tissues measured, especially in the brain. These PIMT-knockout (PIMT-KO) mice have perturbed glutamate metabolism and die prematurely of epileptic seizures. To elucidate the role of PIMT further, brain proteomes of PIMT-KO mice and controls were analyzed. The isoAsp levels from two of the detected 67 isoAsp sites (residue 98 from calmodulin and 68 from glyceraldehyde-3-phosphate dehydrogenase) were quantified and found to be significantly increased in PIMT-KO mice (p < 0.01). Additionally, the abundance of at least 151 out of the 1017 quantified proteins was found to be altered in PIMT-KO mouse brains. Gene ontology analysis revealed that many down-regulated proteins are involved in cellular amino acid biosynthesis. For example, the serine synthesis pathway was suppressed, possibly leading to reduced serine production in PIMT-KO mice. Additionally, the abundances of enzymes in the glutamate-glutamine cycle were altered toward the accumulation of glutamate. These findings support the involvement of PIMT in glutamate metabolism and suggest that the absence of PIMT also affects other processes involving amino acid synthesis and metabolism.", "doi": "10.1021/pr400688r", "pmid": "23947766", "labels": {"Advanced Mass Spectrometry Proteomics": null}, "xrefs": [{"db": "pmc", "key": "PMC3818641"}, {"db": "mid", "key": "NIHMS523577"}], "notes": [], "created": "2017-05-04T15:02:43.071Z", "modified": "2021-07-08T08:58:46.782Z"}, {"entity": "publication", "iuid": "ecd33147407149de9276b0a5ad1a1889", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecd33147407149de9276b0a5ad1a1889.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecd33147407149de9276b0a5ad1a1889"}}, "title": "Aneuploidy in neuroblastoma tumors is not associated with inactivating point mutations in the STAG2 gene.", "authors": [{"family": "Djos", "given": "Anna", "initials": "A"}, {"family": "Fransson", "given": "Susanne", "initials": "S"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Martinsson", "given": "Tommy", "initials": "T"}], "type": "journal article", "published": "2013-10-02", "journal": {"volume": "14", "issn": "1471-2350", "issue": null, "pages": "102", "title": "BMC Med. Genet.", "issn-l": "1471-2350"}, "abstract": "Chromosomal instability is a hallmark of human cancer caused by errors in mitotic control and chromosome segregation. STAG2 encodes a subunit of the cohesion complex that participates in mitotic chromatid separation and was recently found to show low expression and inactivating mutations in Ewing's sarcoma, melanoma and glioblastoma.In the childhood tumor neuroblastoma (NB) segmental chromosomal alterations are associated with poor prognosis whereas tumors displaying whole chromosome gains and losses have a much better prognosis.\n\nAs the genetic contribution to aneuploidy is unknown in NB, we investigated the presence of STAG2 mutations through sequence analysis of all 33 coding exons in 37 primary NB tumors.\n\nAs no STAG2 mutation was detected in this study, we conclude that inactivating mutation of STAG2 is not likely causative to neuroblastoma aneuploidy.", "doi": "10.1186/1471-2350-14-102", "pmid": "24088605", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2350-14-102"}, {"db": "pmc", "key": "PMC3853135"}], "notes": [], "created": "2017-05-04T14:57:49.997Z", "modified": "2020-01-21T13:56:06.046Z"}, {"entity": "publication", "iuid": "b9bc7928871643598f2d013eada8cf22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9bc7928871643598f2d013eada8cf22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9bc7928871643598f2d013eada8cf22"}}, "title": "Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells.", "authors": [{"family": "Wang", "given": "Xuan", "initials": "X"}, {"family": "Jiang", "given": "Lin", "initials": "L"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Engstr\u00f6m", "given": "Ulla", "initials": "U"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Gupta", "given": "Rajesh Kumar", "initials": "RK"}, {"family": "Qi", "given": "Yu", "initials": "Y"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Welsh", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2013-10-01", "journal": {"volume": "110", "issn": "1091-6490", "issue": "40", "pages": "15997-16002", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "We have investigated whether the recently discovered transcription factor, zinc finger BED domain-containing protein 6 (ZBED6), is expressed in insulin-producing cells and, if so, to what extent it affects beta cell function. ZBED6 was translated from a ZC3H11A transcript in which the ZBED6-containing intron was retained. ZBED6 was present in mouse \u03b2TC-6 cells and human islets as a double nuclear band at 115/120 kDa and as a single cytoplasmic band at 95-100 kDa, which lacked N-terminal nuclear localization signals. We propose that ZBED6 supports proliferation and survival of beta cells, possibly at the expense of specialized beta cell function-i.e., insulin production-because (i) the nuclear ZBED6 were the predominant forms in rapidly proliferating \u03b2TC-6 cells, but not in human islet cells; (ii) down-regulation of ZBED6 in \u03b2TC-6 cells resulted in altered morphology, decreased proliferation, a partial S/G2 cell-cycle arrest, increased expression of beta cell-specific genes, and higher rates of apoptosis; (iii) silencing of ZBED6 in the human PANC-1 duct cell line reduced proliferation rates; and (iv) ZBED6 binding was preferentially to genes that control transcription, macromolecule biosynthesis, and apoptosis. Furthermore, it is possible that beta cells, by switching from full length to a truncated form of ZBED6, can decide the subcellular localization of ZBED6, thereby achieving differential ZBED6-mediated transcriptional regulation.", "doi": "10.1073/pnas.1303625110", "pmid": "24043816", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1303625110"}, {"db": "pmc", "key": "PMC3791784"}], "notes": [], "created": "2017-05-04T14:58:10.454Z", "modified": "2021-07-07T14:37:06.582Z"}, {"entity": "publication", "iuid": "0a743e63bdd2424f925baf5c563bbc0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a743e63bdd2424f925baf5c563bbc0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a743e63bdd2424f925baf5c563bbc0d"}}, "title": "Structural diversity of signal recognition particle RNAs in plastids.", "authors": [{"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}, {"family": "Tr\u00e4ger", "given": "Chantal", "initials": "C"}, {"family": "Sch\u00fcnemann", "given": "Danja", "initials": "D"}], "type": "journal article", "published": "2013-10-00", "journal": {"volume": "8", "issn": "1559-2324", "issue": "10", "pages": "doi: 10.4161/psb.26848", "title": "Plant Signal Behav", "issn-l": "1559-2316"}, "abstract": "One of the pathways for protein targeting to the plasma membrane in bacteria utilizes the co-translationally acting signal recognition particle (SRP), a universally conserved ribonucleoprotein complex consisting of a 54 kDa protein and a functional RNA. An interesting exception is the higher plant chloroplast SRP, which lacks the otherwise essential RNA component. Furthermore, green plant chloroplasts have an additional post-translational SRP-dependent transport system in which the chloroplast-specific cpSRP43 protein binds to imported substrate proteins and to the conserved 54 kDa SRP subunit (cpSRP54). While homologs to the bacterial SRP protein and RNA component previously have been identified in genome sequences of red algae and diatoms, a recent study investigated the evolution of the green plant SRP system.1 Analysis of hundreds of plastid and nuclear genomes showed a surprising pattern of multiple losses of the plastid SRP RNA during evolution and a widespread presence in all non-spermatophyte plants and green algae. Contrary to expectations, all green organisms that have an identified cpSRP RNA also contain a cpSRP43. Notably, the structure of the plastid SRP RNAs is much more diverse than that of bacterial SRP RNAs. The apical GNRA tetraloop is only conserved in organisms of the red lineage and basal organisms of the green lineage, whereas further chloroplast SRP RNAs are characterized by atypical, mostly enlarged apical loops.", "doi": "10.4161/psb.26848", "pmid": "24494244", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:26.872Z", "modified": "2020-01-21T13:53:21.747Z"}, {"entity": "publication", "iuid": "089c9e5e58f14db48a50552141e03f81", "links": {"self": {"href": "https://publications.scilifelab.se/publication/089c9e5e58f14db48a50552141e03f81.json"}, "display": {"href": "https://publications.scilifelab.se/publication/089c9e5e58f14db48a50552141e03f81"}}, "title": "Recent advances in crayfish hematopoietic stem cell culture: a model for studies of hemocyte differentiation and immunity.", "authors": [{"family": "S\u00f6derh\u00e4ll", "given": "Irene", "initials": "I"}], "type": "journal article", "published": "2013-10-00", "journal": {"volume": "65", "issn": "0920-9069", "issue": "5", "pages": "691-695", "title": "Cytotechnology", "issn-l": null}, "abstract": "Hematopoiesis is the process by which blood cells (hemocytes) mature and subsequently enter the circulation and we have developed a new technique to culture the hematopoietic progenitor cells in vitro. The reason for the successful culture was the isolation of a plasma protein that turned out to be a novel cytokine, astakine 1 (Ast1) containing a domain present in several vertebrates, so-called prokineticins. Now we have detected several astakines from other invertebrate species. Depending on our discovery of the cytokine Ast1 we have an opportunity to study in detail the differentiation of cells in the hematopoietic tissue of a crustacean, a tissue of evolutionary interest for studies of the connection between the vascular system and the nervous system. We have been able to isolate the entire hematopoietic tissue and for the first time detected a link between this tissue and the brain. We have further localized a proliferation center in the tissue and characterized its different parts. We have also used this system to isolate a new hematopoietic factor CHF that is important in the crossroad between apoptosis and hemocyte differentiation. Our technique for culture of crayfish hematopoietic stem cells provides a simple tool for studying the mechanism of hematopoiesis, but also enables detailed studies of immune defense reactions. Further, the culture system has been used for studies of viral defense and the system is suitable for gene silencing which allows functional characterization of different molecules involved in host defense as well as in hemocyte differentiation.", "doi": "10.1007/s10616-013-9578-y", "pmid": "23686548", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC3967606"}], "notes": [], "created": "2017-05-04T14:57:51.285Z", "modified": "2020-01-21T13:56:00.614Z"}, {"entity": "publication", "iuid": "04c2765944244265b5ee6785dee5925f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04c2765944244265b5ee6785dee5925f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04c2765944244265b5ee6785dee5925f"}}, "title": "Profiling of atherosclerotic lesions by gene and tissue microarrays reveals PCSK6 as a novel protease in unstable carotid atherosclerosis.", "authors": [{"family": "Perisic", "given": "Ljubica", "initials": "L"}, {"family": "Hedin", "given": "Erika", "initials": "E"}, {"family": "Razuvaev", "given": "Anton", "initials": "A"}, {"family": "Lengquist", "given": "Mariette", "initials": "M"}, {"family": "Osterholm", "given": "Cecilia", "initials": "C"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Gillgren", "given": "Peter", "initials": "P"}, {"family": "Paulsson-Berne", "given": "Gabrielle", "initials": "G"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Hedin", "given": "Ulf", "initials": "U"}], "type": "comparative study", "published": "2013-10-00", "journal": {"volume": "33", "issn": "1524-4636", "issue": "10", "pages": "2432-2443", "title": "Arterioscler. Thromb. Vasc. Biol.", "issn-l": "1079-5642"}, "abstract": "Carotid plaque instability is a major cause of ischemic stroke, but detailed knowledge about underlying molecular pathways is still lacking. Here, we evaluated large-scale transcriptomic and protein expression profiling in a biobank of carotid endarterectomies followed by characterization of identified candidates, as a platform for discovery of novel proteins differentially regulated in unstable carotid lesions.\n\nGenes highly upregulated in symptomatic versus asymptomatic plaques were selected from Affymetrix microarray analyses (n=127 plaques), and tissue microarrays constructed from 34 lesions were assayed for 21 corresponding proteins by immunohistochemistry. Quantification of stainings demonstrated differential expression of CD36, CD137, and DOCK7 (P<0.05) in unstable versus stable lesions and the most significant upregulation of a proprotein convertase, PCSK6 (P<0.0001). Increased expression of PCSK6 in symptomatic lesions was verified by quantitative real-time polymerase chain reaction (n=233), and the protein was localized to smooth muscle \u03b1-actin positive cells and extracellular matrix of the fibrous cap by immunohistochemistry. PCSK6 expression positively correlated to genes associated with inflammation, matrix degradation, and mitogens in microarrays. Stimulation of human carotid smooth muscle cells in vitro with cytokines caused rapid induction of PCSK6 mRNA.\n\nUsing a combination of transcriptomic and tissue microarray profiling, we demonstrate a novel approach to identify proteins differentially expressed in unstable carotid atherosclerosis. The proprotein convertase PCSK6 was detected at increased levels in the fibrous cap of symptomatic carotid plaques, possibly associated with key processes in plaque rupture such as inflammation and extracellular matrix remodeling. Further studies are needed to clarify the role of PCSK6 in atherosclerosis.", "doi": "10.1161/ATVBAHA.113.301743", "pmid": "23908247", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "ATVBAHA.113.301743"}], "notes": [], "created": "2017-05-04T14:55:54.714Z", "modified": "2017-05-30T12:51:11.115Z"}, {"entity": "publication", "iuid": "d5e57e39e5de46b9b3c64baa5a8542d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d5e57e39e5de46b9b3c64baa5a8542d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d5e57e39e5de46b9b3c64baa5a8542d0"}}, "title": "Heart research advances using database search engines, Human Protein Atlas and the Sydney Heart Bank.", "authors": [{"family": "Li", "given": "Amy", "initials": "A"}, {"family": "Estigoy", "given": "Colleen", "initials": "C"}, {"family": "Raftery", "given": "Mark", "initials": "M"}, {"family": "Cameron", "given": "Darryl", "initials": "D"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Lal", "given": "Sean", "initials": "S"}, {"family": "Dos Remedios", "given": "Cristobal G", "initials": "CG"}], "type": "journal article", "published": "2013-10-00", "journal": {"volume": "22", "issn": "1444-2892", "issue": "10", "pages": "819-826", "title": "Heart Lung Circ", "issn-l": "1443-9506"}, "abstract": "This Methodological Review is intended as a guide for research students who may have just discovered a human \"novel\" cardiac protein, but it may also help hard-pressed reviewers of journal submissions on a \"novel\" protein reported in an animal model of human heart failure. Whether you are an expert or not, you may know little or nothing about this particular protein of interest. In this review we provide a strategic guide on how to proceed. We ask: How do you discover what has been published (even in an abstract or research report) about this protein? Everyone knows how to undertake literature searches using PubMed and Medline but these are usually encyclopaedic, often producing long lists of papers, most of which are either irrelevant or only vaguely relevant to your query. Relatively few will be aware of more advanced search engines such as Google Scholar and even fewer will know about Quertle. Next, we provide a strategy for discovering if your \"novel\" protein is expressed in the normal, healthy human heart, and if it is, we show you how to investigate its subcellular location. This can usually be achieved by visiting the website \"Human Protein Atlas\" without doing a single experiment. Finally, we provide a pathway to discovering if your protein of interest changes its expression level with heart failure/disease or with ageing.", "doi": "10.1016/j.hlc.2013.06.006", "pmid": "23856366", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "S1443-9506(13)01036-6"}], "notes": [], "created": "2017-05-04T14:55:58.350Z", "modified": "2017-05-30T12:57:31.075Z"}, {"entity": "publication", "iuid": "b9f1a7f8e9a44cf49d440aba63a377d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9f1a7f8e9a44cf49d440aba63a377d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9f1a7f8e9a44cf49d440aba63a377d1"}}, "title": "Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.", "authors": [{"family": "Fortunato", "given": "Caroline S", "initials": "CS"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Herfort", "given": "Lydie", "initials": "L"}, {"family": "Needoba", "given": "Joseph A", "initials": "JA"}, {"family": "Peterson", "given": "Tawnya D", "initials": "TD"}, {"family": "Crump", "given": "Byron C", "initials": "BC"}], "type": "journal article", "published": "2013-10-00", "journal": {"volume": "7", "issn": "1751-7370", "issue": "10", "pages": "1899-1911", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (\u03c1=-0.664) and residence time (\u03c1=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.", "doi": "10.1038/ismej.2013.79", "pmid": "23719153", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ismej201379"}, {"db": "pmc", "key": "PMC3965310"}, {"db": "SRA", "key": "SRA058065"}, {"db": "SRA", "key": "SRP006412"}], "notes": [], "created": "2017-05-04T14:57:59.395Z", "modified": "2020-01-21T13:56:04.870Z"}, {"entity": "publication", "iuid": "ec2fc81f72e94c4cbdce3b15d3ea585c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec2fc81f72e94c4cbdce3b15d3ea585c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec2fc81f72e94c4cbdce3b15d3ea585c"}}, "title": "Comprehensive genetic analysis identifies a pathognomonic NAB2/STAT6 fusion gene, nonrandom secondary genomic imbalances, and a characteristic gene expression profile in solitary fibrous tumor.", "authors": [{"family": "Mohajeri", "given": "Arezoo", "initials": "A"}, {"family": "Tayebwa", "given": "Johnbosco", "initials": "J"}, {"family": "Collin", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Jenny", "initials": "J"}, {"family": "Magnusson", "given": "Linda", "initials": "L"}, {"family": "von Steyern", "given": "Fredrik Vult", "initials": "FV"}, {"family": "Brosj\u00f6", "given": "Otte", "initials": "O"}, {"family": "Domanski", "given": "Henryk A", "initials": "HA"}, {"family": "Larsson", "given": "Olle", "initials": "O"}, {"family": "Sciot", "given": "Raf", "initials": "R"}, {"family": "Debiec-Rychter", "given": "Maria", "initials": "M"}, {"family": "Hornick", "given": "Jason L", "initials": "JL"}, {"family": "Mandahl", "given": "Nils", "initials": "N"}, {"family": "Nord", "given": "Karolin H", "initials": "KH"}, {"family": "Mertens", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2013-10-00", "journal": {"volume": "52", "issn": "1098-2264", "issue": "10", "pages": "873-886", "title": "Genes Chromosomes Cancer", "issn-l": "1045-2257"}, "abstract": "Solitary fibrous tumor (SFT) is a mesenchymal neoplasm displaying variable morphologic and clinical features. To identify pathogenetically important genetic rearrangements, 44 SFTs were analyzed using a variety of techniques. Chromosome banding and fluorescence in situ hybridization (FISH) showed recurrent breakpoints in 12q13, clustering near the NAB2 and STAT6 genes, and single nucleotide polymorphism array analysis disclosed frequent deletions affecting STAT6. Quantitative real-time PCR revealed high expression levels of the 5'-end of NAB2 and the 3'-end of STAT6, which at deep sequencing of enriched DNA corresponded to NAB2/STAT6 fusions. Subsequent reverse-transcriptase PCR (RT-PCR) analysis identified a NAB2/STAT6 fusion in 37/41 cases, confirming that this fusion gene underlies the pathogenesis of SFT. The hypothesis that the NAB2/STAT6 fusions will result in altered properties of the transcriptional co-repressor NAB2--a key regulator of the early growth response 1 (EGR1) transcription factor - was corroborated by global gene expression analysis; SFTs showed deregulated expression of EGR1 target genes, as well as of other, developmentally important genes. We also identified several nonrandom secondary changes, notably loss of material from 13q and 14q. As neither chromosome banding nor FISH analysis identify more than a minor fraction of the fusion-positive cases, and because multiple primer combinations are required to identify all possible fusion transcripts by RT-PCR, alternative diagnostic markers might instead be found among deregulated genes identified at global gene expression analysis. Indeed, using immunohistochemistry on tissue microarrays, the top up-regulated gene, GRIA2, was found to be differentially expressed also at the protein level.", "doi": "10.1002/gcc.22083", "pmid": "23761323", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:54.758Z", "modified": "2020-01-21T13:56:05.993Z"}, {"entity": "publication", "iuid": "8a1b3c9e426b4ad6a5a941ef27ffbd42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a1b3c9e426b4ad6a5a941ef27ffbd42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a1b3c9e426b4ad6a5a941ef27ffbd42"}}, "title": "Transcriptome and genome sequencing uncovers functional variation in humans.", "authors": [{"family": "Lappalainen", "given": "Tuuli", "initials": "T"}, {"family": "Sammeth", "given": "Michael", "initials": "M"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "'t Hoen", "given": "Peter A C", "initials": "PA"}, {"family": "Monlong", "given": "Jean", "initials": "J"}, {"family": "Rivas", "given": "Manuel A", "initials": "MA"}, {"family": "Gonz\u00e0lez-Porta", "given": "Mar", "initials": "M"}, {"family": "Kurbatova", "given": "Natalja", "initials": "N"}, {"family": "Griebel", "given": "Thasso", "initials": "T"}, {"family": "Ferreira", "given": "Pedro G", "initials": "PG"}, {"family": "Barann", "given": "Matthias", "initials": "M"}, {"family": "Wieland", "given": "Thomas", "initials": "T"}, {"family": "Greger", "given": "Liliana", "initials": "L"}, {"family": "van Iterson", "given": "Maarten", "initials": "M"}, {"family": "Alml\u00f6f", "given": "Jonas", "initials": "J"}, {"family": "Ribeca", "given": "Paolo", "initials": "P"}, {"family": "Pulyakhina", "given": "Irina", "initials": "I"}, {"family": "Esser", "given": "Daniela", "initials": "D"}, {"family": "Giger", "given": "Thomas", "initials": "T"}, {"family": "Tikhonov", "given": "Andrew", "initials": "A"}, {"family": "Sultan", "given": "Marc", "initials": "M"}, {"family": "Bertier", "given": "Gabrielle", "initials": "G"}, {"family": "MacArthur", "given": "Daniel G", "initials": "DG"}, {"family": "Lek", "given": "Monkol", "initials": "M"}, {"family": "Lizano", "given": "Esther", "initials": "E"}, {"family": "Buermans", "given": "Henk P J", "initials": "HP"}, {"family": "Padioleau", "given": "Ismael", "initials": "I"}, {"family": "Schwarzmayr", "given": "Thomas", "initials": "T"}, {"family": "Karlberg", "given": "Olof", "initials": "O"}, {"family": "Ongen", "given": "Halit", "initials": "H"}, {"family": "Kilpinen", "given": "Helena", "initials": "H"}, {"family": "Beltran", "given": "Sergi", "initials": "S"}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Kahlem", "given": "Katja", "initials": "K"}, {"family": "Amstislavskiy", "given": "Vyacheslav", "initials": "V"}, {"family": "Stegle", "given": "Oliver", "initials": "O"}, {"family": "Pirinen", "given": "Matti", "initials": "M"}, {"family": "Montgomery", "given": "Stephen B", "initials": "SB"}, {"family": "Donnelly", "given": "Peter", "initials": "P"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Flicek", "given": "Paul", "initials": "P"}, {"family": "Strom", "given": "Tim M", "initials": "TM"}, {"family": "Geuvadis Consortium", "given": null, "initials": null}, {"family": "Lehrach", "given": "Hans", "initials": "H"}, {"family": "Schreiber", "given": "Stefan", "initials": "S"}, {"family": "Sudbrak", "given": "Ralf", "initials": "R"}, {"family": "Carracedo", "given": "Angel", "initials": "A"}, {"family": "Antonarakis", "given": "Stylianos E", "initials": "SE"}, {"family": "H\u00e4sler", "given": "Robert", "initials": "R"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "van Ommen", "given": "Gert-Jan", "initials": "GJ"}, {"family": "Brazma", "given": "Alvis", "initials": "A"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Rosenstiel", "given": "Philip", "initials": "P"}, {"family": "Guig\u00f3", "given": "Roderic", "initials": "R"}, {"family": "Gut", "given": "Ivo G", "initials": "IG"}, {"family": "Estivill", "given": "Xavier", "initials": "X"}, {"family": "Dermitzakis", "given": "Emmanouil T", "initials": "ET"}], "type": "journal article", "published": "2013-09-26", "journal": {"volume": "501", "issn": "1476-4687", "issue": "7468", "pages": "506-511", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Genome sequencing projects are discovering millions of genetic variants in humans, and interpretation of their functional effects is essential for understanding the genetic basis of variation in human traits. Here we report sequencing and deep analysis of messenger RNA and microRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project--the first uniformly processed high-throughput RNA-sequencing data from multiple human populations with high-quality genome sequences. We discover extremely widespread genetic variation affecting the regulation of most genes, with transcript structure and expression level variation being equally common but genetically largely independent. Our characterization of causal regulatory variation sheds light on the cellular mechanisms of regulatory and loss-of-function variation, and allows us to infer putative causal variants for dozens of disease-associated loci. Altogether, this study provides a deep understanding of the cellular mechanisms of transcriptome variation and of the landscape of functional variants in the human genome.", "doi": "10.1038/nature12531", "pmid": "24037378", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "nature12531"}, {"db": "pmc", "key": "PMC3918453"}, {"db": "mid", "key": "NIHMS512974"}], "notes": [], "created": "2017-05-04T15:01:24.216Z", "modified": "2021-07-07T15:11:02.576Z"}, {"entity": "publication", "iuid": "f867fad229be45769f13368f45cf3d6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f867fad229be45769f13368f45cf3d6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f867fad229be45769f13368f45cf3d6a"}}, "title": "FHOD1, a formin upregulated in epithelial-mesenchymal transition, participates in cancer cell migration and invasion.", "authors": [{"family": "Gardberg", "given": "Maria", "initials": "M"}, {"family": "Kaipio", "given": "Katja", "initials": "K"}, {"family": "Lehtinen", "given": "Laura", "initials": "L"}, {"family": "Mikkonen", "given": "Piia", "initials": "P"}, {"family": "Heuser", "given": "Vanina D", "initials": "VD"}, {"family": "Talvinen", "given": "Kati", "initials": "K"}, {"family": "Iljin", "given": "Kristiina", "initials": "K"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Gr\u00e9nman", "given": "Reidar", "initials": "R"}, {"family": "Koivisto", "given": "Mari", "initials": "M"}, {"family": "Carp\u00e9n", "given": "Olli", "initials": "O"}], "type": "journal article", "published": "2013-09-26", "journal": {"volume": "8", "issn": "1932-6203", "issue": "9", "pages": "e74923", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Cancer cells can obtain their ability to invade and metastasise by undergoing epithelial-to-mesenchymal transition (EMT). Exploiting this mechanism of cellular plasticity, malignant cells can remodel their actin cytoskeleton and down-regulate proteins needed for cell-cell contacts. The mechanisms of cytoskeletal reorganisation resulting in mesenchymal morphology and increased invasive potential are poorly understood. Actin nucleating formins have been implicated as key players in EMT. Here, we analysed which formins are altered in squamous cell carcinoma related EMT. FHOD1, a poorly studied formin, appeared to be markedly upregulated upon EMT. In human tissues FHOD1 was primarily expressed in mesenchymal cells, with little expression in epithelia. However, specimens from oral squamous cell cancers demonstrated consistent FHOD1 upregulation in mesenchymally transformed cells at the invasive edge. This upregulation was confirmed in an oral squamous carcinoma model, where FHOD1 expression was markedly increased upon EMT in a PI3K signalling dependent manner. In the EMT cells FHOD1 contributed to the spindle-shaped morphology and mesenchymal F-actin organization. Furthermore, functional assays demonstrated that FHOD1 contributes to cell migration and invasion. Finally, FHOD1 depletion reduced the ability of EMT cancer cells to form invadopodia and to degrade extracellular matrix. Our results indicate that FHOD1 participates in cytoskeletal changes in EMT. In addition, we show that FHOD1 upregulation occurs during cancer cell EMT in vivo, which indicates that FHOD1 may contribute to tumour progression.", "doi": "10.1371/journal.pone.0074923", "pmid": "24086398", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-15073"}, {"db": "pmc", "key": "PMC3784416"}], "notes": [], "created": "2017-05-04T14:56:02.087Z", "modified": "2021-07-08T13:44:33.750Z"}, {"entity": "publication", "iuid": "bc1e42cbc2e44261af352dd2611d68a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc1e42cbc2e44261af352dd2611d68a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc1e42cbc2e44261af352dd2611d68a7"}}, "title": "Genetic variants of coagulation factor XI show association with ischemic stroke up to 70 years of age.", "authors": [{"family": "Hanson", "given": "Ellen", "initials": "E"}, {"family": "Nilsson", "given": "Staffan", "initials": "S"}, {"family": "Jood", "given": "Katarina", "initials": "K"}, {"family": "Norrving", "given": "Bo", "initials": "B"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Blomstrand", "given": "Christian", "initials": "C"}, {"family": "Lindgren", "given": "Arne", "initials": "A"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Jern", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2013-09-25", "journal": {"volume": "8", "issn": "1932-6203", "issue": "9", "pages": "e75286", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Coagulation factor XI (FXI) has an important role in the propagation and stabilization of a thrombus upon vessel injury. High FXI levels have been implicated in thrombotic diseases including ischemic stroke. The aim of our study was to investigate whether FXI gene (F11) variants are associated with ischemic stroke.\r\n\r\nThe discovery sample, the Sahlgrenska Academy Study on Ischemic Stroke (SAHLSIS), included 844 patients with ischemic stroke and 668 controls, all aged 18-70 years. Replication was performed in the Lund Stroke Register (LSR) and Malm\u00f6 Diet and Cancer study (MDC), together including 1213 patients and 788 controls up to 70 years of age, and in total 3145 patients and 1793 controls (18-102 years). Seven F11 single-nucleotide polymorphisms (SNPs) were selected using a tagging approach.\r\n\r\nThe SNPs rs3733403, rs925451, and rs1593 showed independent associations with overall ischemic stroke in SAHLSIS, ORs of 0.74 (95% CI 0.59-0.94), 1.24 (95% CI 1.06-1.46), and 0.70 (95% CI 0.55-0.90), respectively. The association for rs925451 was replicated in the LSR and MDC sample in a pre-specified analysis of subjects aged 70 years or younger, OR of 1.16 (95% CI 1.00-1.34), whereas no SNP was replicated when all ages were included. In line with this, one F11 haplotype was associated with overall ischemic stroke in the discovery sample and in the replication sample \u226470 years.\r\n\r\nWe found significant associations between F11 variation and overall ischemic stroke up to 70 years of age. These findings motivate further studies on the role of F11 in ischemic stroke, especially in younger individuals.", "doi": "10.1371/journal.pone.0075286", "pmid": "24086496", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-15903"}, {"db": "pmc", "key": "PMC3783404"}], "notes": [], "created": "2017-05-04T14:58:15.558Z", "modified": "2020-01-21T13:56:08.766Z"}, {"entity": "publication", "iuid": "71b0cc52b64d44fd86a7e9431f2451a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71b0cc52b64d44fd86a7e9431f2451a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71b0cc52b64d44fd86a7e9431f2451a1"}}, "title": "Spinal deformity in aged zebrafish is accompanied by degenerative changes to their vertebrae that resemble osteoarthritis.", "authors": [{"family": "Hayes", "given": "Anthony J", "initials": "AJ"}, {"family": "Reynolds", "given": "Scott", "initials": "S"}, {"family": "Nowell", "given": "Mari A", "initials": "MA"}, {"family": "Meakin", "given": "Lee B", "initials": "LB"}, {"family": "Habicher", "given": "Judith", "initials": "J"}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}, {"family": "Bashford", "given": "Andrew", "initials": "A"}, {"family": "Caterson", "given": "Bruce", "initials": "B"}, {"family": "Hammond", "given": "Chrissy L", "initials": "CL"}], "type": "journal article", "published": "2013-09-24", "journal": {"volume": "8", "issn": "1932-6203", "issue": "9", "pages": "e75787", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Age-related degenerative changes within the vertebral column are a significant cause of morbidity with considerable socio-economic impact worldwide. An improved understanding of these changes through the development of experimental models may lead to improvements in existing clinical treatment options. The zebrafish is a well-established model for the study of skeletogenesis with significant potential in gerontological research. With advancing age, zebrafish frequently develop gross deformities of their vertebral column, previously ascribed to reduced trunk muscle tone. In this study, we assess degenerative changes specifically within the bone and cartilage of the vertebral column of zebrafish at 1, 2 and 3-years of age. We show increased frequency and severity of spinal deformities/curvatures with age. Underlying the most severe phenotypes are partial or complete vertebral dislocations and focal thickening of the vertebral bone at the joint margins. MicroCT examination demonstrates small defects, fractures and morphological evidence suggestive of bone erosion and remodeling (i.e. osteophytes) within the vertebrae during aging, but no significant change in bone density. Light and electron microscopic examination reveal striking age-related changes in cell morphology, suggestive of chondroptosis, and tissue remodelling of the vertebral cartilage, particularly within the pericellular micro-environment. Glycosaminoglycan analysis of the vertebral column by HPLC demonstrates a consistent, age-related increase in the yield of total chondroitin sulfate disaccharide, but no change in sulfation pattern, supported by immunohistochemical analysis. Immunohistochemistry strongly identifies all three chondroitin/dermatan sulphate isoforms (C-0-S, C-4-S/DS and C-6-S) within the vertebral cartilage, particularly within the pericellular micro-environment. In contrast, keratan sulfate immunolocalises specifically with the notochordal tissue of the intervertebral disc, and its labelling diminishes with age. In summary, these observations raise the prospect that zebrafish, in addition to modelling skeletal development, may have utility in modelling age-related degenerative changes that affect the skeleton during senescence.", "doi": "10.1371/journal.pone.0075787", "pmid": "24086633", "labels": {"Genome Engineering Zebrafish": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-26599"}, {"db": "pmc", "key": "PMC3782452"}], "notes": [], "created": "2017-05-04T15:03:44.039Z", "modified": "2021-07-06T14:27:46.361Z"}, {"entity": "publication", "iuid": "a6d05cf5e7f842cdb241891f6d3309d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6d05cf5e7f842cdb241891f6d3309d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6d05cf5e7f842cdb241891f6d3309d8"}}, "title": "Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia.", "authors": [{"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "B\u00e4cklin", "given": "Christofer L", "initials": "CL"}, {"family": "Wahlberg", "given": "Per", "initials": "P"}, {"family": "Busche", "given": "Stephan", "initials": "S"}, {"family": "Berglund", "given": "Eva C", "initials": "EC"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Flaegstad", "given": "Trond", "initials": "T"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Frost", "given": "Britt-Marie", "initials": "BM"}, {"family": "Harila-Saari", "given": "Arja", "initials": "A"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "J\u00f3nsson", "given": "Olafur G", "initials": "OG"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Sinnett", "given": "Daniel", "initials": "D"}, {"family": "S\u00f6derh\u00e4ll", "given": "Stefan", "initials": "S"}, {"family": "Pastinen", "given": "Tomi", "initials": "T"}, {"family": "Gustafsson", "given": "Mats G", "initials": "MG"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2013-09-24", "journal": {"volume": "14", "issn": "1474-760X", "issue": "9", "pages": "r105", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic background, drug resistance and relapse in ALL is poorly understood.\n\nWe surveyed the DNA methylation levels of 435,941 CpG sites in samples from 764 children at diagnosis of ALL and from 27 children at relapse. This survey uncovered four characteristic methylation signatures. First, compared with control blood cells, the methylomes of ALL cells shared 9,406 predominantly hypermethylated CpG sites, independent of cytogenetic background. Second, each cytogenetic subtype of ALL displayed a unique set of hyper- and hypomethylated CpG sites. The CpG sites that constituted these two signatures differed in their functional genomic enrichment to regions with marks of active or repressed chromatin. Third, we identified subtype-specific differential methylation in promoter and enhancer regions that were strongly correlated with gene expression. Fourth, a set of 6,612 CpG sites was predominantly hypermethylated in ALL cells at relapse, compared with matched samples at diagnosis. Analysis of relapse-free survival identified CpG sites with subtype-specific differential methylation that divided the patients into different risk groups, depending on their methylation status.\n\nOur results suggest an important biological role for DNA methylation in the differences between ALL subtypes and in their clinical outcome after treatment.", "doi": "10.1186/gb-2013-14-9-r105", "pmid": "24063430", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "gb-2013-14-9-r105"}, {"db": "pmc", "key": "PMC4014804"}], "notes": [], "created": "2017-05-04T14:57:55.716Z", "modified": "2021-07-07T15:11:02.635Z"}, {"entity": "publication", "iuid": "15e65aa935ec4c23b4b4c8f004ac16a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15e65aa935ec4c23b4b4c8f004ac16a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15e65aa935ec4c23b4b4c8f004ac16a9"}}, "title": "Equine multiple congenital ocular anomalies and silver coat colour result from the pleiotropic effects of mutant PMEL.", "authors": [{"family": "Andersson", "given": "Lisa S", "initials": "LS"}, {"family": "Wilbe", "given": "Maria", "initials": "M"}, {"family": "Viluma", "given": "Agnese", "initials": "A"}, {"family": "Cothran", "given": "Gus", "initials": "G"}, {"family": "Ekesten", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ewart", "given": "Susan", "initials": "S"}, {"family": "Lindgren", "given": "Gabriella", "initials": "G"}], "type": "journal article", "published": "2013-09-23", "journal": {"volume": "8", "issn": "1932-6203", "issue": "9", "pages": "e75639", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Equine Multiple Congenital Ocular Anomalies (MCOA) syndrome is a heritable eye disorder mainly affecting silver colored horses. Clinically, the disease manifests in two distinct classes depending on the horse genotype. Horses homozygous for the mutant allele present with a wide range of ocular defects, such as iris stromal hypoplasia, abnormal pectinate ligaments, megaloglobus, iridociliary cysts and cataracts. The phenotype of heterozygous horses is less severe and predominantly includes iridociliary cysts, which occasionally extend into the temporal retina. In order to determine the genetic cause of MCOA syndrome we sequenced the entire previously characterized 208 kilobase region on chromosome 6 in ten individuals; five MCOA affected horses from three different breeds, one horse with the intermediate Cyst phenotype and four unaffected controls from two different breeds. This was performed using Illumina TruSeq technology with paired-end reads. Through the systematic exclusion of all polymorphisms barring two SNPs in PMEL, a missense mutation previously reported to be associated with the silver coat colour and a non-conserved intronic SNP, we establish that this gene is responsible for MCOA syndrome. Our finding, together with recent advances that show aberrant protein function due to the coding mutation, suggests that the missense mutation is causative and has pleiotrophic effect, causing both the horse silver coat color and MCOA syndrome.", "doi": "10.1371/journal.pone.0075639", "pmid": "24086599", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-06293"}, {"db": "pmc", "key": "PMC3781063"}], "notes": [], "created": "2017-05-04T15:01:27.058Z", "modified": "2020-01-21T13:56:00.859Z"}, {"entity": "publication", "iuid": "a59fc855052c46eabd6c08e2a220e98b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a59fc855052c46eabd6c08e2a220e98b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a59fc855052c46eabd6c08e2a220e98b"}}, "title": "A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities.", "authors": [{"family": "Thureborn", "given": "Petter", "initials": "P"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Plathan", "given": "Josefin", "initials": "J"}, {"family": "Poole", "given": "Anthony M", "initials": "AM"}, {"family": "Sj\u00f6berg", "given": "Britt-Marie", "initials": "BM"}, {"family": "Sj\u00f6ling", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2013-09-23", "journal": {"volume": "8", "issn": "1932-6203", "issue": "9", "pages": "e74983", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The Baltic Sea is characterized by hyposaline surface waters, hypoxic and anoxic deep waters and sediments. These conditions, which in turn lead to a steep oxygen gradient, are particularly evident at Landsort Deep in the Baltic Proper. Given these substantial differences in environmental parameters at Landsort Deep, we performed a metagenomic census spanning surface to sediment to establish whether the microbial communities at this site are as stratified as the physical environment. We report strong stratification across a depth transect for both functional capacity and taxonomic affiliation, with functional capacity corresponding most closely to key environmental parameters of oxygen, salinity and temperature. We report similarities in functional capacity between the hypoxic community and hadal zone communities, underscoring the substantial degree of eutrophication in the Baltic Proper. Reconstruction of the nitrogen cycle at Landsort deep shows potential for syntrophy between archaeal ammonium oxidizers and bacterial denitrification at anoxic depths, while anaerobic ammonium oxidation genes are absent, despite substantial ammonium levels below the chemocline. Our census also reveals enrichment in genetic prerequisites for a copiotrophic lifestyle and resistance mechanisms reflecting adaptation to prevalent eutrophic conditions and the accumulation of environmental pollutants resulting from ongoing anthropogenic pressures in the Baltic Sea.", "doi": "10.1371/journal.pone.0074983", "pmid": "24086414", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-23027"}, {"db": "pmc", "key": "PMC3781128"}], "notes": [], "created": "2017-05-04T14:58:17.383Z", "modified": "2020-01-21T13:56:04.264Z"}, {"entity": "publication", "iuid": "f860b4e98f3044179bb6ac075c1296ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f860b4e98f3044179bb6ac075c1296ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f860b4e98f3044179bb6ac075c1296ff"}}, "title": "Ebsulfur is a benzisothiazolone cytocidal inhibitor targeting the trypanothione reductase of Trypanosoma brucei.", "authors": [{"family": "Lu", "given": "Jun", "initials": "J"}, {"family": "Vodnala", "given": "Suman K", "initials": "SK"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Gustafsson", "given": "Tomas N", "initials": "TN"}, {"family": "Sj\u00f6berg", "given": "Birger", "initials": "B"}, {"family": "Johansson", "given": "Henrik A", "initials": "HA"}, {"family": "Kumar", "given": "Sangit", "initials": "S"}, {"family": "Tjernberg", "given": "Agneta", "initials": "A"}, {"family": "Engman", "given": "Lars", "initials": "L"}, {"family": "Rottenberg", "given": "Martin E", "initials": "ME"}, {"family": "Holmgren", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-09-20", "journal": {"volume": "288", "issn": "1083-351X", "issue": "38", "pages": "27456-27468", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Trypanosoma brucei is the causing agent of African trypanosomiasis. These parasites possess a unique thiol redox system required for DNA synthesis and defense against oxidative stress. It includes trypanothione and trypanothione reductase (TryR) instead of the thioredoxin and glutaredoxin systems of mammalian hosts. Here, we show that the benzisothiazolone compound ebsulfur (EbS), a sulfur analogue of ebselen, is a potent inhibitor of T. brucei growth with a favorable selectivity index over mammalian cells. EbS inhibited the TryR activity and decreased non-protein thiol levels in cultured parasites. The inhibition of TryR by EbS was irreversible and NADPH-dependent. EbS formed a complex with TryR and caused oxidation and inactivation of the enzyme. EbS was more toxic for T. brucei than for Trypanosoma cruzi, probably due to lower levels of TryR and trypanothione in T. brucei. Furthermore, inhibition of TryR produced high intracellular reactive oxygen species. Hydrogen peroxide, known to be constitutively high in T. brucei, enhanced the EbS inhibition of TryR. The elevation of reactive oxygen species production in parasites caused by EbS induced a programmed cell death. Soluble EbS analogues were synthesized and cured T. brucei brucei infection in mice when used together with nifurtimox. Altogether, EbS and EbS analogues disrupt the trypanothione system, hampering the defense against oxidative stress. Thus, EbS is a promising lead for development of drugs against African trypanosomiasis.", "doi": "10.1074/jbc.M113.495101", "pmid": "23900839", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0021-9258(20)49012-X"}, {"db": "pmc", "key": "PMC3779740"}], "notes": [], "created": "2017-10-20T14:49:29.162Z", "modified": "2025-10-17T13:04:30.291Z"}, {"entity": "publication", "iuid": "1a635d4304824c54b6edcca43eb98c0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a635d4304824c54b6edcca43eb98c0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a635d4304824c54b6edcca43eb98c0e"}}, "title": "Hydrogenosomes in the diplomonad Spironucleus salmonicida.", "authors": [{"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Einarsson", "given": "Elin", "initials": "E"}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "Hjort", "given": "Karin", "initials": "K"}, {"family": "Ek", "given": "Bo", "initials": "B"}, {"family": "Steinhauf", "given": "Daniel", "initials": "D"}, {"family": "Hultenby", "given": "Kjell", "initials": "K"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Andersson", "given": "Jan O", "initials": "JO"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "journal article", "published": "2013-09-18", "journal": {"volume": "4", "issn": "2041-1723", "issue": null, "pages": "2493", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Acquisition of the mitochondrion is a key event in the evolution of the eukaryotic cell, but diversification of the organelle has occurred during eukaryotic evolution. One example of such mitochondria-related organelles (MROs) are hydrogenosomes, which produce ATP by substrate-level phosphorylation with hydrogen as a byproduct. The diplomonad parasite Giardia intestinalis harbours mitosomes, another type of MRO. Here we identify MROs in the salmon parasite Spironucleus salmonicida with similar protein import and Fe-S cluster assembly machineries as in Giardia mitosomes. We find that hydrogen production is prevalent in the diplomonad genus Spironucleus, and that S. salmonicida MROs contain enzymes characteristic of hydrogenosomes. Evolutionary analyses of known hydrogenosomal components indicate their presence in the diplomonad ancestor, and subsequent loss in Giardia. Our results suggest that hydrogenosomes are metabolic adaptations predating the split between parabasalids and diplomonads, which is deeper than the split between animals and fungi in the eukaryotic tree.", "doi": "10.1038/ncomms3493", "pmid": "24042146", "labels": {"Mass Spectrometry-based Proteomics, Uppsala": null}, "xrefs": [{"db": "pii", "key": "ncomms3493"}, {"db": "pmc", "key": "PMC3778541"}], "notes": [], "created": "2017-05-04T15:03:26.011Z", "modified": "2017-05-30T12:43:14.061Z"}, {"entity": "publication", "iuid": "96d1d883dc3749999572787646fb4357", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96d1d883dc3749999572787646fb4357.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96d1d883dc3749999572787646fb4357"}}, "title": "Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease.", "authors": [{"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Chasman", "given": "Daniel", "initials": "D"}, {"family": "Naitza", "given": "Silvia", "initials": "S"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Basu", "given": "Saonli", "initials": "S"}, {"family": "Rudnicka", "given": "Alicja R", "initials": "AR"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Baumert", "given": "Jens", "initials": "J"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Hottenga", "given": "Jouke J", "initials": "JJ"}, {"family": "Shin", "given": "So-Youn", "initials": "SY"}, {"family": "Lopez", "given": "Lorna M", "initials": "LM"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Yanek", "given": "Lisa R", "initials": "LR"}, {"family": "Oudot-Mellakh", "given": "Tiphaine", "initials": "T"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Redline", "given": "Susan", "initials": "S"}, {"family": "Mehra", "given": "Reena", "initials": "R"}, {"family": "Pulanic", "given": "Drazen", "initials": "D"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Curb", "given": "J David", "initials": "JD"}, {"family": "Wallace", "given": "Robert", "initials": "R"}, {"family": "Liu", "given": "Simin", "initials": "S"}, {"family": "Eaton", "given": "Charles B", "initials": "CB"}, {"family": "Becker", "given": "Diane M", "initials": "DM"}, {"family": "Becker", "given": "Lewis C", "initials": "LC"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Green", "given": "David", "initials": "D"}, {"family": "Gross", "given": "Myron", "initials": "M"}, {"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Liewald", "given": "David C", "initials": "DC"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Williams", "given": "Frances M K", "initials": "FM"}, {"family": "Grant", "given": "Peter J", "initials": "PJ"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "van Dongen", "given": "Jenny", "initials": "J"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Swords Jenny", "given": "Nancy", "initials": "N"}, {"family": "Haritunians", "given": "Talin", "initials": "T"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Lumley", "given": "Thomas", "initials": "T"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Grotevendt", "given": "Anne", "initials": "A"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Kocher", "given": "Thomas", "initials": "T"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Franzosi", "given": "Maria Grazia", "initials": "MG"}, {"family": "Seedorf", "given": "Udo", "initials": "U"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Steri", "given": "Maristella", "initials": "M"}, {"family": "Tarasov", "given": "Kirill V", "initials": "KV"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Stott", "given": "David J", "initials": "DJ"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Buckley", "given": "Brendan M", "initials": "BM"}, {"family": "Rumley", "given": "Ann", "initials": "A"}, {"family": "Lowe", "given": "Gordon D", "initials": "GD"}, {"family": "McArdle", "given": "Wendy L", "initials": "WL"}, {"family": "Chen", "given": "Ming-Huei", "initials": "MH"}, {"family": "Tofler", "given": "Geoffrey H", "initials": "GH"}, {"family": "Song", "given": "Jaejoon", "initials": "J"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Folsom", "given": "Aaron R", "initials": "AR"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Teichert", "given": "Martina", "initials": "M"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Mosley", "given": "Thomas H", "initials": "TH"}, {"family": "Bevan", "given": "Steve", "initials": "S"}, {"family": "Dichgans", "given": "Martin", "initials": "M"}, {"family": "Rothwell", "given": "Peter M", "initials": "PM"}, {"family": "Sudlow", "given": "Cathie L M", "initials": "CL"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Morange", "given": "Pierre-Emmanuel", "initials": "PE"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Jacobs", "given": "David", "initials": "D"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "Tracy", "given": "Russell P", "initials": "RP"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Markus", "given": "Hugh S", "initials": "HS"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "VTE Consortium", "given": null, "initials": null}, {"family": "STROKE Consortium", "given": null, "initials": null}, {"family": "Wellcome Trust Case Control Consortium 2 (WTCCC2)", "given": null, "initials": null}, {"family": "C4D Consortium", "given": null, "initials": null}, {"family": "CARDIoGRAM Consortium", "given": null, "initials": null}, {"family": "Wallaschofski", "given": "Henri", "initials": "H"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Tregouet", "given": "David", "initials": "D"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Tang", "given": "Weihong", "initials": "W"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}], "type": "journal article", "published": "2013-09-17", "journal": {"volume": "128", "issn": "1524-4539", "issue": "12", "pages": "1310-1324", "title": "Circulation", "issn-l": "0009-7322"}, "abstract": "Estimates of the heritability of plasma fibrinogen concentration, an established predictor of cardiovascular disease, range from 34% to 50%. Genetic variants so far identified by genome-wide association studies explain only a small proportion (<2%) of its variation.\n\nWe conducted a meta-analysis of 28 genome-wide association studies including >90 000 subjects of European ancestry, the first genome-wide association meta-analysis of fibrinogen levels in 7 studies in blacks totaling 8289 samples, and a genome-wide association study in Hispanics totaling 1366 samples. Evaluation for association of single-nucleotide polymorphisms with clinical outcomes included a total of 40 695 cases and 85 582 controls for coronary artery disease, 4752 cases and 24 030 controls for stroke, and 3208 cases and 46 167 controls for venous thromboembolism. Overall, we identified 24 genome-wide significant (P<5\u00d710(-8)) independent signals in 23 loci, including 15 novel associations, together accounting for 3.7% of plasma fibrinogen variation. Gene-set enrichment analysis highlighted key roles in fibrinogen regulation for the 3 structural fibrinogen genes and pathways related to inflammation, adipocytokines, and thyrotrophin-releasing hormone signaling. Whereas lead single-nucleotide polymorphisms in a few loci were significantly associated with coronary artery disease, the combined effect of all 24 fibrinogen-associated lead single-nucleotide polymorphisms was not significant for coronary artery disease, stroke, or venous thromboembolism.\n\nWe identify 23 robustly associated fibrinogen loci, 15 of which are new. Clinical outcome analysis of these loci does not support a causal relationship between circulating levels of fibrinogen and coronary artery disease, stroke, or venous thromboembolism.", "doi": "10.1161/CIRCULATIONAHA.113.002251", "pmid": "23969696", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "CIRCULATIONAHA.113.002251"}, {"db": "pmc", "key": "PMC3842025"}, {"db": "mid", "key": "NIHMS518819"}], "notes": [], "created": "2017-05-04T14:57:50.942Z", "modified": "2020-01-21T13:56:03.878Z"}, {"entity": "publication", "iuid": "5558f49c0d14434ca91aaa3af36c3a83", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5558f49c0d14434ca91aaa3af36c3a83.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5558f49c0d14434ca91aaa3af36c3a83"}}, "title": "Blood plasma IgG Fc glycans are significantly altered in Alzheimer's disease and progressive mild cognitive impairment.", "authors": [{"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "Yang", "given": "Hongqian", "initials": "H"}, {"family": "Lyutvinskiy", "given": "Yaroslav", "initials": "Y"}, {"family": "Rutishauser", "given": "Dorothea", "initials": "D"}, {"family": "Herukka", "given": "Sanna-Kaisa", "initials": "SK"}, {"family": "Soininen", "given": "Hilkka", "initials": "H"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2013-09-14", "journal": {"volume": "38", "issn": "1875-8908", "issue": "3", "pages": "567-579", "title": "J. Alzheimers Dis.", "issn-l": "1387-2877"}, "abstract": "Blood-based anti-amyloid-\u03b2 (A\u03b2) immunoglobulins (IgGs) and peripheral inflammation are factors correlating with development of Alzheimer's disease (AD). IgG functionality can drastically change from anti- to pro-inflammatory via alterations in the IgG-Fc N-glycan structure. Herein, we tested if IgG-Fc glycosylation in plasma is indeed altered during the development of AD. Samples from age-matched subjects of 23 controls, 58 patients with stable mild cognitive impairment (SMCI), 34 patients with progressive (P)MCI, and 31 patients with AD were investigated. Label-free shotgun proteomics was applied without glycoprotein enrichment. Glycans on peptides EEQYNSTYR (IgG1) and EEQFNSTFR (IgG2) were quantified, and their abundances were normalized to total IgGn glycoform abundance. Univariate and multivariate statistics were employed to investigate the correlations between the patients groups and the abundances of the IgG glycoforms as well as those of inflammatory mediating proteins. Significant differences (p \u2264 0.05) were found, with a lower abundance of complex galactosylated and sialylated forms in AD. For females, a decline in glycoform complexity correlated with disease progress but an inverse change was found in males prior to the onset of AD. Principal component analysis (PCA; Males: R(2)X(cum) = 0.65, Q(2)(cum) = 0.34; Females: R(2)X(cum) = 0.62, Q(2)(cum) = 0.36), confirmed the gender similarities (for controls, SMCI and AD) as well as differences (for PMCI), and showed a close correlation between pro-inflammatory protein markers, AD, female PMCI, and truncated IgG-Fc glycans. The differences observed between genders prior to the onset of AD may indicate a lower ability in females to suppress peripheral inflammation, which may lead to exacerbated disease progression.", "doi": "10.3233/JAD-131088", "pmid": "24028868", "labels": {"Advanced Mass Spectrometry Proteomics": null}, "xrefs": [{"db": "pii", "key": "D06G67816GG7R671"}], "notes": [], "created": "2017-05-04T15:02:46.089Z", "modified": "2021-07-08T08:58:46.765Z"}, {"entity": "publication", "iuid": "d81c4c7c42fa48b1aab8d96dcec59d9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d81c4c7c42fa48b1aab8d96dcec59d9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d81c4c7c42fa48b1aab8d96dcec59d9e"}}, "title": "Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis.", "authors": [{"family": "Beaudoin", "given": "M\u00e9lissa", "initials": "M"}, {"family": "Goyette", "given": "Philippe", "initials": "P"}, {"family": "Boucher", "given": "Gabrielle", "initials": "G"}, {"family": "Lo", "given": "Ken Sin", "initials": "KS"}, {"family": "Rivas", "given": "Manuel A", "initials": "MA"}, {"family": "Stevens", "given": "Christine", "initials": "C"}, {"family": "Alikashani", "given": "Azadeh", "initials": "A"}, {"family": "Ladouceur", "given": "Martin", "initials": "M"}, {"family": "Ellinghaus", "given": "David", "initials": "D"}, {"family": "T\u00f6rkvist", "given": "Leif", "initials": "L"}, {"family": "Goel", "given": "Gautam", "initials": "G"}, {"family": "Lagac\u00e9", "given": "Caroline", "initials": "C"}, {"family": "Annese", "given": "Vito", "initials": "V"}, {"family": "Bitton", "given": "Alain", "initials": "A"}, {"family": "Begun", "given": "Jakob", "initials": "J"}, {"family": "Brant", "given": "Steve R", "initials": "SR"}, {"family": "Bresso", "given": "Francesca", "initials": "F"}, {"family": "Cho", "given": "Judy H", "initials": "JH"}, {"family": "Duerr", "given": "Richard H", "initials": "RH"}, {"family": "Halfvarson", "given": "Jonas", "initials": "J"}, {"family": "McGovern", "given": "Dermot P B", "initials": "DP"}, {"family": "Radford-Smith", "given": "Graham", "initials": "G"}, {"family": "Schreiber", "given": "Stefan", "initials": "S"}, {"family": "Schumm", "given": "Philip L", "initials": "PL"}, {"family": "Sharma", "given": "Yashoda", "initials": "Y"}, {"family": "Silverberg", "given": "Mark S", "initials": "MS"}, {"family": "Weersma", "given": "Rinse K", "initials": "RK"}, {"family": "Quebec IBD Genetics Consortium", "given": null, "initials": null}, {"family": "NIDDK IBD Genetics Consortium", "given": null, "initials": null}, {"family": "International IBD Genetics Consortium", "given": null, "initials": null}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "Vermeire", "given": "Severine", "initials": "S"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Lettre", "given": "Guillaume", "initials": "G"}, {"family": "Xavier", "given": "Ramnik J", "initials": "RJ"}, {"family": "Daly", "given": "Mark J", "initials": "MJ"}, {"family": "Rioux", "given": "John D", "initials": "JD"}], "type": "journal article", "published": "2013-09-12", "journal": {"volume": "9", "issn": "1553-7404", "issue": "9", "pages": "e1003723", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Genome-wide association studies and follow-up meta-analyses in Crohn's disease (CD) and ulcerative colitis (UC) have recently identified 163 disease-associated loci that meet genome-wide significance for these two inflammatory bowel diseases (IBD). These discoveries have already had a tremendous impact on our understanding of the genetic architecture of these diseases and have directed functional studies that have revealed some of the biological functions that are important to IBD (e.g. autophagy). Nonetheless, these loci can only explain a small proportion of disease variance (~14% in CD and 7.5% in UC), suggesting that not only are additional loci to be found but that the known loci may contain high effect rare risk variants that have gone undetected by GWAS. To test this, we have used a targeted sequencing approach in 200 UC cases and 150 healthy controls (HC), all of French Canadian descent, to study 55 genes in regions associated with UC. We performed follow-up genotyping of 42 rare non-synonymous variants in independent case-control cohorts (totaling 14,435 UC cases and 20,204 HC). Our results confirmed significant association to rare non-synonymous coding variants in both IL23R and CARD9, previously identified from sequencing of CD loci, as well as identified a novel association in RNF186. With the exception of CARD9 (OR = 0.39), the rare non-synonymous variants identified were of moderate effect (OR = 1.49 for RNF186 and OR = 0.79 for IL23R). RNF186 encodes a protein with a RING domain having predicted E3 ubiquitin-protein ligase activity and two transmembrane domains. Importantly, the disease-coding variant is located in the ubiquitin ligase domain. Finally, our results suggest that rare variants in genes identified by genome-wide association in UC are unlikely to contribute significantly to the overall variance for the disease. Rather, these are expected to help focus functional studies of the corresponding disease loci.", "doi": "10.1371/journal.pgen.1003723", "pmid": "24068945", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-13-00555"}, {"db": "pmc", "key": "PMC3772057"}], "notes": [], "created": "2017-05-04T15:03:36.533Z", "modified": "2017-05-30T14:52:46.089Z"}, {"entity": "publication", "iuid": "9a73e95a9e86494aa06f2bd3acab89d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a73e95a9e86494aa06f2bd3acab89d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a73e95a9e86494aa06f2bd3acab89d9"}}, "title": "A tosyl-activated magnetic bead cellulose as solid support for sensitive protein detection.", "authors": [{"family": "Yan", "given": "Junhong", "initials": "J"}, {"family": "Hor\u00e1k", "given": "Daniel", "initials": "D"}, {"family": "Lenfeld", "given": "Ji\u0159\u00ed", "initials": "J"}, {"family": "Hammond", "given": "Maria", "initials": "M", "orcid": "0000-0002-8375-6676", "researcher": {"href": "https://publications.scilifelab.se/researcher/78703c93891e4827aabb35c2011be9f2.json"}}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2013-09-10", "journal": {"volume": "167", "issn": "1873-4863", "issue": "3", "pages": "235-240", "title": "J. Biotechnol.", "issn-l": "0168-1656"}, "abstract": "Magnetic bead cellulose (MBC) was prepared using sol-gel transition of viscose in the presence of maghemite (\u03b3-Fe\u2082O\u2083) nanoparticles. The MBC particles were then activated with p-toluenesulfonyl chloride to yield tosyl-activated magnetic bead cellulose (MBC-Ts). The microspheres were characterized by light and electron microscopy, elemental analysis and atomic absorption spectroscopy to determine morphology, size, polydispersity and content of iron and tosyl groups. The functionality of the MBC-Ts microspheres was demonstrated using proximity ligation assay (PLA) to detect vascular endothelial growth factor in femtomolar concentration range. The MBC-Ts microspheres performed equally well as commercially available microparticles that are routinely used as solid support in solid phase PLA.", "doi": "10.1016/j.jbiotec.2013.06.010", "pmid": "23811391", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0168-1656(13)00266-6"}], "notes": [], "created": "2017-05-04T14:55:24.653Z", "modified": "2023-04-14T13:56:28.204Z"}, {"entity": "publication", "iuid": "2b57558de7fe4a87857ad29f0c641235", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b57558de7fe4a87857ad29f0c641235.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b57558de7fe4a87857ad29f0c641235"}}, "title": "The Oct1 homolog Nubbin is a repressor of NF-\u03baB-dependent immune gene expression that increases the tolerance to gut microbiota.", "authors": [{"family": "Dantoft", "given": "Widad", "initials": "W"}, {"family": "Davis", "given": "Monica M", "initials": "MM"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Tang", "given": "Xiongzhuo", "initials": "X"}, {"family": "Uvell", "given": "Hanna", "initials": "H"}, {"family": "Junell", "given": "Anna", "initials": "A"}, {"family": "Beskow", "given": "Anne", "initials": "A"}, {"family": "Engstr\u00f6m", "given": "Ylva", "initials": "Y"}], "type": "journal article", "published": "2013-09-06", "journal": {"volume": "11", "issn": "1741-7007", "issue": null, "pages": "99", "title": "BMC Biol.", "issn-l": "1741-7007"}, "abstract": "Innate immune responses are evolutionarily conserved processes that provide crucial protection against invading organisms. Gene activation by potent NF-\u03baB transcription factors is essential both in mammals and Drosophila during infection and stress challenges. If not strictly controlled, this potent defense system can activate autoimmune and inflammatory stress reactions, with deleterious consequences for the organism. Negative regulation to prevent gene activation in healthy organisms, in the presence of the commensal gut flora, is however not well understood.\n\nWe show that the Drosophila homolog of mammalian Oct1/POU2F1 transcription factor, called Nubbin (Nub), is a repressor of NF-\u03baB/Relish-driven antimicrobial peptide gene expression in flies. In nub1 mutants, which lack Nub-PD protein, excessive expression of antimicrobial peptide genes occurs in the absence of infection, leading to a significant reduction of the numbers of cultivatable gut commensal bacteria. This aberrant immune gene expression was effectively blocked by expression of Nub from a transgene. We have identified an upstream regulatory region, containing a cluster of octamer sites, which is required for repression of antimicrobial peptide gene expression in healthy flies. Chromatin immunoprecipitation experiments demonstrated that Nub binds to octamer-containing promoter fragments of several immune genes. Gene expression profiling revealed that Drosophila Nub negatively regulates many genes that are involved in immune and stress responses, while it is a positive regulator of genes involved in differentiation and metabolism.\n\nThis study demonstrates that a large number of genes that are activated by NF-\u03baB/Relish in response to infection are normally repressed by the evolutionarily conserved Oct/POU transcription factor Nub. This prevents uncontrolled gene activation and supports the existence of a normal gut flora. We suggest that Nub protein plays an ancient role, shared with mammalian Oct/POU transcription factors, to moderate responses to immune challenge, thereby increasing the tolerance to biotic stress.", "doi": "10.1186/1741-7007-11-99", "pmid": "24010524", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "1741-7007-11-99"}, {"db": "pmc", "key": "PMC3849502"}], "notes": [], "created": "2017-05-04T15:03:14.247Z", "modified": "2021-07-05T12:48:15.963Z"}, {"entity": "publication", "iuid": "f76e9c19c0b74aaba112e0f708d80622", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f76e9c19c0b74aaba112e0f708d80622.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f76e9c19c0b74aaba112e0f708d80622"}}, "title": "Post-zygotic and inter-individual structural genetic variation in a presumptive enhancer element of the locus between the IL10R\u03b2 and IFNAR1 genes.", "authors": [{"family": "Razzaghian", "given": "Hamid Reza", "initials": "HR"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA"}, {"family": "Prakash", "given": "Kancherla Reddy", "initials": "KR"}, {"family": "Przerada", "given": "Szymon", "initials": "S"}, {"family": "Paprocka", "given": "Hanna", "initials": "H"}, {"family": "Zywicka", "given": "Anna", "initials": "A"}, {"family": "Westerman", "given": "Maxwell P", "initials": "MP"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "O'Hanlon", "given": "Terrance P", "initials": "TP"}, {"family": "Rider", "given": "Lisa G", "initials": "LG"}, {"family": "Miller", "given": "Frederick W", "initials": "FW"}, {"family": "Srutek", "given": "Ewa", "initials": "E"}, {"family": "Jankowski", "given": "Michal", "initials": "M"}, {"family": "Zegarski", "given": "Wojciech", "initials": "W"}, {"family": "Piotrowski", "given": "Arkadiusz", "initials": "A"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}], "type": "journal article", "published": "2013-09-04", "journal": {"volume": "8", "issn": "1932-6203", "issue": "9", "pages": "e67752", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Although historically considered as junk-DNA, tandemly repeated sequence motifs can affect human phenotype. For example, variable number tandem repeats (VNTR) with embedded enhancers have been shown to regulate gene transcription. The post-zygotic variation is the presence of genetically distinct populations of cells in an individual derived from a single zygote, and this is an understudied aspect of genome biology. We report somatically variable VNTR with sequence properties of an enhancer, located upstream of IFNAR1. Initially, SNP genotyping of 63 monozygotic twin pairs and multiple tissues from 21 breast cancer patients suggested a frequent post-zygotic mosaicism. The VNTR displayed a repeated 32 bp core motif in the center of the repeat, which was flanked by similar variable motifs. A total of 14 alleles were characterized based on combinations of segments, which showed post-zygotic and inter-individual variation, with up to 6 alleles in a single subject. Somatic variation occurred in \u223c24% of cases. In this hypervariable region, we found a clustering of transcription factor binding sites with strongest sequence similarity to mouse Foxg1 transcription factor binding motif. This study describes a VNTR with sequence properties of an enhancer that displays post-zygotic and inter-individual genetic variation. This element is within a locus containing four related cytokine receptors: IFNAR2, IL10R\u03b2, IFNAR1 and IFNGR2, and we hypothesize that it might function in transcriptional regulation of several genes in this cluster. Our findings add another level of complexity to the variation among VNTR-based enhancers. Further work may unveil the normal function of this VNTR in transcriptional control and its possible involvement in diseases connected with these receptors, such as autoimmune conditions and cancer.", "doi": "10.1371/journal.pone.0067752", "pmid": "24023707", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-04402"}, {"db": "pmc", "key": "PMC3762855"}], "notes": [], "created": "2017-05-04T15:01:29.971Z", "modified": "2020-01-21T13:56:06.389Z"}, {"entity": "publication", "iuid": "14e9532cc5b04ab5b73ec0e0ef75acff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14e9532cc5b04ab5b73ec0e0ef75acff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14e9532cc5b04ab5b73ec0e0ef75acff"}}, "title": "Structural insights into substrate recognition in proton-dependent oligopeptide transporters.", "authors": [{"family": "Guettou", "given": "Fatma", "initials": "F"}, {"family": "Quistgaard", "given": "Esben M", "initials": "EM"}, {"family": "Tr\u00e9saugues", "given": "Lionel", "initials": "L"}, {"family": "Moberg", "given": "Per", "initials": "P"}, {"family": "Jegersch\u00f6ld", "given": "Caroline", "initials": "C"}, {"family": "Zhu", "given": "Lin", "initials": "L"}, {"family": "Jong", "given": "Agnes Jin Oi", "initials": "AJ"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}, {"family": "L\u00f6w", "given": "Christian", "initials": "C"}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "14", "issn": "1469-3178", "issue": "9", "pages": "804-810", "title": "EMBO Rep.", "issn-l": "1469-221X"}, "abstract": "Short-chain peptides are transported across membranes through promiscuous proton-dependent oligopeptide transporters (POTs)--a subfamily of the major facilitator superfamily (MFS). The human POTs, PEPT1 and PEPT2, are also involved in the absorption of various drugs in the gut as well as transport to target cells. Here, we present a structure of an oligomeric POT transporter from Shewanella oneidensis (PepTSo2), which was crystallized in the inward open conformation in complex with the peptidomimetic alafosfalin. All ligand-binding residues are highly conserved and the structural insights presented here are therefore likely to also apply to human POTs.", "doi": "10.1038/embor.2013.107", "pmid": "23867627", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "embor2013107"}, {"db": "pmc", "key": "PMC3790050"}, {"db": "PDB", "key": "4LEP"}], "notes": [], "created": "2017-05-04T15:03:47.294Z", "modified": "2017-09-06T11:42:08.981Z"}, {"entity": "publication", "iuid": "1586cc24013f4a42a0b1fa3294c39f98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1586cc24013f4a42a0b1fa3294c39f98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1586cc24013f4a42a0b1fa3294c39f98"}}, "title": "Role of individual MARK isoforms in phosphorylation of tau at Ser\u00b2\u2076\u00b2 in Alzheimer's disease.", "authors": [{"family": "Gu", "given": "Gucci Jijuan", "initials": "GJ"}, {"family": "Lund", "given": "Harald", "initials": "H"}, {"family": "Wu", "given": "Di", "initials": "D"}, {"family": "Blokzijl", "given": "Andries", "initials": "A"}, {"family": "Classon", "given": "Christina", "initials": "C"}, {"family": "von Euler", "given": "Gabriel", "initials": "G"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Sunnemark", "given": "Dan", "initials": "D"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "15", "issn": "1559-1174", "issue": "3", "pages": "458-469", "title": "Neuromolecular Med.", "issn-l": "1535-1084"}, "abstract": "The microtubule-affinity regulating kinase (MARK) family consists of four highly conserved members that have been implicated in phosphorylation of tau protein, causing formation of neurofibrillary tangles in Alzheimer's disease (AD). Understanding of roles by individual MARK isoform in phosphorylating tau has been limited due to lack of antibodies selective for each MARK isoform. In this study, we first applied the proximity ligation assay on cells to select antibodies specific for each MARK isoform. In cells, a CagA peptide specifically and significantly inhibited tau phosphorylation at Ser\u00b2\u2076\u00b2 mediated by MARK4 but not other MARK isoforms. We then used these antibodies to study expression levels of MARK isoforms and interactions between tau and individual MARK isoforms in postmortem human brains. We found a strong and significant elevation of MARK4 expression and MARK4-tau interactions in AD brains, correlating with the Braak stages of the disease. These results suggest the MARK4-tau interactions are of functional importance in the progression of AD and the results also identify MARK4 as a promising target for AD therapy.", "doi": "10.1007/s12017-013-8232-3", "pmid": "23666762", "labels": {"Clinical Biomarkers": "", "PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:25.558Z", "modified": "2023-04-14T13:56:28.379Z"}, {"entity": "publication", "iuid": "0a2bb6fdb7254f0c9c89f417df79602e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a2bb6fdb7254f0c9c89f417df79602e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a2bb6fdb7254f0c9c89f417df79602e"}}, "title": "Progesterone receptor negativity is an independent risk factor for relapse in patients with early stage endometrioid endometrial adenocarcinoma.", "authors": [{"family": "Huvila", "given": "Jutta", "initials": "J"}, {"family": "Talve", "given": "Lauri", "initials": "L"}, {"family": "Carp\u00e9n", "given": "Olli", "initials": "O"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Gr\u00e9nman", "given": "Seija", "initials": "S"}, {"family": "Auranen", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "130", "issn": "1095-6859", "issue": "3", "pages": "463-469", "title": "Gynecol. Oncol.", "issn-l": "0090-8258"}, "abstract": "In endometrioid endometrial adenocarcinoma (EEA), the currently established prognostic factors in clinical guidelines are stage and grade. Many guidelines include lymphovascular invasion (LVI) and tumor size as prognostic factors. Although several studies have associated lack of estrogen (ER) and progesterone receptor (PR) expression with reduced outcome, the prognostic use of these markers is uncommon. Better prognostication of clinical behavior would be useful in patients with early stage (I-II) disease. In this study we evaluated ER and PR as prognostic factors in EEA, and compared their expression with other potential biomarkers and clinical parameters.\n\nTissue microarrays were constructed from 182 patients with stages I-II EEA. ER, PR, p53, Ki-67, PTEN, MLH and HER-2 expression were assessed by immunohistochemical staining and HER-2 was confirmed with SISH. The results were correlated with clinicopathologic parameters and to disease-free survival.\n\nEleven patients (6%) developed recurrent disease during a median follow up time of 62.8 months. In univariate analysis FIGO grade (p=0.019), positive expression of p53 (p=0.010) and negative PR expression (p=0.001) were associated with a shorter disease-free survival. In multivariate analysis only negative PR expression (p=0.019) was significantly associated with a shorter disease-free survival. LVI and tumor size where not of prognostic value.\n\nLack of PR expression is a strong, independent risk factor for tumor recurrence in patients with stages I-II endometrioid endometrial cancer. The use of this easily measurable biomarker as a prognostic factor in the clinical context should be considered and tested in a larger patient population.", "doi": "10.1016/j.ygyno.2013.06.015", "pmid": "23777659", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "S0090-8258(13)00848-2"}], "notes": [], "created": "2017-05-04T14:55:58.050Z", "modified": "2017-05-30T12:51:20.624Z"}, {"entity": "publication", "iuid": "98979524ca9f43c49fa6b51d69edd243", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98979524ca9f43c49fa6b51d69edd243.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98979524ca9f43c49fa6b51d69edd243"}}, "title": "Phylogeography of willow grouse (Lagopus lagopus) in the Arctic: taxonomic discordance as inferred from molecular data", "authors": [{"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Wang", "given": "Biao", "initials": "B"}, {"family": "Axelsson", "given": "Thomas", "initials": "T"}, {"family": "Quintela", "given": "Mar\u00eda", "initials": "M"}], "type": "journal-article", "published": "2013-09-00", "journal": {"volume": "110", "issn": "0024-4066", "issue": "1", "pages": "77-90", "title": "Biol J Linn Soc Lond", "issn-l": null}, "abstract": null, "doi": "10.1111/bij.12109", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T13:44:24.683Z", "modified": "2021-06-22T12:04:18.241Z"}, {"entity": "publication", "iuid": "611d82b47d8b4be493d2d1d27197ef99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/611d82b47d8b4be493d2d1d27197ef99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/611d82b47d8b4be493d2d1d27197ef99"}}, "title": "Multilocus genetic risk scores for coronary heart disease prediction.", "authors": [{"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Reilly", "given": "Marie", "initials": "M"}, {"family": "Arnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}], "type": "evaluation studies", "published": "2013-09-00", "journal": {"volume": "33", "issn": "1524-4636", "issue": "9", "pages": "2267-2272", "title": "Arterioscler. Thromb. Vasc. Biol.", "issn-l": "1079-5642"}, "abstract": "Current guidelines do not support the use of genetic profiles in risk assessment of coronary heart disease (CHD). However, new single nucleotide polymorphisms associated with CHD and intermediate cardiovascular traits have recently been discovered. We aimed to compare several multilocus genetic risk score (MGRS) in terms of association with CHD and to evaluate clinical use.\r\n\r\nWe investigated 6 Swedish prospective cohort studies with 10 612 participants free of CHD at baseline. We developed 1 overall MGRS based on 395 single nucleotide polymorphisms reported as being associated with cardiovascular traits, 1 CHD-specific MGRS, including 46 single nucleotide polymorphisms, and 6 trait-specific MGRS for each established CHD risk factors. Both the overall and the CHD-specific MGRS were significantly associated with CHD risk (781 incident events; hazard ratios for fourth versus first quartile, 1.54 and 1.52; P<0.001) and improved risk classification beyond established risk factors (net reclassification improvement, 4.2% and 4.9%; P=0.006 and 0.017). Discrimination improvement was modest (C-index improvement, 0.004). A polygene MGRS performed worse than the CHD-specific MGRS. We estimate that 1 additional CHD event for every 318 people screened at intermediate risk could be saved by measuring the CHD-specific genetic score in addition to the established risk factors.\r\n\r\nOur results indicate that genetic information could be of some clinical value for prediction of CHD, although further studies are needed to address aspects, such as feasibility, ethics, and cost efficiency of genetic profiling in the primary prevention setting.", "doi": "10.1161/ATVBAHA.113.301218", "pmid": "23685553", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ATVBAHA.113.301218"}], "notes": [], "created": "2017-05-04T14:57:48.478Z", "modified": "2020-01-21T13:56:08.744Z"}, {"entity": "publication", "iuid": "6e0af6826e6d4032a7a49441bd18017b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e0af6826e6d4032a7a49441bd18017b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e0af6826e6d4032a7a49441bd18017b"}}, "title": "Identification of candidate oncogenes in human colorectal cancers with microsatellite instability.", "authors": [{"family": "Gylfe", "given": "Alexandra E", "initials": "AE"}, {"family": "Kondelin", "given": "Johanna", "initials": "J"}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "Ristolainen", "given": "Heikki", "initials": "H"}, {"family": "Katainen", "given": "Riku", "initials": "R"}, {"family": "Pitk\u00e4nen", "given": "Esa", "initials": "E"}, {"family": "Kaasinen", "given": "Eevi", "initials": "E"}, {"family": "Rantanen", "given": "Ville", "initials": "V"}, {"family": "Tanskanen", "given": "Tomas", "initials": "T"}, {"family": "Varjosalo", "given": "Markku", "initials": "M"}, {"family": "Lehtonen", "given": "Heli", "initials": "H"}, {"family": "Palin", "given": "Kimmo", "initials": "K"}, {"family": "Taipale", "given": "Minna", "initials": "M"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}, {"family": "Renkonen-Sinisalo", "given": "Laura", "initials": "L"}, {"family": "J\u00e4rvinen", "given": "Heikki", "initials": "H"}, {"family": "B\u00f6hm", "given": "Jan", "initials": "J"}, {"family": "Mecklin", "given": "Jukka-Pekka", "initials": "JP"}, {"family": "Ristim\u00e4ki", "given": "Ari", "initials": "A"}, {"family": "Kilpivaara", "given": "Outi", "initials": "O"}, {"family": "Tuupanen", "given": "Sari", "initials": "S"}, {"family": "Karhu", "given": "Auli", "initials": "A"}, {"family": "Vahteristo", "given": "Pia", "initials": "P"}, {"family": "Aaltonen", "given": "Lauri A", "initials": "LA"}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "145", "issn": "1528-0012", "issue": "3", "pages": "540-3.e22", "title": "Gastroenterology", "issn-l": "0016-5085"}, "abstract": "Microsatellite instability can be found in approximately 15% of all colorectal cancers. To detect new oncogenes we sequenced the exomes of 25 colorectal tumors and respective healthy colon tissue. Potential mutation hot spots were confirmed in 15 genes; ADAR, DCAF12L2, GLT1D1, ITGA7, MAP1B, MRGPRX4, PSRC1, RANBP2, RPS6KL1, SNCAIP, TCEAL6, TUBB6, WBP5, VEGFB, and ZBTB2; these were validated in 86\u00a0tumors with microsatellite instability. ZBTB2, RANBP2, and PSRC1 also were found to contain hot spot mutations in the validation set. The form of ZBTB2 associated with colorectal cancer increased cell proliferation. The mutation hot spots might be used to develop personalized tumor profiling and therapy.", "doi": "10.1053/j.gastro.2013.05.015", "pmid": "23684749", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "S0016-5085(13)00747-6"}], "notes": [], "created": "2017-05-04T14:57:06.286Z", "modified": "2017-05-30T11:44:14.625Z"}, {"entity": "publication", "iuid": "6ba32815774c43b8b25856bd5108600c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ba32815774c43b8b25856bd5108600c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ba32815774c43b8b25856bd5108600c"}}, "title": "High modal number and triple trisomies are highly correlated favorable factors in childhood B-cell precursor high hyperdiploid acute lymphoblastic leukemia treated according to the NOPHO ALL 1992/2000 protocols.", "authors": [{"family": "Paulsson", "given": "Kajsa", "initials": "K"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Andersen", "given": "Mette K", "initials": "MK"}, {"family": "Autio", "given": "Kirsi", "initials": "K"}, {"family": "Barbany", "given": "Gisela", "initials": "G"}, {"family": "Borgstr\u00f6m", "given": "Georg", "initials": "G"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Golovleva", "given": "Irina", "initials": "I"}, {"family": "Heim", "given": "Sverre", "initials": "S"}, {"family": "Heinonen", "given": "Kristiina", "initials": "K"}, {"family": "Hovland", "given": "Randi", "initials": "R"}, {"family": "Johannsson", "given": "Johann H", "initials": "JH"}, {"family": "Kjeldsen", "given": "Eigil", "initials": "E"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Palmqvist", "given": "Lars", "initials": "L", "orcid": "0000-0001-9274-360X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e50c0057dcb47f39e085b16580806c2.json"}}, {"family": "Johansson", "given": "Bertil", "initials": "B"}, {"family": "Nordic Society of Pediatric Hematology and Oncology (NOPHO)", "given": "", "initials": ""}, {"family": "Swedish Cytogenetic Leukemia Study Group (SCLSG)", "given": "", "initials": ""}, {"family": "NOPHO Leukemia Cytogenetic Study Group (NLCSG)", "given": "", "initials": ""}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "98", "issn": "1592-8721", "issue": "9", "pages": "1424-1432", "title": "Haematologica", "issn-l": "0390-6078"}, "abstract": "Between 1992 and 2008, 713 high hyperdiploid acute lymphoblastic leukemias in children aged 1-15 years were diagnosed and treated according to the Nordic Society for Pediatric Hematology and Oncology acute lymphoblastic leukemia 1992/2000 protocols. Twenty (2.8%) harbored t(1;19), t(9;22), der(11q23), or t(12;21). The median age of patients with \"classic\" high hyperdiploidy was lower than that of patients with translocation-positive high hyperdiploidy (P<0.001). Cases with triple trisomies (+4, +10, +17), comprising 50%, had higher modal numbers than the triple trisomy-negative cases (P<0.0001). The probabilities of event-free survival and overall survival were lower for those with white blood cell counts \u2265 50 \u00d7 10(9)/L (P=0.017/P=0.009), \u2265 5% bone marrow blasts at day 29 (P=0.001/0.002), and for high-risk patients (P<0.001/P=0.003), whereas event-free, but not overall, survival, was higher for cases with gains of chromosomes 4 (P<0.0001), 6 (P<0.003), 17 (P=0.010), 18 (P=0.049), and 22 (P=0.040), triple trisomies (P=0.002), and modal numbers >53/55 (P=0.020/0.024). In multivariate analyses, modal number and triple trisomies were significantly associated with superior event-free survival in separate analyses with age and white blood cell counts. When including both modal numbers and triple trisomies, only low white blood cell counts were significantly associated with superior event-free survival (P=0.009). We conclude that high modal chromosome numbers and triple trisomies are highly correlated prognostic factors and that these two parameters identify the same subgroup of patients characterized by a particularly favorable outcome.", "doi": "10.3324/haematol.2013.085852", "pmid": "23645689", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "haematol.2013.085852"}, {"db": "pmc", "key": "PMC3762100"}], "notes": [], "created": "2017-05-04T14:57:56.324Z", "modified": "2021-07-08T12:52:24.374Z"}, {"entity": "publication", "iuid": "e2ec88ee0b9b493cae196ed552db72f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2ec88ee0b9b493cae196ed552db72f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2ec88ee0b9b493cae196ed552db72f9"}}, "title": "Glutamatergic GRIN2B and polyaminergic ODC1 genes in suicide attempts: associations and gene-environment interactions with childhood/adolescent physical assault.", "authors": [{"family": "Sokolowski", "given": "M", "initials": "M"}, {"family": "Ben-Efraim", "given": "Y J", "initials": "YJ"}, {"family": "Wasserman", "given": "J", "initials": "J"}, {"family": "Wasserman", "given": "D", "initials": "D"}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "18", "issn": "1476-5578", "issue": "9", "pages": "985-992", "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "The complex etiology of suicidal behavior has frequently been investigated in relation to monoaminergic neurotransmission, but other neurosystems have shown alterations as well, involving excitatory glutamatergic and inhibitory \u03b3-aminobutyric acid (GABA) molecular components, together with the modulating polyamines. Sufficiently powered and family-based association studies of glutamatergic and GABAergic genes with suicidal behavior are nonexistent, but several studies have been reported for polyamines. We therefore conducted, for the first time ever, an extensive family-based study of 113 candidate single-nucleotide polymorphisms (SNPs) located in 24 glutamatergic and GABA genes, in addition to interrelated polyaminergic genes, on the outcome of severe suicide attempts (SAs). The family-based analysis (n=660 trios) was supplemented with gene-environment interaction (G \u00d7 E), case-control (n=519 controls) and subgroup analyses. The main observations were the previously unreported association and linkage of SNPs rs2268115 and rs220557 in GRIN2B, as well as of SNPs rs1049500 and rs2302614 in ODC1 (P<10(-2)). Furthermore, GRIN2B haplotypic associations were observed, in particular with a four-SNP AGGC haplotype (rs1805247-rs1806201-rs1805482-rs2268115; P<10(-5)), and a third SNP rs7559979 in ODC1 showed G \u00d7 E with serious childhood/adolescent physical assault (P<10(-4)). SA subjects were characterized by transdiagnostic trait anger and past year alcohol-drug use disorders, but not by alcohol-drug use at SA, depression, anxiety or psychosis diagnoses. We also discuss a first ever confirmatory observation of SNP rs6526342 (polyaminergic SAT1) in SA, originally identified in completed suicides. The results suggest that specific genetic variants in a subset of glutamatergic (GRIN2B) and polyaminergic (ODC1) neurosystem genes may be of importance in certain suicidal subjects.", "doi": "10.1038/mp.2012.112", "pmid": "22850629", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "mp2012112"}], "notes": [], "created": "2017-05-04T15:01:21.826Z", "modified": "2020-01-21T13:56:05.815Z"}, {"entity": "publication", "iuid": "f7e5cebc7cd645fa92a27650fe79b2c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f7e5cebc7cd645fa92a27650fe79b2c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f7e5cebc7cd645fa92a27650fe79b2c9"}}, "title": "Global DNA hypermethylation is associated with high serum levels of persistent organic pollutants in an elderly population.", "authors": [{"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Penell", "given": "Johanna", "initials": "J"}, {"family": "Luttropp", "given": "Karin", "initials": "K"}, {"family": "Nordfors", "given": "Louise", "initials": "L"}, {"family": "Syv\u00e4nen", "given": "Anne-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Salihovic", "given": "Samira", "initials": "S"}, {"family": "van Bavel", "given": "Bert", "initials": "B"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Lind", "given": "P Monica", "initials": "PM"}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "59", "issn": "1873-6750", "issue": null, "pages": "456-461", "title": "Environ Int", "issn-l": "0160-4120"}, "abstract": "Dioxin exposure has experimentally been associated with changes in DNA methylation, an epigenetic change that is associated with disease. The present study aims to investigate if serum levels of dioxin and other persistent environmental pollutants are related to global DNA methylation in a human sample. In the population-based Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) study (all aged 70), global DNA methylation was measured by the Luminometric Methylation Assay in 524 subjects. Twenty-three different POPs, including 16 PCBs, five pesticides, one dioxin (OCDD) and one brominated flame retardant (BDE47) were analysed by HRGC/HRMS. Ten single nucleotide polymorphisms (SNPs) in the Aryl hydrocarbon (Ah)-receptor were analysed by mini-sequencing. High levels of toxic equivalency (TEQ) for PCBs and dioxin were associated with DNA hypermethylation (p=0.030). This was mainly attributed to coplanar non-ortho PCBs. While no significant associations were found between DNA methylation and SNPs in the Ah-receptor, an interaction was found between the SNP rs2237297 and TEQ so that TEQ was associated with hypermethylation (p=0.009) only in subjects with one G-allele (n=103). Also high levels of the PCB126 congener, the OCDD, and the pesticide metabolite p,p'-DDE were related to DNA hypermethylation (p=0.01, 0.03 and 0.003, respectively). In conclusion, in a sample of elderly subjects, high TEQ including PCBs and the dioxin OCDD and high serum levels of PCB126, OCDD, and p,p'-DDE were related to global DNA hypermethylation in a cross-sectional analysis.", "doi": "10.1016/j.envint.2013.07.008", "pmid": "23933504", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0160-4120(13)00152-9"}], "notes": [], "created": "2017-05-04T15:01:16.527Z", "modified": "2021-07-07T15:11:02.809Z"}, {"entity": "publication", "iuid": "7a67f7bf9bdb47b2af025f254c8aa4e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a67f7bf9bdb47b2af025f254c8aa4e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a67f7bf9bdb47b2af025f254c8aa4e3"}}, "title": "Genome-wide analysis shows association of epigenetic changes in regulators of Rab and Rho GTPases with spinal muscular atrophy severity.", "authors": [{"family": "Zheleznyakova", "given": "Galina Y", "initials": "GY"}, {"family": "Voisin", "given": "Sarah", "initials": "S"}, {"family": "Kiselev", "given": "Anton V", "initials": "AV"}, {"family": "S\u00e4llman Alm\u00e9n", "given": "Markus", "initials": "M"}, {"family": "Xavier", "given": "Miguel J", "initials": "MJ"}, {"family": "Maretina", "given": "Marianna A", "initials": "MA"}, {"family": "Tishchenko", "given": "Lyudmila I", "initials": "LI"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Baranov", "given": "Vladislav S", "initials": "VS"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "21", "issn": "1476-5438", "issue": "9", "pages": "988-993", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Spinal muscular atrophy (SMA) is a monogenic disorder that is subdivided into four different types and caused by survival motor neuron gene 1 (SMN1) deletion. Discordant cases of SMA suggest that there exist additional severity modifying factors, apart from the SMN2 gene copy number. Here we performed the first genome-wide methylation profiling of SMA patients and healthy individuals to study the association of DNA methylation status with the severity of the SMA phenotype. We identified strong significant differences in methylation level between SMA patients and healthy controls in CpG sites close to the genes CHML, ARHGAP22, CYTSB, CDK2AP1 and SLC23A2. Interestingly, the CHML and ARHGAP22 genes are associated with the activity of Rab and Rho GTPases, which are important regulators of vesicle formation, actin dynamics, axonogenesis, processes that could be critical for SMA development. We suggest that epigenetic modifications may influence the severity of SMA and that these novel genetic positions could prove to be valuable biomarkers for the understanding of SMA pathogenesis.", "doi": "10.1038/ejhg.2012.293", "pmid": "23299920", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ejhg2012293"}, {"db": "pmc", "key": "PMC3746269"}], "notes": [], "created": "2017-05-04T15:02:23.799Z", "modified": "2020-01-21T13:56:03.175Z"}, {"entity": "publication", "iuid": "b02e8bb899ba4039b9b40e26090fbe16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b02e8bb899ba4039b9b40e26090fbe16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b02e8bb899ba4039b9b40e26090fbe16"}}, "title": "Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.", "authors": [{"family": "Cross-Disorder Group of the Psychiatric Genomics Consortium", "given": "None", "initials": "N"}, {"family": "Lee", "given": "S Hong", "initials": "SH"}, {"family": "Ripke", "given": "Stephan", "initials": "S"}, {"family": "Neale", "given": "Benjamin M", "initials": "BM"}, {"family": "Faraone", "given": "Stephen V", "initials": "SV"}, {"family": "Purcell", "given": "Shaun M", "initials": "SM"}, {"family": "Perlis", "given": "Roy H", "initials": "RH"}, {"family": "Mowry", "given": "Bryan J", "initials": "BJ"}, {"family": "Thapar", "given": "Anita", "initials": "A"}, {"family": "Goddard", "given": "Michael E", "initials": "ME"}, {"family": "Witte", "given": "John S", "initials": "JS"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Akil", "given": "Huda", "initials": "H"}, {"family": "Amin", "given": "Farooq", "initials": "F"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Anjorin", "given": "Adebayo", "initials": "A"}, {"family": "Anney", "given": "Richard", "initials": "R"}, {"family": "Anttila", "given": "Verneri", "initials": "V"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Asherson", "given": "Philip", "initials": "P"}, {"family": "Azevedo", "given": "Maria H", "initials": "MH"}, {"family": "Backlund", "given": "Lena", "initials": "L"}, {"family": "Badner", "given": "Judith A", "initials": "JA"}, {"family": "Bailey", "given": "Anthony J", "initials": "AJ"}, {"family": "Banaschewski", "given": "Tobias", "initials": "T"}, {"family": "Barchas", "given": "Jack D", "initials": "JD"}, {"family": "Barnes", "given": "Michael R", "initials": "MR"}, {"family": "Barrett", "given": "Thomas B", "initials": "TB"}, {"family": "Bass", "given": "Nicholas", "initials": "N"}, {"family": "Battaglia", "given": "Agatino", "initials": "A"}, {"family": "Bauer", "given": "Michael", "initials": "M"}, {"family": "Bay\u00e9s", "given": "M\u00f2nica", "initials": "M"}, {"family": "Bellivier", "given": "Frank", "initials": "F"}, {"family": "Bergen", "given": "Sarah E", "initials": "SE"}, {"family": "Berrettini", "given": "Wade", "initials": "W"}, {"family": "Betancur", "given": "Catalina", "initials": "C"}, {"family": "Bettecken", "given": "Thomas", "initials": "T"}, {"family": "Biederman", "given": "Joseph", "initials": "J"}, {"family": "Binder", "given": "Elisabeth B", "initials": "EB"}, {"family": "Black", "given": "Donald W", "initials": "DW"}, {"family": "Blackwood", "given": "Douglas H R", "initials": "DHR"}, {"family": "Bloss", "given": "Cinnamon S", "initials": "CS"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "Breuer", "given": "Ren\u00e9", "initials": "R"}, {"family": "Bruggeman", "given": "Richard", "initials": "R"}, {"family": "Cormican", "given": "Paul", "initials": "P"}, {"family": "Buccola", "given": "Nancy G", "initials": "NG"}, {"family": "Buitelaar", "given": "Jan K", "initials": "JK"}, {"family": "Bunney", "given": "William E", "initials": "WE"}, {"family": "Buxbaum", "given": "Joseph D", "initials": "JD"}, {"family": "Byerley", "given": "William F", "initials": "WF"}, {"family": "Byrne", "given": "Enda M", "initials": "EM"}, {"family": "Caesar", "given": "Sian", "initials": "S"}, {"family": "Cahn", "given": "Wiepke", "initials": "W"}, {"family": "Cantor", "given": "Rita M", "initials": "RM"}, {"family": "Casas", "given": "Miguel", "initials": "M"}, {"family": "Chakravarti", "given": "Aravinda", "initials": "A"}, {"family": "Chambert", "given": "Kimberly", "initials": "K"}, {"family": "Choudhury", "given": "Khalid", "initials": "K"}, {"family": "Cichon", "given": "Sven", "initials": "S"}, {"family": "Cloninger", "given": "C Robert", "initials": "CR"}, {"family": "Collier", "given": "David A", "initials": "DA"}, {"family": "Cook", "given": "Edwin H", "initials": "EH"}, {"family": "Coon", "given": "Hilary", "initials": "H"}, {"family": "Cormand", "given": "Bru", "initials": "B"}, {"family": "Corvin", "given": "Aiden", "initials": "A"}, {"family": "Coryell", "given": "William H", "initials": "WH"}, {"family": "Craig", "given": "David W", "initials": "DW"}, {"family": "Craig", "given": "Ian W", "initials": "IW"}, {"family": "Crosbie", "given": "Jennifer", "initials": "J"}, {"family": "Cuccaro", "given": "Michael L", "initials": "ML"}, {"family": "Curtis", "given": "David", "initials": "D"}, {"family": "Czamara", "given": "Darina", "initials": "D"}, {"family": "Datta", "given": "Susmita", "initials": "S"}, {"family": "Dawson", "given": "Geraldine", "initials": "G"}, {"family": "Day", "given": "Richard", "initials": "R"}, {"family": "De Geus", "given": "Eco J", "initials": "EJ"}, {"family": "Degenhardt", "given": "Franziska", "initials": "F"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Donohoe", "given": "Gary J", "initials": "GJ"}, {"family": "Doyle", "given": "Alysa E", "initials": "AE"}, {"family": "Duan", "given": "Jubao", "initials": "J"}, {"family": "Dudbridge", "given": "Frank", "initials": "F"}, {"family": "Duketis", "given": "Eftichia", "initials": "E"}, {"family": "Ebstein", "given": "Richard P", "initials": "RP"}, {"family": "Edenberg", "given": "Howard J", "initials": "HJ"}, {"family": "Elia", "given": "Josephine", "initials": "J"}, {"family": "Ennis", "given": "Sean", "initials": "S"}, {"family": "Etain", "given": "Bruno", "initials": "B"}, {"family": "Fanous", "given": "Ayman", "initials": "A"}, {"family": "Farmer", "given": "Anne E", "initials": "AE"}, {"family": "Ferrier", "given": "I Nicol", "initials": "IN"}, {"family": "Flickinger", "given": "Matthew", "initials": "M"}, {"family": "Fombonne", "given": "Eric", "initials": "E"}, {"family": "Foroud", "given": "Tatiana", "initials": "T"}, {"family": "Frank", "given": "Josef", "initials": "J"}, {"family": "Franke", "given": "Barbara", "initials": "B"}, {"family": "Fraser", "given": "Christine", "initials": "C"}, {"family": "Freedman", "given": "Robert", "initials": "R"}, {"family": "Freimer", "given": "Nelson B", "initials": "NB"}, {"family": "Freitag", "given": "Christine M", "initials": "CM"}, {"family": "Friedl", "given": "Marion", "initials": "M"}, {"family": "Fris\u00e9n", "given": "Louise", "initials": "L"}, {"family": "Gallagher", "given": "Louise", "initials": "L"}, {"family": "Gejman", "given": "Pablo V", "initials": "PV"}, {"family": "Georgieva", "given": "Lyudmila", "initials": "L"}, {"family": "Gershon", "given": "Elliot S", "initials": "ES"}, {"family": "Geschwind", "given": "Daniel H", "initials": "DH"}, {"family": "Giegling", "given": "Ina", "initials": "I"}, {"family": "Gill", "given": "Michael", "initials": "M"}, {"family": "Gordon", "given": "Scott D", "initials": "SD"}, {"family": "Gordon-Smith", "given": "Katherine", "initials": "K"}, {"family": "Green", "given": "Elaine K", "initials": "EK"}, {"family": "Greenwood", "given": "Tiffany A", "initials": "TA"}, {"family": "Grice", "given": "Dorothy E", "initials": "DE"}, {"family": "Gross", "given": "Magdalena", "initials": "M"}, {"family": "Grozeva", "given": "Detelina", "initials": "D"}, {"family": "Guan", "given": "Weihua", "initials": "W"}, {"family": "Gurling", "given": "Hugh", "initials": "H"}, {"family": "De Haan", "given": "Lieuwe", "initials": "L"}, {"family": "Haines", "given": "Jonathan L", "initials": "JL"}, {"family": "Hakonarson", "given": "Hakon", "initials": "H"}, {"family": "Hallmayer", "given": "Joachim", "initials": "J"}, {"family": "Hamilton", "given": "Steven P", "initials": "SP"}, {"family": "Hamshere", "given": "Marian L", "initials": "ML"}, {"family": "Hansen", "given": "Thomas F", "initials": "TF"}, {"family": "Hartmann", "given": "Annette M", "initials": "AM"}, {"family": "Hautzinger", "given": "Martin", "initials": "M"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Henders", "given": "Anjali K", "initials": "AK"}, {"family": "Herms", "given": "Stefan", "initials": "S"}, {"family": "Hickie", "given": "Ian B", "initials": "IB"}, {"family": "Hipolito", "given": "Maria", "initials": "M"}, {"family": "Hoefels", "given": "Susanne", "initials": "S"}, {"family": "Holmans", "given": "Peter A", "initials": "PA"}, {"family": "Holsboer", "given": "Florian", "initials": "F"}, {"family": "Hoogendijk", "given": "Witte J", "initials": "WJ"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "J"}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Hus", "given": "Vanessa", "initials": "V"}, {"family": "Ingason", "given": "Andr\u00e9s", "initials": "A"}, {"family": "Ising", "given": "Marcus", "initials": "M"}, {"family": "Jamain", "given": "St\u00e9phane", "initials": "S"}, {"family": "Jones", "given": "Edward G", "initials": "EG"}, {"family": "Jones", "given": "Ian", "initials": "I"}, {"family": "Jones", "given": "Lisa", "initials": "L"}, {"family": "Tzeng", "given": "Jung-Ying", "initials": "J"}, {"family": "K\u00e4hler", "given": "Anna K", "initials": "AK"}, {"family": "Kahn", "given": "Ren\u00e9 S", "initials": "RS"}, {"family": "Kandaswamy", "given": "Radhika", "initials": "R"}, {"family": "Keller", "given": "Matthew C", "initials": "MC"}, {"family": "Kennedy", "given": "James L", "initials": "JL"}, {"family": "Kenny", "given": "Elaine", "initials": "E"}, {"family": "Kent", "given": "Lindsey", "initials": "L"}, {"family": "Kim", "given": "Yunjung", "initials": "Y"}, {"family": "Kirov", "given": "George K", "initials": "GK"}, {"family": "Klauck", "given": "Sabine M", "initials": "SM"}, {"family": "Klei", "given": "Lambertus", "initials": "L"}, {"family": "Knowles", "given": "James A", "initials": "JA"}, {"family": "Kohli", "given": "Martin A", "initials": "MA"}, {"family": "Koller", "given": "Daniel L", "initials": "DL"}, {"family": "Konte", "given": "Bettina", "initials": "B"}, {"family": "Korszun", "given": "Ania", "initials": "A"}, {"family": "Krabbendam", "given": "Lydia", "initials": "L"}, {"family": "Krasucki", "given": "Robert", "initials": "R"}, {"family": "Kuntsi", "given": "Jonna", "initials": "J"}, {"family": "Kwan", "given": "Phoenix", "initials": "P"}, {"family": "Land\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "L\u00e5ngstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Lathrop", "given": "Mark", "initials": "M"}, {"family": "Lawrence", "given": "Jacob", "initials": "J"}, {"family": "Lawson", "given": "William B", "initials": "WB"}, {"family": "Leboyer", "given": "Marion", "initials": "M"}, {"family": "Ledbetter", "given": "David H", "initials": "DH"}, {"family": "Lee", "given": "Phil H", "initials": "PH"}, {"family": "Lencz", "given": "Todd", "initials": "T"}, {"family": "Lesch", "given": "Klaus-Peter", "initials": "K"}, {"family": "Levinson", "given": "Douglas F", "initials": "DF"}, {"family": "Lewis", "given": "Cathryn M", "initials": "CM"}, {"family": "Li", "given": "Jun", "initials": "J"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Lieberman", "given": "Jeffrey A", "initials": "JA"}, {"family": "Lin", "given": "Dan-Yu", "initials": "D"}, {"family": "Linszen", "given": "Don H", "initials": "DH"}, {"family": "Liu", "given": "Chunyu", "initials": "C"}, {"family": "Lohoff", "given": "Falk W", "initials": "FW"}, {"family": "Loo", "given": "Sandra K", "initials": "SK"}, {"family": "Lord", "given": "Catherine", "initials": "C"}, {"family": "Lowe", "given": "Jennifer K", "initials": "JK"}, {"family": "Lucae", "given": "Susanne", "initials": "S"}, {"family": "MacIntyre", "given": "Donald J", "initials": "DJ"}, {"family": "Madden", "given": "Pamela A F", "initials": "PAF"}, {"family": "Maestrini", "given": "Elena", "initials": "E"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Mahon", "given": "Pamela B", "initials": "PB"}, {"family": "Maier", "given": "Wolfgang", "initials": "W"}, {"family": "Malhotra", "given": "Anil K", "initials": "AK"}, {"family": "Mane", "given": "Shrikant M", "initials": "SM"}, {"family": "Martin", "given": "Christa L", "initials": "CL"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Mattheisen", "given": "Manuel", "initials": "M"}, {"family": "Matthews", "given": "Keith", "initials": "K"}, {"family": "Mattingsdal", "given": "Morten", "initials": "M"}, {"family": "McCarroll", "given": "Steven A", "initials": "SA"}, {"family": "McGhee", "given": "Kevin A", "initials": "KA"}, {"family": "McGough", "given": "James J", "initials": "JJ"}, {"family": "McGrath", "given": "Patrick J", "initials": "PJ"}, {"family": "McGuffin", "given": "Peter", "initials": "P"}, {"family": "McInnis", "given": "Melvin G", "initials": "MG"}, {"family": "McIntosh", "given": "Andrew", "initials": "A"}, {"family": "McKinney", "given": "Rebecca", "initials": "R"}, {"family": "McLean", "given": "Alan W", "initials": "AW"}, {"family": "McMahon", "given": "Francis J", "initials": "FJ"}, {"family": "McMahon", "given": "William M", "initials": "WM"}, {"family": "McQuillin", "given": "Andrew", "initials": "A"}, {"family": "Medeiros", "given": "Helena", "initials": "H"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Meier", "given": "Sandra", "initials": "S"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Meng", "given": "Fan", "initials": "F"}, {"family": "Meyer", "given": "Jobst", "initials": "J"}, {"family": "Middeldorp", "given": "Christel M", "initials": "CM"}, {"family": "Middleton", "given": "Lefkos", "initials": "L"}, {"family": "Milanova", "given": "Vihra", "initials": "V"}, {"family": "Miranda", "given": "Ana", "initials": "A"}, {"family": "Monaco", "given": "Anthony P", "initials": "AP"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Moran", "given": "Jennifer L", "initials": "JL"}, {"family": "Moreno-De-Luca", "given": "Daniel", "initials": "D"}, {"family": "Morken", "given": "Gunnar", "initials": "G"}, {"family": "Morris", "given": "Derek W", "initials": "DW"}, {"family": "Morrow", "given": "Eric M", "initials": "EM"}, {"family": "Moskvina", "given": "Valentina", "initials": "V"}, {"family": "Muglia", "given": "Pierandrea", "initials": "P"}, {"family": "M\u00fchleisen", "given": "Thomas W", "initials": "TW"}, {"family": "Muir", "given": "Walter J", "initials": "WJ"}, {"family": "M\u00fcller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Murtha", "given": "Michael", "initials": "M"}, {"family": "Myers", "given": "Richard M", "initials": "RM"}, {"family": "Myin-Germeys", "given": "Inez", "initials": "I"}, {"family": "Neale", "given": "Michael C", "initials": "MC"}, {"family": "Nelson", "given": "Stan F", "initials": "SF"}, {"family": "Nievergelt", "given": "Caroline M", "initials": "CM"}, {"family": "Nikolov", "given": "Ivan", "initials": "I"}, {"family": "Nimgaonkar", "given": "Vishwajit", "initials": "V"}, {"family": "Nolen", "given": "Willem A", "initials": "WA"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Nurnberger", "given": "John I", "initials": "JI"}, {"family": "Nwulia", "given": "Evaristus A", "initials": "EA"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "O'Dushlaine", "given": "Colm", "initials": "C"}, {"family": "Oades", "given": "Robert D", "initials": "RD"}, {"family": "Olincy", "given": "Ann", "initials": "A"}, {"family": "Oliveira", "given": "Guiomar", "initials": "G"}, {"family": "Olsen", "given": "Line", "initials": "L"}, {"family": "Ophoff", "given": "Roel A", "initials": "RA"}, {"family": "Osby", "given": "Urban", "initials": "U"}, {"family": "Owen", "given": "Michael J", "initials": "MJ"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Parr", "given": "Jeremy R", "initials": "JR"}, {"family": "Paterson", "given": "Andrew D", "initials": "AD"}, {"family": "Pato", "given": "Carlos N", "initials": "CN"}, {"family": "Pato", "given": "Michele T", "initials": "MT"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Pergadia", "given": "Michele L", "initials": "ML"}, {"family": "Pericak-Vance", "given": "Margaret A", "initials": "MA"}, {"family": "Pickard", "given": "Benjamin S", "initials": "BS"}, {"family": "Pimm", "given": "Jonathan", "initials": "J"}, {"family": "Piven", "given": "Joseph", "initials": "J"}, {"family": "Posthuma", "given": "Danielle", "initials": "D"}, {"family": "Potash", "given": "James B", "initials": "JB"}, {"family": "Poustka", "given": "Fritz", "initials": "F"}, {"family": "Propping", "given": "Peter", "initials": "P"}, {"family": "Puri", "given": "Vinay", "initials": "V"}, {"family": "Quested", "given": "Digby J", "initials": "DJ"}, {"family": "Quinn", "given": "Emma M", "initials": "EM"}, {"family": "Ramos-Quiroga", "given": "Josep Antoni", "initials": "JA"}, {"family": "Rasmussen", "given": "Henrik B", "initials": "HB"}, {"family": "Raychaudhuri", "given": "Soumya", "initials": "S"}, {"family": "Rehnstr\u00f6m", "given": "Karola", "initials": "K"}, {"family": "Reif", "given": "Andreas", "initials": "A"}, {"family": "Ribas\u00e9s", "given": "Marta", "initials": "M"}, {"family": "Rice", "given": "John P", "initials": "JP"}, {"family": "Rietschel", "given": "Marcella", "initials": "M"}, {"family": "Roeder", "given": "Kathryn", "initials": "K"}, {"family": "Roeyers", "given": "Herbert", "initials": "H"}, {"family": "Rossin", "given": "Lizzy", "initials": "L"}, {"family": "Rothenberger", "given": "Aribert", "initials": "A"}, {"family": "Rouleau", "given": "Guy", "initials": "G"}, {"family": "Ruderfer", "given": "Douglas", "initials": "D"}, {"family": "Rujescu", "given": "Dan", "initials": "D"}, {"family": "Sanders", "given": "Alan R", "initials": "AR"}, {"family": "Sanders", "given": "Stephan J", "initials": "SJ"}, {"family": "Santangelo", "given": "Susan L", "initials": "SL"}, {"family": "Sergeant", "given": "Joseph A", "initials": "JA"}, {"family": "Schachar", "given": "Russell", "initials": "R"}, {"family": "Schalling", "given": "Martin", "initials": "M"}, {"family": "Schatzberg", "given": "Alan F", "initials": "AF"}, {"family": "Scheftner", "given": "William A", "initials": "WA"}, {"family": "Schellenberg", "given": "Gerard D", "initials": "GD"}, {"family": "Scherer", "given": "Stephen W", "initials": "SW"}, {"family": "Schork", "given": "Nicholas J", "initials": "NJ"}, {"family": "Schulze", "given": "Thomas G", "initials": "TG"}, {"family": "Schumacher", "given": "Johannes", "initials": "J"}, {"family": "Schwarz", "given": "Markus", "initials": "M"}, {"family": "Scolnick", "given": "Edward", "initials": "E"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "Shi", "given": "Jianxin", "initials": "J"}, {"family": "Shilling", "given": "Paul D", "initials": "PD"}, {"family": "Shyn", "given": "Stanley I", "initials": "SI"}, {"family": "Silverman", "given": "Jeremy M", "initials": "JM"}, {"family": "Slager", "given": "Susan L", "initials": "SL"}, {"family": "Smalley", "given": "Susan L", "initials": "SL"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Smith", "given": "Erin N", "initials": "EN"}, {"family": "Sonuga-Barke", "given": "Edmund J S", "initials": "EJS"}, {"family": "St Clair", "given": "David", "initials": "D"}, {"family": "State", "given": "Matthew", "initials": "M"}, {"family": "Steffens", "given": "Michael", "initials": "M"}, {"family": "Steinhausen", "given": "Hans-Christoph", "initials": "H"}, {"family": "Strauss", "given": "John S", "initials": "JS"}, {"family": "Strohmaier", "given": "Jana", "initials": "J"}, {"family": "Stroup", "given": "T Scott", "initials": "TS"}, {"family": "Sutcliffe", "given": "James S", "initials": "JS"}, {"family": "Szatmari", "given": "Peter", "initials": "P"}, {"family": "Szelinger", "given": "Szabocls", "initials": "S"}, {"family": "Thirumalai", "given": "Srinivasa", "initials": "S"}, {"family": "Thompson", "given": "Robert C", "initials": "RC"}, {"family": "Todorov", "given": "Alexandre A", "initials": "AA"}, {"family": "Tozzi", "given": "Federica", "initials": "F"}, {"family": "Treutlein", "given": "Jens", "initials": "J"}, {"family": "Uhr", "given": "Manfred", "initials": "M"}, {"family": "van den Oord", "given": "Edwin J C G", "initials": "EJCG"}, {"family": "Van Grootheest", "given": "Gerard", "initials": "G"}, {"family": "Van Os", "given": "Jim", "initials": "J"}, {"family": "Vicente", "given": "Astrid M", "initials": "AM"}, {"family": "Vieland", "given": "Veronica J", "initials": "VJ"}, {"family": "Vincent", "given": "John B", "initials": "JB"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Walsh", "given": "Christopher A", "initials": "CA"}, {"family": "Wassink", "given": "Thomas H", "initials": "TH"}, {"family": "Watson", "given": "Stanley J", "initials": "SJ"}, {"family": "Weissman", "given": "Myrna M", "initials": "MM"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Wienker", "given": "Thomas F", "initials": "TF"}, {"family": "Wijsman", "given": "Ellen M", "initials": "EM"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Williams", "given": "Nigel", "initials": "N"}, {"family": "Willsey", "given": "A Jeremy", "initials": "AJ"}, {"family": "Witt", "given": "Stephanie H", "initials": "SH"}, {"family": "Xu", "given": "Wei", "initials": "W"}, {"family": "Young", "given": "Allan H", "initials": "AH"}, {"family": "Yu", "given": "Timothy W", "initials": "TW"}, {"family": "Zammit", "given": "Stanley", "initials": "S"}, {"family": "Zandi", "given": "Peter P", "initials": "PP"}, {"family": "Zhang", "given": "Peng", "initials": "P"}, {"family": "Zitman", "given": "Frans G", "initials": "FG"}, {"family": "Z\u00f6llner", "given": "Sebastian", "initials": "S"}, {"family": "Devlin", "given": "Bernie", "initials": "B"}, {"family": "Kelsoe", "given": "John R", "initials": "JR"}, {"family": "Sklar", "given": "Pamela", "initials": "P"}, {"family": "Daly", "given": "Mark J", "initials": "MJ"}, {"family": "O'Donovan", "given": "Michael C", "initials": "MC"}, {"family": "Craddock", "given": "Nicholas", "initials": "N"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Smoller", "given": "Jordan W", "initials": "JW"}, {"family": "Kendler", "given": "Kenneth S", "initials": "KS"}, {"family": "Wray", "given": "Naomi R", "initials": "NR"}, {"family": "International Inflammatory Bowel Disease Genetics Consortium (IIBDGC)", "given": "None", "initials": "N"}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "45", "issn": "1546-1718", "issue": "9", "pages": "984-994", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17-29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 \u00b1 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 \u00b1 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 \u00b1 0.06 s.e.), and ADHD and major depressive disorder (0.32 \u00b1 0.07 s.e.), low between schizophrenia and ASD (0.16 \u00b1 0.06 s.e.) and non-significant for other pairs of disorders as well as between psychiatric disorders and the negative control of Crohn's disease. This empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders.", "doi": "10.1038/ng.2711", "pmid": "23933821", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ng.2711"}, {"db": "pmc", "key": "PMC3800159"}, {"db": "mid", "key": "NIHMS516146"}], "notes": [], "created": "2017-05-04T14:58:06.283Z", "modified": "2020-01-21T13:56:08.652Z"}, {"entity": "publication", "iuid": "22d0bfd4cf7a4bdfaca700da148cbe5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22d0bfd4cf7a4bdfaca700da148cbe5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22d0bfd4cf7a4bdfaca700da148cbe5d"}}, "title": "Genes identified in Asian SLE GWASs are also associated with SLE in Caucasian populations.", "authors": [{"family": "Wang", "given": "Chuan", "initials": "C"}, {"family": "Ahlford", "given": "Annika", "initials": "A"}, {"family": "J\u00e4rvinen", "given": "Tiina M", "initials": "TM"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Sturfelt", "given": "Gunnar", "initials": "G"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Truedsson", "given": "Lennart", "initials": "L"}, {"family": "Eriksson", "given": "Catharina", "initials": "C"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Julkunen", "given": "Heikki", "initials": "H"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "Graham", "given": "Robert R", "initials": "RR"}, {"family": "Behrens", "given": "Timothy W", "initials": "TW"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "21", "issn": "1476-5438", "issue": "9", "pages": "994-999", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Recent genome-wide association studies (GWASs) conducted in Asian populations have identified novel risk loci for systemic lupus erythematosus (SLE). Here, we genotyped 10 single-nucleotide polymorphisms (SNPs) in eight such loci and investigated their disease associations in three independent Caucasian SLE case-control cohorts recruited from Sweden, Finland and the United States. The disease associations of the SNPs in ETS1, IKZF1, LRRC18-WDFY4, RASGRP3, SLC15A4, TNIP1 and 16p11.2 were replicated, whereas no solid evidence of association was observed for the 7q11.23 locus in the Caucasian cohorts. SLC15A4 was significantly associated with renal involvement in SLE. The association of TNIP1 was more pronounced in SLE patients with renal and immunological disorder, which is corroborated by two previous studies in Asian cohorts. The effects of all the associated SNPs, either conferring risk for or being protective against SLE, were in the same direction in Caucasians and Asians. The magnitudes of the allelic effects for most of the SNPs were also comparable across different ethnic groups. On the contrary, remarkable differences in allele frequencies between Caucasian and Asian populations were observed for all associated SNPs. In conclusion, most of the novel SLE risk loci identified by GWASs in Asian populations were also associated with SLE in Caucasian populations. We observed both similarities and differences with respect to the effect sizes and risk allele frequencies across ethnicities.", "doi": "10.1038/ejhg.2012.277", "pmid": "23249952", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ejhg2012277"}, {"db": "pmc", "key": "PMC3746253"}], "notes": [], "created": "2017-05-04T15:01:17.659Z", "modified": "2021-07-07T15:11:02.329Z"}, {"entity": "publication", "iuid": "0d26cf1338444ca88be5a65923130cb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d26cf1338444ca88be5a65923130cb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d26cf1338444ca88be5a65923130cb5"}}, "title": "Autoantibody profiling in multiple sclerosis using arrays of human protein fragments.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "12", "issn": "1535-9484", "issue": "9", "pages": "2657-2672", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Profiling the autoantibody repertoire with large antigen collections is emerging as a powerful tool for the identification of biomarkers for autoimmune diseases. Here, a systematic and undirected approach was taken to screen for profiles of IgG in human plasma from 90 individuals with multiple sclerosis related diagnoses. Reactivity pattern of 11,520 protein fragments (representing \u223c38% of all human protein encoding genes) were generated on planar protein microarrays built within the Human Protein Atlas. For more than 2,000 antigens IgG reactivity was observed, among which 64% were found only in single individuals. We used reactivity distributions among multiple sclerosis subgroups to select 384 antigens, which were then re-evaluated on planar microarrays, corroborated with suspension bead arrays in a larger cohort (n = 376) and confirmed for specificity in inhibition assays. Among the heterogeneous pattern within and across multiple sclerosis subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation. In conclusion, using protein fragments and complementary high-throughput protein array platforms facilitated an alternative route to discovery and verification of potentially disease-associated autoimmunity signatures, that are now proposed as additional antigens for large-scale validation studies across multiple sclerosis biobanks.", "doi": "10.1074/mcp.M112.026757", "pmid": "23732997", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "M112.026757"}, {"db": "pmc", "key": "PMC3769337"}], "notes": [], "created": "2017-05-04T14:55:38.084Z", "modified": "2021-07-08T13:44:33.014Z"}, {"entity": "publication", "iuid": "783c318d16164bebb17391a256efe62c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/783c318d16164bebb17391a256efe62c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/783c318d16164bebb17391a256efe62c"}}, "title": "Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins.", "authors": [{"family": "Demina", "given": "Irina V", "initials": "IV"}, {"family": "Persson", "given": "Tomas", "initials": "T"}, {"family": "Santos", "given": "Patricia", "initials": "P"}, {"family": "Plaszczyca", "given": "Marian", "initials": "M"}, {"family": "Pawlowski", "given": "Katharina", "initials": "K"}], "type": "journal article", "published": "2013-08-29", "journal": {"volume": "8", "issn": "1932-6203", "issue": "8", "pages": "e72442", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Actinorhizal root nodule symbioses are very diverse, and the symbiosis of Datisca glomerata has previously been shown to have many unusual aspects. In order to gain molecular information on the infection mechanism, nodule development and nodule metabolism, we compared the transcriptomes of D. glomerata roots and nodules. Root and nodule libraries representing the 3'-ends of cDNAs were subjected to high-throughput parallel 454 sequencing. To identify the corresponding genes and to improve the assembly, Illumina sequencing of the nodule transcriptome was performed as well. The evaluation revealed 406 differentially regulated genes, 295 of which (72.7%) could be assigned a function based on homology. Analysis of the nodule transcriptome showed that genes encoding components of the common symbiosis signaling pathway were present in nodules of D. glomerata, which in combination with the previously established function of SymRK in D. glomerata nodulation suggests that this pathway is also active in actinorhizal Cucurbitales. Furthermore, comparison of the D. glomerata nodule transcriptome with nodule transcriptomes from actinorhizal Fagales revealed a new subgroup of nodule-specific defensins that might play a role specific to actinorhizal symbioses. The D. glomerata members of this defensin subgroup contain an acidic C-terminal domain that was never found in plant defensins before.", "doi": "10.1371/journal.pone.0072442", "pmid": "24009681", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-21713"}, {"db": "pmc", "key": "PMC3756986"}], "notes": [], "created": "2017-05-04T14:58:14.340Z", "modified": "2020-01-21T13:56:03.128Z"}, {"entity": "publication", "iuid": "5165d78ca9f243f09656046db2957cec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5165d78ca9f243f09656046db2957cec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5165d78ca9f243f09656046db2957cec"}}, "title": "Genome-wide transcriptional analysis of Drosophila larvae infected by entomopathogenic nematodes shows involvement of complement, recognition and extracellular matrix proteins.", "authors": [{"family": "Arefin", "given": "Badrul", "initials": "B"}, {"family": "Kucerova", "given": "Lucie", "initials": "L"}, {"family": "Dobes", "given": "Pavel", "initials": "P"}, {"family": "Markus", "given": "Robert", "initials": "R"}, {"family": "Strnad", "given": "Hynek", "initials": "H"}, {"family": "Wang", "given": "Zhi", "initials": "Z"}, {"family": "Hyrsl", "given": "Pavel", "initials": "P"}, {"family": "Zurovec", "given": "Michal", "initials": "M"}, {"family": "Theopold", "given": "Ulrich", "initials": "U"}], "type": "journal article", "published": "2013-08-27", "journal": {"volume": "6", "issn": "1662-8128", "issue": "2", "pages": "192-204", "title": "J Innate Immun", "issn-l": "1662-811X"}, "abstract": "Heterorhabditis bacteriophora is an entomopathogenic nematode (EPN) which infects its host by accessing the hemolymph where it releases endosymbiotic bacteria of the species Photorhabdus luminescens. We performed a genome-wide transcriptional analysis of the Drosophila response to EPN infection at the time point at which the nematodes reached the hemolymph either via the cuticle or the gut and the bacteria had started to multiply. Many of the most strongly induced genes have been implicated in immune responses in other infection models. Mapping of the complete set of differentially regulated genes showed the hallmarks of a wound response, but also identified a large fraction of EPN-specific transcripts. Several genes identified by transcriptome profiling or their homologues play protective roles during nematode infections. Genes that positively contribute to controlling nematobacterial infections encode: a homolog of thioester-containing complement protein 3, a basement membrane component (glutactin), a recognition protein (GNBP-like 3) and possibly several small peptides. Of note is that several of these genes have not previously been implicated in immune responses.", "doi": "10.1159/000353734", "pmid": "23988573", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "000353734"}], "notes": [], "created": "2017-05-04T14:58:42.042Z", "modified": "2020-01-21T13:56:02.286Z"}, {"entity": "publication", "iuid": "798604e143a640fdb25e6d793786aa4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/798604e143a640fdb25e6d793786aa4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/798604e143a640fdb25e6d793786aa4b"}}, "title": "Structure-Guided Design of Novel Thiazolidine Inhibitors ofO-Acetyl Serine Sulfhydrylase from Mycobacterium tuberculosis", "authors": [{"family": "Poyraz", "given": "\u00d6mer", "initials": "\u00d6"}, {"family": "Jeankumar", "given": "Variam Ullas", "initials": "VU"}, {"family": "Saxena", "given": "Shalini", "initials": "S"}, {"family": "Schnell", "given": "Robert", "initials": "R"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "Yogeeswari", "given": "Perumal", "initials": "P"}, {"family": "Sriram", "given": "Dharmarajan", "initials": "D"}, {"family": "Schneider", "given": "Gunter", "initials": "G"}], "type": "journal-article", "published": "2013-08-22", "journal": {"volume": "56", "issn": "1520-4804", "issue": "16", "pages": "6457-6466", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": null, "doi": "10.1021/jm400710k", "pmid": "23879381", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:17:31.897Z", "modified": "2025-10-17T13:04:30.302Z"}, {"entity": "publication", "iuid": "7a0e6263a1364ea68b51f14d2b910718", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a0e6263a1364ea68b51f14d2b910718.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a0e6263a1364ea68b51f14d2b910718"}}, "title": "Genome-wide relatedness of Treponema pedis, from gingiva and necrotic skin lesions of pigs, with the human oral pathogen Treponema denticola.", "authors": [{"family": "Svartstr\u00f6m", "given": "Olov", "initials": "O"}, {"family": "Mushtaq", "given": "Memoona", "initials": "M"}, {"family": "Pringle", "given": "M\u00e4rit", "initials": "M"}, {"family": "Segerman", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2013-08-19", "journal": {"volume": "8", "issn": "1932-6203", "issue": "8", "pages": "e71281", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Treponema pedis and T. denticola are two genetically related species with different origins of isolation. Treponema denticola is part of the human oral microbiota and is associated with periodontitis while T. pedis has been isolated from skin lesions in animals, e.g., digital dermatitis in cattle and necrotic ulcers in pigs. Although multiple Treponema phylotypes may exist in ulcerative lesions in pigs, T. pedis appears to be a predominant spirochete in these lesions. Treponema pedis can also be present in pig gingiva. In this study, we determined the complete genome sequence of T. pedis strain T A4, isolated from a porcine necrotic ear lesion, and compared its genome with that of T. denticola. Most genes in T. pedis were homologous to those in T. denticola and the two species were similar in general genomic features such as size, G+C content, and number of genes. In addition, many homologues of specific virulence-related genes in T. denticola were found in T. pedis. Comparing a selected pair of strains will usually not give a complete picture of the relatedness between two species. We therefore complemented the analysis with draft genomes from six T. pedis isolates, originating from gingiva and necrotic ulcers in pigs, and from twelve T. denticola strains. Each strain carried a considerable amount of accessory genetic material, of which a large part was strain specific. There was also extensive sequence variability in putative virulence-related genes between strains belonging to the same species. Signs of lateral gene-transfer events from bacteria known to colonize oral environments were found. This suggests that the oral cavity is an important habitat for T. pedis. In summary, we found extensive genomic similarities between T. pedis and T. denticola but also large variability within each species.", "doi": "10.1371/journal.pone.0071281", "pmid": "23977007", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-11951"}, {"db": "pmc", "key": "PMC3747143"}], "notes": [], "created": "2017-05-04T14:58:17.068Z", "modified": "2020-01-21T13:56:03.159Z"}, {"entity": "publication", "iuid": "c73f418613754fe9bb3f7bf2fd8fd74d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c73f418613754fe9bb3f7bf2fd8fd74d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c73f418613754fe9bb3f7bf2fd8fd74d"}}, "title": "Automated serial extraction of DNA and RNA from biobanked tissue specimens.", "authors": [{"family": "Mathot", "given": "Lucy", "initials": "L"}, {"family": "Wallin", "given": "Monica", "initials": "M"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2013-08-19", "journal": {"volume": "13", "issn": "1472-6750", "issue": null, "pages": "66", "title": "BMC Biotechnol.", "issn-l": "1472-6750"}, "abstract": "With increasing biobanking of biological samples, methods for large scale extraction of nucleic acids are in demand. The lack of such techniques designed for extraction from tissues results in a bottleneck in downstream genetic analyses, particularly in the field of cancer research. We have developed an automated procedure for tissue homogenization and extraction of DNA and RNA into separate fractions from the same frozen tissue specimen. A purpose developed magnetic bead based technology to serially extract both DNA and RNA from tissues was automated on a Tecan Freedom Evo robotic workstation.\n\n864 fresh-frozen human normal and tumor tissue samples from breast and colon were serially extracted in batches of 96 samples. Yields and quality of DNA and RNA were determined. The DNA was evaluated in several downstream analyses, and the stability of RNA was determined after 9 months of storage. The extracted DNA performed consistently well in processes including PCR-based STR analysis, HaloPlex selection and deep sequencing on an Illumina platform, and gene copy number analysis using microarrays. The RNA has performed well in RT-PCR analyses and maintains integrity upon storage.\n\nThe technology described here enables the processing of many tissue samples simultaneously with a high quality product and a time and cost reduction for the user. This reduces the sample preparation bottleneck in cancer research. The open automation format also enables integration with upstream and downstream devices for automated sample quantitation or storage.", "doi": "10.1186/1472-6750-13-66", "pmid": "23957867", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1472-6750-13-66"}, {"db": "pmc", "key": "PMC3751724"}], "notes": [], "created": "2017-05-04T15:02:19.266Z", "modified": "2020-01-21T13:56:05.138Z"}, {"entity": "publication", "iuid": "2fe62b124481426587ced9de3110f34c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fe62b124481426587ced9de3110f34c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fe62b124481426587ced9de3110f34c"}}, "title": "PARP inhibitor with selectivity toward ADP-ribosyltransferase ARTD3/PARP3.", "authors": [{"family": "Lindgren", "given": "Anders E G", "initials": "AE"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Thorsell", "given": "Ann-Gerd", "initials": "AG"}, {"family": "Hesse", "given": "Mareike", "initials": "M"}, {"family": "Spjut", "given": "Sara", "initials": "S"}, {"family": "Ekblad", "given": "Torun", "initials": "T"}, {"family": "Andersson", "given": "C David", "initials": "CD"}, {"family": "Pinto", "given": "Ana Filipa", "initials": "AF"}, {"family": "Weigelt", "given": "Johan", "initials": "J"}, {"family": "Hottiger", "given": "Michael O", "initials": "MO"}, {"family": "Linusson", "given": "Anna", "initials": "A"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H"}], "type": "journal article", "published": "2013-08-16", "journal": {"volume": "8", "issn": "1554-8937", "issue": "8", "pages": "1698-1703", "title": "ACS Chem. Biol.", "issn-l": "1554-8929"}, "abstract": "Inhibiting ADP-ribosyl transferases with PARP-inhibitors is considered a promising strategy for the treatment of many cancers and ischemia, but most of the cellular targets are poorly characterized. Here, we describe an inhibitor of ADP-ribosyltransferase-3/poly(ADP-ribose) polymerase-3 (ARTD3), a regulator of DNA repair and mitotic progression. In vitro profiling against 12 members of the enzyme family suggests selectivity for ARTD3, and crystal structures illustrate the molecular basis for inhibitor selectivity. The compound is active in cells, where it elicits ARTD3-specific effects at submicromolar concentration. Our results show that by targeting the nicotinamide binding site, selective inhibition can be achieved among the closest relatives of the validated clinical target, ADP-ribosyltransferase-1/poly(ADP-ribose) polymerase-1.", "doi": "10.1021/cb4002014", "pmid": "23742272", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "PDB", "key": "4GV0"}, {"db": "PDB", "key": "4GV2"}, {"db": "PDB", "key": "4GV4"}, {"db": "PDB", "key": "4GV7"}], "notes": [], "created": "2017-05-04T15:03:46.378Z", "modified": "2017-09-06T11:42:09.033Z"}, {"entity": "publication", "iuid": "001c2c5c3ab14854a718c5ef123f9951", "links": {"self": {"href": "https://publications.scilifelab.se/publication/001c2c5c3ab14854a718c5ef123f9951.json"}, "display": {"href": "https://publications.scilifelab.se/publication/001c2c5c3ab14854a718c5ef123f9951"}}, "title": "Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites.", "authors": [{"family": "Yan", "given": "Jian", "initials": "J"}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Whitington", "given": "Thomas", "initials": "T"}, {"family": "Dave", "given": "Kashyap", "initials": "K"}, {"family": "Liu", "given": "Jianping", "initials": "J"}, {"family": "Sur", "given": "Inderpreet", "initials": "I"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Jolma", "given": "Arttu", "initials": "A"}, {"family": "Kivioja", "given": "Teemu", "initials": "T"}, {"family": "Taipale", "given": "Minna", "initials": "M"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2013-08-15", "journal": {"volume": "154", "issn": "1097-4172", "issue": "4", "pages": "801-813", "title": "Cell", "issn-l": "0092-8674"}, "abstract": "During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered and that the clusters are enriched in binding motifs for several major TF classes. Strikingly, almost all clusters are formed around cohesin, and loss of cohesin decreases both DNA accessibility and binding of TFs to clusters. We show that cohesin remains bound in S phase, holding the nascent sister chromatids together at the TF cluster sites. Furthermore, cohesin remains bound to the cluster sites when TFs are evicted in early M phase. These results suggest that cohesin-binding functions as a cellular memory that promotes re-establishment of TF clusters after DNA replication and chromatin condensation.", "doi": "10.1016/j.cell.2013.07.034", "pmid": "23953112", "labels": {"Bioinformatics and Expression Analysis (BEA)": null, "Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "S0092-8674(13)00942-2"}, {"db": "GEO", "key": "GSE48448"}, {"db": "GEO", "key": "GSE49402"}], "notes": [], "created": "2017-05-04T14:57:05.169Z", "modified": "2021-07-06T14:42:14.615Z"}, {"entity": "publication", "iuid": "e6647b124ffc46a0b90cfb3df3a6c409", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e6647b124ffc46a0b90cfb3df3a6c409.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e6647b124ffc46a0b90cfb3df3a6c409"}}, "title": "The STK33-linked SNP rs4929949 is associated with obesity and BMI in two independent cohorts of Swedish and Greek children.", "authors": [{"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Moschonis", "given": "George", "initials": "G"}, {"family": "Chrousos", "given": "George P", "initials": "GP"}, {"family": "Marcus", "given": "Claude", "initials": "C"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2013-08-15", "journal": {"volume": "8", "issn": "1932-6203", "issue": "8", "pages": "e71353", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Recent genome wide association studies (GWAS) have identified a locus on chromosome 11p15.5, closely associated with serine/threonine kinase 33 (STK33), to be associated with body mass. STK33, a relatively understudied protein, has been linked to KRAS mutation-driven cancers and explored as a potential antineoplastic drug target. The strongest association with body mass observed at this loci in GWAS was rs4929949, a single nucleotide polymorphism located within intron 1 of the gene encoding STK33. The functional implications of rs4929949 or related variants have not been explored as of yet. We have genotyped rs4929949 in two cohorts, an obesity case-control cohort of 991 Swedish children, and a cross-sectional cohort of 2308 Greek school children. We found that the minor allele of rs4929949 was associated with obesity in the cohort of Swedish children and adolescents (OR\u200a=\u200a1.199 (95%CI: 1.002-1.434), p\u200a=\u200a0.047), and with body mass in the cross-sectional cohort of Greek children (\u03b2\u200a=\u200a0.08147 (95% CI: 0.1345-0.1618), p\u200a=\u200a0.021). We observe the effects of rs4929949 on body mass to be detectable already at adolescence. Subsequent analysis did not detect any association of rs4929949 to phenotypic measurements describing body adiposity or to metabolic factors such as insulin levels, triglycerides and insulin resistance (HOMA).", "doi": "10.1371/journal.pone.0071353", "pmid": "23967198", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-07092"}, {"db": "pmc", "key": "PMC3744548"}], "notes": [], "created": "2017-05-04T15:02:30.354Z", "modified": "2020-01-21T13:56:05.893Z"}, {"entity": "publication", "iuid": "1efdd142441c48c3958ebd462bd19953", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1efdd142441c48c3958ebd462bd19953.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1efdd142441c48c3958ebd462bd19953"}}, "title": "Investigation of six testicular germ cell tumor susceptibility genes suggests a parent-of-origin effect in SPRY4.", "authors": [{"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Andreassen", "given": "Kristine E", "initials": "KE"}, {"family": "Kristiansen", "given": "Wenche", "initials": "W"}, {"family": "Aschim", "given": "Elin L", "initials": "EL"}, {"family": "Bremnes", "given": "Roy M", "initials": "RM"}, {"family": "Dahl", "given": "Olav", "initials": "O"}, {"family": "Foss\u00e5", "given": "Sophie D", "initials": "SD"}, {"family": "Klepp", "given": "Olbj\u00f8rn", "initials": "O"}, {"family": "Langberg", "given": "Carl W", "initials": "CW"}, {"family": "Solberg", "given": "Arne", "initials": "A"}, {"family": "Tretli", "given": "Steinar", "initials": "S"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Adami", "given": "Hans-Olov", "initials": "H"}, {"family": "Haugen", "given": "Trine B", "initials": "TB"}, {"family": "Grotmol", "given": "Tom", "initials": "T"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2013-08-15", "journal": {"volume": "22", "issn": "1460-2083", "issue": "16", "pages": "3373-3380", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Recent genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) associated with testicular germ cell tumor (TGCT) risk in the genes ATF7IP, BAK1, DMRT1, KITLG, SPRY4 and TERT. In the present study, we validate these associations in a Scandinavian population, and explore effect modification by parental sex and differences in associations between the major histological subtypes seminoma and non-seminoma. A total of 118 SNPs in the six genes were genotyped in a population-based Swedish-Norwegian sample comprising 831 TGCT case-parent triads, 474 dyads, 712 singletons and 3919 population controls. Seven hundred and thirty-four additional SNPs were imputed using reference haplotypes from the 1000 genomes project. SNP-TGCT association was investigated using a likelihood-based association test for nuclear families and unrelated subjects implemented in the software package UNPHASED. Forward stepwise regression within each gene was applied to determine independent association signals. Effect modifications by parent-of-origin and effect differences between histological subtypes were explored. We observed strong association between SNPs in all six genes and TGCT (lowest P-value per gene: ATF7IP 6.2 \u00d7 10(-6); BAK1 2.1 \u00d7 10(-10); DMRT1 6.7 \u00d7 10(-25); KITLG 2.1 \u00d7 10(-48); SPRY4 1.4 \u00d7 10(-29); TERT 1.8 \u00d7 10(-18)). Stepwise regression indicated three independent signals for BAK1 and TERT, two for SPRY4 and one each for DMRT1, ATF7IP and KITLG. A significant parent-of-origin effect was observed for rs10463352 in SPRY4 (maternal odds ratio = 1.72, paternal odds ratio = 0.99, interaction P = 0.0013). No significant effect differences between seminomas and non-seminomas were found. In summary, we validated previously reported genetic associations with TGCT in a Scandinavian population, and observed suggestive evidence of a parent-of-origin effect in SPRY4.", "doi": "10.1093/hmg/ddt188", "pmid": "23640991", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ddt188"}], "notes": [], "created": "2017-05-04T14:57:57.270Z", "modified": "2020-01-21T13:56:08.632Z"}, {"entity": "publication", "iuid": "da3b438cfbb54b0193d7b1fec0680681", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da3b438cfbb54b0193d7b1fec0680681.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da3b438cfbb54b0193d7b1fec0680681"}}, "title": "Structural and biophysical characterization of the cytoplasmic domains of human BAP29 and BAP31.", "authors": [{"family": "Quistgaard", "given": "Esben M", "initials": "EM"}, {"family": "L\u00f6w", "given": "Christian", "initials": "C"}, {"family": "Moberg", "given": "Per", "initials": "P"}, {"family": "Guettou", "given": "Fatma", "initials": "F"}, {"family": "Maddi", "given": "Karthik", "initials": "K"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2013-08-13", "journal": {"volume": "8", "issn": "1932-6203", "issue": "8", "pages": "e71111", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Two members of the B-cell associated 31 (BAP31) family are found in humans; BAP29 and BAP31. These are ubiquitously expressed receptors residing in the endoplasmic reticulum. BAP31 functions in sorting of membrane proteins and in caspase-8 mediated apoptosis, while BAP29 appears to mainly corroborate with BAP31 in sorting. The N-terminal half of these proteins is membrane-bound while the C-terminal half is cytoplasmic. The latter include the so called variant of death effector domain (vDED), which shares weak sequence homology with DED domains. Here we present two structures of BAP31 vDED determined from a single and a twinned crystal, grown at pH 8.0 and pH 4.2, respectively. These structures show that BAP31 vDED forms a dimeric parallel coiled coil with no structural similarity to DED domains. Solution studies support this conclusion and strongly suggest that an additional \u03b1-helical domain is present in the C-terminal cytoplasmic region, probably forming a second coiled coil. The thermal stability of BAP31 vDED is quite modest at neutral pH, suggesting that it may assemble in a dynamic fashion in vivo. Surprisingly, BAP29 vDED is partially unfolded at pH 7, while a coiled coil is formed at pH 4.2 in vitro. It is however likely that folding of the domain is triggered by other factors than low pH in vivo. We found no evidence for direct interaction of the cytoplasmic domains of BAP29 and BAP31.", "doi": "10.1371/journal.pone.0071111", "pmid": "23967155", "labels": {"Protein Science Facility (PSF)": null, "Advanced Mass Spectrometry Proteomics": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-14318"}, {"db": "pmc", "key": "PMC3742741"}, {"db": "PDB", "key": "4JZL"}, {"db": "PDB", "key": "4JZP"}], "notes": [], "created": "2017-05-04T15:02:44.571Z", "modified": "2017-09-06T11:42:09.421Z"}, {"entity": "publication", "iuid": "2a6d5589972f48ed8e8c7b2523aeba35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a6d5589972f48ed8e8c7b2523aeba35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a6d5589972f48ed8e8c7b2523aeba35"}}, "title": "Meta-analysis of gene-level associations for rare variants based on single-variant statistics.", "authors": [{"family": "Hu", "given": "Yi-Juan", "initials": "Y"}, {"family": "Berndt", "given": "Sonja I", "initials": "SI"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Genetic Investigation of ANthropometric Traits (GIANT) Consortium", "given": "None", "initials": "N"}, {"family": "Hirschhorn", "given": "Joel", "initials": "J"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Lin", "given": "Dan-Yu", "initials": "D"}], "type": "journal article", "published": "2013-08-08", "journal": {"volume": "93", "issn": "1537-6605", "issue": "2", "pages": "236-248", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Meta-analysis of genome-wide association studies (GWASs) has led to the discoveries of many common variants associated with complex human diseases. There is a growing recognition that identifying \"causal\" rare variants also requires large-scale meta-analysis. The fact that association tests with rare variants are performed at the gene level rather than at the variant level poses unprecedented challenges in the meta-analysis. First, different studies may adopt different gene-level tests, so the results are not compatible. Second, gene-level tests require multivariate statistics (i.e., components of the test statistic and their covariance matrix), which are difficult to obtain. To overcome these challenges, we propose to perform gene-level tests for rare variants by combining the results of single-variant analysis (i.e., p values of association tests and effect estimates) from participating studies. This simple strategy is possible because of an insight that multivariate statistics can be recovered from single-variant statistics, together with the correlation matrix of the single-variant test statistics, which can be estimated from one of the participating studies or from a publicly available database. We show both theoretically and numerically that the proposed meta-analysis approach provides accurate control of the type I error and is as powerful as joint analysis of individual participant data. This approach accommodates any disease phenotype and any study design and produces all commonly used gene-level tests. An application to the GWAS summary results of the Genetic Investigation of ANthropometric Traits (GIANT) consortium reveals rare and low-frequency variants associated with human height. The relevant software is freely available.", "doi": "10.1016/j.ajhg.2013.06.011", "pmid": "23891470", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9297(13)00280-2"}, {"db": "pmc", "key": "PMC3738834"}], "notes": [], "created": "2017-05-04T14:57:47.877Z", "modified": "2020-01-21T13:56:08.583Z"}, {"entity": "publication", "iuid": "61ca84461a3b40a093bb55d33f13aa3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61ca84461a3b40a093bb55d33f13aa3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61ca84461a3b40a093bb55d33f13aa3b"}}, "title": "Temperament and character in the Child and Adolescent Twin Study in Sweden (CATSS): comparison to the general population, and genetic structure analysis.", "authors": [{"family": "Garcia", "given": "Danilo", "initials": "D"}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S"}, {"family": "Br\u00e4ndstr\u00f6m", "given": "Sven", "initials": "S"}, {"family": "R\u00e5stam", "given": "Maria", "initials": "M"}, {"family": "Cloninger", "given": "C Robert", "initials": "CR"}, {"family": "Kerekes", "given": "N\u00f3ra", "initials": "N"}, {"family": "Nilsson", "given": "Thomas", "initials": "T"}, {"family": "Anckars\u00e4ter", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2013-08-05", "journal": {"volume": "8", "issn": "1932-6203", "issue": "8", "pages": "e70475", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The Child and Adolescent Twin Study in Sweden (CATSS) is an on-going, large population-based longitudinal twin study. We aimed (1) to investigate the reliability of two different versions (125-items and 238-items) of Cloninger's Temperament and Character Inventory (TCI) used in the CATSS and the validity of extracting the short version from the long version, (2) to compare these personality dimensions between twins and adolescents from the general population, and (3) to investigate the genetic structure of Cloninger's model.\n\nReliability and correlation analyses were conducted for both TCI versions, 2,714 CATSS-twins were compared to 631 adolescents from the general population, and the genetic structure was investigated through univariate genetic analyses, using a model-fitting approach with structural equation-modeling techniques based on same-sex twin pairs from the CATSS (423 monozygotic and 408 dizygotic pairs).\n\nThe TCI scores from the short and long versions showed comparable reliability coefficients and were strongly correlated. Twins scored about half a standard deviation higher in the character scales. Three of the four temperament dimensions (Novelty Seeking, Harm Avoidance, and Persistence) had strong genetic and non-shared environmental effects, while Reward Dependence and the three character dimensions had moderate genetic effects, and both shared and non-shared environmental effects.\n\nTwins showed higher scores in character dimensions compared to adolescents from the general population. At least among adolescents there is a shared environmental influence for all of the character dimensions, but only for one of the temperament dimensions (i.e., Reward Dependence). This specific finding regarding the existence of shared environmental factors behind the character dimensions in adolescence, together with earlier findings showing a small shared environmental effects on character among young adults and no shared environmental effects on character among adults, suggest that there is a shift in type of environmental influence from adolescence to adulthood regarding character.", "doi": "10.1371/journal.pone.0070475", "pmid": "23940581", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-13063"}, {"db": "pmc", "key": "PMC3734246"}], "notes": [], "created": "2017-05-04T15:03:37.458Z", "modified": "2017-05-30T14:53:00.208Z"}, {"entity": "publication", "iuid": "f228840f7683454eaba3ee2c988cb29a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f228840f7683454eaba3ee2c988cb29a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f228840f7683454eaba3ee2c988cb29a"}}, "title": "An Integratedin VitroModel for Simultaneous Assessment of Drug Uptake, Metabolism, and Efflux", "authors": [{"family": "Neve", "given": "Etienne P A", "initials": "EPA"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Ingelman-Sundberg", "given": "Magnus", "initials": "M"}, {"family": "Karlgren", "given": "Maria", "initials": "M"}], "type": "journal-article", "published": "2013-08-05", "journal": {"volume": "10", "issn": "1543-8384", "issue": "8", "pages": "3152-3163", "title": "Mol. Pharmaceutics", "issn-l": "1543-8384"}, "abstract": null, "doi": "10.1021/mp400202d", "pmid": "23822632", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:18:54.236Z", "modified": "2025-10-17T13:04:30.314Z"}, {"entity": "publication", "iuid": "8d3ee82789cd475d9bf3c5b4a32d3dd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d3ee82789cd475d9bf3c5b4a32d3dd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d3ee82789cd475d9bf3c5b4a32d3dd2"}}, "title": "Improved production of membrane proteins in Escherichia coli by selective codon substitutions.", "authors": [{"family": "N\u00f8rholm", "given": "Morten H H", "initials": "MH"}, {"family": "Toddo", "given": "Stephen", "initials": "S"}, {"family": "Virkki", "given": "Minttu T I", "initials": "MT"}, {"family": "Light", "given": "Sara", "initials": "S"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/f663c0a9e9e1455cbbf8e6aea13af4a9.json"}}, {"family": "Daley", "given": "Daniel O", "initials": "DO"}], "type": "journal article", "published": "2013-08-02", "journal": {"volume": "587", "issn": "1873-3468", "issue": "15", "pages": "2352-2358", "title": "FEBS Lett.", "issn-l": "0014-5793"}, "abstract": "Membrane proteins are extremely challenging to produce in sufficient quantities for biochemical and structural analysis and there is a growing demand for solutions to this problem. In this study we attempted to improve expression of two difficult-to-express coding sequences (araH and narK) for membrane transporters. For both coding sequences, synonymous codon substitutions in the region adjacent to the AUG start led to significant improvements in expression, whereas multi-parameter sequence optimization of codons throughout the coding sequence failed. We conclude that coding sequences can be re-wired for high-level protein expression by selective engineering of the 5' coding sequence with synonymous codons, thus circumventing the need to consider whole sequence optimization.", "doi": "10.1016/j.febslet.2013.05.063", "pmid": "23769986", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S0014-5793(13)00442-0"}], "notes": [], "created": "2017-05-04T14:56:23.649Z", "modified": "2021-06-16T15:21:58.662Z"}, {"entity": "publication", "iuid": "ea8ac9f5dfe4413aadfed4d405e8ddca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea8ac9f5dfe4413aadfed4d405e8ddca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea8ac9f5dfe4413aadfed4d405e8ddca"}}, "title": "Identification of adenovirus-encoded small RNAs by deep RNA sequencing.", "authors": [{"family": "Zhao", "given": "Hongxing", "initials": "H"}, {"family": "Chen", "given": "Maoshan", "initials": "M"}, {"family": "Pettersson", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2013-08-01", "journal": {"volume": "442", "issn": "1096-0341", "issue": "2", "pages": "148-155", "title": "Virology", "issn-l": "0042-6822"}, "abstract": "Using deep RNA sequencing, we have studied the expression of adenovirus-encoded small RNAs at different times after infection. Nineteen small RNAs which comprised more than 1% of the total pool of small RNAs at least one time point were identified. These small RNAs were between 25 and 35 nucleotides long and mapped in the region of the VA RNAI and RNAII genes. However, the overlap was incomplete and some contained a few extra nucleotides at the 3' end. This finding together with the observation that some of the small RNAs were detected before VA RNA expression had started might indicate that they are derived from other precursors than VA RNAI and II. Interestingly, the small RNAs displayed different expression profiles during the course of the infection suggesting that they have different functions. An effort was made to identify their mRNA targets by using computer prediction and deep cDNA sequencing. The most significant targets for the earliest small RNAs were genes involved in signaling pathways.", "doi": "10.1016/j.virol.2013.04.006", "pmid": "23659909", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0042-6822(13)00200-6"}], "notes": [], "created": "2017-05-04T15:02:31.277Z", "modified": "2020-01-21T13:56:05.980Z"}, {"entity": "publication", "iuid": "dacfd5d04ff5435d8275cccc7613b623", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dacfd5d04ff5435d8275cccc7613b623.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dacfd5d04ff5435d8275cccc7613b623"}}, "title": "Chronic airway-induced allergy in mice modifies gene expression in the brain toward insulin resistance and inflammatory responses.", "authors": [{"family": "Sarlus", "given": "Heela", "initials": "H"}, {"family": "Wang", "given": "Xiuzhe", "initials": "X"}, {"family": "Cedazo-Minguez", "given": "Angel", "initials": "A"}, {"family": "Schultzberg", "given": "Marianne", "initials": "M"}, {"family": "Oprica", "given": "Mircea", "initials": "M"}], "type": "journal article", "published": "2013-08-01", "journal": {"volume": "10", "issn": "1742-2094", "issue": null, "pages": "99", "title": "J Neuroinflammation", "issn-l": "1742-2094"}, "abstract": "Chronic systemic inflammation affects brain functionality and may negatively influence the progression of neurodegenerative disorders. Allergy is a chronic inflammatory disease affecting more than 20% of the Western population. Little is known regarding the influence of allergy on brain functions. The aim of the present study was to obtain a global overview of the genes that drive the effects of peripheral inflammation associated with chronic airway-induced allergy in the brain.\n\nAirway allergy was induced in C57B/6J mice using ovalbumin as the allergen. Microarray analysis was performed in the hippocampus and frontal cortex in association with Affymetrix. For the data analysis, principal component analysis and orthogonal to latent structures discriminant analysis followed by pathway analysis were used. Quantitative polymerase chain reaction (qPCR) and protein analysis by Western blotting were performed for the validation of microarray results.\n\nMicroarray analysis showed low-grade changes in gene expression in the brain induced by airway-associated allergy. Changes in expression were observed for genes involved in antigen processing and presentation, cytokine-cytokine interaction, Toll-like receptor and mitogen-activated protein kinase signaling, as determined by pathway analysis. We confirmed a reduction of insulin-degrading enzyme at the protein level and a decrease in insulin receptor phosphorylation in the brains of allergic mice. Other allergy-induced gene expression changes were confirmed by qPCR, including increased levels of tumor necrosis factor receptor superfamily member 23 and lipopolysaccharide-binding protein.\n\nAirway-associated allergy induces changes in brain gene expression toward induction of insulin resistance and inflammatory responses with potential implications for neurodegenerative disorders.", "doi": "10.1186/1742-2094-10-99", "pmid": "23915208", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "1742-2094-10-99"}, {"db": "pmc", "key": "PMC3750454"}], "notes": [], "created": "2017-05-04T15:03:15.374Z", "modified": "2017-05-30T14:51:21.228Z"}, {"entity": "publication", "iuid": "cef090910edf4b94892344f87f1a3426", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cef090910edf4b94892344f87f1a3426.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cef090910edf4b94892344f87f1a3426"}}, "title": "Tumour expression of bladder cancer-associated urinary proteins.", "authors": [{"family": "Lind\u00e9n", "given": "M\u00e5rten", "initials": "M"}, {"family": "Segersten", "given": "Ulrika", "initials": "U"}, {"family": "Runeson", "given": "Marcus", "initials": "M"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Busch", "given": "Christer", "initials": "C"}, {"family": "Pettersson", "given": "Ulf", "initials": "U"}, {"family": "Lind", "given": "Sara Bergstr\u00f6m", "initials": "SB"}, {"family": "Malmstr\u00f6m", "given": "Per-Uno", "initials": "PU"}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "112", "issn": "1464-410X", "issue": "3", "pages": "407-415", "title": "BJU Int.", "issn-l": "1464-4096"}, "abstract": "WHAT'S KNOWN ON THE SUBJECT? AND WHAT DOES THE STUDY ADD?: The current basis for diagnosis and prognosis in urinary bladder cancer is based on the pathologists' assessment of a biopsy of the tumour. Urinary biomarkers are preferable as they can be non-invasively sampled. Urinary cytology is the only test with widespread use but is hampered by poor reproducibility and low sensitivity. By studying the protein expression in bladder tumour tissue samples of proteins previously found in elevated levels in the urine of patients with bladder cancer, we have been able to show that these proteins originate from the tumour. The immunoreactivity of three of the investigated proteins increased with higher stage. Also a serine peptidase inhibitor was found to be predictive of progression from non-muscle-invasive to muscle-invasive tumours.\n\nTo analyse the expression of five bladder cancer-associated urinary proteins and investigate if expression is related to the malignant phenotype of the tumour. To explore the possible prognostic value of these proteins.\n\nUrine samples, 16 from patients with bladder cancer and 26 from controls, were used in Western Blotting experiments. Tissue microarrays with bladder tissue from 344 patients diagnosed with bladder cancer between 1984 and 2005 was used in immunohistochemistry experiments. The proteins apolipoprotein E (APOE), fibrinogen \u03b2 chain precursor (FGB), leucine-rich \u03b12-glycoprotein (LRG1), polymerase (RNA) I polypeptide E (POLR1E), \u03b11-antitrypsin (SERPINA1) and topoisomerase 2A (TOP2A) were probed with antibodies validated by the Human Protein Atlas.\n\nIncreased expressions of APOE, FGB and POLR1E were correlated with increased tumour stage (P < 0.001). Expression of SERPINA1 in Ta and T1 tumours was found to increase the risk of tumour progression (hazard ratio 2.57, 95% confidence interval 1.13-5.87; P = 0.025) CONCLUSIONS: All proteins previously detected in urine from patients with bladder cancer were also expressed in bladder cancer tissue. The expression of APOE, FGB and POLR1E increased with stage and they are potential diagnostic markers. SERPINA1 was identified as a prognostic marker candidate.", "doi": "10.1111/j.1464-410X.2012.11653.x", "pmid": "23470167", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:55.017Z", "modified": "2017-05-30T12:57:21.895Z"}, {"entity": "publication", "iuid": "61168500d6b84e0fb73a7ba0abd8158c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61168500d6b84e0fb73a7ba0abd8158c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61168500d6b84e0fb73a7ba0abd8158c"}}, "title": "Synergistic interactions between camptothecin and EGFR or RAC1 inhibitors and between imatinib and Notch signaling or RAC1 inhibitors in glioblastoma cell lines.", "authors": [{"family": "Sooman", "given": "Linda", "initials": "L"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Kultima", "given": "Hanna G\u00f6ransson", "initials": "HG"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Johansson", "given": "Fredrik", "initials": "F"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Blomquist", "given": "Erik", "initials": "E"}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "72", "issn": "1432-0843", "issue": "2", "pages": "329-340", "title": "Cancer Chemother. Pharmacol.", "issn-l": "0344-5704"}, "abstract": "The current treatment strategies for glioblastoma have limited health and survival benefits for the patients. A common obstacle in the treatment is chemoresistance. A possible strategy to evade this problem may be to combine chemotherapeutic drugs with agents inhibiting resistance mechanisms. The aim with this study was to identify molecular pathways influencing drug resistance in glioblastoma-derived cells and to evaluate the potential of pharmacological interference with these pathways to identify synergistic drug combinations.\n\nGlobal gene expressions and drug sensitivities to three chemotherapeutic drugs (imatinib, camptothecin and temozolomide) were measured in six human glioblastoma-derived cell lines. Gene expressions that correlated to drug sensitivity or resistance were identified and mapped to specific pathways. Selective inhibitors of these pathways were identified. The effects of six combinations of inhibitors and chemotherapeutic drugs were evaluated in glioblastoma-derived cell lines. Drug combinations with synergistic effects were also evaluated in non-cancerous epithelial cells.\n\nFour drug combinations had synergistic effects in at least one of the tested glioblastoma-derived cell lines; camptothecin combined with gefitinib (epidermal growth factor receptor inhibitor) or NSC 23766 (ras-related C3 botulinum toxin substrate 1 inhibitor) and imatinib combined with DAPT (Notch signaling inhibitor) or NSC 23766. Of these, imatinib combined with DAPT or NSC 23766 did not have synergistic effects in non-cancerous epithelial cells. Two drug combinations had at least additive effects in one of the tested glioblastoma-derived cell lines; temozolomide combined with gefitinib or PF-573228 (focal adhesion kinase inhibitor).\n\nFour synergistic and two at least additive drug combinations were identified in glioblastoma-derived cells. Pathways targeted by these drug combinations may serve as targets for future drug development with the potential to increase efficacy of currently used/evaluated chemotherapy.", "doi": "10.1007/s00280-013-2197-7", "pmid": "23736154", "labels": {"Array and Analysis Facility": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:00.782Z", "modified": "2017-05-30T12:37:50.801Z"}, {"entity": "publication", "iuid": "f8642f169e964e94bb3ea82333586b5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8642f169e964e94bb3ea82333586b5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8642f169e964e94bb3ea82333586b5d"}}, "title": "Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.", "authors": [{"family": "Andersson", "given": "Karl-Magnus", "initials": "KM"}, {"family": "Meerupati", "given": "Tejashwari", "initials": "T"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Friman", "given": "Eva", "initials": "E"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Tunlid", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "79", "issn": "1098-5336", "issue": "16", "pages": "4993-5004", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "Many nematophagous fungi use morphological structures called traps to capture nematodes by adhesion or mechanically. To better understand the cellular functions of adhesive traps, the trap cell proteome of the fungus Monacrosporium haptotylum was characterized. The trap of M. haptotylum consists of a unicellular structure called a knob that develops at the apex of a hypha. Proteins extracted from knobs and mycelia were analyzed using SDS-PAGE and liquid chromatography-tandem mass spectrometry (LC-MS-MS). The peptide sequences were matched against predicted gene models from the recently sequenced M. haptotylum genome. In total, 336 proteins were identified, with 54 expressed at significantly higher levels in the knobs than in the mycelia. The upregulated knob proteins included peptidases, small secreted proteins with unknown functions, and putative cell surface adhesins containing carbohydrate-binding domains, including the WSC domain. Phylogenetic analysis showed that all upregulated WSC domain proteins belonged to a large, expanded cluster of paralogs in M. haptotylum. Several peptidases and homologs of experimentally verified proteins in other pathogenic fungi were also upregulated in the knob proteome. Complementary profiling of gene expression at the transcriptome level showed poor correlation between the upregulation of knob proteins and their corresponding transcripts. We propose that the traps of M. haptotylum contain many of the proteins needed in the early stages of infection and that the trap cells can tightly control the translation and degradation of these proteins to minimize the cost of protein synthesis.", "doi": "10.1128/AEM.01390-13", "pmid": "23770896", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "AEM.01390-13"}, {"db": "pmc", "key": "PMC3754708"}], "notes": [], "created": "2017-05-04T14:56:20.335Z", "modified": "2020-01-21T13:53:20.969Z"}, {"entity": "publication", "iuid": "1d15511588be4f849c3a84cddc2b0bd3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d15511588be4f849c3a84cddc2b0bd3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d15511588be4f849c3a84cddc2b0bd3"}}, "title": "Molecular identification and phylogenic analysis by sequencing the rDNA of copper-tolerant soft-rot Phialophora spp.", "authors": [{"family": "Karunasekera", "given": "Hasanthi", "initials": "H"}, {"family": "Daniel", "given": "Geoffrey", "initials": "G"}], "type": "journal-article", "published": "2013-08-00", "journal": {"volume": "82", "issn": "0964-8305", "issue": null, "pages": "45-52", "title": "International Biodeterioration & Biodegradation", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ibiod.2013.01.019", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:09:21.315Z", "modified": "2021-06-22T12:04:39.924Z"}, {"entity": "publication", "iuid": "d427c64c64cb4bd1b98b6e311acb9593", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d427c64c64cb4bd1b98b6e311acb9593.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d427c64c64cb4bd1b98b6e311acb9593"}}, "title": "In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models.", "authors": [{"family": "Lyutvinskiy", "given": "Yaroslav", "initials": "Y"}, {"family": "Yang", "given": "Hongqian", "initials": "H"}, {"family": "Rutishauser", "given": "Dorothea", "initials": "D"}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "12", "issn": "1535-9484", "issue": "8", "pages": "2324-2331", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "In the analysis of proteome changes arising during the early stages of a biological process (e.g. disease or drug treatment) or from the indirect influence of an important factor, the biological variations of interest are often small (\u223c10%). The corresponding requirements for the precision of proteomics analysis are high, and this often poses a challenge, especially when employing label-free quantification. One of the main contributors to the inaccuracy of label-free proteomics experiments is the variability of the instrumental response during LC-MS/MS runs. Such variability might include fluctuations in the electrospray current, transmission efficiency from the air-vacuum interface to the detector, and detection sensitivity. We have developed an in silico post-processing method of reducing these variations, and have thus significantly improved the precision of label-free proteomics analysis. For abundant blood plasma proteins, a coefficient of variation of approximately 1% was achieved, which allowed for sex differentiation in pooled samples and \u224890% accurate differentiation of individual samples by means of a single LC-MS/MS analysis. This method improves the precision of measurements and increases the accuracy of predictive models based on the measurements. The post-acquisition nature of the correction technique and its generality promise its widespread application in LC-MS/MS-based methods such as proteomics and metabolomics.", "doi": "10.1074/mcp.O112.023804", "pmid": "23589346", "labels": {"Advanced Mass Spectrometry Proteomics": null}, "xrefs": [{"db": "pii", "key": "O112.023804"}, {"db": "pmc", "key": "PMC3734588"}], "notes": [], "created": "2017-05-04T15:02:43.669Z", "modified": "2021-07-08T08:58:46.853Z"}, {"entity": "publication", "iuid": "8073104337864e828f6d9304523cfb9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8073104337864e828f6d9304523cfb9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8073104337864e828f6d9304523cfb9b"}}, "title": "High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation.", "authors": [{"family": "Anandapadamanaban", "given": "Madhanagopal", "initials": "M"}, {"family": "Andresen", "given": "Cecilia", "initials": "C"}, {"family": "Helander", "given": "Sara", "initials": "S"}, {"family": "Ohyama", "given": "Yoshifumi", "initials": "Y"}, {"family": "Siponen", "given": "Marina I", "initials": "MI"}, {"family": "Lundstr\u00f6m", "given": "Patrik", "initials": "P"}, {"family": "Kokubo", "given": "Tetsuro", "initials": "T"}, {"family": "Ikura", "given": "Mitsuhiko", "initials": "M"}, {"family": "Moche", "given": "Martin", "initials": "M"}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "20", "issn": "1545-9985", "issue": "8", "pages": "1008-1014", "title": "Nat. Struct. Mol. Biol.", "issn-l": "1545-9985"}, "abstract": "The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 \u00c5) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 bound to yeast TBP, together with mutational data. We find that yeast TAF1-TAND1, which in itself acts as a transcriptional activator, binds TBP's concave DNA-binding surface by presenting similar anchor residues to TBP as does Mot1 but from a distinct structural scaffold. Furthermore, we show how TAF1-TAND2 uses an aromatic and acidic anchoring pattern to bind a conserved TBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides insight into the competitive multiprotein TBP interplay critical to transcriptional regulation.", "doi": "10.1038/nsmb.2611", "pmid": "23851461", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "nsmb.2611"}, {"db": "pmc", "key": "PMC4972576"}, {"db": "mid", "key": "CAMS4086"}, {"db": "PDB", "key": "4B0A"}], "notes": [], "created": "2017-05-04T15:03:49.726Z", "modified": "2017-09-06T11:42:09.178Z"}, {"entity": "publication", "iuid": "310df3ee55bb4cc8a6dfd9aa72931760", "links": {"self": {"href": "https://publications.scilifelab.se/publication/310df3ee55bb4cc8a6dfd9aa72931760.json"}, "display": {"href": "https://publications.scilifelab.se/publication/310df3ee55bb4cc8a6dfd9aa72931760"}}, "title": "Genetic variation in the dimethylarginine dimethylaminohydrolase 1 gene (DDAH1) is related to asymmetric dimethylarginine (ADMA) levels, but not to endothelium-dependent vasodilation.", "authors": [{"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kumar", "given": "Jitender", "initials": "J"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Teerlink", "given": "Tom", "initials": "T"}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "18", "issn": "1477-0377", "issue": "4", "pages": "192-199", "title": "Vasc Med", "issn-l": "1358-863X"}, "abstract": "Asymmetric dimethylarginine (ADMA) is an endogenous inhibitor of nitric oxide synthase. The breakdown of ADMA is mainly governed by the activity of dimethylarginine dimethylaminohydrolases (DDAHs). We investigated if genetic variation in the DDAH1 and DDAH2 genes were related to ADMA and l-arginine levels, as well as measures of endothelium-dependent vasodilation.\n\nIn 1016 70-year-old participants of the population-based Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) study (50% women), we measured endothelium-dependent vasodilation (EDV) using the invasive forearm technique with acetylcholine given in the brachial artery and the brachial artery ultrasound technique with measurement of flow-mediated dilatation (FMD). Plasma l-arginine and ADMA levels were measured by high-performance liquid chromatography and 55 single nucleotide polymorphisms (SNPs) in the DDAH1 and DDAH2 genes were genotyped.\n\nSeveral of the genotypes in the DDAH1 gene were highly significantly related to ADMA levels (p = 10(-7) at best), but not to the l-arginine levels. No relationships between the genotypes in the DDAH2 gene and ADMA or l-arginine levels were found. None of the DDAH1 genotypes being closely related to ADMA levels were significantly related to EDV or FMD. Neither were any of the DDAH2 genotypes closely related to any of the measurements of vasoreactivity.\n\nA close relationship was seen between SNPs in the DDAH1, but not DDAH2, gene and ADMA levels. However, variation in those genes was not related to measures of EDV in this elderly population.", "doi": "10.1177/1358863X13496488", "pmid": "23892448", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1358863X13496488"}], "notes": [], "created": "2017-05-04T15:01:31.413Z", "modified": "2021-07-07T15:11:02.377Z"}, {"entity": "publication", "iuid": "4cd28ffb0bb040aeb1d18f01821866e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4cd28ffb0bb040aeb1d18f01821866e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4cd28ffb0bb040aeb1d18f01821866e5"}}, "title": "Expression of chondroitin/dermatan sulfate glycosyltransferases during early zebrafish development.", "authors": [{"family": "Filipek-G\u00f3rniok", "given": "Beata", "initials": "B", "orcid": "0000-0002-6757-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f0b7b3e0b045f082d2aff1dd23ec0e.json"}}, {"family": "Holmborn", "given": "Katarina", "initials": "K"}, {"family": "Haitina", "given": "Tatjana", "initials": "T"}, {"family": "Habicher", "given": "Judith", "initials": "J"}, {"family": "Oliveira", "given": "Marta Bastos", "initials": "MB"}, {"family": "Hellgren", "given": "Charlotte", "initials": "C"}, {"family": "Eriksson", "given": "Inger", "initials": "I"}, {"family": "Kjell\u00e9n", "given": "Lena", "initials": "L"}, {"family": "Kreuger", "given": "Johan", "initials": "J"}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "242", "issn": "1097-0177", "issue": "8", "pages": "964-975", "title": "Dev. Dyn.", "issn-l": "1058-8388"}, "abstract": "Chondroitin/dermatan sulfate (CS/DS) proteoglycans present in the extracellular matrix have important structural and regulatory functions.\n\nSix human genes have previously been shown to catalyze CS/DS polymerization. Here we show that one of these genes, chpf, is represented by two copies in the zebrafish genome, chpfa and chpfb, while the other five human CS/DS glycosyltransferases csgalnact1, csgalnact2, chpf2, chsy1, and chsy3 all have single zebrafish orthologues. The putative zebrafish CS/DS glycosyltransferases are spatially and temporally expressed. Interestingly, overlapping expression of multiple glycosyltransferases coincides with high CS/DS deposition. Finally, whereas the relative levels of the related polysaccharide HS reach steady-state at around 2 days post fertilization, there is a continued relative increase of the CS amounts per larvae during the first 6 days of development, matching the increased cartilage formation.\n\nThere are 7 CS/DS glycosyltransferases in zebrafish, which, based on homology, can be divided into the CSGALNACT, CHSY, and CHPF families. The overlap between intense CS/DS production and the expression of multiple CS/DS glycosyltransferases suggests that efficient CS/DS biosynthesis requires a combination of several glycosyltransferases.", "doi": "10.1002/dvdy.23981", "pmid": "23703795", "labels": {"Genome Engineering Zebrafish": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:43.737Z", "modified": "2021-07-06T16:05:51.247Z"}, {"entity": "publication", "iuid": "38c3875a34454e4da87d1656e59b66ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38c3875a34454e4da87d1656e59b66ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38c3875a34454e4da87d1656e59b66ce"}}, "title": "Design of a highly selective and potent class of non-planar estrogen receptor \u03b2 agonists.", "authors": [{"family": "Sund\u00e9n", "given": "Henrik", "initials": "H"}, {"family": "Ma", "given": "Jian-Nong", "initials": "JN"}, {"family": "Hansen", "given": "Lars K", "initials": "LK"}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Burstein", "given": "Ethan S", "initials": "ES"}, {"family": "Olsson", "given": "Roger", "initials": "R"}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "8", "issn": "1860-7187", "issue": "8", "pages": "1283-1294", "title": "ChemMedChem", "issn-l": "1860-7179"}, "abstract": "Selective activation of the estrogen receptor \u03b2 (ER\u03b2) could be a safe approach to hormone replacement therapy for both women and men, in contrast to the estrogens currently used for women which activate both ER\u03b2 and ER\u03b1, occasionally causing severe side effects. The selective ER\u03b2 agonist AC-131 has shown efficacy in animal models of Parkinson's disease and neuropathic pain. With the use of AC-131 as template, herein we report the discovery, synthesis, and structure-activity relationship (SAR) study of a new class of dihydrobenzofurans as potent and selective ER\u03b2 agonists. The SAR was established by enantioselective synthesis, molecular modeling, and whole-cell-based functional assays. The most potent diastereomer, cis-10-SR, was shown to have an EC50 value of <1 nM, potency 100-fold higher than that of AC-131. Even more interestingly, compound trans-10-SS exhibited 1000-fold ER\u03b2/ER\u03b1 selectivity while still maintaining good potency (\u223c10 nM). In addition, trans-10-SS showed only partial agonist activity (30-60 % Eff.) toward ER\u03b1 at 10 \u03bcM. This unprecedented selectivity could be rationalized by molecular modeling. Compound trans-10-SS appears to be the first molecule to take advantage of both conservative amino acid differences found in the \u03b1- and \u03b2-faces of the binding cavities of ER\u03b1 and ER\u03b2.", "doi": "10.1002/cmdc.201300175", "pmid": "23784708", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-20T14:59:35.171Z", "modified": "2025-10-17T13:04:30.324Z"}, {"entity": "publication", "iuid": "135f821176884e3480bb7c2a8062b568", "links": {"self": {"href": "https://publications.scilifelab.se/publication/135f821176884e3480bb7c2a8062b568.json"}, "display": {"href": "https://publications.scilifelab.se/publication/135f821176884e3480bb7c2a8062b568"}}, "title": "Antibody-based profiling of cerebrospinal fluid within multiple sclerosis.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "15", "pages": "2256-2267", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Antibody suspension bead arrays have proven to enable multiplexed and high-throughput protein profiling in unfractionated plasma and serum samples through a direct labeling approach. We here describe the development and application of an assay for protein profiling of cerebrospinal fluid (CSF). While setting up the assay, systematic intensity differences between sample groups were observed that reflected inherent sample specific total protein amounts. Supplementing the labeling reaction with BSA and IgG diminished these differences without impairing the apparent sensitivity of the assay. We also assessed the effects of heat treatment on the analysis of CSF proteins and applied the assay to profile 43 selected proteins by 101 antibodies in 339 CSF samples from a multiple sclerosis (MS) cohort. Two proteins, GAP43 and SERPINA3 were found to have a discriminating potential with altered intensity levels between sample groups. GAP43 was detected at significantly lower levels in secondary progressive MS compared to early stages of MS and the control group of other neurological diseases. SERPINA3 instead was detected at higher levels in all MS patients compared to controls. The developed assay procedure now offers new possibilities for broad-scale protein profiling of CSF within neurological disorders.", "doi": "10.1002/pmic.201200580", "pmid": "23696371", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:38.686Z", "modified": "2021-07-08T13:44:33.026Z"}, {"entity": "publication", "iuid": "a1face33528a44f296d40e15ed6e2d6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a1face33528a44f296d40e15ed6e2d6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a1face33528a44f296d40e15ed6e2d6a"}}, "title": "A novel intellectual disability syndrome caused by GPI anchor deficiency due to homozygous mutations in PIGT.", "authors": [{"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Korenke", "given": "G Christoph", "initials": "GC"}, {"family": "Chiang", "given": "Samuel C C", "initials": "SC"}, {"family": "Blennow", "given": "Elisabeth", "initials": "E"}, {"family": "Bergmann", "given": "Markus", "initials": "M"}, {"family": "St\u00f6dberg", "given": "Tommy", "initials": "T"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Bryceson", "given": "Yenan T", "initials": "YT"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "50", "issn": "1468-6244", "issue": "8", "pages": "521-528", "title": "J. Med. Genet.", "issn-l": "0022-2593"}, "abstract": "To delineate the molecular basis for a novel autosomal recessive syndrome, characterised by distinct facial features, intellectual disability, hypotonia and seizures, in combination with abnormal skeletal, endocrine, and ophthalmologic findings.\n\nWe examined four patients from a consanguineous kindred with a strikingly similar phenotype, by using whole exome sequencing (WES). Functional validation of the initial results were performed by flow cytometry determining surface expression of glycosylphosphatidylinositol (GPI) and GPI anchored proteins and, in addition, by in vivo assays on zebrafish embryos.\n\nThe results from WES identified a homozygous mutation, c.547A>C (p.Thr183Pro), in PIGT; Sanger sequencing of additional family members confirmed segregation with the disease. PIGT encodes phosphatidylinositol-glycan biosynthesis class T (PIG-T) protein, which is a subunit of the transamidase complex that catalyses the attachment of proteins to GPI. By flow cytometry, we found that granulocytes from the patients had reduced levels of the GPI anchored protein CD16b, supporting pathogenicity of the mutation. Further functional in vivo validation via morpholino mediated knockdown of the PIGT ortholog in zebrafish (pigt) showed that, unlike human wild-type PIGT mRNA, the p.Thr183Pro encoding mRNA failed to rescue gastrulation defects induced by the suppression of pigt.\n\nWe identified mutations in PIGT as the cause of a novel autosomal recessive intellectual disability syndrome. Our results demonstrate a new pathogenic mechanism in the GPI anchor pathway and expand the clinical spectrum of disorders belonging to the group of GPI anchor deficiencies.", "doi": "10.1136/jmedgenet-2013-101654", "pmid": "23636107", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "jmedgenet-2013-101654"}], "notes": [], "created": "2017-05-04T14:58:00.901Z", "modified": "2020-01-21T13:56:04.174Z"}, {"entity": "publication", "iuid": "ea85e337297a48128a0dd4b9783a7f0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea85e337297a48128a0dd4b9783a7f0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea85e337297a48128a0dd4b9783a7f0d"}}, "title": "New viruses in veterinary medicine, detected by metagenomic approaches.", "authors": [{"family": "Bel\u00e1k", "given": "S\u00e1ndor", "initials": "S"}, {"family": "Karlsson", "given": "Oskar E", "initials": "OE"}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}, {"family": "Berg", "given": "Mikael", "initials": "M"}, {"family": "Granberg", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2013-07-26", "journal": {"volume": "165", "issn": "1873-2542", "issue": "1-2", "pages": "95-101", "title": "Vet. Microbiol.", "issn-l": "0378-1135"}, "abstract": "In our world, which is faced today with exceptional environmental changes and dramatically intensifying globalisation, we are encountering challenges due to many new factors, including the emergence or re-emergence of novel, so far \"unknown\" infectious diseases. Although a broad arsenal of diagnostic methods is at our disposal, the majority of the conventional diagnostic tests is highly virus-specific or is targeted entirely towards a limited group of infectious agents. This specificity complicates or even hinders the detection of new or unexpected pathogens, such as new, emerging or re-emerging viruses or novel viral variants. The recently developed approaches of viral metagenomics provide an effective novel way to screen samples and detect viruses without previous knowledge of the infectious agent, thereby enabling a better diagnosis and disease control, in line with the \"One World, One Health\" principles (www.oneworldonehealth.org). Using metagenomic approaches, we have recently identified a broad variety of new viruses, such as novel bocaviruses, Torque Teno viruses, astroviruses, rotaviruses and kobuviruses in porcine disease syndromes, new virus variants in honeybee populations, as well as a range of other infectious agents in further host species. These findings indicate that the metagenomic detection of viral pathogens is becoming now a powerful, cultivation-independent, and useful novel diagnostic tool in veterinary diagnostic virology.", "doi": "10.1016/j.vetmic.2013.01.022", "pmid": "23428379", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0378-1135(13)00074-6"}], "notes": [], "created": "2017-05-04T15:02:30.977Z", "modified": "2020-01-21T13:56:05.973Z"}, {"entity": "publication", "iuid": "77a017da07e24a4d955f1fcde71b5124", "links": {"self": {"href": "https://publications.scilifelab.se/publication/77a017da07e24a4d955f1fcde71b5124.json"}, "display": {"href": "https://publications.scilifelab.se/publication/77a017da07e24a4d955f1fcde71b5124"}}, "title": "Gene \u00d7 physical activity interactions in obesity: combined analysis of 111,421 individuals of European ancestry.", "authors": [{"family": "Ahmad", "given": "Shafqat", "initials": "S"}, {"family": "Rukh", "given": "Gull", "initials": "G"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Kurbasic", "given": "Azra", "initials": "A"}, {"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Ericson", "given": "Ulrika", "initials": "U"}, {"family": "Koivula", "given": "Robert W", "initials": "RW"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Qi", "given": "Qibin", "initials": "Q"}, {"family": "Stan\u010d\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Sandholt", "given": "Camilla H", "initials": "CH"}, {"family": "Elks", "given": "Cathy E", "initials": "CE"}, {"family": "Curhan", "given": "Gary", "initials": "G"}, {"family": "Jensen", "given": "Majken K", "initials": "MK"}, {"family": "Tamimi", "given": "Rulla M", "initials": "RM"}, {"family": "Allin", "given": "Kristine H", "initials": "KH"}, {"family": "J\u00f8rgensen", "given": "Torben", "initials": "T"}, {"family": "Brage", "given": "Soren", "initials": "S"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Aadahl", "given": "Mette", "initials": "M"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "InterAct Consortium", "given": "", "initials": ""}, {"family": "DIRECT Consortium", "given": "", "initials": ""}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Pasquale", "given": "Louis T", "initials": "LT"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}], "type": "journal article", "published": "2013-07-25", "journal": {"volume": "9", "issn": "1553-7404", "issue": "7", "pages": "e1003607", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Numerous obesity loci have been identified using genome-wide association studies. A UK study indicated that physical activity may attenuate the cumulative effect of 12 of these loci, but replication studies are lacking. Therefore, we tested whether the aggregate effect of these loci is diminished in adults of European ancestry reporting high levels of physical activity. Twelve obesity-susceptibility loci were genotyped or imputed in 111,421 participants. A genetic risk score (GRS) was calculated by summing the BMI-associated alleles of each genetic variant. Physical activity was assessed using self-administered questionnaires. Multiplicative interactions between the GRS and physical activity on BMI were tested in linear and logistic regression models in each cohort, with adjustment for age, age(2), sex, study center (for multicenter studies), and the marginal terms for physical activity and the GRS. These results were combined using meta-analysis weighted by cohort sample size. The meta-analysis yielded a statistically significant GRS \u00d7 physical activity interaction effect estimate (Pinteraction \u200a=\u200a0.015). However, a statistically significant interaction effect was only apparent in North American cohorts (n\u200a=\u200a39,810, Pinteraction \u200a=\u200a0.014 vs. n\u200a=\u200a71,611, Pinteraction \u200a=\u200a0.275 for Europeans). In secondary analyses, both the FTO rs1121980 (Pinteraction \u200a=\u200a0.003) and the SEC16B rs10913469 (Pinteraction \u200a=\u200a0.025) variants showed evidence of SNP \u00d7 physical activity interactions. This meta-analysis of 111,421 individuals provides further support for an interaction between physical activity and a GRS in obesity disposition, although these findings hinge on the inclusion of cohorts from North America, indicating that these results are either population-specific or non-causal.", "doi": "10.1371/journal.pgen.1003607", "pmid": "23935507", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-03208"}, {"db": "pmc", "key": "PMC3723486"}], "notes": [], "created": "2017-05-04T14:58:11.058Z", "modified": "2020-01-21T13:56:08.567Z"}, {"entity": "publication", "iuid": "fc780965960b47328827dd5902f87022", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc780965960b47328827dd5902f87022.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc780965960b47328827dd5902f87022"}}, "title": "NCR3/NKp30 contributes to pathogenesis in primary Sjogren's syndrome.", "authors": [{"family": "Rusakiewicz", "given": "Sylvie", "initials": "S"}, {"family": "Nocturne", "given": "Gaetane", "initials": "G"}, {"family": "Lazure", "given": "Thierry", "initials": "T"}, {"family": "Semeraro", "given": "Michaela", "initials": "M"}, {"family": "Flament", "given": "Caroline", "initials": "C"}, {"family": "Caillat-Zucman", "given": "Sophie", "initials": "S"}, {"family": "S\u00e8ne", "given": "Damien", "initials": "D"}, {"family": "Delahaye", "given": "Nicolas", "initials": "N"}, {"family": "Vivier", "given": "Eric", "initials": "E"}, {"family": "Chaba", "given": "Kariman", "initials": "K"}, {"family": "Poirier-Colame", "given": "Vichnou", "initials": "V"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Theander", "given": "Elke", "initials": "E"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Nititham", "given": "Joanne", "initials": "J"}, {"family": "Taylor", "given": "Kimberly E", "initials": "KE"}, {"family": "Lessard", "given": "Christopher J", "initials": "CJ"}, {"family": "Sivils", "given": "Kathy L Moser", "initials": "KL"}, {"family": "Gottenberg", "given": "Jacques-Eric", "initials": "JE"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "Miceli-Richard", "given": "Corinne", "initials": "C"}, {"family": "Zitvogel", "given": "Laurence", "initials": "L"}, {"family": "Mariette", "given": "Xavier", "initials": "X"}], "type": "journal article", "published": "2013-07-24", "journal": {"volume": "5", "issn": "1946-6242", "issue": "195", "pages": "195ra96", "title": "Sci Transl Med", "issn-l": "1946-6234"}, "abstract": "Primary Sj\u00f6gren's syndrome (pSS) is a chronic autoimmune disease characterized by a lymphocytic exocrinopathy. However, patients often have evidence of systemic autoimmunity, and they are at markedly increased risk for the development of non- Hodgkin's lymphoma. Similar to other autoimmune disorders, a strong interferon (IFN) signature is present among subsets of pSS patients, although the precise etiology remains uncertain. NCR3/NKp30 is a natural killer (NK)-specific activating receptor regulating the cross talk between NK and dendritic cells and type II IFN secretion. We performed a case-control study of genetic polymorphisms of the NCR3/NKp30 gene and found that rs11575837 (G>A) residing in the promoter was associated with reduced gene transcription and function as well as protection to pSS. We also demonstrated that circulating levels of NCR3/NKp30 were significantly increased among pSS patients compared with controls and correlated with higher NCR3/NKp30 but not CD16-dependent IFN-\u03b3 secretion by NK cells. Excess accumulation of NK cells in minor salivary glands correlated with the severity of the exocrinopathy. B7H6, the ligand of NKp30, was expressed by salivary epithelial cells. These findings suggest that NK cells may promote an NKp30-dependent inflammatory state in salivary glands and that blockade of the B7H6/NKp30 axis could be clinically relevant in pSS.", "doi": "10.1126/scitranslmed.3005727", "pmid": "23884468", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "5/195/195ra96"}, {"db": "pmc", "key": "PMC4237161"}, {"db": "mid", "key": "NIHMS638202"}], "notes": [], "created": "2017-05-04T15:01:31.108Z", "modified": "2020-01-21T13:56:06.481Z"}, {"entity": "publication", "iuid": "64b1a650dbca4d7fae474646e27d6298", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64b1a650dbca4d7fae474646e27d6298.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64b1a650dbca4d7fae474646e27d6298"}}, "title": "Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer.", "authors": [{"family": "Johansson", "given": "Henrik J", "initials": "HJ"}, {"family": "Sanchez", "given": "Betzabe C", "initials": "BC"}, {"family": "Mundt", "given": "Filip", "initials": "F"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "Kovacs", "given": "Aniko", "initials": "A"}, {"family": "Panizza", "given": "Elena", "initials": "E"}, {"family": "Hultin-Rosenberg", "given": "Lina", "initials": "L"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "M\u00e1th\u00e9", "given": "Gy\u00f6ngyv\u00e9r", "initials": "G"}, {"family": "Yakhini", "given": "Zohar", "initials": "Z"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Krawiec", "given": "Kamilla", "initials": "K"}, {"family": "Kanter", "given": "Lena", "initials": "L"}, {"family": "Hjerpe", "given": "Anders", "initials": "A"}, {"family": "St\u00e5l", "given": "Olle", "initials": "O"}, {"family": "Linderholm", "given": "Barbro K", "initials": "BK"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2013-07-23", "journal": {"volume": "4", "issn": "2041-1723", "issue": null, "pages": "2175", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "About one-third of oestrogen receptor alpha-positive breast cancer patients treated with tamoxifen relapse. Here we identify the nuclear receptor retinoic acid receptor alpha as a marker of tamoxifen resistance. Using quantitative mass spectrometry-based proteomics, we show that retinoic acid receptor alpha protein networks and levels differ in a tamoxifen-sensitive (MCF7) and a tamoxifen-resistant (LCC2) cell line. High intratumoural retinoic acid receptor alpha protein levels also correlate with reduced relapse-free survival in oestrogen receptor alpha-positive breast cancer patients treated with adjuvant tamoxifen solely. A similar retinoic acid receptor alpha expression pattern is seen in a comparable independent patient cohort. An oestrogen receptor alpha and retinoic acid receptor alpha ligand screening reveals that tamoxifen-resistant LCC2 cells have increased sensitivity to retinoic acid receptor alpha ligands and are less sensitive to oestrogen receptor alpha ligands compared with MCF7 cells. Our data indicate that retinoic acid receptor alpha may be a novel therapeutic target and a predictive factor for oestrogen receptor alpha-positive breast cancer patients treated with adjuvant tamoxifen.", "doi": "10.1038/ncomms3175", "pmid": "23868472", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms3175"}, {"db": "pmc", "key": "PMC3759040"}], "notes": "Biochemical and Cellular Screening", "created": "2017-05-04T14:57:01.894Z", "modified": "2025-10-17T13:05:09.700Z"}, {"entity": "publication", "iuid": "d117d952634e42d88473d791e950f070", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d117d952634e42d88473d791e950f070.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d117d952634e42d88473d791e950f070"}}, "title": "Genetic variants in hormone-related genes and risk of breast cancer.", "authors": [{"family": "Clendenen", "given": "Tess", "initials": "T"}, {"family": "Zeleniuch-Jacquotte", "given": "Anne", "initials": "A"}, {"family": "Wirgin", "given": "Isaac", "initials": "I"}, {"family": "Koenig", "given": "Karen L", "initials": "KL"}, {"family": "Afanasyeva", "given": "Yelena", "initials": "Y"}, {"family": "Lundin", "given": "Eva", "initials": "E"}, {"family": "Arslan", "given": "Alan A", "initials": "AA"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "F\u00f6rsti", "given": "Asta", "initials": "A"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Hemminki", "given": "Kari", "initials": "K"}, {"family": "Lenner", "given": "Per", "initials": "P"}, {"family": "Roy", "given": "Nirmal", "initials": "N"}, {"family": "Shore", "given": "Roy E", "initials": "RE"}, {"family": "Chen", "given": "Yu", "initials": "Y"}], "type": "journal article", "published": "2013-07-23", "journal": {"volume": "8", "issn": "1932-6203", "issue": "7", "pages": "e69367", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Sex hormones play a key role in the development of breast cancer. Certain polymorphic variants (SNPs and repeat polymorphisms) in hormone-related genes are associated with sex hormone levels. However, the relationship observed between these genetic variants and breast cancer risk has been inconsistent. We conducted a case-control study nested within two prospective cohorts to assess the relationship between specific genetic variants in hormone-related genes and breast cancer risk. In total, 1164 cases and 2111 individually-matched controls were included in the study. We did not observe an association between potential functional genetic polymorphisms in the estrogen pathway, SHBG rs6259, ESR1 rs2234693, CYP19 rs10046 and rs4775936, and UGT1A1 rs8175347, or the progesterone pathway, PGR rs1042838, with the risk of breast cancer. Our results suggest that these genetic variants do not have a strong effect on breast cancer risk.", "doi": "10.1371/journal.pone.0069367", "pmid": "23935996", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-05381"}, {"db": "pmc", "key": "PMC3720532"}], "notes": [], "created": "2017-05-04T15:01:27.976Z", "modified": "2020-01-21T13:56:05.321Z"}, {"entity": "publication", "iuid": "8ceea6d27ed644f7b3a8459069a59292", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ceea6d27ed644f7b3a8459069a59292.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ceea6d27ed644f7b3a8459069a59292"}}, "title": "SNP in TXNRD2 associated with radiation-induced fibrosis: a study of genetic variation in reactive oxygen species metabolism and signaling.", "authors": [{"family": "Edvardsen", "given": "Hege", "initials": "H"}, {"family": "Landmark-H\u00f8yvik", "given": "Hege", "initials": "H"}, {"family": "Reinertsen", "given": "Kristin V", "initials": "KV"}, {"family": "Zhao", "given": "Xi", "initials": "X"}, {"family": "Grenaker-Aln\u00e6s", "given": "Grethe Irene", "initials": "GI"}, {"family": "Nebdal", "given": "Daniel", "initials": "D"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "R\u00f8dningen", "given": "Olaug", "initials": "O"}, {"family": "Alsner", "given": "Jan", "initials": "J"}, {"family": "Overgaard", "given": "Jens", "initials": "J"}, {"family": "Borresen-Dale", "given": "Anne-Lise", "initials": "AL"}, {"family": "Foss\u00e5", "given": "Sophie D", "initials": "SD"}, {"family": "Kristensen", "given": "Vessela N", "initials": "VN"}], "type": "journal article", "published": "2013-07-15", "journal": {"volume": "86", "issn": "1879-355X", "issue": "4", "pages": "791-799", "title": "Int. J. Radiat. Oncol. Biol. Phys.", "issn-l": "0360-3016"}, "abstract": "The aim of the study was to identify noninvasive markers of treatment-induced side effects. Reactive oxygen species (ROS) are generated after irradiation, and genetic variation in genes related to ROS metabolism might influence the level of radiation-induced adverse effects (AEs).\n\n92 breast cancer (BC) survivors previously treated with hypofractionated radiation therapy were assessed for the AEs subcutaneous atrophy and fibrosis, costal fractures, lung fibrosis, pleural thickening, and telangiectasias (median follow-up time 17.1 years). Single-nucleotide polymorphisms (SNPs) in 203 genes were analyzed for association to AE grade. SNPs associated with subcutaneous fibrosis were validated in an independent BC survivor material (n=283). The influence of the studied genetic variation on messenger ribonucleic acid (mRNA) expression level of 18 genes previously associated with fibrosis was assessed in fibroblast cell lines from BC patients.\n\nSubcutaneous fibrosis and atrophy had the highest correlation (r=0.76) of all assessed AEs. The nonsynonymous SNP rs1139793 in TXNRD2 was associated with grade of subcutaneous fibrosis, the reference T-allele being more prevalent in the group experiencing severe levels of fibrosis. This was confirmed in another sample cohort of 283 BC survivors, and rs1139793 was found significantly associated with mRNA expression level of TXNRD2 in blood. Genetic variation in 24 ROS-related genes, including EGFR, CENPE, APEX1, and GSTP1, was associated with mRNA expression of 14 genes previously linked to fibrosis (P\u2264.005).\n\nDevelopment of subcutaneous fibrosis can be associated with genetic variation in the mitochondrial enzyme TXNRD2, critically involved in removal of ROS, and maintenance of the intracellular redox balance.", "doi": "10.1016/j.ijrobp.2013.02.025", "pmid": "23597419", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0360-3016(13)00217-4"}], "notes": [], "created": "2017-05-04T15:01:19.734Z", "modified": "2021-07-07T15:11:02.591Z"}, {"entity": "publication", "iuid": "c377029014784be6aa1c7671aa6953aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c377029014784be6aa1c7671aa6953aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c377029014784be6aa1c7671aa6953aa"}}, "title": "Novel signatures of cancer-associated fibroblasts.", "authors": [{"family": "Boz\u00f3ky", "given": "Benedek", "initials": "B"}, {"family": "Savchenko", "given": "Andrii", "initials": "A"}, {"family": "Csermely", "given": "P\u00e9ter", "initials": "P"}, {"family": "Korcsm\u00e1ros", "given": "Tam\u00e1s", "initials": "T"}, {"family": "D\u00fal", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Sz\u00e9kely", "given": "L\u00e1szl\u00f3", "initials": "L"}, {"family": "Klein", "given": "George", "initials": "G"}], "type": "journal article", "published": "2013-07-15", "journal": {"volume": "133", "issn": "1097-0215", "issue": "2", "pages": "286-293", "title": "Int. J. Cancer", "issn-l": "0020-7136"}, "abstract": "Increasing evidence indicates the importance of the tumor microenvironment, in particular cancer-associated fibroblasts, in cancer development and progression. In our study, we developed a novel, visually based method to identify new immunohistochemical signatures of these fibroblasts. The method employed a protein list based on 759 protein products of genes identified by RNA profiling from our previous study, comparing fibroblasts with differential growth-modulating effect on human cancers cells, and their first neighbors in the human protein interactome. These 2,654 proteins were analyzed in the Human Protein Atlas online database by comparing their immunohistochemical expression patterns in normal versus tumor-associated fibroblasts. Twelve new proteins differentially expressed in cancer-associated fibroblasts were identified (DLG1, BHLHE40, ROCK2, RAB31, AZI2, PKM2, ARHGAP31, ARHGAP26, ITCH, EGLN1, RNF19A and PLOD2), four of them can be connected to the Rho kinase signaling pathway. They were further analyzed in several additional tumor stromata and revealed that the majority showed congruence among the different tumors. Many of them were also positive in normal myofibroblast-like cells. The new signatures can be useful in immunohistochemical analysis of different tumor stromata and may also give us an insight into the pathways activated in them in their true in vivo context. The method itself could be used for other similar analysis to identify proteins expressed in other cell types in tumors and their surrounding microenvironment.", "doi": "10.1002/ijc.28035", "pmid": "23319410", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:59.257Z", "modified": "2017-05-30T12:56:58.377Z"}, {"entity": "publication", "iuid": "9c88915dcf384e9cb72f4a45e6ad5891", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c88915dcf384e9cb72f4a45e6ad5891.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c88915dcf384e9cb72f4a45e6ad5891"}}, "title": "Prevalence, comorbidity and heritability of hoarding symptoms in adolescence: a population based twin study in 15-year olds.", "authors": [{"family": "Ivanov", "given": "Volen Z", "initials": "VZ"}, {"family": "Mataix-Cols", "given": "David", "initials": "D"}, {"family": "Serlachius", "given": "Eva", "initials": "E"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Anckars\u00e4ter", "given": "Henrik", "initials": "H"}, {"family": "Chang", "given": "Zheng", "initials": "Z"}, {"family": "Gumpert", "given": "Clara Hellner", "initials": "CH"}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S"}, {"family": "L\u00e5ngstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "R\u00fcck", "given": "Christian", "initials": "C"}], "type": "journal article", "published": "2013-07-10", "journal": {"volume": "8", "issn": "1932-6203", "issue": "7", "pages": "e69140", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Hoarding Disorder (HD) is often assumed to be an 'old age' problem, but many individuals diagnosed with HD retrospectively report first experiencing symptoms in childhood or adolescence. We examined the prevalence, comorbidity and etiology of hoarding symptoms in adolescence.\n\nTo determine the presence of clinically significant hoarding symptoms, a population-based sample of 15-year old twins (N\u200a=\u200a3,974) completed the Hoarding Rating Scale-Self Report. Co-occurring Obsessive Compulsive Disorder (OCD), Autism Spectrum Disorders (ASD) and Attention Deficit Hyperactivity Disorder (ADHD) were estimated from parental report. Model-fitting analyses divided hoarding symptom scores into additive genetic, shared, and non-shared environmental effects.\n\nThe prevalence of clinically significant hoarding symptoms was 2% (95% CI 1.6-2.5%), with a significantly higher prevalence in girls than boys. Exclusion of the clutter criterion (as adolescents do not have control over their environment) increased the prevalence rate to 3.7% (95% CI 3.1-4.3%). Excessive acquisition was reported by 30-40% among those with clinically significant hoarding symptoms. The prevalence of co-occurring OCD (2.9%), ASD (2.9%) and ADHD (10.0%) was comparable in hoarding and non-hoarding teenagers. Model-fitting analyses suggested that, in boys, additive genetic (32%; 95% CI 13-44%) and non-shared environmental effects accounted for most of the variance. In contrast, among girls, shared and non-shared environmental effects explained most of the variance, while additive genetic factors played a negligible role.\n\nHoarding symptoms are relatively prevalent in adolescents, particularly in girls, and cause distress and/or impairment. Hoarding was rarely associated with other common neurodevelopmental disorders, supporting its DSM-5 status as an independent diagnosis. The relative importance of genetic and shared environmental factors for hoarding differed across sexes. The findings are suggestive of dynamic developmental genetic and environmental effects operating from adolescence onto adulthood.", "doi": "10.1371/journal.pone.0069140", "pmid": "23874893", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-13943"}, {"db": "pmc", "key": "PMC3707873"}], "notes": [], "created": "2017-05-04T15:03:37.759Z", "modified": "2017-05-30T14:53:04.918Z"}, {"entity": "publication", "iuid": "fc718dc9e6634204b3ed32257abed223", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc718dc9e6634204b3ed32257abed223.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc718dc9e6634204b3ed32257abed223"}}, "title": "Amyloid-\u03b2 protofibrils: size, morphology and synaptotoxicity of an engineered mimic.", "authors": [{"family": "Dubnovitsky", "given": "Anatoly", "initials": "A"}, {"family": "Sandberg", "given": "Anders", "initials": "A"}, {"family": "Rahman", "given": "M Mahafuzur", "initials": "MM"}, {"family": "Benilova", "given": "Iryna", "initials": "I"}, {"family": "Lendel", "given": "Christofer", "initials": "C"}, {"family": "H\u00e4rd", "given": "Torleif", "initials": "T"}], "type": "journal article", "published": "2013-07-02", "journal": {"volume": "8", "issn": "1932-6203", "issue": "7", "pages": "e66101", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Structural and biochemical studies of the aggregation of the amyloid-\u03b2 peptide (A\u03b2) are important to understand the mechanisms of Alzheimer's disease, but research is complicated by aggregate inhomogeneity and instability. We previously engineered a hairpin form of A\u03b2 called A\u03b2cc, which forms stable protofibrils that do not convert into amyloid fibrils. Here we provide a detailed characterization of A\u03b242cc protofibrils. Like wild type A\u03b2 they appear as smooth rod-like particles with a diameter of 3.1 (\u00b10.2) nm and typical lengths in the range 60 to 220 nm when observed by atomic force microscopy. Non-perturbing analytical ultracentrifugation and nanoparticle tracking analyses are consistent with such rod-like protofibrils. A\u03b242cc protofibrils bind the ANS dye indicating that they, like other toxic protein aggregates, expose hydrophobic surface. Assays with the OC/A11 pair of oligomer specific antibodies put A\u03b242cc protofibrils into the same class of species as fibrillar oligomers of wild type A\u03b2. A\u03b242cc protofibrils may be used to extract binding proteins in biological fluids and apolipoprotein E is readily detected as a binder in human serum. Finally, A\u03b242cc protofibrils act to attenuate spontaneous synaptic activity in mouse hippocampal neurons. The experiments indicate considerable structural and chemical similarities between protofibrils formed by A\u03b242cc and aggregates of wild type A\u03b242. We suggest that A\u03b242cc protofibrils may be used in research and applications that require stable preparations of protofibrillar A\u03b2.", "doi": "10.1371/journal.pone.0066101", "pmid": "23843949", "labels": {"Mass Spectrometry-based Proteomics, Uppsala": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-01978"}, {"db": "pmc", "key": "PMC3699592"}], "notes": [], "created": "2017-05-04T15:03:26.336Z", "modified": "2017-05-30T14:51:53.812Z"}, {"entity": "publication", "iuid": "adaf08f7cdf54005af3210ec5aa6aa34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/adaf08f7cdf54005af3210ec5aa6aa34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/adaf08f7cdf54005af3210ec5aa6aa34"}}, "title": "Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.", "authors": [{"family": "Cousminer", "given": "Diana L", "initials": "DL"}, {"family": "Berry", "given": "Diane J", "initials": "DJ"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Ang", "given": "Wei", "initials": "W"}, {"family": "Thiering", "given": "Elisabeth", "initials": "E"}, {"family": "Byrne", "given": "Enda M", "initials": "EM"}, {"family": "Taal", "given": "H Rob", "initials": "HR"}, {"family": "Huikari", "given": "Ville", "initials": "V"}, {"family": "Bradfield", "given": "Jonathan P", "initials": "JP"}, {"family": "Kerkhof", "given": "Marjan", "initials": "M"}, {"family": "Groen-Blokhuis", "given": "Maria M", "initials": "MM"}, {"family": "Kreiner-M\u00f8ller", "given": "Eskil", "initials": "E"}, {"family": "Marinelli", "given": "Marcella", "initials": "M"}, {"family": "Holst", "given": "Claus", "initials": "C"}, {"family": "Leinonen", "given": "Jaakko T", "initials": "JT"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Pietil\u00e4inen", "given": "Olli", "initials": "O"}, {"family": "Kettunen", "given": "Johannes", "initials": "J"}, {"family": "Anttila", "given": "Verneri", "initials": "V"}, {"family": "Kaakinen", "given": "Marika", "initials": "M"}, {"family": "Sovio", "given": "Ulla", "initials": "U"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Das", "given": "Shikta", "initials": "S"}, {"family": "Lagou", "given": "Vasiliki", "initials": "V"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Evans", "given": "David M", "initials": "DM"}, {"family": "Kemp", "given": "John P", "initials": "JP"}, {"family": "St Pourcain", "given": "Beate", "initials": "B"}, {"family": "Ring", "given": "Susan", "initials": "S"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Kajantie", "given": "Eero", "initials": "E"}, {"family": "Osmond", "given": "Clive", "initials": "C"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Viikari", "given": "Jorma S", "initials": "JS"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Warrington", "given": "Nicole M", "initials": "NM"}, {"family": "Lye", "given": "Stephen J", "initials": "SJ"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Tiesler", "given": "Carla M T", "initials": "CMT"}, {"family": "Flexeder", "given": "Claudia", "initials": "C"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Hakonarson", "given": "Hakon", "initials": "H"}, {"family": "Guxens", "given": "M\u00f2nica", "initials": "M"}, {"family": "Bartels", "given": "Meike", "initials": "M"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "ReproGen Consortium", "given": "", "initials": ""}, {"family": "Murabito", "given": "Joanne M", "initials": "JM"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TIA"}, {"family": "Ballester", "given": "Ferran", "initials": "F"}, {"family": "Bisgaard", "given": "Hans", "initials": "H"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH"}, {"family": "Grant", "given": "Struan F A", "initials": "SFA"}, {"family": "Jaddoe", "given": "Vincent W V", "initials": "VWV"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Heinrich", "given": "Joachim", "initials": "J"}, {"family": "Pennell", "given": "Craig E", "initials": "CE"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Wid\u00e9n", "given": "Elisabeth", "initials": "E"}, {"family": "Early Growth Genetics (EGG) Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2013-07-01", "journal": {"volume": "22", "issn": "1460-2083", "issue": "13", "pages": "2735-2747", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "The pubertal height growth spurt is a distinctive feature of childhood growth reflecting both the central onset of puberty and local growth factors. Although little is known about the underlying genetics, growth variability during puberty correlates with adult risks for hormone-dependent cancer and adverse cardiometabolic health. The only gene so far associated with pubertal height growth, LIN28B, pleiotropically influences childhood growth, puberty and cancer progression, pointing to shared underlying mechanisms. To discover genetic loci influencing pubertal height and growth and to place them in context of overall growth and maturation, we performed genome-wide association meta-analyses in 18 737 European samples utilizing longitudinally collected height measurements. We found significant associations (P < 1.67 \u00d7 10(-8)) at 10 loci, including LIN28B. Five loci associated with pubertal timing, all impacting multiple aspects of growth. In particular, a novel variant correlated with expression of MAPK3, and associated both with increased prepubertal growth and earlier menarche. Another variant near ADCY3-POMC associated with increased body mass index, reduced pubertal growth and earlier puberty. Whereas epidemiological correlations suggest that early puberty marks a pathway from rapid prepubertal growth to reduced final height and adult obesity, our study shows that individual loci associating with pubertal growth have variable longitudinal growth patterns that may differ from epidemiological observations. Overall, this study uncovers part of the complex genetic architecture linking pubertal height growth, the timing of puberty and childhood obesity and provides new information to pinpoint processes linking these traits.", "doi": "10.1093/hmg/ddt104", "pmid": "23449627", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ddt104"}, {"db": "pmc", "key": "PMC3674797"}], "notes": [], "created": "2017-05-04T14:57:56.946Z", "modified": "2020-01-21T13:56:08.548Z"}, {"entity": "publication", "iuid": "8a7b8e5545af42fe83c2bdc222607eca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a7b8e5545af42fe83c2bdc222607eca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a7b8e5545af42fe83c2bdc222607eca"}}, "title": "Somatic mutations in H-RAS in sporadic pheochromocytoma and paraganglioma identified by exome sequencing.", "authors": [{"family": "Crona", "given": "Joakim", "initials": "J"}, {"family": "Delgado Verdugo", "given": "Alberto", "initials": "A"}, {"family": "Maharjan", "given": "Rajani", "initials": "R"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}, {"family": "Granberg", "given": "Dan", "initials": "D"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "Peyman", "initials": "P"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "98", "issn": "1945-7197", "issue": "7", "pages": "E1266-E1271", "title": "J. Clin. Endocrinol. Metab.", "issn-l": "0021-972X"}, "abstract": "Up to 60% of pheochromocytoma (PCC) and paraganglioma (PGL) are associated with either somatic or germline mutations in established PCC and PGL susceptibility loci. Most unexplained cases are characterized by an increased activity of the RAS/RAF/ERK signaling pathway. Mutations in RAS subtypes H, K, and N are common in human cancers; however, previous studies have been inconsistent regarding the mutational status of RAS in PCC and PGL.\n\nThe aim of this study was to identify novel disease causing genes in PCC and PGL tumors.\n\nFour benign and sporadic PCC and PGL tumors were subjected to whole exome sequencing using the Illumina HiSeq Platform. Sequences were processed by CLC genomics 4.9 bioinformatics software and the acquired list of genetic variants was filtered against the Catalogue of Somatic Mutations in Cancer database. Findings were validated in an additional 78 PCC and PGL tumor lesions.\n\nExome sequencing identified 2 cases with somatic mutations in the H-RAS. In total, 6.9% (n = 4/58) of tumors negative for mutations in major PCC and PGL loci had mutations in H-RAS: G13R, Q61K, and Q61R. There were 3 PCC and 1 PGL; all had sporadic presentation with benign tumor characteristics and substantial increases in norepinephrine and/or epinephrine. H-RAS tumors were exclusively found in male patients (P = .007).\n\nWe identified recurrent somatic H-RAS mutations in pheochromocytoma and paraganglioma. Tumors with H-RAS mutations had activation of the RAS/RAF/ERK signaling pathway and were associated with male PCC patients having benign and sporadic disease characteristics. H-RAS could serve as a prognostic and predictive marker as well as a novel therapeutic target.", "doi": "10.1210/jc.2012-4257", "pmid": "23640968", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "jc.2012-4257"}], "notes": [], "created": "2017-05-04T15:01:20.041Z", "modified": "2020-01-21T13:56:03.543Z"}, {"entity": "publication", "iuid": "ae438fb9b85c4feab4abc585bcd67553", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae438fb9b85c4feab4abc585bcd67553.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae438fb9b85c4feab4abc585bcd67553"}}, "title": "Response of Acidithiobacillus\u00a0caldus toward suboptimal pH conditions.", "authors": [{"family": "Mangold", "given": "Stefanie", "initials": "S"}, {"family": "Rao Jonna", "given": "Venkateswara", "initials": "V"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "17", "issn": "1433-4909", "issue": "4", "pages": "689-696", "title": "Extremophiles", "issn-l": "1431-0651"}, "abstract": "Maintenance of a circumneutral intracellular pH is important for any organism. Acidophilic microorganisms thrive at low pH while maintaining their intracellular pH around 6.5. However, the mechanisms contributing to acidophile pH homeostasis are not well characterized. The authors investigated the proteomic response and cytoplasmic membrane fatty acid profiles of Acidithiobacillus caldus toward three pH values: 1.1, 2.5, and 4.0. Major rearrangements were observed but lower pH elicited larger changes. Differentially expressed transcription factors suggested tight transcriptional control of pH induced genes. Enzymes involved in sulfur metabolism were up-regulated at pH 1.1 suggesting either that: (1) cells required more energy for maintenance or (2) increased metabolic activity was a specific acid stress response to export intracellular protons via 1\u00b0 electron transport proton pumps. Furthermore, glutamate decarboxylase, an important enzyme in Escherichia coli acid resistance, was uniquely expressed at pH 1.1. Other proteins previously shown to be involved in neutrophilic acid response, such as spermidine synthase, PspA, and toluene tolerance protein, were differentially expressed in At. caldus but require further investigation to show a direct link to pH homeostasis. Their roles in acidophilic organisms are discussed. Active modulation of fatty acid profiles was detected and suggested a more rigid membrane at low pH.", "doi": "10.1007/s00792-013-0553-5", "pmid": "23712908", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:23.349Z", "modified": "2020-01-21T13:53:20.770Z"}, {"entity": "publication", "iuid": "30ad36931bf84a5796ba662da42ac3a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30ad36931bf84a5796ba662da42ac3a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30ad36931bf84a5796ba662da42ac3a8"}}, "title": "Republished: Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime.", "authors": [{"family": "Forsberg", "given": "Lars Anders", "initials": "LA"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Dumanski", "given": "Jan Piotr", "initials": "JP"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "89", "issn": "1469-0756", "issue": "1053", "pages": "417-426", "title": "Postgrad Med J", "issn-l": "0032-5473"}, "abstract": "The heritability of most common, multifactorial diseases is rather modest and known genetic effects account for a small part of it. The remaining portion of disease aetiology has been conventionally ascribed to environmental effects, with an unknown part being stochastic. This review focuses on recent studies highlighting stochastic events of potentially great importance in human disease-the accumulation of post-zygotic structural aberrations with age in phenotypically normal humans. These findings are in agreement with a substantial mutational load predicted to occur during lifetime within the human soma. A major consequence of these results is that the genetic profile of a single tissue collected at one time point should be used with caution as a faithful portrait of other tissues from the same subject or the same tissue throughout life. Thus, the design of studies in human genetics interrogating a single sample per subject or applying lymphoblastoid cell lines may come into question. Sporadic disorders are common in medicine. We wish to stress the non-heritable genetic variation as a potentially important factor behind the development of sporadic diseases. Moreover, associations between post-zygotic mutations, clonal cell expansions and their relation to cancer predisposition are central in this context. Post-zygotic mutations are amenable to robust examination and are likely to explain a sizable part of non-heritable disease causality, which has routinely been thought of as synonymous with environmental factors. In view of the widespread accumulation of genetic aberrations with age and strong predictions of disease risk from such analyses, studies of post-zygotic mutations may be a fruitful approach for delineation of variants that are causative for common human disorders.", "doi": "10.1136/postgradmedj-2012-101322rep", "pmid": "23781115", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "postgradmedj-2012-101322rep"}, {"db": "pmc", "key": "PMC3711362"}], "notes": [], "created": "2017-05-04T15:01:30.499Z", "modified": "2020-01-21T13:56:01.348Z"}, {"entity": "publication", "iuid": "605f4a936bcb4643ab7978a8d82e0c9a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/605f4a936bcb4643ab7978a8d82e0c9a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/605f4a936bcb4643ab7978a8d82e0c9a"}}, "title": "Massive functional mapping of a 5'-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing.", "authors": [{"family": "Holmqvist", "given": "Erik", "initials": "E"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Wagner", "given": "E Gerhart H", "initials": "EG"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "41", "issn": "1362-4962", "issue": "12", "pages": "e122", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "We present here a method that enables functional screening of large number of mutations in a single experiment through the combination of random mutagenesis, phenotypic cell sorting and high-throughput sequencing. As a test case, we studied post-transcriptional gene regulation of the bacterial csgD messenger RNA, which is regulated by a small RNA (sRNA). A 109 bp sequence within the csgD 5'-UTR, containing all elements for expression and sRNA-dependent control, was mutagenized close to saturation. We monitored expression from a translational gfp fusion and collected fractions of cells with distinct expression levels by fluorescence-activated cell sorting. Deep sequencing of mutant plasmids from cells in different activity-sorted fractions identified functionally important positions in the messenger RNA that impact on intrinsic (translational activity per se) and extrinsic (sRNA-based) gene regulation. The results obtained corroborate previously published data. In addition to pinpointing nucleotide positions that change expression levels, our approach also reveals mutations that are silent in terms of gene expression and/or regulation. This method provides a simple and informative tool for studies of regulatory sequences in RNA, in particular addressing RNA structure-function relationships (e.g. sRNA-mediated control, riboswitch elements). However, slight protocol modifications also permit mapping of functional DNA elements and functionally important regions in proteins.", "doi": "10.1093/nar/gkt267", "pmid": "23609548", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "gkt267"}, {"db": "pmc", "key": "PMC3695526"}], "notes": [], "created": "2017-05-04T15:01:25.050Z", "modified": "2020-01-21T13:56:02.631Z"}, {"entity": "publication", "iuid": "9ce1b64f05d749e9bc4847a76b807c87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ce1b64f05d749e9bc4847a76b807c87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ce1b64f05d749e9bc4847a76b807c87"}}, "title": "Implications of baseline polymorphisms for potential resistance to NS3 protease inhibitors in Hepatitis C virus genotypes 1a, 2b and 3a.", "authors": [{"family": "Palanisamy", "given": "Navaneethan", "initials": "N"}, {"family": "Danielsson", "given": "Axel", "initials": "A"}, {"family": "Kokkula", "given": "Chakradhar", "initials": "C"}, {"family": "Yin", "given": "Hong", "initials": "H"}, {"family": "Bondeson", "given": "K\u00e5re", "initials": "K"}, {"family": "Wessl\u00e9n", "given": "Lars", "initials": "L"}, {"family": "Duberg", "given": "Ann-Sofi", "initials": "AS"}, {"family": "Lennerstrand", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "99", "issn": "1872-9096", "issue": "1", "pages": "12-17", "title": "Antiviral Res.", "issn-l": "0166-3542"}, "abstract": "The future interferon-free treatment of hepatitis C virus (HCV) infection could include NS3 protease inhibitors (PIs) for potent pan-genotypic effect. We studied the prevalence of pre-existing PI resistance associated amino acid variants (RAVs) in 126 treatment-naive patient samples of HCV genotypes 1a, 2b and 3a, the most common genotypes in Sweden. The NS3 genes were each amplified by nested PCR method with degenerated primers to enable a broad genotype analysis. Population sequencing method was used, and the sequences were aligned with the NS3 sequence from HCV genotype 1a H77 strain. Interpretation of fold-change resistance to NS3 candidate drugs were done from already published phenotypic resistance data. The prevalence of known PI RAVs at baseline in genotype 1a was 28% (15/53), either single (V36L or Q80K/R) or combinations (T54A/S and V55A/I) of mutation(s). In genotype 2b, specific mutations like V36L, Q80G and S122R of viral NS3 protease gene were found in 100% (11/11). These may be the natural polymorphisms unique to genotype 2b. Similarly, specific mutations like V36L and D168Q were found uniquely in all 3a samples (30/30). The natural PI RAVs found in genotype 1a, although with relatively weak resistance, could still render up to 10-fold-resistance to the approved (boceprevir and telaprevir) and the 2nd generation PIs (faldaprevir and simeprevir). Moreover, the natural polymorphisms in genotype 2b (i.e. S122R) and 3a (i.e. D168Q), with inherent PI drug resistance of up to 20 and 700 fold respectively, would explain why current PIs are primarily directed against genotype 1.", "doi": "10.1016/j.antiviral.2013.04.018", "pmid": "23648709", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0166-3542(13)00117-4"}], "notes": [], "created": "2017-05-04T15:02:18.233Z", "modified": "2020-01-21T13:56:04.067Z"}, {"entity": "publication", "iuid": "11d2225f3a49441792b37f668708d895", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11d2225f3a49441792b37f668708d895.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11d2225f3a49441792b37f668708d895"}}, "title": "Family-based study of HTR2A in suicide attempts: observed gene, gene \u00d7 environment and parent-of-origin associations.", "authors": [{"family": "Ben-Efraim", "given": "Y J", "initials": "YJ"}, {"family": "Wasserman", "given": "D", "initials": "D"}, {"family": "Wasserman", "given": "J", "initials": "J"}, {"family": "Sokolowski", "given": "M", "initials": "M"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "18", "issn": "1476-5578", "issue": "7", "pages": "758-766", "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "While suicidal behavior is frequently accompanied by serotonergic system alterations, specific associations with genetic variation in the serotonin 2A receptor (HTR2A) gene have been inconsistent. Using a family-based study design of 660 offspring who have made a suicide attempt (SA) and both parents, we conducted an association and linkage analysis using single-nucleotide polymorphisms (SNPs) with extensive gene coverage, and included the study of parent-of-origin (POE) and gene-environment interaction (G \u00d7 E), also using previously unstudied exposures. The main finding was a G \u00d7 E between the exon 1 SNP rs6313 and exposure to cumulative types of lifetime stressful life events (SLEs), driven by overtransmission of CT and undertransmission of TT, both in relation to other genotypes. Further exploratory analysis revealed a significant POE in this G \u00d7 E in female subjects, which followed a polar overdominant inheritance pattern. In addition, rs6310 and rs6305 were found to significantly associate with SA in the total sample. A G \u00d7 E in female subjects (rs7322347 \u00d7 physical assault in childhood/adolescence) confirmed features of a previously observed association with SA. Other potentially interesting nominally significant findings were observed, but like the G \u00d7 E of rs7322347 did not pass a false-discovery rate cutoff. Taken together, this study found multiple associations of HTR2A SNPs on SA, with strongest statistical evidence for a G \u00d7 E involving rs6313, and further suggested the importance of taking into account different inheritance patterns and G \u00d7 Es with regard to HTR2A.", "doi": "10.1038/mp.2012.86", "pmid": "22751492", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "mp201286"}], "notes": [], "created": "2017-05-04T15:01:21.524Z", "modified": "2020-01-21T13:56:00.764Z"}, {"entity": "publication", "iuid": "b2e66f827add48e794f545bbca1165f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2e66f827add48e794f545bbca1165f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2e66f827add48e794f545bbca1165f9"}}, "title": "Family-based study of AVPR1B association and interaction with stressful life events on depression and anxiety in suicide attempts.", "authors": [{"family": "Ben-Efraim", "given": "Yair J", "initials": "YJ"}, {"family": "Wasserman", "given": "Danuta", "initials": "D"}, {"family": "Wasserman", "given": "Jerzy", "initials": "J"}, {"family": "Sokolowski", "given": "Marcus", "initials": "M"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "38", "issn": "1740-634X", "issue": "8", "pages": "1504-1511", "title": "Neuropsychopharmacology", "issn-l": "0893-133X"}, "abstract": "The cortisol response to psychosocial stress may become dysregulated in stress-related disorders. It is potentiated by pituitary secretion of adrenocorticotropic hormone (ACTH), which is, in part, regulated by arginine vasopressin receptor-1B (AVPR1B). AVPR1B variants were previously reported to associate with mood and anxiety disorders. This study aims, for the first time, to investigate association of AVPR1B genetic variants with mood and anxiety outcomes in suicidal behavior.Using a family-based study design of 660 complete nuclear family trios with offspring who have made a suicide attempt (SA), we tested the direct association and linkage of AVPR1B single nucleotide polymorphisms (SNPs) with SA, as well as with depression and anxiety in SA. Main findings were the association and linkage of AVPR1B exon 1 SNP rs33990840 and a major 6-SNP haplotype representative of all common AVPR1B-SNPs, on the outcome of high Beck Depression Inventory scores in SA. By contrast, genetic associations with lifetime diagnoses of depression and anxiety in SA or gene-environment interactions between AVPR1B variants and stressful life events (SLEs) were not significant. An exploratory screen of interactions between AVPR1B and CRHR1 (corticotropin-releasing hormone receptor-1), the principal pituitary regulator of ACTH secretion, showed no support for gene-gene interactions on the studied outcomes. The results suggest that AVPR1B genetic variation, eg, non-synonymous SNP rs33990840 mediating putative consequences on ligand binding, has a role in SA etiology characterized by elevated depression symptoms, without involving AVPR1B-moderation of SLEs.", "doi": "10.1038/npp.2013.49", "pmid": "23422793", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "npp201349"}, {"db": "pmc", "key": "PMC3682145"}], "notes": [], "created": "2017-05-04T15:01:24.534Z", "modified": "2020-01-21T13:56:04.712Z"}, {"entity": "publication", "iuid": "8cd8cffcaad846af80039b4c8931588c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cd8cffcaad846af80039b4c8931588c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cd8cffcaad846af80039b4c8931588c"}}, "title": "Estrogen receptor \u03b2 expression induces changes in the microRNA pool in human colon cancer cells.", "authors": [{"family": "Edvardsson", "given": "Karin", "initials": "K"}, {"family": "Nguyen-Vu", "given": "Trang", "initials": "T"}, {"family": "Kalasekar", "given": "Sharanya M", "initials": "SM"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Gustafsson", "given": "Jan-\u00c5ke", "initials": "J\u00c5"}, {"family": "Williams", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "34", "issn": "1460-2180", "issue": "7", "pages": "1431-1441", "title": "Carcinogenesis", "issn-l": "0143-3334"}, "abstract": "There is epidemiological, animal and in vitro evidence that estrogen receptor \u03b2 (ER\u03b2) can mediate protective effects against colon cancer, but the mechanism is not completely understood. Previous research has indicated critical pathways whereby ER\u03b2 acts in an antitumorigenic fashion. In this study, we investigate ER\u03b2's impact on the microRNA (miRNA) pool in colon cancer cells using large-scale genomic approaches, bioinformatics and focused functional studies. We detect and confirm 27 miRNAs to be significantly changed following ER\u03b2 expression in SW480 colon cancer cells. Among these, the oncogenic miR-17-92 cluster and miR-200a/b are strongly downregulated. Using target prediction and anticorrelation to gene expression data followed by focused mechanistic studies, we demonstrate that repression of miR-17 is a secondary event following ER\u03b2's downregulatory effect on MYC. We show that re-introduction of miR-17 can reverse the antiproliferative effects of ER\u03b2. The repression of miR-17 also influences cell death upon DNA damage and mediates regulation of NCOA3 (SRC-3) and CLU in colon cancer cells. We further determine that the downregulation of miR-200a/b mediates increased ZEB1 while decreasing E-cadherin levels in ER\u03b2-expressing colon cancer cells. Changes in these genes correspond to significant alterations in morphology and migration. Our work contributes novel data of ER\u03b2 and miRNA in the colon. Elucidating the mechanism of ER\u03b2 and biomarkers of its activity has significant potential to impact colon cancer prevention and treatment.", "doi": "10.1093/carcin/bgt067", "pmid": "23436804", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "bgt067"}], "notes": [], "created": "2017-05-04T14:55:56.227Z", "modified": "2017-05-30T12:55:29.874Z"}, {"entity": "publication", "iuid": "f85ef18fd5854691a4f47be275d4168a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f85ef18fd5854691a4f47be275d4168a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f85ef18fd5854691a4f47be275d4168a"}}, "title": "Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides.", "authors": [{"family": "Ducani", "given": "Cosimo", "initials": "C"}, {"family": "Kaul", "given": "Corinna", "initials": "C"}, {"family": "Moche", "given": "Martin", "initials": "M"}, {"family": "Shih", "given": "William M", "initials": "WM"}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "10", "issn": "1548-7105", "issue": "7", "pages": "647-652", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": "Single-stranded oligonucleotides are important as research tools, as diagnostic probes, in gene therapy and in DNA nanotechnology. Oligonucleotides are typically produced via solid-phase synthesis, using polymer chemistries that are limited relative to what biological systems produce. The number of errors in synthetic DNA increases with oligonucleotide length, and the resulting diversity of sequences can be a problem. Here we present the 'monoclonal stoichiometric' (MOSIC) method for enzyme-mediated production of DNA oligonucleotides. We amplified oligonucleotides from clonal templates derived from single bacterial colonies and then digested cutter hairpins in the products, which released pools of oligonucleotides with precisely controlled relative stoichiometric ratios. We prepared 14-378-nucleotide MOSIC oligonucleotides either by in vitro rolling-circle amplification or by amplification of phagemid DNA in Escherichia coli. Analyses of the formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides.", "doi": "10.1038/nmeth.2503", "pmid": "23727986", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "nmeth.2503"}, {"db": "pmc", "key": "PMC3843646"}, {"db": "mid", "key": "NIHMS528250"}, {"db": "PDB", "key": "4B8D"}], "notes": [], "created": "2017-05-04T15:03:49.103Z", "modified": "2017-09-06T11:42:09.473Z"}, {"entity": "publication", "iuid": "5130693ce09f4fe0b874c25e95858efd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5130693ce09f4fe0b874c25e95858efd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5130693ce09f4fe0b874c25e95858efd"}}, "title": "Computational Prospecting for Drug\u2013Transporter Interactions", "authors": [{"family": "Matsson", "given": "P", "initials": "P"}, {"family": "Artursson", "given": "P", "initials": "P"}], "type": "journal-article", "published": "2013-07-00", "journal": {"volume": "94", "issn": "0009-9236", "issue": "1", "pages": "30-32", "title": "Clin Pharmacol Ther", "issn-l": null}, "abstract": null, "doi": "10.1038/clpt.2013.67", "pmid": "23588306", "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:15:40.775Z", "modified": "2025-10-17T13:04:30.334Z"}, {"entity": "publication", "iuid": "d351e65476b84c9bbdcebfac581eb1df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d351e65476b84c9bbdcebfac581eb1df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d351e65476b84c9bbdcebfac581eb1df"}}, "title": "Clinical depression, antidepressant use and risk of future cardiovascular disease.", "authors": [{"family": "Rahman", "given": "Iffat", "initials": "I"}, {"family": "Humphreys", "given": "Keith", "initials": "K"}, {"family": "Bennet", "given": "Anna Michaela", "initials": "AM"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Pedersen", "given": "Nancy Lee", "initials": "NL"}, {"family": "Magnusson", "given": "Patrik Karl Erik", "initials": "PK"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "28", "issn": "1573-7284", "issue": "7", "pages": "589-595", "title": "Eur. J. Epidemiol.", "issn-l": "0393-2990"}, "abstract": "Many studies have shown that depression contributes to a higher risk of developing cardiovascular disease (CVD). Use of antidepressants and its association with CVD development has also been investigated previously but the results have been conflicting. Further, depression and use of antidepressants have been more widely studied in relation to coronary heart disease rather than stroke. A population-based cohort study consisting of 36,654 Swedish elderly twins was conducted with a follow-up of maximum 4\u00a0years. Information on exposures, outcomes and covariates were collected from the Swedish national patient registers, the Swedish prescribed drug registry and the Swedish twin registry. Depression and antidepressant use were both associated with CVD development. The risk was most pronounced among depressed patients who did not use antidepressants (HR 1. 48, CI 1.10-2.00). When assessing the two main CVD outcomes coronary heart disease and ischemic stroke separately, the predominant association was found for ischemic stroke while it was absent for coronary heart disease. The association between depression and stroke also remained significant when restricting to depression diagnoses occurring at least 10\u00a0years before baseline. The study supports that depression is a possible risk factor for development of CVD. Moreover, the hazard rate for CVD outcomes was highest among depressed patients who had not used antidepressants. The association with clinical depression is more marked in relation to stroke and disappears in relation to development of coronary heart disease.", "doi": "10.1007/s10654-013-9821-z", "pmid": "23836399", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:53.117Z", "modified": "2020-01-21T13:56:05.395Z"}, {"entity": "publication", "iuid": "ec5addbe8a004dc9be3de2406c51efeb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec5addbe8a004dc9be3de2406c51efeb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec5addbe8a004dc9be3de2406c51efeb"}}, "title": "Cenani-Lenz syndrome restricted to limb and kidney anomalies associated with a novel LRP4 missense mutation.", "authors": [{"family": "Khan", "given": "Tahir Naeem", "initials": "TN"}, {"family": "Klar", "given": "J", "initials": "J"}, {"family": "Ali", "given": "Zafar", "initials": "Z"}, {"family": "Khan", "given": "F", "initials": "F"}, {"family": "Baig", "given": "S M", "initials": "SM"}, {"family": "Dahl", "given": "N", "initials": "N"}], "type": "case reports", "published": "2013-07-00", "journal": {"volume": "56", "issn": "1878-0849", "issue": "7", "pages": "371-374", "title": "Eur J Med Genet", "issn-l": "1769-7212"}, "abstract": "Cenani-Lenz syndrome (CLS) is a rare autosomal recessive developmental disorder of the limbs. The disorder is characterized by complete syndactyly with metacarpal fusions and/or oligodactyly sometimes accompanied by radioulnar synostosis. The clinical expression is variable and kidney agenesis/hypoplasia, craniofacial dysmorphism and teeth abnormalities are frequent features as well as lower limb involvement. CLS was recently associated with mutations in the low-density lipoprotein receptor-related protein 4 (LRP4) gene and dysregulated canonical WNT signaling. We have identified a large consanguineous Pakistani pedigree with 9 members affected by CLS. The affected individuals present with a consistent expression of the syndrome restricted to the limbs and kidneys. Symptoms from the lower limb are mild or absent and there were no radioulnar synostosis or craniofacial involvement. Genetic analysis using autozygosity mapping and sequencing revealed homozygosity for a novel missense mutation c.2858T\u00a0>\u00a0C (p.L953P) in the LRP4 gene. The mutation is located in a region encoding the highly conserved low-density lipoprotein receptor repeat class B domain of LRP4. Our findings add to the genotype-phenotype correlations in CLS and support kidney anomalies as a frequent associated feature.", "doi": "10.1016/j.ejmg.2013.04.007", "pmid": "23664847", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1769-7212(13)00091-8"}], "notes": [], "created": "2017-05-04T14:57:53.417Z", "modified": "2020-01-21T13:56:06.007Z"}, {"entity": "publication", "iuid": "b866fb216f3d4d56ae6d8df86a91b97d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b866fb216f3d4d56ae6d8df86a91b97d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b866fb216f3d4d56ae6d8df86a91b97d"}}, "title": "CDK-mediated activation of the SCF(FBXO) (28) ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer.", "authors": [{"family": "Cepeda", "given": "Diana", "initials": "D"}, {"family": "Ng", "given": "Hwee-Fang", "initials": "HF"}, {"family": "Sharifi", "given": "Hamid Reza", "initials": "HR"}, {"family": "Mahmoudi", "given": "Salah", "initials": "S"}, {"family": "Cerrato", "given": "Vanessa Soto", "initials": "VS"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "Magnusson", "given": "Kristina", "initials": "K"}, {"family": "Nilsson", "given": "Hel\u00e9n", "initials": "H"}, {"family": "Malyukova", "given": "Alena", "initials": "A"}, {"family": "Rantala", "given": "Juha", "initials": "J"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Vi\u00f1als", "given": "Francesc", "initials": "F"}, {"family": "Bhaskaran", "given": "Nimesh", "initials": "N"}, {"family": "Zakaria", "given": "Siti Mariam", "initials": "SM"}, {"family": "Rahmanto", "given": "Aldwin Suryo", "initials": "AS"}, {"family": "Grotegut", "given": "Stefan", "initials": "S"}, {"family": "Nielsen", "given": "Michael Lund", "initials": "ML"}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Sun", "given": "Dahui", "initials": "D"}, {"family": "Lerner", "given": "Mikael", "initials": "M"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Widschwendter", "given": "Martin", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Wohlschlegel", "given": "James", "initials": "J"}, {"family": "Grand\u00e9r", "given": "Dan", "initials": "D"}, {"family": "Spruck", "given": "Charles", "initials": "C"}, {"family": "Larsson", "given": "Lars-Gunnar", "initials": "LG"}, {"family": "Sangfelt", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "5", "issn": "1757-4684", "issue": "7", "pages": "1067-1086", "title": "EMBO Mol Med", "issn-l": "1757-4676"}, "abstract": "SCF (Skp1/Cul1/F-box) ubiquitin ligases act as master regulators of cellular homeostasis by targeting key proteins for ubiquitylation. Here, we identified a hitherto uncharacterized F-box protein, FBXO28 that controls MYC-dependent transcription by non-proteolytic ubiquitylation. SCF(FBXO28) activity and stability are regulated during the cell cycle by CDK1/2-mediated phosphorylation of FBXO28, which is required for its efficient ubiquitylation of MYC and downsteam enhancement of the MYC pathway. Depletion of FBXO28 or overexpression of an F-box mutant unable to support MYC ubiquitylation results in an impairment of MYC-driven transcription, transformation and tumourigenesis. Finally, in human breast cancer, high FBXO28 expression and phosphorylation are strong and independent predictors of poor outcome. In conclusion, our data suggest that SCF(FBXO28) plays an important role in transmitting CDK activity to MYC function during the cell cycle, emphasizing the CDK-FBXO28-MYC axis as a potential molecular drug target in MYC-driven cancers, including breast cancer.", "doi": "10.1002/emmm.201202341", "pmid": "23776131", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pmc", "key": "PMC3721474"}], "notes": [], "created": "2017-05-04T14:55:57.444Z", "modified": "2021-07-08T13:44:33.547Z"}, {"entity": "publication", "iuid": "053dcdf7a470487bbc007fafb09de734", "links": {"self": {"href": "https://publications.scilifelab.se/publication/053dcdf7a470487bbc007fafb09de734.json"}, "display": {"href": "https://publications.scilifelab.se/publication/053dcdf7a470487bbc007fafb09de734"}}, "title": "Active nitrogen-fixing heterotrophic bacteria at and below the chemocline of the central Baltic Sea.", "authors": [{"family": "Farnelid", "given": "Hanna", "initials": "H"}, {"family": "Bentzon-Tilia", "given": "Mikkel", "initials": "M"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Jost", "given": "G\u00fcnter", "initials": "G"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "7", "issn": "1751-7370", "issue": "7", "pages": "1413-1423", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "The Baltic Sea receives large nitrogen inputs by diazotrophic (N2-fixing) heterocystous cyanobacteria but the significance of heterotrophic N2 fixation has not been studied. Here, the diversity, abundance and transcription of the nifH fragment of the nitrogenase enzyme in two basins of the Baltic Sea proper was examined. N2 fixation was measured at the surface (5\u2009m) and in anoxic water (200\u2009m). Vertical sampling profiles of >10 and <10\u2009\u03bcm size fractions were collected in 2007, 2008 and 2011 at the Gotland Deep and in 2011 in the Bornholm Basin. Both of these stations are characterized by permanently anoxic bottom water. The 454-pyrosequencing nifH analysis revealed a diverse assemblage of nifH genes related to alpha-, beta- and gammaproteobacteria (nifH cluster I) and anaerobic bacteria (nifH cluster III) at and below the chemocline. Abundances of genes and transcripts of seven diazotrophic phylotypes were investigated using quantitative polymerase chain reaction revealing abundances of heterotrophic nifH phylotypes of up to 2.1 \u00d7 10(7) nifH copies\u2009l(-1). Abundant nifH transcripts (up to 3.2 \u00d7 10(4) transcripts\u2009l(-1)) within nifH cluster III and co-occurring N2 fixation (0.44\u00b10.26\u2009nmol\u2009l(-1)\u2009day(-1)) in deep water suggests that heterotrophic diazotrophs are fixing N2 in anoxic ammonium-rich waters. Our results reveal that N2 fixation in the Baltic Sea is not limited to illuminated N-deplete surface waters and suggest that N2 fixation could also be of importance in other suboxic regions of the world's oceans.", "doi": "10.1038/ismej.2013.26", "pmid": "23446833", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ismej201326"}, {"db": "pmc", "key": "PMC3695292"}], "notes": [], "created": "2017-05-04T14:57:59.082Z", "modified": "2020-01-21T13:56:00.584Z"}, {"entity": "publication", "iuid": "f38394d1b1e64917ac8938cf9d41eed4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f38394d1b1e64917ac8938cf9d41eed4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f38394d1b1e64917ac8938cf9d41eed4"}}, "title": "Unbiased approach for virus detection in skin lesions.", "authors": [{"family": "Bzhalava", "given": "Davit", "initials": "D"}, {"family": "Johansson", "given": "Hanna", "initials": "H"}, {"family": "Ekstr\u00f6m", "given": "Johanna", "initials": "J"}, {"family": "Faust", "given": "Helena", "initials": "H"}, {"family": "M\u00f6ller", "given": "Birgitta", "initials": "B"}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Nordin", "given": "Peter", "initials": "P"}, {"family": "Stenquist", "given": "Bo", "initials": "B"}, {"family": "Paoli", "given": "John", "initials": "J"}, {"family": "Persson", "given": "Bengt", "initials": "B"}, {"family": "Forslund", "given": "Ola", "initials": "O"}, {"family": "Dillner", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2013-06-28", "journal": {"volume": "8", "issn": "1932-6203", "issue": "6", "pages": "e65953", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "To assess presence of virus DNA in skin lesions, swab samples from 82 squamous cell carcinomas of the skin (SCCs), 60 actinic keratoses (AKs), paraffin-embedded biopsies from 28 SCCs and 72 kerathoacanthomas (KAs) and fresh-frozen biopsies from 92 KAs, 85 SCCs and 92 AKs were analyzed by high throughput sequencing (HTS) using 454 or Ion Torrent technology. We found total of 4,284 viral reads, out of which 4,168 were Human Papillomavirus (HPV)-related, belonging to 15 known (HPV8, HPV12, HPV20, HPV36, HPV38, HPV45, HPV57, HPV59, HPV104, HPV105, HPV107, HPV109, HPV124, HPV138, HPV147), four previously described putative (HPV 915 F 06 007 FD1, FA73, FA101, SE42) and two putatively new HPV types (SE46, SE47). SE42 was cloned, sequenced, designated as HPV155 and found to have 76% similarity to the most closely related known HPV type. In conclusion, an unbiased approach for viral DNA detection in skin tumors has found that, although some new putative HPVs were found, known HPV types constituted most of the viral DNA.", "doi": "10.1371/journal.pone.0065953", "pmid": "23840382", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-36687"}, {"db": "pmc", "key": "PMC3696016"}], "notes": [], "created": "2017-05-04T14:58:13.736Z", "modified": "2020-01-21T13:56:06.295Z"}, {"entity": "publication", "iuid": "8c27147b1b3644bcae3ec3efca1a153c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c27147b1b3644bcae3ec3efca1a153c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c27147b1b3644bcae3ec3efca1a153c"}}, "title": "Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan.", "authors": [{"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2013-06-27", "journal": {"volume": "8", "issn": "1932-6203", "issue": "6", "pages": "e67378", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "DNA methylation plays an important role in development of disease and the process of aging. In this study we examine DNA methylation at 476,366 sites throughout the genome of white blood cells from a population cohort (N\u200a=\u200a421) ranging in age from 14 to 94 years old. Age affects DNA methylation at almost one third (29%) of the sites (Bonferroni adjusted P-value <0.05), of which 60.5% becomes hypomethylated and 39.5% hypermethylated with increasing age. DNA methylation sites that are located within CpG islands (CGIs) more often become hypermethylated compared to sites outside an island. CpG sites in promoters are more unaffected by age, whereas sites in enhancers more often becomes hypo- or hypermethylated. Hypermethylated sites are overrepresented among genes that are involved in DNA binding, transcription regulation, processes of anatomical structure and developmental process and cortex neuron differentiation (P-value down to P\u200a=\u200a9.14*10(-67)). By contrast, hypomethylated sites are not strongly overrepresented among any biological function or process. Our results indicate that the 23% of the variation in DNA methylation is attributed chronological age, and that hypermethylation is more site-specific than hypomethylation. It appears that the change in DNA methylation partly overlap with regions that change histone modifications with age, indicating an interaction between the two major epigenetic mechanisms. Epigenetic modifications and change in gene expression over time most likely reflects the natural process of aging and variation between individuals might contribute to the development of age-related phenotypes and diseases such as type II diabetes, autoimmune and cardiovascular disease.", "doi": "10.1371/journal.pone.0067378", "pmid": "23826282", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-02458"}, {"db": "pmc", "key": "PMC3695075"}], "notes": [], "created": "2017-05-04T14:58:15.857Z", "modified": "2020-01-21T13:56:09.007Z"}, {"entity": "publication", "iuid": "be5f0d8555da45f9b6061300e0ee83a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be5f0d8555da45f9b6061300e0ee83a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be5f0d8555da45f9b6061300e0ee83a0"}}, "title": "Constrained H-Phe-Phe-NH2 analogues with high affinity to the substance P 1-7 binding site and with improved metabolic stability and cell permeability.", "authors": [{"family": "Fransson", "given": "Rebecca", "initials": "R"}, {"family": "Sk\u00f6ld", "given": "Christian", "initials": "C"}, {"family": "Kratz", "given": "Jadel M", "initials": "JM"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Nyberg", "given": "Fred", "initials": "F"}, {"family": "Hallberg", "given": "Mathias", "initials": "M"}, {"family": "Sandstr\u00f6m", "given": "Anja", "initials": "A"}], "type": "journal article", "published": "2013-06-27", "journal": {"volume": "56", "issn": "1520-4804", "issue": "12", "pages": "4953-4965", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": "We recently reported the discovery of H-Phe-Phe-NH2 as a small and high affinity ligand for the substance P 1-7 (SP(1-7), H-Arg-Pro-Lys-Pro-Gln-Gln-Phe-OH) specific binding site and its intriguing ability to reduce neuropathic pain. With the overall aim to develop stable and orally bioavailable SP(1-7) mimetics, the dipeptide was chosen as a lead compound. Herein the structure-activity relationship (SAR) of a set of modified H-Phe-Phe-NH2 analogues is presented together with their potential active uptake by PEPT1 transporter, intestinal permeability, and metabolic stability. Local constraints via peptide backbone methylation or preparation of cyclized analogues based on pyrrolidine were evaluated and were shown to significantly improve the in vitro pharmacokinetic properties. The SAR was rationalized by deriving a plausible binding pose for the high affinity ligands. Rigidification using a 3-phenylpyrrolidine moiety in the C-terminal of H-Phe-Phe-NH2 resulted in high affinity and improved intrinsic clearance and intestinal epithelial permeability.", "doi": "10.1021/jm400209h", "pmid": "23735006", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": "Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)\r\nADME of Therapeutics (UDOPP)", "created": "2017-05-04T14:56:47.101Z", "modified": "2025-10-17T13:04:30.362Z"}, {"entity": "publication", "iuid": "c10e9ac0ad744d8a8b53ceb56e53a0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c10e9ac0ad744d8a8b53ceb56e53a0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c10e9ac0ad744d8a8b53ceb56e53a0e5"}}, "title": "The crystal structure of the lumenal domain of Erv41p, a protein involved in transport between the endoplasmic reticulum and Golgi apparatus.", "authors": [{"family": "Biterova", "given": "Ekaterina I", "initials": "EI"}, {"family": "Sv\u00e4rd", "given": "Maria", "initials": "M"}, {"family": "Possner", "given": "Dominik D D", "initials": "DD"}, {"family": "Guy", "given": "Jodie E", "initials": "JE"}], "type": "journal article", "published": "2013-06-26", "journal": {"volume": "425", "issn": "1089-8638", "issue": "12", "pages": "2208-2218", "title": "J. Mol. Biol.", "issn-l": "0022-2836"}, "abstract": "Erv41p is a conserved integral membrane protein that is known to play a role in transport between the endoplasmic reticulum and Golgi apparatus, part of the early secretory pathway of eukaryotes. However, the exact function of the protein is not known, and it shares very low sequence identity with proteins of known structure or function. Here we present the structure of the full lumenal domain of Erv41p from Saccharomyces cerevisiae, determined by X-ray crystallography to a resolution of 2.0\u00c5. The structure reveals the protein to be composed predominantly of two large \u03b2-sheets that form a twisted \u03b2-sandwich. Comparison to structures in the Protein Data Bank shows that the Erv41p lumenal domain displays only limited similarity to \u03b2-sandwich domains of other proteins. Analysis of the surface properties of the protein identifies an extensive patch of negative electrostatic potential on the exposed surface of one of the \u03b2-sheets, which likely forms a binding site for a ligand or interaction partner. A predominantly hydrophobic region close to the membrane interface is identified as a likely site for protein-protein interaction. This structure, the first of Erv41p or any of its homologues, provides a new starting point for studies of the roles of Erv41p and its interaction partners in the eukaryotic secretory pathway.", "doi": "10.1016/j.jmb.2013.03.024", "pmid": "23524136", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "S0022-2836(13)00173-3"}, {"db": "PDB", "key": "3ZLC"}], "notes": [], "created": "2017-05-04T15:03:48.202Z", "modified": "2017-09-06T11:42:09.289Z"}, {"entity": "publication", "iuid": "c2744079070a474986d37354abb62585", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2744079070a474986d37354abb62585.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2744079070a474986d37354abb62585"}}, "title": "The role of adiposity in cardiometabolic traits: a Mendelian randomization analysis.", "authors": [{"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Ploner", "given": "Alexander", "initials": "A"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Horikoshi", "given": "Momoko", "initials": "M"}, {"family": "Sarin", "given": "Antti-Pekka", "initials": "A"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Kals", "given": "Mart", "initials": "M"}, {"family": "Kuningas", "given": "Maris", "initials": "M"}, {"family": "Draisma", "given": "Harmen H M", "initials": "HHM"}, {"family": "Ried", "given": "Janina S", "initials": "JS"}, {"family": "van Zuydam", "given": "Natalie R", "initials": "NR"}, {"family": "Huikari", "given": "Ville", "initials": "V"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Sonestedt", "given": "Emily", "initials": "E"}, {"family": "Benyamin", "given": "Beben", "initials": "B"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Rivera", "given": "Natalia V", "initials": "NV"}, {"family": "Kristiansson", "given": "Kati", "initials": "K"}, {"family": "Shen", "given": "Huei-Yi", "initials": "H"}, {"family": "Havulinna", "given": "Aki S", "initials": "AS"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Donnelly", "given": "Louise A", "initials": "LA"}, {"family": "Kaakinen", "given": "Marika", "initials": "M"}, {"family": "Nuotio", "given": "Marja-Liisa", "initials": "M"}, {"family": "Robertson", "given": "Neil", "initials": "N"}, {"family": "de Bruijn", "given": "Ren\u00e9e F A G", "initials": "RFAG"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Balmforth", "given": "Anthony J", "initials": "AJ"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Doney", "given": "Alexander S F", "initials": "ASF"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Gretarsdottir", "given": "Solveig", "initials": "S"}, {"family": "Hartikainen", "given": "Anna-Liisa", "initials": "A"}, {"family": "Heikkil\u00e4", "given": "Kauko", "initials": "K"}, {"family": "Herzig", "given": "Karl-Heinz", "initials": "K"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "Karssen", "given": "Lennart C", "initials": "LC"}, {"family": "Kettunen", "given": "Johannes", "initials": "J"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Kuulasmaa", "given": "Kari", "initials": "K"}, {"family": "Laatikainen", "given": "Tiina", "initials": "T"}, {"family": "Laitinen", "given": "Jaana", "initials": "J"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "L\u00e4\u00e4r\u00e4", "given": "Esa", "initials": "E"}, {"family": "Rayner", "given": "Nigel W", "initials": "NW"}, {"family": "M\u00e4nnist\u00f6", "given": "Satu", "initials": "S"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Rathmann", "given": "Wolfgang", "initials": "W"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Ruokonen", "given": "Aimo", "initials": "A"}, {"family": "Savolainen", "given": "Markku J", "initials": "MJ"}, {"family": "Sijbrands", "given": "Eric J G", "initials": "EJG"}, {"family": "Small", "given": "Kerrin S", "initials": "KS"}, {"family": "Smit", "given": "Jan H", "initials": "JH"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Taanila", "given": "Anja", "initials": "A"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Witteman", "given": "Jacqueline", "initials": "J"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Evans", "given": "Alun", "initials": "A"}, {"family": "Ferri\u00e8res", "given": "Jean", "initials": "J"}, {"family": "Virtamo", "given": "Jarmo", "initials": "J"}, {"family": "Kee", "given": "Frank", "initials": "F"}, {"family": "Tregouet", "given": "David-Alexandre", "initials": "D"}, {"family": "Arveiler", "given": "Dominique", "initials": "D"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Ferrario", "given": "Marco M", "initials": "MM"}, {"family": "Brambilla", "given": "Paolo", "initials": "P"}, {"family": "Hall", "given": "Alistair S", "initials": "AS"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Madden", "given": "Pamela A F", "initials": "PAF"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Knekt", "given": "Paul", "initials": "P"}, {"family": "Oostra", "given": "Ben", "initials": "B"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Wichmann", "given": "H Erich", "initials": "HE"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Tuomi", "given": "TiinaMaija", "initials": "T"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "Hammond", "given": "Christopher J", "initials": "CJ"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Palmer", "given": "Colin Neil Alexander", "initials": "CNA"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Vartiainen", "given": "Erkki", "initials": "E"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "European Network for Genetic and Genomic Epidemiology (ENGAGE) consortium", "given": "None", "initials": "N"}], "type": "journal article", "published": "2013-06-25", "journal": {"volume": "10", "issn": "1549-1676", "issue": "6", "pages": "e1001474", "title": "PLoS Med.", "issn-l": "1549-1277"}, "abstract": "The association between adiposity and cardiometabolic traits is well known from epidemiological studies. Whilst the causal relationship is clear for some of these traits, for others it is not. We aimed to determine whether adiposity is causally related to various cardiometabolic traits using the Mendelian randomization approach.\r\n\r\nWe used the adiposity-associated variant rs9939609 at the FTO locus as an instrumental variable (IV) for body mass index (BMI) in a Mendelian randomization design. Thirty-six population-based studies of individuals of European descent contributed to the analyses. Age- and sex-adjusted regression models were fitted to test for association between (i) rs9939609 and BMI (n\u200a =\u200a 198,502), (ii) rs9939609 and 24 traits, and (iii) BMI and 24 traits. The causal effect of BMI on the outcome measures was quantified by IV estimators. The estimators were compared to the BMI-trait associations derived from the same individuals. In the IV analysis, we demonstrated novel evidence for a causal relationship between adiposity and incident heart failure (hazard ratio, 1.19 per BMI-unit increase; 95% CI, 1.03-1.39) and replicated earlier reports of a causal association with type 2 diabetes, metabolic syndrome, dyslipidemia, and hypertension (odds ratio for IV estimator, 1.1-1.4; all p < 0.05). For quantitative traits, our results provide novel evidence for a causal effect of adiposity on the liver enzymes alanine aminotransferase and gamma-glutamyl transferase and confirm previous reports of a causal effect of adiposity on systolic and diastolic blood pressure, fasting insulin, 2-h post-load glucose from the oral glucose tolerance test, C-reactive protein, triglycerides, and high-density lipoprotein cholesterol levels (all p < 0.05). The estimated causal effects were in agreement with traditional observational measures in all instances except for type 2 diabetes, where the causal estimate was larger than the observational estimate (p\u200a = \u200a0.001).\r\n\r\nWe provide novel evidence for a causal relationship between adiposity and heart failure as well as between adiposity and increased liver enzymes.", "doi": "10.1371/journal.pmed.1001474", "pmid": "23824655", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PMEDICINE-D-12-03573"}, {"db": "pmc", "key": "PMC3692470"}], "notes": [], "created": "2017-05-04T14:58:13.038Z", "modified": "2021-07-07T15:11:02.201Z"}, {"entity": "publication", "iuid": "ef809a1996704838a59705082f7f5b37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef809a1996704838a59705082f7f5b37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef809a1996704838a59705082f7f5b37"}}, "title": "Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data.", "authors": [{"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Dahl\u00f6", "given": "Martin", "initials": "M"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Hagberg", "given": "Jonas", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2013-06-25", "journal": {"volume": "2", "issn": "2047-217X", "issue": "1", "pages": "9", "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": ": Analyzing and storing data and results from next-generation sequencing (NGS) experiments is a challenging task, hampered by ever-increasing data volumes and frequent updates of analysis methods and tools. Storage and computation have grown beyond the capacity of personal computers and there is a need for suitable e-infrastructures for processing. Here we describe UPPNEX, an implementation of such an infrastructure, tailored to the needs of data storage and analysis of NGS data in Sweden serving various labs and multiple instruments from the major sequencing technology platforms. UPPNEX comprises resources for high-performance computing, large-scale and high-availability storage, an extensive bioinformatics software suite, up-to-date reference genomes and annotations, a support function with system and application experts as well as a web portal and support ticket system. UPPNEX applications are numerous and diverse, and include whole genome-, de novo- and exome sequencing, targeted resequencing, SNP discovery, RNASeq, and methylation analysis. There are over 300 projects that utilize UPPNEX and include large undertakings such as the sequencing of the flycatcher and Norwegian spruce. We describe the strategic decisions made when investing in hardware, setting up maintenance and support, allocating resources, and illustrate major challenges such as managing data growth. We conclude with summarizing our experiences and observations with UPPNEX to date, providing insights into the successful and less successful decisions made.", "doi": "10.1186/2047-217X-2-9", "pmid": "23800020", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "2047-217X-2-9"}, {"db": "pmc", "key": "PMC3704847"}], "notes": [], "created": "2017-05-04T14:56:23.957Z", "modified": "2020-01-21T13:53:20.946Z"}, {"entity": "publication", "iuid": "7ef6e8359a244573a60a04db1afe077c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7ef6e8359a244573a60a04db1afe077c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7ef6e8359a244573a60a04db1afe077c"}}, "title": "Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates.", "authors": [{"family": "Chen", "given": "Ming Wei", "initials": "MW"}, {"family": "Lohkamp", "given": "Bernhard", "initials": "B"}, {"family": "Schnell", "given": "Robert", "initials": "R"}, {"family": "Lescar", "given": "Julien", "initials": "J"}, {"family": "Schneider", "given": "Gunter", "initials": "G"}], "type": "journal article", "published": "2013-06-21", "journal": {"volume": "8", "issn": "1932-6203", "issue": "6", "pages": "e66936", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Biosynthesis of UDP-N-acetylmuramic acid in bacteria is a committed step towards peptidoglycan production. In an NADPH- and FAD-dependent reaction, the UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) reduces UDP-N-acetylglucosamine-enolpyruvate to UDP-N-acetylmuramic acid. We determined the three-dimensional structures of the ternary complex of Pseudomonas aeruginosa MurB with FAD and NADP(+) in two crystal forms to resolutions of 2.2 and 2.1 \u00c5, respectively, to investigate the structural basis of the first half-reaction, hydride transfer from NADPH to FAD. The nicotinamide ring of NADP(+) stacks against the si face of the isoalloxazine ring of FAD, suggesting an unusual mode of hydride transfer to flavin. Comparison with the structure of the Escherichia coli MurB complex with UDP-N-acetylglucosamine-enolpyruvate shows that both substrates share the binding site located between two lobes of the substrate-binding domain III, consistent with a ping pong mechanism with sequential substrate binding. The nicotinamide and the enolpyruvyl moieties are strikingly well-aligned upon superimposition, both positioned for hydride transfer to and from FAD. However, flexibility of the substrate channel allows the non-reactive parts of the two substrates to bind in different conformations. A potassium ion in the active site may assist in substrate orientation and binding. These structural models should help in structure-aided drug design against MurB, which is essential for cell wall biogenesis and hence bacterial survival.", "doi": "10.1371/journal.pone.0066936", "pmid": "23805286", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-09972"}, {"db": "pmc", "key": "PMC3689657"}], "notes": [], "created": "2017-05-04T15:03:50.562Z", "modified": "2017-09-06T11:42:09.172Z"}, {"entity": "publication", "iuid": "eccffea99fad46728185a5e961c32f32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eccffea99fad46728185a5e961c32f32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eccffea99fad46728185a5e961c32f32"}}, "title": "GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.", "authors": [{"family": "Rietveld", "given": "Cornelius A", "initials": "CA"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Derringer", "given": "Jaime", "initials": "J"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Martin", "given": "Nicolas W", "initials": "NW"}, {"family": "Westra", "given": "Harm-Jan", "initials": "H"}, {"family": "Shakhbazov", "given": "Konstantin", "initials": "K"}, {"family": "Abdellaoui", "given": "Abdel", "initials": "A"}, {"family": "Agrawal", "given": "Arpana", "initials": "A"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Alizadeh", "given": "Behrooz Z", "initials": "BZ"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Barnard", "given": "John", "initials": "J"}, {"family": "Baumeister", "given": "Sebastian E", "initials": "SE"}, {"family": "Benke", "given": "Kelly S", "initials": "KS"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Boatman", "given": "Jeffrey A", "initials": "JA"}, {"family": "Boyle", "given": "Patricia A", "initials": "PA"}, {"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "de Leeuw", "given": "Christiaan", "initials": "C"}, {"family": "Eklund", "given": "Niina", "initials": "N"}, {"family": "Evans", "given": "Daniel S", "initials": "DS"}, {"family": "Ferhmann", "given": "Rudolf", "initials": "R"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Gjessing", "given": "H\u00e5kon K", "initials": "HK"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Harris", "given": "Jennifer R", "initials": "JR"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Holzapfel", "given": "Christina", "initials": "C"}, {"family": "Ibrahim-Verbaas", "given": "Carla A", "initials": "CA"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Jacobsson", "given": "Bo", "initials": "B"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Jugessur", "given": "Astanand", "initials": "A"}, {"family": "Kaakinen", "given": "Marika", "initials": "M"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Karjalainen", "given": "Juha", "initials": "J"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Kristiansson", "given": "Kati", "initials": "K"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Lee", "given": "Sang H", "initials": "SH"}, {"family": "Lin", "given": "Peng", "initials": "P"}, {"family": "Lind", "given": "Penelope A", "initials": "PA"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Lohman", "given": "Kurt", "initials": "K"}, {"family": "Loitfelder", "given": "Marisa", "initials": "M"}, {"family": "McMahon", "given": "George", "initials": "G"}, {"family": "Vidal", "given": "Pedro Marques", "initials": "PM"}, {"family": "Meirelles", "given": "Osorio", "initials": "O"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Myhre", "given": "Ronny", "initials": "R"}, {"family": "Nuotio", "given": "Marja-Liisa", "initials": "M"}, {"family": "Oldmeadow", "given": "Christopher J", "initials": "CJ"}, {"family": "Petrovic", "given": "Katja E", "initials": "KE"}, {"family": "Peyrot", "given": "Wouter J", "initials": "WJ"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Quaye", "given": "Lydia", "initials": "L"}, {"family": "Reinmaa", "given": "Eva", "initials": "E"}, {"family": "Rice", "given": "John P", "initials": "JP"}, {"family": "Rizzi", "given": "Thais S", "initials": "TS"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Terracciano", "given": "Antonio", "initials": "A"}, {"family": "van der Loos", "given": "Matthijs J H M", "initials": "MJHM"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wellmann", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Yu", "given": "Lei", "initials": "L"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Allik", "given": "J\u00fcri", "initials": "J"}, {"family": "Attia", "given": "John R", "initials": "JR"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Bastardot", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Beauchamp", "given": "Jonathan", "initials": "J"}, {"family": "Bennett", "given": "David A", "initials": "DA"}, {"family": "Berger", "given": "Klaus", "initials": "K"}, {"family": "Bierut", "given": "Laura J", "initials": "LJ"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "B\u00fcltmann", "given": "Ute", "initials": "U"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Chabris", "given": "Christopher F", "initials": "CF"}, {"family": "Cherkas", "given": "Lynn", "initials": "L"}, {"family": "Chung", "given": "Mina K", "initials": "MK"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "de Andrade", "given": "Mariza", "initials": "M"}, {"family": "De Jager", "given": "Philip L", "initials": "PL"}, {"family": "De Neve", "given": "Jan-Emmanuel", "initials": "J"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Dimitriou", "given": "Maria", "initials": "M"}, {"family": "Eir\u00edksd\u00f3ttir", "given": "Gu\u00f0ny", "initials": "G"}, {"family": "Elderson", "given": "Martin F", "initials": "MF"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Evans", "given": "David M", "initials": "DM"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Garcia", "given": "Melissa E", "initials": "ME"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Gu\u00f0nason", "given": "Vilmundur", "initials": "V"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Harris", "given": "Juliette M", "initials": "JM"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hastie", "given": "Nicholas D", "initials": "ND"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Hernandez", "given": "Dena G", "initials": "DG"}, {"family": "Hoffmann", "given": "Wolfgang", "initials": "W"}, {"family": "Hofman", "given": "Adriaan", "initials": "A"}, {"family": "Holle", "given": "Rolf", "initials": "R"}, {"family": "Holliday", "given": "Elizabeth G", "initials": "EG"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "J"}, {"family": "Iacono", "given": "William G", "initials": "WG"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Kirkpatrick", "given": "Robert M", "initials": "RM"}, {"family": "Kowgier", "given": "Matthew", "initials": "M"}, {"family": "Latvala", "given": "Antti", "initials": "A"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Lawlor", "given": "Debbie A", "initials": "DA"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Li", "given": "Jingmei", "initials": "J"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Lichtner", "given": "Peter", "initials": "P"}, {"family": "Liewald", "given": "David C", "initials": "DC"}, {"family": "Madden", "given": "Pamela A", "initials": "PA"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "M\u00e4kinen", "given": "Tomi E", "initials": "TE"}, {"family": "Masala", "given": "Marco", "initials": "M"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Mielck", "given": "Andreas", "initials": "A"}, {"family": "Miller", "given": "Michael B", "initials": "MB"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Mukherjee", "given": "Sutapa", "initials": "S"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Preisig", "given": "Martin", "initials": "M"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Realo", "given": "Anu", "initials": "A"}, {"family": "Ring", "given": "Susan M", "initials": "SM"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Rustichini", "given": "Aldo", "initials": "A"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Sarin", "given": "Antti-Pekka", "initials": "A"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Scott", "given": "Rodney J", "initials": "RJ"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "St Pourcain", "given": "Beate", "initials": "B"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Sul", "given": "Jae Hoon", "initials": "JH"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Svento", "given": "Rauli", "initials": "R"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "LifeLines Cohort Study", "given": "None", "initials": "N"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "van Rooij", "given": "Frank J A", "initials": "FJA"}, {"family": "Van Wagoner", "given": "David R", "initials": "DR"}, {"family": "Vartiainen", "given": "Erkki", "initials": "E"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Vonk", "given": "Judith M", "initials": "JM"}, {"family": "Waeber", "given": "G\u00e9rard", "initials": "G"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Wichmann", "given": "H-Erich", "initials": "H"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Conley", "given": "Dalton", "initials": "D"}, {"family": "Davey-Smith", "given": "George", "initials": "G"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Groenen", "given": "Patrick J F", "initials": "PJF"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Johannesson", "given": "Magnus", "initials": "M"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Krueger", "given": "Robert F", "initials": "RF"}, {"family": "Laibson", "given": "David", "initials": "D"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Meyer", "given": "Michelle N", "initials": "MN"}, {"family": "Posthuma", "given": "Danielle", "initials": "D"}, {"family": "Thurik", "given": "A Roy", "initials": "AR"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Benjamin", "given": "Daniel J", "initials": "DJ"}, {"family": "Cesarini", "given": "David", "initials": "D"}, {"family": "Koellinger", "given": "Philipp D", "initials": "PD"}], "type": "journal article", "published": "2013-06-21", "journal": {"volume": "340", "issn": "1095-9203", "issue": "6139", "pages": "1467-1471", "title": "Science", "issn-l": "0036-8075"}, "abstract": "A genome-wide association study (GWAS) of educational attainment was conducted in a discovery sample of 101,069 individuals and a replication sample of 25,490. Three independent single-nucleotide polymorphisms (SNPs) are genome-wide significant (rs9320913, rs11584700, rs4851266), and all three replicate. Estimated effects sizes are small (coefficient of determination R(2) \u2248 0.02%), approximately 1 month of schooling per allele. A linear polygenic score from all measured SNPs accounts for \u22482% of the variance in both educational attainment and cognitive function. Genes in the region of the loci have previously been associated with health, cognitive, and central nervous system phenotypes, and bioinformatics analyses suggest the involvement of the anterior caudate nucleus. These findings provide promising candidate SNPs for follow-up work, and our effect size estimates can anchor power analyses in social-science genetics.", "doi": "10.1126/science.1235488", "pmid": "23722424", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "science.1235488"}, {"db": "pmc", "key": "PMC3751588"}, {"db": "mid", "key": "NIHMS495960"}], "notes": [], "created": "2017-05-04T14:58:18.626Z", "modified": "2020-01-21T13:56:08.612Z"}, {"entity": "publication", "iuid": "bbbb90a3332e4601827c71c44bfacee9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbbb90a3332e4601827c71c44bfacee9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbbb90a3332e4601827c71c44bfacee9"}}, "title": "Vandetanib combined with a p38 MAPK inhibitor synergistically reduces glioblastoma cell survival.", "authors": [{"family": "Sooman", "given": "Linda", "initials": "L"}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Tsakonas", "given": "Georgios", "initials": "G"}, {"family": "Johansson", "given": "Fredrik", "initials": "F"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Jaiswal", "given": "Archita", "initials": "A"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Alafuzoff", "given": "Irina", "initials": "I"}, {"family": "Popova", "given": "Svetlana", "initials": "S"}, {"family": "Blomquist", "given": "Erik", "initials": "E"}, {"family": "Ekman", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2013-06-20", "journal": {"volume": "30", "issn": "1559-131X", "issue": "3", "pages": "638", "title": "Med. Oncol.", "issn-l": "1357-0560"}, "abstract": "The survival for patients with high-grade glioma is poor, and only a limited number of patients respond to the therapy. The aim of this study was to analyze the significance of using p38 MAPK phosphorylation as a prognostic marker in high-grade glioma patients and as a therapeutic target in combination chemotherapy with vandetanib. p38 MAPK phosphorylation was analyzed with immunohistochemistry in 90 high-grade glioma patients. Correlation between p38 MAPK phosphorylation and overall survival was analyzed with Mann-Whitney U test analysis. The effects on survival of glioblastoma cells of combining vandetanib with the p38 MAPK inhibitor SB 203580 were analyzed in vitro with the median-effect method with the fluorometric microculture cytotoxicity assay. Two patients had phosphorylated p38 MAPK in both the cytoplasm and nucleus, and these two presented with worse survival than patients with no detectable p38 MAPK phosphorylation or phosphorylated p38 MAPK only in the nucleus. This was true for both high-grade glioma patients (WHO grade III and IV, n = 90, difference in median survival: 6.1 months, 95 % CI [0.20, 23], p = 0.039) and for the subgroup with glioblastoma patients (WHO grade IV, n = 70, difference in median survival: 6.1 months, 95 % CI [0.066, 23], p = 0.043). The combination of vandetanib and the p38 MAPK inhibitor SB 203580 had synergistic effects on cell survival for glioblastoma-derived cells in vitro. In conclusion, p38 MAPK phosphorylation may be a prognostic marker for high-grade glioma patients, and vandetanib combined with a p38 MAPK inhibitor may be useful combination chemotherapy for glioma patients.", "doi": "10.1007/s12032-013-0638-0", "pmid": "23783486", "labels": {"Tissue Profiling": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:00.970Z", "modified": "2020-01-21T13:53:20.826Z"}, {"entity": "publication", "iuid": "1b4fd9ae526a4deeb6366d4755d572a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b4fd9ae526a4deeb6366d4755d572a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b4fd9ae526a4deeb6366d4755d572a1"}}, "title": "Behavioural and Brain Gene Expression Profiling in Pigs during Tail Biting Outbreaks - Evidence of a Tail Biting Resistant Phenotype.", "authors": [{"family": "Brunberg", "given": "Emma", "initials": "E"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Keeling", "given": "Linda J", "initials": "LJ"}], "type": "journal article", "published": "2013-06-18", "journal": {"volume": "8", "issn": "1932-6203", "issue": "6", "pages": "e66513", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Abnormal tail biting behaviour is a major welfare problem for pigs receiving the behaviour, as well as an indication of decreased welfare in the pigs performing it. However, not all pigs in a pen perform or receive tail biting behaviour and it has recently been shown that these 'neutral' pigs not only differ in their behaviour, but also in their gene expression compared to performers and receivers of tail biting in the same pen. To investigate whether this difference was linked to the cause or a consequence of them not being involved in the outbreak of tail biting, behaviour and brain gene expression was compared with 'control' pigs housed in pens with no tail biting. It was shown that the pigs housed in control pens performed a wider variety of pig-directed abnormal behaviour (belly nosing 0.95\u00b11.59, tail in mouth 0.31\u00b10.60 and 'other' abnormal 1.53\u00b14.26; mean\u00b1S.D) compared to the neutral pigs (belly nosing 0.30\u00b10.62, tail in mouth 0.13\u00b10.50 and \"other\" abnormal 0.42\u00b11.06). With Affymetrix gene expression arrays, 107 transcripts were identified as differently expressed (p<0.05) between these two categories of pigs. Several of these transcripts had already been shown to be differently expressed in the neutral pigs when they were compared to performers and receivers of tail biting in the same pen in an earlier study. Hence, the different expression of these genes cannot be a consequence of the neutral pigs not being involved in tail biting behaviour, but rather linked to the cause contributing to why they were not involved in tail biting interactions. These neutral pigs seem to have a genetic and behavioural profile that somehow contributes to them being resistant to performing or receiving pig-directed abnormal behaviour, such as tail biting, even when housed in an environment that elicits that behaviour in other pigs.", "doi": "10.1371/journal.pone.0066513", "pmid": "23824700", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-16862"}, {"db": "pmc", "key": "PMC3688911"}], "notes": [], "created": "2017-05-04T15:03:02.113Z", "modified": "2017-05-30T14:50:01.676Z"}, {"entity": "publication", "iuid": "0fe1e59a92db484ead8642f49cef0d4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0fe1e59a92db484ead8642f49cef0d4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0fe1e59a92db484ead8642f49cef0d4b"}}, "title": "Stable isotope labeling methods in protein profiling.", "authors": [{"family": "Lengqvist", "given": "Johan", "initials": "J"}, {"family": "Sandberg", "given": "AnnSofi", "initials": "A"}], "type": "journal article", "published": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "21-51", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Mass spectrometry (MS) analysis of peptides and proteins has evolved dramatically over the last 20 years. Improvement of MS instrumentation, computational data analysis, and the availability of complete sequence databases for many species have made large-scale proteomics analyses possible. The measurement of global protein abundance by quantitative mass spectrometry has the potential to increase both speed and impact of biological and clinical research. However, to be able to detect and identify potential biomarkers, reproducible and accurate quantification is essential. The following chapter describes how to perform quantitative protein profiling using stable isotope labeling methods. Throughout, there is a focus on guidance in selection of an appropriate labeling strategy. With that in mind, we have included a section on acquisition and understanding of the liquid chromatography-mass spectrometry (LC-MS) data format. Further, we describe the different stable isotope labeling methods and their pros and cons. We start by giving an overview of the overall quantitative proteomics workflow in which extracting relevant biological information from the acquired data is the ultimate goal.", "doi": "10.1007/978-1-4614-7209-4_3", "pmid": "23765618", "labels": {"Clinical Proteomics Mass spectrometry": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:23.801Z", "modified": "2023-06-19T12:55:00.440Z"}, {"entity": "publication", "iuid": "2e42e8d0491849e18636a9542a65ef10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e42e8d0491849e18636a9542a65ef10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e42e8d0491849e18636a9542a65ef10"}}, "title": "Protein quantification by peptide quality control (PQPQ) of shotgun proteomics data.", "authors": [{"family": "Forshed", "given": "Jenny", "initials": "J"}], "type": "journal article", "published": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "149-158", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "This chapter describes how to improve quantitative accuracy and precision in shotgun proteomics by PQPQ (protein quantification by peptide quality control). The method is based on the assumption that the quantitative pattern of peptides derived from one protein will correlate over several samples. Dissonant patterns are assumed to arise either from mismatched peptides or due to the presence of different protein species. PQPQ identifies and excludes outliers and detects the existence of different protein species by correlation analysis. Alternative protein species can then be quantified separately. PQPQ can handle shotgun proteomics data from several MS instruments, data from different kinds of labeling, and label-free data. We have previously shown that data processing by PQPQ improves the information output from shotgun proteomics by validating the algorithm on seven datasets related to different cancer studies (Forshed et al., Mol Cell Proteomics 10(10):M111.010264, 2011). Data from two labeling procedures and three different instrumental platforms was included in the evaluation. With this unique method using both peptide sequence data and quantitative data, we can improve the quantitative accuracy and precision on the protein level and detect different protein species (Forshed et al., Mol Cell Proteomics 10(10):M111.010264, 2011).", "doi": "10.1007/978-1-4614-7209-4_9", "pmid": "23765624", "labels": {"Clinical Proteomics Mass spectrometry": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:23.206Z", "modified": "2017-05-30T12:42:45.953Z"}, {"entity": "publication", "iuid": "2e1fe44fabcf483abdd700396ed83d4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e1fe44fabcf483abdd700396ed83d4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e1fe44fabcf483abdd700396ed83d4e"}}, "title": "Narrow-range peptide isoelectric focusing as peptide prefractionation method prior to tandem mass spectrometry analysis.", "authors": [{"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}], "type": "journal article", "published": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "3-11", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "High sample complexity is one of the major challenges in mass spectrometry-based proteomics today. Despite massive improvement in instrumentation, sample prefractionation is still needed to reduce sample complexity and improve proteome coverage. Isoelectric focusing (IEF) has been traditionally used as a first-dimension protein separation technique in two-dimensional gel electrophoresis-based proteomics. Recently, peptide IEF has emerged as appealing alternative for anion exchange chromatography in multidimensional LC-MS/MS workflows. The rationale behind using narrow-range peptide isoelectric focusing as a prefractionation method prior to ms/ms is to reduce the complexity induced by tryptic digestion. This is done by selectively analyzing a sub-fraction of peptides with an acidic pI. The pI range is chosen as it has previously been shown that 96 % of human proteins have at least one tryptic peptide between pH 3.4 and 4.9. This ensures high proteome coverage while reducing the number of peptides with 2/3. In addition the focusing precision is optimal in this range. Therefore, by analyzing this sub-fraction of peptides the complexity of the sample can be reduced without significant loss of proteome coverage. As the theoretical pI of peptides can be calculated, the pI of the identified peptides can be used to validate the peptide sequence (identified peptides with pI outside the pH range 3.4-4.9 are more likely to be false positives). In addition, this approach is compatible with iTRAQ labelling as the different iTRAQ labels migrate similarly in IEF.", "doi": "10.1007/978-1-4614-7209-4_1", "pmid": "23765616", "labels": {"Clinical Proteomics Mass spectrometry": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:24.100Z", "modified": "2021-07-08T11:36:54.632Z"}, {"entity": "publication", "iuid": "f1a748adc53d487b9c3cf711b8237af8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1a748adc53d487b9c3cf711b8237af8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1a748adc53d487b9c3cf711b8237af8"}}, "title": "Highly multiplexed antibody suspension bead arrays for plasma protein profiling.", "authors": [{"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "137-145", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Alongside the increasing availability of affinity reagents, antibody microarrays have become a powerful tool to screen for target proteins in complex samples. Applying directly labeled samples onto arrays instead of using sandwich assays offers an approach to facilitate a systematic, high-throughput, and flexible exploration of protein profiles in body fluids such as serum or plasma. As an alternative to planar arrays, a system based on color-coded beads for the creation of antibody arrays in suspension has become available to offer a microtiter plate-based option for screening larger number of samples with variable sets of capture reagents. A procedure was established for analyzing biotinylated samples without the necessity to remove excess labeling substance. We have shown that this assay system allows detecting proteins down into lower pico-molar and higher pg/ml levels with dynamic ranges over three orders of magnitude. Presently, this workflow enables the profiling of 384 samples for up to 384 proteins per assay.", "doi": "10.1007/978-1-4614-7209-4_8", "pmid": "23765623", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:37.784Z", "modified": "2021-07-08T12:07:34.315Z"}, {"entity": "publication", "iuid": "afd562f281744bc99a19b35dbd0c972d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afd562f281744bc99a19b35dbd0c972d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afd562f281744bc99a19b35dbd0c972d"}}, "title": "Comprehensive analysis of MHC ligands in clinical material by immunoaffinity-mass spectrometry.", "authors": [{"family": "Kasuga", "given": "Kie", "initials": "K"}], "type": "journal article", "published": "2013-06-15", "journal": {"volume": "1023", "issn": "1940-6029", "issue": null, "pages": "203-218", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Major histocompatibility complexes (MHC) are expressed on antigen-presenting cells (APC) that display peptide antigens. This is a crucial step to activate a T-cell response. Since immunogenic ligand of MHC is closely related with autoimmunity, inflammatory diseases, and cancer, comprehensive analysis of MHC ligands (the so-called Ligandome) is essential to unveil disease pathogenesis. Recently, immunotherapies such as vaccination have been focused on as new therapies of cancer, HIV, and infectious diseases. Therefore, the importance of comprehensive analysis of MHC ligands is increasing. Mass spectrometry has been the core technology of ligand identification since the 1990s. The sensitivity of mass spectrometers has been improved dramatically in recent years; thus, it enables to identify MHC ligands in clinical materials. This chapter lays out the workflow of MHC ligand identification in clinical materials, especially human bronchoalveolar (BAL) cells. MHC-ligand complexes are enriched by immunoaffinity extraction and captured ligand peptides are identified by LC-MS/MS. MHC class II ligand in BAL cells is described in this text; however, this approach is applicable to MHC class I and other clinical materials such as tissues.", "doi": "10.1007/978-1-4614-7209-4_14", "pmid": "23765629", "labels": {"Clinical Proteomics Mass spectrometry": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:23.503Z", "modified": "2017-05-30T12:42:50.697Z"}, {"entity": "publication", "iuid": "c90bf34b19344d5c958e846513c6c7e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c90bf34b19344d5c958e846513c6c7e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c90bf34b19344d5c958e846513c6c7e1"}}, "title": "Molecular genetics and subjective well-being.", "authors": [{"family": "Rietveld", "given": "Cornelius A", "initials": "CA"}, {"family": "Cesarini", "given": "David", "initials": "D"}, {"family": "Benjamin", "given": "Daniel J", "initials": "DJ"}, {"family": "Koellinger", "given": "Philipp D", "initials": "PD"}, {"family": "De Neve", "given": "Jan-Emmanuel", "initials": "JE"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "Johannesson", "given": "Magnus", "initials": "M"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Krueger", "given": "Robert F", "initials": "RF"}, {"family": "Bartels", "given": "Meike", "initials": "M"}], "type": "journal article", "published": "2013-06-11", "journal": {"volume": "110", "issn": "1091-6490", "issue": "24", "pages": "9692-9697", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Subjective well-being (SWB) is a major topic of research across the social sciences. Twin and family studies have found that genetic factors may account for as much as 30-40% of the variance in SWB. Here, we study genetic contributions to SWB in a pooled sample of \u2248 11,500 unrelated, comprehensively-genotyped Swedish and Dutch individuals. We apply a recently developed method to estimate \"common narrow heritability\": the fraction of variance in SWB that can be explained by the cumulative additive effects of genetic polymorphisms that are common in the population. Our estimates are 5-10% for single-question survey measures of SWB, and 12-18% after correction for measurement error in the SWB measures. Our results suggest guarded optimism about the prospects of using genetic data in SWB research because, although the common narrow heritability is not large, the polymorphisms that contribute to it could feasibly be discovered with a sufficiently large sample of individuals.", "doi": "10.1073/pnas.1222171110", "pmid": "23708117", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1222171110"}, {"db": "pmc", "key": "PMC3683731"}], "notes": [], "created": "2017-05-04T14:58:10.155Z", "modified": "2020-01-21T13:56:05.158Z"}, {"entity": "publication", "iuid": "3a49c2d5569449b2bf18a5ee7bac7009", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a49c2d5569449b2bf18a5ee7bac7009.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a49c2d5569449b2bf18a5ee7bac7009"}}, "title": "The prognostic relevance of tumour-infiltrating plasma cells and immunoglobulin kappa C indicates an important role of the humoral immune response in non-small cell lung cancer.", "authors": [{"family": "Lohr", "given": "Miriam", "initials": "M"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Hammad", "given": "Seddik", "initials": "S"}, {"family": "Hellwig", "given": "Birte", "initials": "B"}, {"family": "Othman", "given": "Amnah", "initials": "A"}, {"family": "Berglund", "given": "Anders", "initials": "A"}, {"family": "Lambe", "given": "Mats", "initials": "M"}, {"family": "Holmberg", "given": "Lars", "initials": "L"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Cadenas", "given": "Cristina", "initials": "C"}, {"family": "Marchan", "given": "Rosemarie", "initials": "R"}, {"family": "Hengstler", "given": "Jan G", "initials": "JG"}, {"family": "Rahnenf\u00fchrer", "given": "J\u00f6rg", "initials": "J"}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2013-06-10", "journal": {"volume": "333", "issn": "1872-7980", "issue": "2", "pages": "222-228", "title": "Cancer Lett.", "issn-l": "0304-3835"}, "abstract": "A prognostic impact of immunoglobulin kappa C (IGKC) expression has been described in cancer. We analysed the influence of B-cell and plasma cell markers, as well as IGKC expression, in non-small lung cancer (NSCLC) using immunohistochemistry on a tissue microarray. IGKC protein expression was independently associated with longer survival, with particular impact in the adenocarcinoma subgroup. Moreover, a correlation was seen with CD138+ cells, but not with CD20. CD138 expression revealed a comparable association with survival. In conclusion, IGKC expression in stroma-infiltrating plasma cells is a prognostic marker in NSCLC, supporting emerging treatment concepts that exploit the humoral immune response.", "doi": "10.1016/j.canlet.2013.01.036", "pmid": "23370224", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "S0304-3835(13)00080-3"}], "notes": [], "created": "2017-05-04T14:55:55.626Z", "modified": "2017-05-30T12:52:58.591Z"}, {"entity": "publication", "iuid": "46fcccfe99494658bf5552e1a28e8a73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46fcccfe99494658bf5552e1a28e8a73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46fcccfe99494658bf5552e1a28e8a73"}}, "title": "Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP).", "authors": [{"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Algen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Sivertsson", "given": "Asa", "initials": "A"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Olsson", "given": "Ingmarie", "initials": "I"}, {"family": "Rydberg", "given": "Urban", "initials": "U"}, {"family": "Hudson", "given": "Paul", "initials": "P"}, {"family": "Ottosson Takanen", "given": "Jenny", "initials": "J"}, {"family": "Berling", "given": "Holger", "initials": "H"}, {"family": "Bj\u00f6rling", "given": "Lisa", "initials": "L"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2013-06-07", "journal": {"volume": "12", "issn": "1535-3907", "issue": "6", "pages": "2439-2448", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few tissue-specific proteins and approximately half of the genes expressed in all the analyzed cells. The status for each gene with regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas ( www.proteinatlas.org ).", "doi": "10.1021/pr300924j", "pmid": "23276153", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:13.479Z", "modified": "2021-07-08T13:44:33.207Z"}, {"entity": "publication", "iuid": "b87432546a9c447f8ecd453937951849", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b87432546a9c447f8ecd453937951849.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b87432546a9c447f8ecd453937951849"}}, "title": "Promoter DNA methylation pattern identifies prognostic subgroups in childhood T-cell acute lymphoblastic leukemia.", "authors": [{"family": "Borss\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Palmqvist", "given": "Lars", "initials": "L", "orcid": "0000-0001-9274-360X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e50c0057dcb47f39e085b16580806c2.json"}}, {"family": "Karrman", "given": "Kristina", "initials": "K"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Behrendtz", "given": "Mikael", "initials": "M"}, {"family": "Heldrup", "given": "Jesper", "initials": "J"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Roos", "given": "G\u00f6ran", "initials": "G"}, {"family": "Degerman", "given": "Sofie", "initials": "S"}], "type": "journal article", "published": "2013-06-06", "journal": {"volume": "8", "issn": "1932-6203", "issue": "6", "pages": "e65373", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has improved, but there is a considerable fraction of patients experiencing a poor outcome. There is a need for better prognostic markers and aberrant DNA methylation is a candidate in other malignancies, but its potential prognostic significance in T-ALL is hitherto undecided.\n\nGenome wide promoter DNA methylation analysis was performed in pediatric T-ALL samples (n = 43) using arrays covering >27000 CpG sites. Clinical outcome was evaluated in relation to methylation status and compared with a contemporary T-ALL group not tested for methylation (n = 32).\n\nBased on CpG island methylator phenotype (CIMP), T-ALL samples were subgrouped as CIMP+ (high methylation) and CIMP- (low methylation). CIMP- T-ALL patients had significantly worse overall and event free survival (p = 0.02 and p = 0.001, respectively) compared to CIMP+ cases. CIMP status was an independent factor for survival in multivariate analysis including age, gender and white blood cell count. Analysis of differently methylated genes in the CIMP subgroups showed an overrepresentation of transcription factors, ligands and polycomb target genes.\n\nWe identified global promoter methylation profiling as being of relevance for subgrouping and prognostication of pediatric T-ALL.", "doi": "10.1371/journal.pone.0065373", "pmid": "23762353", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-31749"}, {"db": "pmc", "key": "PMC3675104"}], "notes": [], "created": "2017-05-04T15:01:27.672Z", "modified": "2021-07-06T16:10:15.504Z"}, {"entity": "publication", "iuid": "4a7238add3f84862ba7a983f4d696379", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a7238add3f84862ba7a983f4d696379.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a7238add3f84862ba7a983f4d696379"}}, "title": "Rapid Measurement of Intracellular Unbound Drug Concentrations", "authors": [{"family": "Mateus", "given": "Andr\u00e9", "initials": "A"}, {"family": "Matsson", "given": "P\u00e4r", "initials": "P"}, {"family": "Artursson", "given": "Per", "initials": "P"}], "type": "journal-article", "published": "2013-06-03", "journal": {"volume": "10", "issn": "1543-8384", "issue": "6", "pages": "2467-2478", "title": "Mol. Pharmaceutics", "issn-l": "1543-8384"}, "abstract": null, "doi": "10.1021/mp4000822", "pmid": "23631740", "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:09:09.573Z", "modified": "2025-10-17T13:04:30.373Z"}, {"entity": "publication", "iuid": "12fc5d0c11d54343befd3f72b23b8ec6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12fc5d0c11d54343befd3f72b23b8ec6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12fc5d0c11d54343befd3f72b23b8ec6"}}, "title": "Next-generation sequencing in the clinical genetic screening of patients with pheochromocytoma and paraganglioma.", "authors": [{"family": "Crona", "given": "Joakim", "initials": "J"}, {"family": "Verdugo", "given": "Alberto Delgado", "initials": "AD"}, {"family": "Granberg", "given": "Dan", "initials": "D"}, {"family": "Welin", "given": "Staffan", "initials": "S"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "Peyman", "initials": "P"}], "type": "journal article", "published": "2013-06-01", "journal": {"volume": "2", "issn": "2049-3614", "issue": "2", "pages": "104-111", "title": "Endocr Connect", "issn-l": "2049-3614"}, "abstract": "Recent findings have shown that up to 60% of pheochromocytomas (PCCs) and paragangliomas (PGLs) are caused by germline or somatic mutations in one of the 11 hitherto known susceptibility genes: SDHA, SDHB, SDHC, SDHD, SDHAF2, VHL, HIF2A (EPAS1), RET, NF1, TMEM127 and MAX. This list of genes is constantly growing and the 11 genes together consist of 144 exons. A genetic screening test is extensively time consuming and expensive. Hence, we introduce next-generation sequencing (NGS) as a time-efficient and cost-effective alternative.\n\nTumour lesions from three patients with apparently sporadic PCC were subjected to whole exome sequencing utilizing Agilent Sureselect target enrichment system and Illumina Hi seq platform. Bioinformatics analysis was performed in-house using commercially available software. Variants in PCC and PGL susceptibility genes were identified.\n\nWe have identified 16 unique genetic variants in PCC susceptibility loci in three different PCC, spending less than a 30-min hands-on, in-house time. Two patients had one unique variant each that was classified as probably and possibly pathogenic: NF1 Arg304Ter and RET Tyr791Phe. The RET variant was verified by Sanger sequencing.\n\nNGS can serve as a fast and cost-effective method in the clinical genetic screening of PCC. The bioinformatics analysis may be performed without expert skills. We identified process optimization, characterization of unknown variants and determination of additive effects of multiple variants as key issues to be addressed by future studies.", "doi": "10.1530/EC-13-0009", "pmid": "23781326", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "EC130009"}, {"db": "pmc", "key": "PMC3682230"}], "notes": [], "created": "2017-05-04T15:01:16.226Z", "modified": "2020-01-21T13:56:00.808Z"}, {"entity": "publication", "iuid": "4bcd1d13ed9344d1b516e49f5d255f69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4bcd1d13ed9344d1b516e49f5d255f69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4bcd1d13ed9344d1b516e49f5d255f69"}}, "title": "The value of selected in vitro and in silico methods to predict acute oral toxicity in a regulatory context: results from the European Project ACuteTox.", "authors": [{"family": "Prieto", "given": "P", "initials": "P"}, {"family": "Kinsner-Ovaskainen", "given": "A", "initials": "A"}, {"family": "Stanzel", "given": "S", "initials": "S"}, {"family": "Albella", "given": "B", "initials": "B"}, {"family": "Artursson", "given": "P", "initials": "P"}, {"family": "Campillo", "given": "N", "initials": "N"}, {"family": "Cecchelli", "given": "R", "initials": "R"}, {"family": "Cerrato", "given": "L", "initials": "L"}, {"family": "D\u00edaz", "given": "L", "initials": "L"}, {"family": "Di Consiglio", "given": "E", "initials": "E"}, {"family": "Guerra", "given": "A", "initials": "A"}, {"family": "Gombau", "given": "L", "initials": "L"}, {"family": "Herrera", "given": "G", "initials": "G"}, {"family": "Honegger", "given": "P", "initials": "P"}, {"family": "Landry", "given": "C", "initials": "C"}, {"family": "O'Connor", "given": "J E", "initials": "JE"}, {"family": "P\u00e1ez", "given": "J A", "initials": "JA"}, {"family": "Quintas", "given": "G", "initials": "G"}, {"family": "Svensson", "given": "R", "initials": "R"}, {"family": "Turco", "given": "L", "initials": "L"}, {"family": "Zurich", "given": "M G", "initials": "MG"}, {"family": "Zurbano", "given": "M J", "initials": "MJ"}, {"family": "Kopp-Schneider", "given": "A", "initials": "A"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "27", "issn": "1879-3177", "issue": "4", "pages": "1357-1376", "title": "Toxicol In Vitro", "issn-l": "0887-2333"}, "abstract": "ACuteTox is a project within the 6th European Framework Programme which had as one of its goals to develop, optimise and prevalidate a non-animal testing strategy for predicting human acute oral toxicity. In its last 6 months, a challenging exercise was conducted to assess the predictive capacity of the developed testing strategies and final identification of the most promising ones. Thirty-two chemicals were tested blind in the battery of in vitro and in silico methods selected during the first phase of the project. This paper describes the classification approaches studied: single step procedures and two step tiered testing strategies. In summary, four in vitro testing strategies were proposed as best performing in terms of predictive capacity with respect to the European acute oral toxicity classification. In addition, a heuristic testing strategy is suggested that combines the prediction results gained from the neutral red uptake assay performed in 3T3 cells, with information on neurotoxicity alerts identified by the primary rat brain aggregates test method. Octanol-water partition coefficients and in silico prediction of intestinal absorption and blood-brain barrier passage are also considered. This approach allows to reduce the number of chemicals wrongly predicted as not classified (LD50>2000 mg/kg b.w.).", "doi": "10.1016/j.tiv.2012.07.013", "pmid": "22922246", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0887-2333(12)00217-2"}], "notes": "Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)\r\nADME of Therapeutics (UDOPP)", "created": "2017-05-04T14:56:49.802Z", "modified": "2025-10-17T13:04:30.384Z"}, {"entity": "publication", "iuid": "d124b89b92db4a0c8b4ec14ab8bb8485", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d124b89b92db4a0c8b4ec14ab8bb8485.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d124b89b92db4a0c8b4ec14ab8bb8485"}}, "title": "The impact of splicing on protein domain architecture.", "authors": [{"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "23", "issn": "1879-033X", "issue": "3", "pages": "451-458", "title": "Curr. Opin. Struct. Biol.", "issn-l": "0959-440X"}, "abstract": "Many proteins are composed of protein domains, functional units of common descent. Multidomain forms are common in all eukaryotes making up more than half of the proteome and the evolution of novel domain architecture has been accelerated in metazoans. It is also becoming increasingly clear that alternative splicing is prevalent among vertebrates. Given that protein domains are defined as structurally, functionally and evolutionarily distinct units, one may speculate that some alternative splicing events may lead to clean excisions of protein domains, thus generating a number of different domain architectures from one gene template. However, recent findings indicate that smaller alternative splicing events, in particular in disordered regions, might be more prominent than domain architectural changes. The problem of identifying protein isoforms is, however, still not resolved. Clearly, many splice forms identified through detection of mRNA sequences appear to produce 'nonfunctional' proteins, such as proteins with missing internal secondary structure elements. Here, we review the state of the art methods for identification of functional isoforms and present a summary of what is known, thus far, about alternative splicing with regard to protein domain architectures.", "doi": "10.1016/j.sbi.2013.02.013", "pmid": "23562110", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S0959-440X(13)00043-2"}], "notes": [], "created": "2017-05-04T14:56:22.753Z", "modified": "2020-01-21T13:53:20.880Z"}, {"entity": "publication", "iuid": "cf2c496c7c344e5a8ad536c44367b83a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf2c496c7c344e5a8ad536c44367b83a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf2c496c7c344e5a8ad536c44367b83a"}}, "title": "Structural basis for substrate transport in the GLUT-homology family of monosaccharide transporters.", "authors": [{"family": "Quistgaard", "given": "Esben M", "initials": "EM"}, {"family": "L\u00f6w", "given": "Christian", "initials": "C"}, {"family": "Moberg", "given": "Per", "initials": "P"}, {"family": "Tr\u00e9saugues", "given": "Lionel", "initials": "L"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "20", "issn": "1545-9985", "issue": "6", "pages": "766-768", "title": "Nat. Struct. Mol. Biol.", "issn-l": "1545-9985"}, "abstract": "Here we present two structures of the major facilitator (MFS) xylose transporter XylE from Escherichia coli in inward open and partially occluded inward open conformations. These structures provide key information about the transport cycle of XylE and the closely related human GLUT transporters. This is, to our knowledge, the first MFS transporter structure determined in more than one conformational state, which may establish XylE as an important MFS model protein.", "doi": "10.1038/nsmb.2569", "pmid": "23624861", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "nsmb.2569"}, {"db": "PDB", "key": "4JA3"}, {"db": "PDB", "key": "4JA4"}], "notes": [], "created": "2017-05-04T15:03:49.415Z", "modified": "2017-09-06T11:42:09.361Z"}, {"entity": "publication", "iuid": "bad4b917f0f94e1c930ce1b0bdc88bd0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bad4b917f0f94e1c930ce1b0bdc88bd0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bad4b917f0f94e1c930ce1b0bdc88bd0"}}, "title": "Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase.", "authors": [{"family": "Lim", "given": "Sing Mei", "initials": "SM"}, {"family": "Chen", "given": "Dan", "initials": "D"}, {"family": "Teo", "given": "Hsiangling", "initials": "H"}, {"family": "Roos", "given": "Annette", "initials": "A"}, {"family": "Jansson", "given": "Anna Elisabet", "initials": "AE"}, {"family": "Nyman", "given": "Tomas", "initials": "T"}, {"family": "Tr\u00e9saugues", "given": "Lionel", "initials": "L"}, {"family": "Pervushin", "given": "Konstantin", "initials": "K"}, {"family": "Nordlund", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "54", "issn": "1539-7262", "issue": "6", "pages": "1630-1643", "title": "J. Lipid Res.", "issn-l": "0022-2275"}, "abstract": "Lipocalin prostaglandin D synthase (L-PGDS) regulates synthesis of an important inflammatory and signaling mediator, prostaglandin D2 (PGD2). Here, we used structural, biophysical, and biochemical approaches to address the mechanistic aspects of substrate entry, catalysis, and product exit of this enzyme. Structure of human L-PGDS was solved in a complex with a substrate analog (SA) and in ligand-free form. Its catalytic Cys 65 thiol group was found in two different conformations, each making a distinct hydrogen bond network to neighboring residues. These help in elucidating the mechanism of the cysteine nucleophile activation. Electron density for ligand observed in the active site defined the substrate binding regions, but did not allow unambiguous fitting of the SA. To further understand ligand binding, we used NMR spectroscopy to map the binding sites and to show the dynamics of protein-substrate and protein-product interactions. A model for ligand binding at the catalytic site is proposed, showing a second binding site involved in ligand exit and entry. NMR chemical shift perturbations and NMR resonance line-width alterations (observed as changes of intensity in two-dimensional cross-peaks in [\u00b9H,\u00b9\u2075N]-transfer relaxation optimization spectroscopy) for residues at the \u03a9 loop (A-B loop), E-F loop, and G-H loop besides the catalytic sites indicate involvement of these residues in ligand entry/egress.", "doi": "10.1194/jlr.M035410", "pmid": "23526831", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "jlr.M035410"}, {"db": "pmc", "key": "PMC3646464"}], "notes": [], "created": "2017-05-04T15:03:47.595Z", "modified": "2017-09-06T11:42:09.269Z"}, {"entity": "publication", "iuid": "89526e500465447fb04d28118f5ed164", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89526e500465447fb04d28118f5ed164.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89526e500465447fb04d28118f5ed164"}}, "title": "Stepping-stone expansion and habitat loss explain a peculiar genetic structure and distribution of a forest insect.", "authors": [{"family": "Cassel-Lundhagen", "given": "Anna", "initials": "A"}, {"family": "Ronn\u00e5s", "given": "Cecilia", "initials": "C"}, {"family": "Battisti", "given": "Andrea", "initials": "A"}, {"family": "Wall\u00e9n", "given": "Johan", "initials": "J"}, {"family": "Larsson", "given": "Stig", "initials": "S"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "22", "issn": "1365-294X", "issue": "12", "pages": "3362-3375", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "It is challenging to unravel the history of organisms with highly scattered populations. Such species may have fragmented distributions because extant populations are remnants of a previously more continuous range, or because the species has narrow habitat requirements in combination with good dispersal capacity (naturally or vector borne). The northern pine processionary moth Thaumetopoea pinivora has a scattered distribution with fragmented populations in two separate regions, northern and south-western Europe. The aims of this study were to explore the glacial and postglacial history of T.\u00a0pinivora, and add to the understanding of its current distribution and level of contemporary gene flow. We surveyed published records of its occurrence and analysed individuals from a representative subset of populations across the range. A 633\u00a0bp long fragment of the mtDNA COI gene was sequenced and nine polymorphic microsatellite loci were genotyped. Only nine nucleotide sites were polymorphic in the COI gene and 90% of the individuals from across its whole range shared the same haplotype. The microsatellite diversity gradually declined towards the north, and unique alleles were found in only three of the northern and three of southern sites. Genetic structuring did not indicate complete isolation among regions, but an increase of genetic isolation by geographic distance. Approximate Bayesian model choice suggested recent divergence during the postglacial period, but glacial refugia remain unidentified. The progressive reduction of suitable habitats is suggested to explain the genetic structure of the populations and we suggest that T.\u00a0pinivora is a cold-tolerant relict species, with situation-dependent dispersal.", "doi": "10.1111/mec.12313", "pmid": "23718200", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "GENBANK", "key": "JX243015"}, {"db": "GENBANK", "key": "JX243021"}], "notes": [], "created": "2017-05-04T15:02:28.977Z", "modified": "2020-01-21T13:56:03.494Z"}, {"entity": "publication", "iuid": "8dddcf2bd4784bea8b3e82160f2f9e4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8dddcf2bd4784bea8b3e82160f2f9e4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8dddcf2bd4784bea8b3e82160f2f9e4c"}}, "title": "Sortilin receptor 1 predicts longitudinal cognitive change.", "authors": [{"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Zavala", "given": "Catalina", "initials": "C"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Vie", "given": "Loryana", "initials": "L"}, {"family": "Johansson", "given": "Boo", "initials": "B"}, {"family": "Malmberg", "given": "Bo", "initials": "B"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "34", "issn": "1558-1497", "issue": "6", "pages": "1710.e11-1710.e18", "title": "Neurobiol. Aging", "issn-l": "0197-4580"}, "abstract": "The gene encoding sortilin receptor 1 (SORL1) has been associated with Alzheimer's disease risk. We examined 15 SORL1 variants and single nucleotide polymorphism (SNP) set risk scores in relation to longitudinal verbal, spatial, memory, and perceptual speed performance, testing for age trends and sex-specific effects. Altogether, 1609 individuals from 3 population-based Swedish twin studies were assessed up to 5 times across 16 years. Controlling for apolipoprotein E genotype (APOE), multiple simple and sex-moderated associations were observed for spatial, episodic memory, and verbal trajectories (p = 1.25E-03 to p = 4.83E-02). Five variants (rs11600875, rs753780, rs7105365, rs11820794, rs2070045) were associated across domains. Notably, in those homozygous for the rs2070045 risk allele, men demonstrated initially favorable performance but accelerating declines, and women showed overall lower performance. SNP set risk scores predicted spatial (Card Rotations, p = 5.92E-03) and episodic memory trajectories (Thurstone Picture Memory, p = 3.34E-02), where higher risk scores benefited men's versus women's performance up to age 75 but with accelerating declines. SORL1 is associated with cognitive aging, and might contribute differentially to change in men and women.", "doi": "10.1016/j.neurobiolaging.2012.12.006", "pmid": "23318115", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0197-4580(12)00621-5"}, {"db": "pmc", "key": "PMC3839667"}, {"db": "mid", "key": "NIHMS435934"}], "notes": [], "created": "2017-05-04T14:58:08.343Z", "modified": "2020-01-21T13:56:08.600Z"}, {"entity": "publication", "iuid": "71aecea2405c40f2beded48c38cb5532", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71aecea2405c40f2beded48c38cb5532.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71aecea2405c40f2beded48c38cb5532"}}, "title": "Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing.", "authors": [{"family": "Nong", "given": "Rachel Yuan", "initials": "RY"}, {"family": "Wu", "given": "Di", "initials": "D"}, {"family": "Yan", "given": "Junhong", "initials": "J"}, {"family": "Hammond", "given": "Maria", "initials": "M", "orcid": "0000-0002-8375-6676", "researcher": {"href": "https://publications.scilifelab.se/researcher/78703c93891e4827aabb35c2011be9f2.json"}}, {"family": "Gu", "given": "Gucci Jijuan", "initials": "GJ"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Darmanis", "given": "Spyros", "initials": "S"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "8", "issn": "1750-2799", "issue": "6", "pages": "1234-1248", "title": "Nat Protoc", "issn-l": null}, "abstract": "Solid-phase proximity ligation assays share properties with the classical sandwich immunoassays for protein detection. The proteins captured via antibodies on solid supports are, however, detected not by single antibodies with detectable functions, but by pairs of antibodies with attached DNA strands. Upon recognition by these sets of three antibodies, pairs of DNA strands brought in proximity are joined by ligation. The ligated reporter DNA strands are then detected via methods such as real-time PCR or next-generation sequencing (NGS). We describe how to construct assays that can offer improved detection specificity by virtue of recognition by three antibodies, as well as enhanced sensitivity owing to reduced background and amplified detection. Finally, we also illustrate how the assays can be applied for parallel detection of proteins, taking advantage of the oligonucleotide ligation step to avoid background problems that might arise with multiplexing. The protocol for the singleplex solid-phase proximity ligation assay takes ~5 h. The multiplex version of the assay takes 7-8 h depending on whether quantitative PCR (qPCR) or sequencing is used as the readout. The time for the sequencing-based protocol includes the library preparation but not the actual sequencing, as times may vary based on the choice of sequencing platform.", "doi": "10.1038/nprot.2013.070", "pmid": "23722261", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "nprot.2013.070"}], "notes": [], "created": "2017-05-04T14:55:25.250Z", "modified": "2023-04-14T13:56:28.601Z"}, {"entity": "publication", "iuid": "bd28801553d742e7ab13c5f300a57f6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd28801553d742e7ab13c5f300a57f6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd28801553d742e7ab13c5f300a57f6e"}}, "title": "Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits.", "authors": [{"family": "Randall", "given": "Joshua C", "initials": "JC"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Berndt", "given": "Sonja I", "initials": "SI"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Monda", "given": "Keri L", "initials": "KL"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Li", "given": "Shengxu", "initials": "S"}, {"family": "Workalemahu", "given": "Tsegaselassie", "initials": "T"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Croteau-Chonka", "given": "Damien C", "initials": "DC"}, {"family": "Day", "given": "Felix R", "initials": "FR"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Ferreira", "given": "Teresa", "initials": "T"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Locke", "given": "Adam E", "initials": "AE"}, {"family": "Mathieson", "given": "Iain", "initials": "I"}, {"family": "Scherag", "given": "Andre", "initials": "A"}, {"family": "Vedantam", "given": "Sailaja", "initials": "S"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Dermitzakis", "given": "Emmanouil T", "initials": "ET"}, {"family": "Dimas", "given": "Antigone S", "initials": "AS"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Min", "given": "Josine L", "initials": "JL"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Clegg", "given": "Deborah J", "initials": "DJ"}, {"family": "Person", "given": "Thomas", "initials": "T"}, {"family": "Krohn", "given": "Jon P", "initials": "JP"}, {"family": "Bauer", "given": "Sabrina", 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"Henrik", "initials": "H"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Li", "given": "Guo", "initials": "G"}, {"family": "Beckmann", "given": "Jacques S", "initials": "JS"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Teder-Laving", "given": "Maris", "initials": "M"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "K"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Kraja", "given": "Aldi T", "initials": "AT"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Heard-Costa", "given": "Nancy L", "initials": "NL"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Saramies", "given": "Jouko", "initials": "J"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Hengstenberg", "given": "Christian", "initials": "C"}, {"family": "Loley", "given": "Christina", "initials": "C"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Lamina", "given": "Claudia", "initials": "C"}, {"family": "Wichmann", "given": "H Erich", "initials": "HE"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Speliotes", "given": "Elizabeth K", "initials": "EK"}, {"family": "Penninx", "given": "Brenda", "initials": "B"}, {"family": "Hartikainen", "given": "Anna-Liisa", "initials": "A"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Chanock", "given": "Stephen J", "initials": "SJ"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Estrada", "given": "Karol", "initials": "K"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "den Heijer", "given": "Martin", "initials": "M"}, {"family": "Kiemeney", "given": "Lambertus A", "initials": "LA"}, {"family": "Maschio", "given": "Andrea", "initials": "A"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Tyrer", "given": "Jonathan", "initials": "J"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Hall", "given": "Alistair S", "initials": "AS"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Attwood", "given": "Antony Paul", "initials": "AP"}, {"family": "Sambrook", "given": "Jennifer G", "initials": "JG"}, {"family": "Hung", "given": "Joseph", "initials": "J"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Lokki", "given": "Marja-Liisa", "initials": "M"}, {"family": "Sinisalo", "given": "Juha", "initials": "J"}, {"family": "Boucher", "given": "Gabrielle", "initials": "G"}, {"family": "Huikuri", "given": "Heikki", "initials": "H"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Eklund", "given": "Niina", "initials": "N"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Barlassina", "given": "Cristina", "initials": "C"}, {"family": "Rivolta", "given": "Carlo", "initials": "C"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Van der Klauw", "given": "Melanie M", "initials": "MM"}, {"family": "Van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV"}, {"family": "Gejman", "given": "Pablo V", "initials": "PV"}, {"family": "Shi", "given": "Jianxin", "initials": "J"}, {"family": "Jacobs", "given": "Kevin B", "initials": "KB"}, {"family": "Wang", "given": "Zhaoming", "initials": "Z"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL"}, {"family": "Mateo Leach", "given": "Irene", "initials": "I"}, {"family": "Navis", "given": "Gerjan", "initials": "G"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Iribarren", "given": "Carlos", "initials": "C"}, {"family": "Basart", "given": "Hanneke", "initials": "H"}, {"family": "Hovingh", "given": "Kees G", "initials": "KG"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "Anderson", "given": "Denise", "initials": "D"}, {"family": "Beilby", "given": "John P", "initials": "JP"}, {"family": "Hui", "given": "Jennie", "initials": "J"}, {"family": "Jolley", "given": "Jennifer", "initials": "J"}, {"family": "Sager", "given": "Hendrik", "initials": "H"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Schwarz", "given": "Peter E 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"Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Keinanen-Kiukaanniemi", "given": "Sirkka M", "initials": "SM"}, {"family": "Saaristo", "given": "Timo E", "initials": "TE"}, {"family": "Edkins", "given": "Sarah", "initials": "S"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Morris", "given": "Andrew David", "initials": "AD"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Erbel", "given": "Raimund", "initials": "R"}, {"family": "Moebus", "given": "Susanne", "initials": "S"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Pechlivanis", "given": "Sonali", "initials": "S"}, {"family": "Hveem", 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"Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Arveiler", "given": "Dominique", "initials": "D"}, {"family": "Cesana", "given": "Giancarlo", "initials": "G"}, {"family": "Kuulasmaa", "given": "Kari", "initials": "K"}, {"family": "Virtamo", "given": "Jarmo", "initials": "J"}, {"family": "Yarnell", "given": "John W G", "initials": "JWG"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Dimitriou", "given": "Maria", "initials": "M"}, {"family": "Kolovou", "given": "Genovefa", "initials": "G"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Stirrups", "given": "Kathleen", "initials": "K"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Nj\u00f8lstad", "given": "Inger", "initials": "I"}, {"family": "Wilsgaard", "given": "Tom", "initials": "T"}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Rehnberg", "given": "Emil", "initials": "E"}, {"family": "Hingorani", "given": "Aroon", "initials": "A"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Frayling", "given": "Timothy", "initials": "T"}, {"family": "Groop", "given": "Leif C", "initials": "LC"}, {"family": "Haritunians", "given": "Talin", "initials": "T"}, {"family": "Hunter", "given": "David", "initials": "D"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kaplan", "given": "Robert", "initials": "R"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "9", "issn": "1553-7404", "issue": "6", "pages": "e1003500", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals) and took forward 348 SNPs into follow-up (additional 137,052 individuals) in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%), including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9) and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG), all of which were genome-wide significant in women (P<5\u00d710(-8)), but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits.", "doi": "10.1371/journal.pgen.1003500", "pmid": "23754948", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-01098"}, {"db": "pmc", "key": "PMC3674993"}], "notes": [], "created": "2017-05-04T14:58:12.018Z", "modified": "2020-01-21T13:56:08.638Z"}, {"entity": "publication", "iuid": "d1604f3658f2436c8f3832d8f27b3b0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1604f3658f2436c8f3832d8f27b3b0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1604f3658f2436c8f3832d8f27b3b0c"}}, "title": "Prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in healthy Swedish preschool children.", "authors": [{"family": "Kaarme", "given": "Johan", "initials": "J"}, {"family": "Molin", "given": "Ylva", "initials": "Y"}, {"family": "Olsen", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Melhus", "given": "Asa", "initials": "A"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "102", "issn": "1651-2227", "issue": "6", "pages": "655-660", "title": "Acta Paediatr.", "issn-l": "0803-5253"}, "abstract": "The objective was to determine the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in faeces from healthy Swedish preschool children and to establish whether transmission took place between children in preschools.\n\nDiapers from children attending preschools in Uppsala city were collected during September to October 2010, and the faeces was cultured. Antibiotic profiles and carriage of CTX-M, TEM, SHV and AmpC type enzymes were determined. PCR-positive isolates were further characterized by sequencing and epidemiological typing. Statistics on antibiotic use and ESBL producers in paediatric patients at Uppsala University Hospital were extracted for comparison.\n\nA total of 313 stool specimens were obtained, representing 24.5% of all preschool children in Uppsala city. The carriage rate of ESBL-producing Enterobacteriaceae was 2.9% among these healthy children. The corresponding figure for patients in the same age group was 8.4%. Escherichia coli with CTX-M type enzymes predominated, and only one E.\u00a0coli isolate carried genes-encoding CMY. CTX-M-producing E.\u00a0coli isolates with identical genotypes were found in children with no familial relation at two different preschools.\n\nUsing diapers, the prevalence of ESBL-producing Enterobacteriaceae in children was quickly established, and, most likely, a transmission of ESBL-producing E.\u00a0coli was for the first time documented between children at the same preschool.", "doi": "10.1111/apa.12206", "pmid": "23419070", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:17.933Z", "modified": "2020-01-21T13:56:05.348Z"}, {"entity": "publication", "iuid": "0c98e0712e2047a588c8a2ef3e4bf000", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c98e0712e2047a588c8a2ef3e4bf000.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c98e0712e2047a588c8a2ef3e4bf000"}}, "title": "Parallel visualization of multiple protein complexes in individual cells in tumor tissue.", "authors": [{"family": "Leuchowius", "given": "Karl-Johan", "initials": "KJ"}, {"family": "Clausson", "given": "Carl-Magnus", "initials": "CM"}, {"family": "Grannas", "given": "Karin", "initials": "K"}, {"family": "Erbilgin", "given": "Y\u00fccel", "initials": "Y"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "12", "issn": "1535-9484", "issue": "6", "pages": "1563-1571", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Cellular functions are regulated and executed by complex protein interaction networks. Accordingly, it is essential to understand the interplay between proteins in determining the activity status of signaling cascades. New methods are therefore required to provide information on different protein interaction events at the single cell level in heterogeneous cell populations such as in tissue sections. Here, we describe a multiplex proximity ligation assay for simultaneous visualization of multiple protein complexes in situ. The assay is an enhancement of the original proximity ligation assay, and it is based on using proximity probes labeled with unique tag sequences that can be used to read out which probes, from a pool of probes, have bound a certain protein complex. Using this approach, it is possible to gain information on the constituents of different protein complexes, the subcellular location of the complexes, and how the balance between different complex constituents can change between normal and malignant cells, for example. As a proof of concept, we used the assay to simultaneously visualize multiple protein complexes involving EGFR, HER2, and HER3 homo- and heterodimers on a single-cell level in breast cancer tissue sections. The ability to study several protein complex formations concurrently at single cell resolution could be of great potential for a systems understanding, paving the way for improved disease diagnostics and possibilities for drug development.", "doi": "10.1074/mcp.O112.023374", "pmid": "23436906", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null, "PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "O112.023374"}, {"db": "pmc", "key": "PMC3675814"}], "notes": [], "created": "2017-05-04T14:55:24.950Z", "modified": "2023-04-14T13:56:28.802Z"}, {"entity": "publication", "iuid": "dfffc27ce20b4e9e828d6e5c0a0bb751", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfffc27ce20b4e9e828d6e5c0a0bb751.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfffc27ce20b4e9e828d6e5c0a0bb751"}}, "title": "No association of primary Sj\u00f6gren's syndrome with Fc\u03b3 receptor gene variants.", "authors": [{"family": "Haldorsen", "given": "K", "initials": "K"}, {"family": "Appel", "given": "S", "initials": "S"}, {"family": "Le Hellard", "given": "S", "initials": "S"}, {"family": "Bruland", "given": "O", "initials": "O"}, {"family": "Brun", "given": "J G", "initials": "JG"}, {"family": "Omdal", "given": "R", "initials": "R"}, {"family": "Kristjansdottir", "given": "G", "initials": "G"}, {"family": "Theander", "given": "E", "initials": "E"}, {"family": "Fernandes", "given": "C P D", "initials": "CP"}, {"family": "Kvarnstr\u00f6m", "given": "M", "initials": "M"}, {"family": "Eriksson", "given": "P", "initials": "P"}, {"family": "R\u00f6nnblom", "given": "L", "initials": "L"}, {"family": "Herlenius", "given": "M W", "initials": "MW"}, {"family": "Nordmark", "given": "G", "initials": "G"}, {"family": "Jonsson", "given": "R", "initials": "R"}, {"family": "Bolstad", "given": "A I", "initials": "AI"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "14", "issn": "1476-5470", "issue": "4", "pages": "234-237", "title": "Genes Immun.", "issn-l": "1466-4879"}, "abstract": "The genetic background of primary Sj\u00f6gren's syndrome (pSS) is partly shared with systemic lupus erythematosus (SLE). Immunoglobulin G Fc receptors are important for clearance of immune complexes. Fc\u03b3 receptor variants and gene deletion have been found to confer SLE risk. In this study, four Fc\u03b3 receptor single-nucleotide polymorphisms (SNPs) and one copy number variation (CNV) were studied. Swedish and Norwegian pSS patients (N=527) and controls (N=528) were genotyped for the Fc\u03b3 receptor gene variant FCGR2A H131R (rs1801274) by the Illumina GoldenGate assay. FCGR3A F158V (rs396991) was analysed in 488 patients and 485 controls, FCGR3B rs447536 was analysed in 471 patients and 467 controls, and FCGR3B rs448740 was analysed in 478 cases and 455 controls, using TaqMan SNP genotyping assays. FCGR3B CNV was analysed in 124 patients and 139 controls using a TaqMan copy number assay. None of the SNPs showed any association with pSS. Also, no FCGR3B CNV association was detected. The lack of association of pSS with Fc\u03b3 receptor gene variants indicates that defective immune complex clearance may not be as important in pSS pathogenesis as in SLE, and may point to important differences between SLE and pSS.", "doi": "10.1038/gene.2013.12", "pmid": "23552400", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "gene201312"}], "notes": [], "created": "2017-05-04T15:01:18.177Z", "modified": "2020-01-21T13:56:05.751Z"}, {"entity": "publication", "iuid": "38deb04ab67148e9bfa7ba2cd6bbf4eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38deb04ab67148e9bfa7ba2cd6bbf4eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38deb04ab67148e9bfa7ba2cd6bbf4eb"}}, "title": "Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.", "authors": [{"family": "Geiger", "given": "Tamar", "initials": "T"}, {"family": "Velic", "given": "Ana", "initials": "A"}, {"family": "Macek", "given": "Boris", "initials": "B"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Nagaraj", "given": "Nagarjuna", "initials": "N"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Cox", "given": "Juergen", "initials": "J"}, {"family": "Mann", "given": "Matthias", "initials": "M"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "12", "issn": "1535-9484", "issue": "6", "pages": "1709-1722", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Identifying the building blocks of mammalian tissues is a precondition for understanding their function. In particular, global and quantitative analysis of the proteome of mammalian tissues would point to tissue-specific mechanisms and place the function of each protein in a whole-organism perspective. We performed proteomic analyses of 28 mouse tissues using high-resolution mass spectrometry and used a mix of mouse tissues labeled via stable isotope labeling with amino acids in cell culture as a \"spike-in\" internal standard for accurate protein quantification across these tissues. We identified a total of 7,349 proteins and quantified 6,974 of them. Bioinformatic data analysis showed that physiologically related tissues clustered together and that highly expressed proteins represented the characteristic tissue functions. Tissue specialization was reflected prominently in the proteomic profiles and is apparent already in their hundred most abundant proteins. The proportion of strictly tissue-specific proteins appeared to be small. However, even proteins with household functions, such as those in ribosomes and spliceosomes, can have dramatic expression differences among tissues. We describe a computational framework with which to correlate proteome profiles with physiological functions of the tissue. Our data will be useful to the broad scientific community as an initial atlas of protein expression of a mammalian species.", "doi": "10.1074/mcp.M112.024919", "pmid": "23436904", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "M112.024919"}, {"db": "pmc", "key": "PMC3675825"}], "notes": [], "created": "2017-05-04T14:55:14.094Z", "modified": "2021-07-08T13:44:33.162Z"}, {"entity": "publication", "iuid": "21d45deb0da74422b84ce38ad7d1ecd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21d45deb0da74422b84ce38ad7d1ecd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21d45deb0da74422b84ce38ad7d1ecd9"}}, "title": "Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.", "authors": [{"family": "den Hoed", "given": "Marcel", "initials": "M"}, {"family": "Eijgelsheim", "given": "Mark", "initials": "M"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Brundel", "given": "Bianca J J M", "initials": "BJJM"}, {"family": "Peal", "given": "David S", "initials": "DS"}, {"family": "Evans", "given": "David M", "initials": "DM"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Segr\u00e8", "given": "Ayellet V", "initials": "AV"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Handsaker", "given": "Robert E", "initials": "RE"}, {"family": "Westra", "given": "Harm-Jan", "initials": "H"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Lundby", "given": "Alicia", "initials": "A"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Kim", "given": "Young Jin", "initials": "YJ"}, {"family": "Go", "given": "Min Jin", "initials": "MJ"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Boucher", "given": "Gabrielle", "initials": "G"}, {"family": "Cornelis", "given": "Marilyn C", "initials": "MC"}, {"family": "Gudbjartsson", "given": "Daniel", "initials": "D"}, {"family": "Hadley", "given": "David", "initials": "D"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "den Heijer", "given": "Martin", "initials": "M"}, {"family": "Igl", "given": "Wilmar", "initials": "W"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Kemp", "given": "John P", "initials": "JP"}, {"family": "Kristiansson", "given": "Kati", "initials": "K"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "Njajou", "given": "Omer T", "initials": "OT"}, {"family": "O'Reilly", "given": "Paul F", "initials": "PF"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "St Pourcain", "given": "Beate", "initials": "B"}, {"family": "Rankinen", "given": "Tuomo", "initials": "T"}, {"family": "Salo", "given": "Perttu", "initials": "P"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Waite", "given": "Lindsay", "initials": "L"}, {"family": "Wheeler", "given": "William", "initials": "W"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Draisma", "given": "Harmen H M", "initials": "HHM"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Kerr", "given": "Kathleen F", "initials": "KF"}, {"family": "Lind", "given": "Penelope A", "initials": "PA"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Onland-Moret", "given": "N Charlotte", "initials": "NC"}, {"family": "Song", "given": "Ci", "initials": "C"}, {"family": "Weedon", "given": "Michael N", "initials": "MN"}, {"family": "Xie", "given": "Weijia", "initials": "W"}, {"family": "Yengo", "given": "Loic", "initials": "L"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Albert", "given": "Christine M", "initials": "CM"}, {"family": "Alonso", "given": "Alvaro", "initials": "A"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "de Bakker", "given": "Paul I W", "initials": "PIW"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Barlassina", "given": "Cristina", "initials": "C"}, {"family": "Benaglio", "given": "Paola", "initials": "P"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "Brage", "given": "S\u00f8ren", "initials": "S"}, {"family": "Chanock", "given": "Stephen J", "initials": "SJ"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Chung", "given": "Mina", "initials": "M"}, {"family": "Darbar", "given": "Dawood", "initials": "D"}, {"family": "Dina", "given": "Christian", "initials": "C"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Felix", "given": "Stephan B", "initials": "SB"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Goyette", "given": "Philippe", "initials": "P"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hartikainen", "given": "Anna-Liisa", "initials": "A"}, {"family": "Havulinna", "given": "Aki S", "initials": "AS"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Holewijn", "given": "Suzanne", "initials": "S"}, {"family": "Hoogstra-Berends", "given": "Femke", "initials": "F"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "J"}, {"family": "Jensen", "given": "Majken K", "initials": "MK"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Junttila", "given": "Juhani", "initials": "J"}, {"family": "K\u00e4\u00e4b", "given": "Stefan", "initials": "S"}, {"family": "Kanon", "given": "Bart", "initials": "B"}, {"family": "Ketkar", "given": "Shamika", "initials": "S"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "K"}, {"family": "Knowles", "given": "Joshua W", "initials": "JW"}, {"family": "Kooner", "given": "Angrad S", "initials": "AS"}, {"family": "Kors", "given": "Jan A", "initials": "JA"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Laiho", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Lakatta", "given": "Edward G", "initials": "EG"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Leusink", "given": "Maarten", "initials": "M"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Luben", "given": "Robert N", "initials": "RN"}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL"}, {"family": "Lynch", "given": "Stacey N", "initials": "SN"}, {"family": "Markus", "given": "Marcello R P", "initials": "MRP"}, {"family": "Marques-Vidal", "given": "Pedro", "initials": "P"}, {"family": "Mateo Leach", "given": "Irene", "initials": "I"}, {"family": "McArdle", "given": "Wendy L", "initials": "WL"}, {"family": "McCarroll", "given": "Steven A", "initials": "SA"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Miller", "given": "Kathryn A", "initials": "KA"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Nelis", "given": "Mari", "initials": "M"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Newman", "given": "Anne B", "initials": "AB"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Ring", "given": "Susan M", "initials": "SM"}, {"family": "Rossin", "given": "Elizabeth J", "initials": "EJ"}, {"family": "Rudan", "given": "Diana", "initials": "D"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Sehmi", "given": "Jaban S", "initials": "JS"}, {"family": "Sharp", "given": "Stephen", "initials": "S"}, {"family": "Shin", "given": "Jordan T", "initials": "JT"}, {"family": "Singleton", "given": "Andrew B", "initials": "AB"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Stewart", "given": "Chip", "initials": "C"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Tarasov", "given": "Kirill V", "initials": "KV"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Vandenput", "given": "Liesbeth", "initials": "L"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "S"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Wijmenga", "given": "Cisca", "initials": "C"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JCM"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Wong", "given": "Quenna", "initials": "Q"}, {"family": "Jamshidi", "given": "Yalda", "initials": "Y"}, {"family": "Zitting", "given": "Paavo", "initials": "P"}, {"family": "Boer", "given": "Jolanda M A", "initials": "JMA"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Ekelund", "given": "Ulf", "initials": "U"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Hingorani", "given": "Aroon", "initials": "A"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Kronmal", "given": "Richard A", "initials": "RA"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Quertermous", "given": "Thomas", "initials": "T"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "van der Schouw", "given": "Yvonne T", "initials": "YT"}, {"family": "Verschuren", "given": "W M Monique", "initials": "WMM"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Albanes", "given": "Demetrius", "initials": "D"}, {"family": "Arnar", "given": "David O", "initials": "DO"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "de Boer", "given": "Rudolf A", "initials": "RA"}, {"family": "Bouchard", "given": "Claude", "initials": "C"}, {"family": "Caulfield", "given": "W L Mark", "initials": "WLM"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Curhan", "given": "Gary", "initials": "G"}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "Eriksson", "given": "Johan", "initials": "J"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "van Gilst", "given": "Wiek H", "initials": "WH"}, {"family": "Glorioso", "given": "Nicola", "initials": "N"}, {"family": "de Graaf", "given": "Jacqueline", "initials": "J"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hsueh", "given": "Wen-Chi", "initials": "W"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Huikuri", "given": "Heikki V", "initials": "HV"}, {"family": "Hunter", "given": "David J", "initials": "DJ"}, {"family": "Iribarren", "given": "Carlos", "initials": "C"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kiemeney", "given": "Lambertus A", "initials": "LA"}, {"family": "van der Klauw", "given": "Melanie M", "initials": "MM"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Iacoviello", "given": "Licia", "initials": "L"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lokki", "given": "Marja-Liisa L", "initials": "ML"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Navis", "given": "Gerjan", "initials": "G"}, {"family": "Nieminen", "given": "Markku S", "initials": "MS"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Poulter", "given": "Neil R", "initials": "NR"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Rimm", "given": "Eric B", "initials": "EB"}, {"family": "Rioux", "given": "John D", "initials": "JD"}, {"family": "Rizzi", "given": "Federica", "initials": "F"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Sever", "given": "Peter S", "initials": "PS"}, {"family": "Shields", "given": "Denis C", "initials": "DC"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Sinisalo", "given": "Juha", "initials": "J"}, {"family": "Stanton", "given": "Alice V", "initials": "AV"}, {"family": "Stolk", "given": "Ronald P", "initials": "RP"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Tardif", "given": "Jean-Claude", "initials": "J"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Tuomilehto", "given": "Jaako", "initials": "J"}, {"family": "van Veldhuisen", "given": "Dirk J", "initials": "DJ"}, {"family": "Virtamo", "given": "Jarmo", "initials": "J"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Waeber", "given": "G\u00e9rard", "initials": "G"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Cho", "given": "Yoon Shin", "initials": "YS"}, {"family": "Olsen", "given": "Jesper V", "initials": "JV"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Willer", "given": "Cristen", "initials": "C"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Global BPgen Consortium", "given": "None", "initials": "N"}, {"family": "CARDIoGRAM Consortium", "given": "None", "initials": "N"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Thompson", "given": "John R", "initials": "JR"}, {"family": "PR GWAS Consortium", "given": "None", "initials": "N"}, {"family": "Pfeufer", "given": "Arne", "initials": "A"}, {"family": "QRS GWAS Consortium", "given": "None", "initials": "N"}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "QT-IGC Consortium", "given": "None", "initials": "N"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "CHARGE-AF Consortium", "given": "None", "initials": "N"}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT"}, {"family": "Stricker", "given": "Bruno H Ch", "initials": "BHC"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Beckmann", "given": "Jacques S", "initials": "JS"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Sibon", "given": "Ody C M", "initials": "OCM"}, {"family": "Milan", "given": "David J", "initials": "DJ"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "45", "issn": "1546-1718", "issue": "6", "pages": "621-631", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Elevated resting heart rate is associated with greater risk of cardiovascular disease and mortality. In a 2-stage meta-analysis of genome-wide association studies in up to 181,171 individuals, we identified 14 new loci associated with heart rate and confirmed associations with all 7 previously established loci. Experimental downregulation of gene expression in Drosophila melanogaster and Danio rerio identified 20 genes at 11 loci that are relevant for heart rate regulation and highlight a role for genes involved in signal transmission, embryonic cardiac development and the pathophysiology of dilated cardiomyopathy, congenital heart failure and/or sudden cardiac death. In addition, genetic susceptibility to increased heart rate is associated with altered cardiac conduction and reduced risk of sick sinus syndrome, and both heart rate-increasing and heart rate-decreasing variants associate with risk of atrial fibrillation. Our findings provide fresh insights into the mechanisms regulating heart rate and identify new therapeutic targets.", "doi": "10.1038/ng.2610", "pmid": "23583979", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.2610"}, {"db": "pmc", "key": "PMC3696959"}, {"db": "mid", "key": "NIHMS473857"}], "notes": [], "created": "2017-05-04T14:58:06.694Z", "modified": "2020-01-21T13:56:08.711Z"}, {"entity": "publication", "iuid": "8fafa408f1fa4183a437402e9e8dbb47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fafa408f1fa4183a437402e9e8dbb47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fafa408f1fa4183a437402e9e8dbb47"}}, "title": "Gambogic acid is cytotoxic to cancer cells through inhibition of the ubiquitin-proteasome system.", "authors": [{"family": "Felth", "given": "Jenny", "initials": "J"}, {"family": "Lesiak-Mieczkowska", "given": "Karolina", "initials": "K"}, {"family": "D'Arcy", "given": "Padraig", "initials": "P"}, {"family": "Haglund", "given": "Caroline", "initials": "C"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Linder", "given": "Stig", "initials": "S"}, {"family": "Bohlin", "given": "Lars", "initials": "L"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Rickardson", "given": "Linda", "initials": "L"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "31", "issn": "1573-0646", "issue": "3", "pages": "587-598", "title": "Invest New Drugs", "issn-l": "0167-6997"}, "abstract": "Gambogic acid (GA), displays cytotoxicity towards a wide variety of tumor cells and has been shown to affect many important cell-signaling pathways. In the present work, we investigated the mechanism of action of GA by analysis of drug-induced changes in gene expression profiles and identified GA and the derivative dihydro GA as possible inhibitors of the ubiquitin-proteasome system (UPS). Both GA and dihydro GA inhibited proteasome function in cells resulting in the accumulation of polyubiquitin complexes. In vitro experiments showed that both GA and dihydro GA inhibited 20S chymotrypsin activity and the inhibitory effects of GA and dihydro GA on proteasome function corresponded with apoptosis induction and cell death. In conclusion, our results show that GA and dihydro GA exert their cytotoxic activity through inhibition of the UPS, specifically by acting as inhibitors of the chymotrypsin activity of the 20S proteasome.", "doi": "10.1007/s10637-012-9902-y", "pmid": "23179339", "labels": {"Array and Analysis Facility": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:58.925Z", "modified": "2017-05-30T12:37:22.819Z"}, {"entity": "publication", "iuid": "a545c6ba60cb45c2997f9f552360db45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a545c6ba60cb45c2997f9f552360db45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a545c6ba60cb45c2997f9f552360db45"}}, "title": "Exome sequencing in diagnostic evaluation of colorectal cancer predisposition in young patients.", "authors": [{"family": "Tanskanen", "given": "Tomas", "initials": "T"}, {"family": "Gylfe", "given": "Alexandra E", "initials": "AE"}, {"family": "Katainen", "given": "Riku", "initials": "R"}, {"family": "Taipale", "given": "Minna", "initials": "M"}, {"family": "Renkonen-Sinisalo", "given": "Laura", "initials": "L"}, {"family": "Mecklin", "given": "Jukka-Pekka", "initials": "JP"}, {"family": "J\u00e4rvinen", "given": "Heikki", "initials": "H"}, {"family": "Tuupanen", "given": "Sari", "initials": "S"}, {"family": "Kilpivaara", "given": "Outi", "initials": "O"}, {"family": "Vahteristo", "given": "Pia", "initials": "P"}, {"family": "Aaltonen", "given": "Lauri A", "initials": "LA"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "48", "issn": "1502-7708", "issue": "6", "pages": "672-678", "title": "Scand. J. Gastroenterol.", "issn-l": "0036-5521"}, "abstract": "Early-onset colorectal cancer (CRC), defined here as age of onset less than 40 years, develops frequently in genetically predisposed individuals. Next-generation sequencing is an increasingly available option in the diagnostic workup of suspected hereditary susceptibility, but little is known about the practical feasibility and additional diagnostic yield of the technology in this patient group.\n\nWe analyzed 38 young CRC patients derived from a set of 1514 CRC cases. All 38 tumors had been tested in our laboratory for microsatellite instability (MSI), and Sanger sequencing had been used to screen for MLH1 and MSH2 mutations in MSI cases. Also, gastrointestinal polyposis had been diagnosed clinically and molecularly. Family histories were acquired from national registries. If inherited syndromes had not been diagnosed in routine diagnostic efforts (n = 23), normal tissue DNA was analyzed for mutations in a comprehensive set of high-penetrance genes (MLH1, MSH2, MSH6, PMS2, APC, MUTYH, SMAD4, BMPR1A, LKB1/STK11, and PTEN) by exome sequencing.\n\nCRC predisposition syndromes were confirmed in 42% (16/38) of early-onset CRC patients. Hereditary nonpolyposis colorectal cancer was diagnosed in 12 (32%) patients, familial adenomatous polyposis in three (7.9%), and juvenile polyposis in one (2.6%) patient. Exome sequencing revealed one additional MLH1 mutation. Over half of the patients had advanced cancers (Dukes C or D, 61%, 23/38). The majority of nonsyndromic patients had unaffected first-degree relatives and microsatellite-stable tumors.\n\nMicrosatellite instability positivity or gastrointestinal polyposis characterized all patients with unambiguous highly penetrant germline mutations. In our series, exome sequencing produced little added value in diagnosing the underlying predisposition conditions.", "doi": "10.3109/00365521.2013.783102", "pmid": "23544471", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:06.890Z", "modified": "2017-05-30T11:44:21.885Z"}, {"entity": "publication", "iuid": "2e1c8dcca9af48ef929ced291f139685", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e1c8dcca9af48ef929ced291f139685.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e1c8dcca9af48ef929ced291f139685"}}, "title": "Coronary heart disease in systemic lupus erythematosus is associated with interferon regulatory factor-8 gene variants.", "authors": [{"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Berggren", "given": "Olof", "initials": "O"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Bengtsson", "given": "Christine", "initials": "C"}, {"family": "Wang", "given": "Chuan", "initials": "C"}, {"family": "Jensen-Urstad", "given": "Kerstin", "initials": "K"}, {"family": "Granstam", "given": "Sven-Olof", "initials": "SO"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Gustafsson", "given": "Johanna T", "initials": "JT"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "6", "issn": "1942-3268", "issue": "3", "pages": "255-263", "title": "Circ Cardiovasc Genet", "issn-l": null}, "abstract": "Patients with systemic lupus erythematosus have increased morbidity and mortality in coronary heart disease (CHD). We asked whether there was a genetic influence on CHD in systemic lupus erythematosus.\n\nThe association between single-nucleotide polymorphisms (SNPs) and CHD in 2 populations of patients with systemic lupus erythematosus was assessed. Patients were genotyped on a custom 12k Illumina Array. The allele frequencies were compared between patients with (n=66) and without (n=509) CHD. We found 61 SNPs with an association (P<0.01) to CHD, with the strongest association for 3 SNPs located in the interferon regulatory factor-8 (IRF8) gene. Comparison of the allele frequencies of these 61 SNPs in patients with (n=27) and without (n=212) CHD in the second study population revealed that 2 SNPs, rs925994 and rs10514610 in IRF8 (linkage disequilibrium, r\u00b2=0.84), were associated with CHD in both study populations. Meta-analysis of the SNP rs925994 gave an odds ratio of 3.6 (2.1-6.3), P value 1.9\u00d710\u207b\u2076. The identified IRF8 allele remained as a risk factor for CHD after adjustment for traditional CHD risk factors. The IRF8 risk allele was associated with the presence of carotid plaques (P<0.001) and increased intima-media thickness (P=0.01). By electrophoretic mobility shift assays, we show weaker binding of protein to the risk allele of the highly linked SNP rs11117415, and by flow cytometry, a reduced frequency of circulating B cells was detected in patients with the IRF8 risk allele.\n\nThere is a considerable genetic component for CHD in systemic lupus erythematosus, with IRF8 as a strong susceptibility locus.", "doi": "10.1161/CIRCGENETICS.113.000044", "pmid": "23661672", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "CIRCGENETICS.113.000044"}], "notes": [], "created": "2017-05-04T15:01:15.613Z", "modified": "2021-07-07T15:11:02.370Z"}, {"entity": "publication", "iuid": "803765ea306c4adb91b9b63b6c26996c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/803765ea306c4adb91b9b63b6c26996c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/803765ea306c4adb91b9b63b6c26996c"}}, "title": "Contribution of IKBKE and IFIH1 gene variants to SLE susceptibility.", "authors": [{"family": "Wang", "given": "C", "initials": "C"}, {"family": "Ahlford", "given": "A", "initials": "A"}, {"family": "Laxman", "given": "N", "initials": "N"}, {"family": "Nordmark", "given": "G", "initials": "G"}, {"family": "Eloranta", "given": "M-L", "initials": "ML"}, {"family": "Gunnarsson", "given": "I", "initials": "I"}, {"family": "Svenungsson", "given": "E", "initials": "E"}, {"family": "Padyukov", "given": "L", "initials": "L"}, {"family": "Sturfelt", "given": "G", "initials": "G"}, {"family": "J\u00f6nsen", "given": "A", "initials": "A"}, {"family": "Bengtsson", "given": "A A", "initials": "AA"}, {"family": "Truedsson", "given": "L", "initials": "L"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "S", "initials": "S"}, {"family": "Sj\u00f6wall", "given": "C", "initials": "C"}, {"family": "Sandling", "given": "J K", "initials": "JK"}, {"family": "R\u00f6nnblom", "given": "L", "initials": "L"}, {"family": "Syv\u00e4nen", "given": "A-C", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "14", "issn": "1476-5470", "issue": "4", "pages": "217-222", "title": "Genes Immun.", "issn-l": "1466-4879"}, "abstract": "The type I interferon system genes IKBKE and IFIH1 are associated with the risk of systemic lupus erythematosus (SLE). To identify the sequence variants that are able to account for the disease association, we resequenced the genes IKBKE and IFIH1. Eighty-six single-nucleotide variants (SNVs) with potentially functional effect or differences in allele frequencies between patients and controls determined by sequencing were further genotyped in 1140 SLE patients and 2060 controls. In addition, 108 imputed sequence variants in IKBKE and IFIH1 were included in the association analysis. Ten IKBKE SNVs and three IFIH1 SNVs were associated with SLE. The SNVs rs1539241 and rs12142086 tagged two independent association signals in IKBKE, and the haplotype carrying their risk alleles showed an odds ratio of 1.68 (P-value=1.0 \u00d7 10(-5)). The risk allele of rs12142086 affects the binding of splicing factor 1 in vitro and could thus influence its transcriptional regulatory function. Two independent association signals were also detected in IFIH1, which were tagged by a low-frequency SNV rs78456138 and a missense SNV rs3747517. Their joint effect is protective against SLE (odds ratio=0.56; P-value=6.6 \u00d7 10(-3)). In conclusion, we have identified new SLE-associated sequence variants in IKBKE and IFIH1, and proposed functional hypotheses for the association signals.", "doi": "10.1038/gene.2013.9", "pmid": "23535865", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "gene20139"}], "notes": [], "created": "2017-05-04T15:01:18.482Z", "modified": "2021-07-07T15:11:02.253Z"}, {"entity": "publication", "iuid": "ac199852b6e74b4fbb9e72bfc2ea70f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac199852b6e74b4fbb9e72bfc2ea70f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac199852b6e74b4fbb9e72bfc2ea70f6"}}, "title": "Circadian regulation of melanization and prokineticin homologues is conserved in the brain of freshwater crayfish and zebrafish.", "authors": [{"family": "Noonin", "given": "Chadanat", "initials": "C"}, {"family": "Watthanasurorot", "given": "Apiruck", "initials": "A"}, {"family": "Winberg", "given": "Svante", "initials": "S"}, {"family": "S\u00f6derh\u00e4ll", "given": "Irene", "initials": "I"}], "type": "comparative study", "published": "2013-06-00", "journal": {"volume": "40", "issn": "1879-0089", "issue": "2", "pages": "218-226", "title": "Dev. Comp. Immunol.", "issn-l": "0145-305X"}, "abstract": "Circadian clock is important to living organisms to adjust to the external environment. This clock has been extensively studied in mammals, and prokineticin 2 (Prok2) acts as one of the messenger between the central nervous system and peripheral tissues. In this study, expression profiles of Prok1 and Prok2 were investigated in a non-mammalian vertebrate brain, zebrafish, and the expression was compared to the Prok homologues, astakines (Ast1 and Ast2) in crayfish. These transcripts exhibited circadian oscillation in the brain, and Ast1 had similar pattern to Prok2. In addition, the expression of tyrosinase, an enzyme which expression is regulated by E-box elements like in Prok2, was also examined in zebrafish brain and was compared with the expression of prophenoloxidase (proPO), the melanization enzyme, in crayfish brain. Interestingly, the expressions of both Tyr and proPO displayed circadian rhythm in a similar pattern to Prok2 and Ast1, respectively. Therefore, this study shows that circadian oscillation of prokineticin homologues and enzymes involved in melanization are conserved.", "doi": "10.1016/j.dci.2013.03.002", "pmid": "23500514", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "Genome Engineering Zebrafish": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0145-305X(13)00057-8"}], "notes": [], "created": "2017-05-04T14:57:51.888Z", "modified": "2020-01-21T13:56:04.515Z"}, {"entity": "publication", "iuid": "335fdcd40a9747538176a8109141ebe6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/335fdcd40a9747538176a8109141ebe6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/335fdcd40a9747538176a8109141ebe6"}}, "title": "A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species.", "authors": [{"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Gyllenstrand", "given": "Niclas", "initials": "N"}, {"family": "Lagercrantz", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "162", "issn": "1532-2548", "issue": "2", "pages": "741-754", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": "Small RNAs (sRNAs), including microRNA (miRNA) and short-interfering RNA (siRNA), are important in the regulation of diverse biological processes. Comparative studies of sRNAs from plants have mainly focused on miRNA, even though they constitute a mere fraction of the total sRNA diversity. In this study, we report results from an in-depth analysis of the sRNA population from the conifer spruce (Picea abies) and compared the results with those of a range of plant species. The vast majority of sRNA sequences in spruce can be assigned to 21-nucleotide-long siRNA sequences, of which a large fraction originate from the degradation of transcribed sequences related to nucleotide-binding site-leucine-rich repeat-type resistance genes. Over 90% of all genes predicted to contain either a Toll/interleukin-1 receptor or nucleotide-binding site domain showed evidence of siRNA degradation. The data further suggest that this phased degradation of resistance-related genes is initiated from miRNA-guided cleavage, often by an abundant 22-nucleotide miRNA. Comparative analysis over a range of plant species revealed a huge variation in the abundance of this phenomenon. The process seemed to be virtually absent in several species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and nonvascular plants, while particularly high frequencies were observed in spruce, grape (Vitis vinifera), and poplar (Populus trichocarpa). This divergent pattern might reflect a mechanism to limit runaway transcription of these genes in species with rapidly expanding nucleotide-binding site-leucine-rich repeat gene families. Alternatively, it might reflect variation in a counter-counter defense mechanism between plant species.", "doi": "10.1104/pp.113.214643", "pmid": "23580593", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "pp.113.214643"}, {"db": "pmc", "key": "PMC3668067"}, {"db": "GENBANK", "key": "ACN49932"}, {"db": "GENBANK", "key": "TC161203"}, {"db": "GEO", "key": "GSE28755"}], "notes": [], "created": "2017-05-04T15:01:25.782Z", "modified": "2020-01-21T13:56:01.434Z"}, {"entity": "publication", "iuid": "c403f99f84324b52bc5e13ce42920772", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c403f99f84324b52bc5e13ce42920772.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c403f99f84324b52bc5e13ce42920772"}}, "title": "The Norway spruce genome sequence and conifer genome evolution.", "authors": [{"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Wetterbom", "given": "Anna", "initials": "A"}, {"family": "Zuccolo", "given": "Andrea", "initials": "A"}, {"family": "Lin", "given": "Yao-Cheng", "initials": "YC"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Vicedomini", "given": "Riccardo", "initials": "R"}, {"family": "Sahlin", "given": "Kristoffer", "initials": "K"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "Gramzow", "given": "Lydia", "initials": "L"}, {"family": "Holmberg", "given": "Kristina", "initials": "K"}, {"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "Keech", "given": "Olivier", "initials": "O"}, {"family": "Klasson", "given": "Lisa", "initials": "L"}, {"family": "Koriabine", "given": "Maxim", "initials": "M"}, {"family": "Kucukoglu", "given": "Melis", "initials": "M"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Luthman", "given": "Johannes", "initials": "J"}, {"family": "Lysholm", "given": "Fredrik", "initials": "F"}, {"family": "Niittyl\u00e4", "given": "Totte", "initials": "T"}, {"family": "Olson", "given": "Ake", "initials": "A"}, {"family": "Rilakovic", "given": "Nemanja", "initials": "N"}, {"family": "Ritland", "given": "Carol", "initials": "C"}, {"family": "Rossell\u00f3", "given": "Josep A", "initials": "JA"}, {"family": "Sena", "given": "Juliana", "initials": "J"}, {"family": "Svensson", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Talavera-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Thei\u00dfen", "given": "G\u00fcnter", "initials": "G"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}, {"family": "Vanneste", "given": "Kevin", "initials": "K"}, {"family": "Wu", "given": "Zhi-Qiang", "initials": "ZQ"}, {"family": "Zhang", "given": "Bo", "initials": "B"}, {"family": "Zerbe", "given": "Philipp", "initials": "P"}, {"family": "Arvestad", "given": "Lars", "initials": "L"}, {"family": "Bhalerao", "given": "Rishikesh", "initials": "R"}, {"family": "Bohlmann", "given": "Joerg", "initials": "J"}, {"family": "Bousquet", "given": "Jean", "initials": "J"}, {"family": "Garcia Gil", "given": "Rosario", "initials": "R"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "de Jong", "given": "Pieter", "initials": "P"}, {"family": "MacKay", "given": "John", "initials": "J"}, {"family": "Morgante", "given": "Michele", "initials": "M"}, {"family": "Ritland", "given": "Kermit", "initials": "K"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Thompson", "given": "Stacey Lee", "initials": "SL"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2013-05-30", "journal": {"volume": "497", "issn": "1476-4687", "issue": "7451", "pages": "579-584", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.", "doi": "10.1038/nature12211", "pmid": "23698360", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support for Computational Resources": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "nature12211"}], "notes": [], "created": "2017-05-04T14:56:13.625Z", "modified": "2024-01-16T13:48:50.828Z"}, {"entity": "publication", "iuid": "64d97f6f868b4d2bbc3249798373be4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64d97f6f868b4d2bbc3249798373be4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64d97f6f868b4d2bbc3249798373be4c"}}, "title": "Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria.", "authors": [{"family": "Herlemann", "given": "Daniel P R", "initials": "DP"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Zheng", "given": "Zongli", "initials": "Z"}, {"family": "Aspeborg", "given": "Henrik", "initials": "H"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2013-05-28", "journal": {"volume": "4", "issn": "2150-7511", "issue": "3", "pages": "e00569-e00512", "title": "MBio", "issn-l": null}, "abstract": "The verrucomicrobial subdivision 2 class Spartobacteria is one of the most abundant bacterial lineages in soil and has recently also been found to be ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of the Spartobacteria is one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within the Spartobacteria exists. Since no aquatic representative from the Spartobacteria has been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic Sea Spartobacteria phylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near-complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates, like cellulose, mannan, xylan, chitin, and starch, as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype's distribution within the Baltic Sea indicate a connection to Cyanobacteria that may be the main source of the polysaccharide substrates.", "doi": "10.1128/mBio.00569-12", "pmid": "23716574", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "mBio.00569-12"}, {"db": "pmc", "key": "PMC3663571"}, {"db": "GENBANK", "key": "ADX05696"}, {"db": "GENBANK", "key": "AF217460"}, {"db": "GENBANK", "key": "AF217461"}, {"db": "GENBANK", "key": "AF217462"}], "notes": [], "created": "2017-05-04T14:58:03.611Z", "modified": "2020-01-21T13:56:02.742Z"}, {"entity": "publication", "iuid": "615d5e0b24d64d0aa511ff1ad6784068", "links": {"self": {"href": "https://publications.scilifelab.se/publication/615d5e0b24d64d0aa511ff1ad6784068.json"}, "display": {"href": "https://publications.scilifelab.se/publication/615d5e0b24d64d0aa511ff1ad6784068"}}, "title": "Dynamic gradients of an intermediate filament-like cytoskeleton are recruited by a polarity landmark during apical growth.", "authors": [{"family": "Fuchino", "given": "Katsuya", "initials": "K"}, {"family": "Bagchi", "given": "Sonchita", "initials": "S"}, {"family": "Cantlay", "given": "Stuart", "initials": "S"}, {"family": "Sandblad", "given": "Linda", "initials": "L", "orcid": "0000-0003-3492-3287", "researcher": {"href": "https://publications.scilifelab.se/researcher/070825e0190a4e9a932e79663d2bc89f.json"}}, {"family": "Wu", "given": "Di", "initials": "D"}, {"family": "Bergman", "given": "Jessica", "initials": "J"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Fl\u00e4rdh", "given": "Klas", "initials": "K"}, {"family": "Ausmees", "given": "Nora", "initials": "N"}], "type": "journal article", "published": "2013-05-21", "journal": {"volume": "110", "issn": "1091-6490", "issue": "21", "pages": "E1889-E1897", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Intermediate filament (IF)-like cytoskeleton emerges as a versatile tool for cellular organization in all kingdoms of life, underscoring the importance of mechanistically understanding its diverse manifestations. We showed previously that, in Streptomyces (a bacterium with a mycelial lifestyle similar to that of filamentous fungi, including extreme cell and growth polarity), the IF protein FilP confers rigidity to the hyphae by an unknown mechanism. Here, we provide a possible explanation for the IF-like function of FilP by demonstrating its ability to self-assemble into a cis-interconnected regular network in vitro and its localization into structures consistent with a cytoskeletal network in vivo. Furthermore, we reveal that a spatially restricted interaction between FilP and DivIVA, the main component of the Streptomyces polarisome complex, leads to formation of apical gradients of FilP in hyphae undergoing active tip extension. We propose that the coupling between the mechanism driving polar growth and the assembly of an IF cytoskeleton provides each new hypha with an additional stress-bearing structure at its tip, where the nascent cell wall is inevitably more flexible and compliant while it is being assembled and matured. Our data suggest that recruitment of cytoskeleton around a cell polarity landmark is a broadly conserved strategy in tip-growing cells.", "doi": "10.1073/pnas.1305358110", "pmid": "23641002", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "1305358110"}, {"db": "pmc", "key": "PMC3666699"}], "notes": [], "created": "2017-05-04T14:55:27.064Z", "modified": "2023-04-14T13:56:29.030Z"}, {"entity": "publication", "iuid": "1dae3a5e0d3f4edfaa37026908d2f20f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1dae3a5e0d3f4edfaa37026908d2f20f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1dae3a5e0d3f4edfaa37026908d2f20f"}}, "title": "A texture based pattern recognition approach to distinguish melanoma from non-melanoma cells in histopathological tissue microarray sections.", "authors": [{"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Agnarsd\u00f3ttir", "given": "Margr\u00e9t", "initials": "M"}, {"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}], "type": "comparative study", "published": "2013-05-17", "journal": {"volume": "8", "issn": "1932-6203", "issue": "5", "pages": "e62070", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Immunohistochemistry is a routine practice in clinical cancer diagnostics and also an established technology for tissue-based research regarding biomarker discovery efforts. Tedious manual assessment of immunohistochemically stained tissue needs to be fully automated to take full advantage of the potential for high throughput analyses enabled by tissue microarrays and digital pathology. Such automated tools also need to be reproducible for different experimental conditions and biomarker targets. In this study we present a novel supervised melanoma specific pattern recognition approach that is fully automated and quantitative.\n\nMelanoma samples were immunostained for the melanocyte specific target, Melan-A. Images representing immunostained melanoma tissue were then digitally processed to segment regions of interest, highlighting Melan-A positive and negative areas. Color deconvolution was applied to each region of interest to separate the channel containing the immunohistochemistry signal from the hematoxylin counterstaining channel. A support vector machine melanoma classification model was learned from a discovery melanoma patient cohort (n = 264) and subsequently validated on an independent cohort of melanoma patient tissue sample images (n = 157).\n\nHere we propose a novel method that takes advantage of utilizing an immuhistochemical marker highlighting melanocytes to fully automate the learning of a general melanoma cell classification model. The presented method can be applied on any protein of interest and thus provides a tool for quantification of immunohistochemistry-based protein expression in melanoma.", "doi": "10.1371/journal.pone.0062070", "pmid": "23690928", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-33946"}, {"db": "pmc", "key": "PMC3656869"}], "notes": [], "created": "2017-05-04T14:55:15.014Z", "modified": "2021-07-08T13:44:33.066Z"}, {"entity": "publication", "iuid": "8cb99d88b98744529ed74d2eed93d1c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cb99d88b98744529ed74d2eed93d1c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cb99d88b98744529ed74d2eed93d1c6"}}, "title": "Adaptive mutations and replacements of virulence traits in the Escherichia coli O104:H4 outbreak population.", "authors": [{"family": "Guy", "given": "Lionel", "initials": "L"}, {"family": "Jernberg", "given": "Cecilia", "initials": "C"}, {"family": "Arv\u00e9n Norling", "given": "Jenny", "initials": "J"}, {"family": "Ivarsson", "given": "Sofie", "initials": "S"}, {"family": "Hedenstr\u00f6m", "given": "Ingela", "initials": "I"}, {"family": "Melefors", "given": "\u00d6jar", "initials": "\u00d6"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Andersson", "given": "Siv G E", "initials": "SGE"}], "type": "journal article", "published": "2013-05-10", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "8", "issue": "5", "pages": "e63027"}, "abstract": "The sequencing of highly virulent Escherichia coli O104:H4 strains isolated during the outbreak of bloody diarrhea and hemolytic uremic syndrome in Europe in 2011 revealed a genome that contained a Shiga toxin encoding prophage and a plasmid encoding enteroaggregative fimbriae. Here, we present the draft genome sequence of a strain isolated in Sweden from a patient who had travelled to Tunisia in 2010 (E112/10) and was found to differ from the outbreak strains by only 38 SNPs in non-repetitive regions, 16 of which were mapped to the branch to the outbreak strain. We identified putatively adaptive mutations in genes for transporters, outer surface proteins and enzymes involved in the metabolism of carbohydrates. A comparative analysis with other historical strains showed that E112/10 contained Shiga toxin prophage genes of the same genotype as the outbreak strain, while these genes have been replaced by a different genotype in two otherwise very closely related strains isolated in the Republic of Georgia in 2009. We also present the genome sequences of two enteroaggregative E. coli strains affiliated with phylogroup A (C43/90 and C48/93) that contain the agg genes for the AAF/I-type fimbriae characteristic of the outbreak population. Interestingly, C43/90 also contained a tet/mer antibiotic resistance island that was nearly identical in sequence to that of the outbreak strain, while the corresponding island in the Georgian strains was most similar to E. coli strains of other serotypes. We conclude that the pan-genome of the outbreak population is shared with strains of the A phylogroup and that its evolutionary history is littered with gene replacement events, including most recently independent acquisitions of antibiotic resistance genes in the outbreak strains and its nearest neighbors. The results are summarized in a refined evolutionary model for the emergence of the O104:H4 outbreak population.", "doi": "10.1371/journal.pone.0063027", "pmid": "23675451", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-13-05699"}, {"db": "pmc", "key": "PMC3651199"}], "notes": [], "created": "2017-05-04T14:58:15.248Z", "modified": "2022-03-31T15:21:14.631Z"}, {"entity": "publication", "iuid": "15185a5ef0034f8ea1dcde6ce36c2c01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15185a5ef0034f8ea1dcde6ce36c2c01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15185a5ef0034f8ea1dcde6ce36c2c01"}}, "title": "Age dependence of tumor genetics in unfavorable neuroblastoma: arrayCGH profiles of 34 consecutive cases, using a Swedish 25-year neuroblastoma cohort for validation.", "authors": [{"family": "Cetinkaya", "given": "Cihan", "initials": "C"}, {"family": "Martinsson", "given": "Tommy", "initials": "T"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "Tr\u00e4ger", "given": "Catarina", "initials": "C"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Dumanski", "given": "Jan", "initials": "J"}, {"family": "D\u00edaz de St\u00e5hl", "given": "Teresita", "initials": "T"}, {"family": "Hedborg", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2013-05-09", "journal": {"volume": "13", "issn": "1471-2407", "issue": null, "pages": "231", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Aggressive neuroblastoma remains a significant cause of childhood cancer death despite current intensive multimodal treatment protocols. The purpose of the present work was to characterize the genetic and clinical diversity of such tumors by high resolution arrayCGH profiling.\n\nBased on a 32K BAC whole-genome tiling path array and using 50-250K Affymetrix SNP array platforms for verification, DNA copy number profiles were generated for 34 consecutive high-risk or lethal outcome neuroblastomas. In addition, age and MYCN amplification (MNA) status were retrieved for 112 unfavorable neuroblastomas of the Swedish Childhood Cancer Registry, representing a 25-year neuroblastoma cohort of Sweden, here used for validation of the findings. Statistical tests used were: Fisher's exact test, Bayes moderated t-test, independent samples t-test, and correlation analysis.\n\nMNA or segmental 11q loss (11q-) was found in 28/34 tumors. With two exceptions, these aberrations were mutually exclusive. Children with MNA tumors were diagnosed at significantly younger ages than those with 11q- tumors (mean: 27.4 vs. 69.5 months; p=0.008; n=14/12), and MNA tumors had significantly fewer segmental chromosomal aberrations (mean: 5.5 vs. 12.0; p<0.001). Furthermore, in the 11q- tumor group a positive correlation was seen between the number of segmental aberrations and the age at diagnosis (Pearson Correlation 0.606; p=0.037). Among nonMNA/non11q- tumors (n=6), one tumor displayed amplicons on 11q and 12q and three others bore evidence of progression from low-risk tumors due to retrospective evidence of disease six years before diagnosis, or due to tumor profiles with high proportions of numerical chromosomal aberrations. An early age at diagnosis of MNA neuroblastomas was verified by registry data, with an average of 29.2 months for 43 cases that were not included in the present study.\n\nMNA and segmental 11q loss define two major genetic variants of unfavorable neuroblastoma with apparent differences in their pace of tumor evolution and in genomic integrity. Other possible, but less common, routes in the development of aggressive tumors are progression of low-risk infant-type lesions, and gene amplifications other than MYCN. Knowledge on such nosological diversity of aggressive neuroblastoma might influence future strategies for therapy.", "doi": "10.1186/1471-2407-13-231", "pmid": "23656755", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2407-13-231"}, {"db": "pmc", "key": "PMC3664071"}], "notes": [], "created": "2017-05-04T14:57:49.386Z", "modified": "2020-01-21T13:56:00.846Z"}, {"entity": "publication", "iuid": "2b008514b5c44b6eae6b951bc4351d20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b008514b5c44b6eae6b951bc4351d20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b008514b5c44b6eae6b951bc4351d20"}}, "title": "Genome-wide association study of susceptibility loci for cervical cancer.", "authors": [{"family": "Chen", "given": "Dan", "initials": "D"}, {"family": "Juko-Pecirep", "given": "Ivana", "initials": "I"}, {"family": "Hammer", "given": "Joanna", "initials": "J"}, {"family": "Ivansson", "given": "Emma", "initials": "E"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Gustavsson", "given": "Inger", "initials": "I"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "McKay", "given": "James D", "initials": "JD"}, {"family": "Wilander", "given": "Erik", "initials": "E"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2013-05-01", "journal": {"volume": "105", "issn": "1460-2105", "issue": "9", "pages": "624-633", "title": "J. Natl. Cancer Inst.", "issn-l": "0027-8874"}, "abstract": "Cervical carcinoma has a heritable genetic component, but the genetic basis of cervical cancer is still not well understood.\n\nWe performed a genome-wide association study of 731 422 single nucleotide polymorphisms (SNPs) in 1075 cervical cancer case subjects and 4014 control subjects and replicated it in 1140 case subjects and 1058 control subjects. The association between top SNPs and cervical cancer was estimated by odds ratios (ORs) and 95% confidence intervals (CIs) with unconditional logistic regression. All statistical tests were two-sided.\n\nThree independent loci in the major histocompatibility complex (MHC) region at 6p21.3 were associated with cervical cancer: the first is adjacent to the MHC class I polypeptide-related sequence A gene (MICA) (rs2516448; OR = 1.42, 95% CI = 1.31 to 1.54; P = 1.6\u00d710(-18)); the second is between HLA-DRB1 and HLA-DQA1 (rs9272143; OR = 0.67, 95% CI = 0.62 to 0.72; P = 9.3\u00d710(-24)); and the third is at HLA-DPB2 (rs3117027; OR=1.25, 95% CI = 1.15 to 1.35; P = 4.9\u00d710(-8)). We also confirmed previously reported associations of B*0702 and DRB1*1501-DQB1*0602 with susceptibility to and DRB1*1301-DQA1*0103-DQB1*0603 with protection against cervical cancer. The three new loci are statistically independent of these specific human leukocyte antigen alleles/haplotypes. MICA encodes a membrane-bound protein that acts as a ligand for NKG2D to activate antitumor effects. The risk allele of rs2516448 is in perfect linkage disequilibrium with a frameshift mutation (A5.1) of MICA, which results in a truncated protein. Functional analysis shows that women carrying this mutation have lower levels of membrane-bound MICA.\n\nThree novel loci in the MHC may affect susceptibility to cervical cancer in situ, including the MICA-A5.1 allele that may cause impaired immune activation and increased risk of tumor development.", "doi": "10.1093/jnci/djt051", "pmid": "23482656", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "djt051"}], "notes": [], "created": "2017-05-04T14:58:02.378Z", "modified": "2021-07-07T14:15:07.518Z"}, {"entity": "publication", "iuid": "24c00563956b47dca65bbcdb397432bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24c00563956b47dca65bbcdb397432bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24c00563956b47dca65bbcdb397432bc"}}, "title": "Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1.", "authors": [{"family": "Arczewska", "given": "Katarzyna D", "initials": "KD"}, {"family": "Tomazella", "given": "Gisele G", "initials": "GG"}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Kassahun", "given": "Henok", "initials": "H"}, {"family": "Maglioni", "given": "Silvia", "initials": "S"}, {"family": "Torgovnick", "given": "Alessandro", "initials": "A"}, {"family": "Henriksson", "given": "Johan", "initials": "J"}, {"family": "Matilainen", "given": "Olli", "initials": "O"}, {"family": "Marquis", "given": "Bryce J", "initials": "BJ"}, {"family": "Nelson", "given": "Bryant C", "initials": "BC"}, {"family": "Jaruga", "given": "Pawel", "initials": "P"}, {"family": "Babaie", "given": "Eshrat", "initials": "E"}, {"family": "Holmberg", "given": "Carina I", "initials": "CI"}, {"family": "B\u00fcrglin", "given": "Thomas R", "initials": "TR"}, {"family": "Ventura", "given": "Natascia", "initials": "N"}, {"family": "Thiede", "given": "Bernd", "initials": "B"}, {"family": "Nilsen", "given": "Hilde", "initials": "H"}], "type": "journal article", "published": "2013-05-01", "journal": {"volume": "41", "issn": "1362-4962", "issue": "10", "pages": "5368-5381", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Transcription-blocking oxidative DNA damage is believed to contribute to aging and to underlie activation of oxidative stress responses and down-regulation of insulin-like signaling (ILS) in Nucleotide Excision Repair (NER) deficient mice. Here, we present the first quantitative proteomic description of the Caenorhabditis elegans NER-defective xpa-1 mutant and compare the proteome and transcriptome signatures. Both methods indicated activation of oxidative stress responses, which was substantiated biochemically by a bioenergetic shift involving increased steady-state reactive oxygen species (ROS) and Adenosine triphosphate (ATP) levels. We identify the lesion-detection enzymes of Base Excision Repair (NTH-1) and global genome NER (XPC-1 and DDB-1) as upstream requirements for transcriptomic reprogramming as RNA-interference mediated depletion of these enzymes prevented up-regulation of genes over-expressed in the xpa-1 mutant. The transcription factors SKN-1 and SLR-2, but not DAF-16, were identified as effectors of reprogramming. As shown in human XPA cells, the levels of transcription-blocking 8,5'-cyclo-2'-deoxyadenosine lesions were reduced in the xpa-1 mutant compared to the wild type. Hence, accumulation of cyclopurines is unlikely to be sufficient for reprogramming. Instead, our data support a model where the lesion-detection enzymes NTH-1, XPC-1 and DDB-1 play active roles to generate a genomic stress signal sufficiently strong to result in transcriptomic reprogramming in the xpa-1 mutant.", "doi": "10.1093/nar/gkt225", "pmid": "23580547", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "gkt225"}, {"db": "pmc", "key": "PMC3664812"}], "notes": [], "created": "2017-05-04T15:03:15.692Z", "modified": "2021-07-05T12:48:15.949Z"}, {"entity": "publication", "iuid": "a134d16c2df64cee8cfa683333518f3f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a134d16c2df64cee8cfa683333518f3f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a134d16c2df64cee8cfa683333518f3f"}}, "title": "Variation in genes in the endothelin pathway and endothelium-dependent and endothelium-independent vasodilation in an elderly population.", "authors": [{"family": "Lind", "given": "L", "initials": "L"}, {"family": "Syv\u00e4nen", "given": "A-C", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Axelsson", "given": "T", "initials": "T"}, {"family": "Lundmark", "given": "P", "initials": "P"}, {"family": "H\u00e4gg", "given": "S", "initials": "S"}, {"family": "Larsson", "given": "A", "initials": "A"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "208", "issn": "1748-1716", "issue": "1", "pages": "88-94", "title": "Acta Physiol (Oxf)", "issn-l": "1748-1708"}, "abstract": "Indirect evidences by blockade of the endothelin receptors have suggested a role of endothelin in endothelium-dependent vasodilation. This study aimed to investigate whether circulating levels of endotehlin-1 or genetic variations in genes in the endothelin pathway were related to endothelium-dependent vasodilation.\n\nIn 1016 seventy-year-old participants of the population-based Prospective Study of the Vasculature in Uppsala Seniors (PIVUS) study (52% women), we measured endothelium-dependent vasodilation using the invasive forearm technique with acetylcholine given in the brachial artery (EDV) and the brachial artery ultrasound technique with measurement of flow-mediated dilatation (FMD). Plasma endothelin-1 levels were measured and 60 SNPs in genes in the endothelin pathway (ECE1, EDN1, EDNRA, EDNRB) were genotyped.\n\nNo significant associations were found between circulating endothelin levels and EDV or FMD. No single genotype was related to EDV or FMD following adjustment for multiple testing, but a genotype score for 3 SNPs (rs11618266 in EDNRB, rs17675063 in EDNRA, rs3026868 in ECE1) was significantly related to EDV (beta coefficient 0.070, 95% CI 0.025-0.12, P = 0.002) when adjusting for gender, systolic blood pressure, HDL and LDL cholesterol, serum triglycerides, BMI, diabetes, smoking, antihypertensive medication or statins and CRP. This score was also related to nitroprusside-induced vasodilation in the forearm.\n\nA combination of genotypes in the endothelin pathway was related to both endothelium-dependent and endothelium-independent vasodilation in forearm resistance vessels, but not in the brachial artery in an elderly population, giving evidence for a role of the endothelin system in resistance vessel reactivity independent of major cardiovascular risk factors.", "doi": "10.1111/apha.12068", "pmid": "23336501", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:13.345Z", "modified": "2021-07-07T15:11:02.266Z"}, {"entity": "publication", "iuid": "6626f21f53574b5185fe6f501426b326", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6626f21f53574b5185fe6f501426b326.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6626f21f53574b5185fe6f501426b326"}}, "title": "The combined effects of single-nucleotide polymorphisms, tobacco products, and ethanol on normal resting blood mononuclear cells.", "authors": [{"family": "Cederblad", "given": "Lena", "initials": "L"}, {"family": "Thunberg", "given": "Ulf", "initials": "U"}, {"family": "Engstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Castro", "given": "Juan", "initials": "J"}, {"family": "Rutqvist", "given": "Lars Erik", "initials": "LE"}, {"family": "Laytragoon-Lewin", "given": "Nongnit", "initials": "N"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "15", "issn": "1469-994X", "issue": "5", "pages": "890-895", "title": "Nicotine Tob. Res.", "issn-l": "1462-2203"}, "abstract": "Tobacco and ethanol consumption are crucial factors in the development of various diseases including cancer. In this investigation, we evaluated the combined effects of a number of single nucleotide polymorphisms (SNPs), with ethanol and tobacco products on healthy individuals.\r\n\r\nPure nicotine, cigarette smoke extract, and Swedish snuff (snus) extract were used. The effects were examined by means of in vitro cell cycle progression and cell death of peripheral blood mononuclear cells (PBMCs) obtained from healthy donors.\r\n\r\nAfter 3 days, in vitro, resting PBMCs entered the S and G2 stage in the presence of 100 \u00b5M nicotine. The PBMCs only proceeded to S stage, in the presence of 0.2% ethanol. The nicotine- and ethanol-induced normal cell cycle progression correlated to a number of SNPs in the IL12RB2, Rad 52, XRCC2, P53, CCND3, and ABCA1 genes. Certain SNPs in Caspases 8, IL12RB2, Rad 52, MMP2, and MDM2 genes appeared to significantly influence the effects of EtOH-, snus-, and snus + EtOH-induced cell death. Importantly, the highest degree of cell death was observed in the presence of smoke + EtOH. The amount of cell death under this treatment condition also correlated to specific SNPs, located in the MDM2, ABCA1, or GASC1 genes.\r\n\r\nCigarette smoke in combination with ethanol strongly induced massive cell death. Long-term exposure to smoke and ethanol could provoke chronic inflammation, and this could be the initiation of disease including the development of cancer at various sites.", "doi": "10.1093/ntr/nts207", "pmid": "23042982", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "nts207"}], "notes": [], "created": "2017-05-04T14:58:08.641Z", "modified": "2020-01-21T13:56:08.808Z"}, {"entity": "publication", "iuid": "04ac029b56624e018c0df25e2c99e400", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04ac029b56624e018c0df25e2c99e400.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04ac029b56624e018c0df25e2c99e400"}}, "title": "The adenovirus VA RNA-derived miRNAs are not essential for lytic virus growth in tissue culture cells.", "authors": [{"family": "Kamel", "given": "Wael", "initials": "W"}, {"family": "Segerman", "given": "Bo", "initials": "B"}, {"family": "\u00d6berg", "given": "Daniel", "initials": "D"}, {"family": "Punga", "given": "Tanel", "initials": "T"}, {"family": "Akusj\u00e4rvi", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "41", "issn": "1362-4962", "issue": "9", "pages": "4802-4812", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "At late times during a lytic infection human adenovirus type 5 produces \u223c10(8) copies per cell of virus-associated RNA I (VA RNAI). This short highly structured RNA polymerase III transcript has previously been shown to be essential for lytic virus growth. A fraction of VA RNAI is processed by Dicer into small RNAs, so-called mivaRNAIs, which are efficiently incorporated into the RNA-induced silencing complex. Here, we constructed recombinant adenoviruses with mutations in the seed sequence of both the 5'- and the 3'-strand of the mivaRNAI duplex. The results showed that late viral protein synthesis, as well as new virus progeny formation, was essentially unaffected by the seed sequence mutations under lytic replicative conditions in HeLa or HEK293 cells. Collectively, our results suggest that either strand of the mivaRNAI duplex does not have target mRNA interactions that are critical for the establishment of virus growth under lytic conditions. Further, by depletion of protein kinase R (PKR) in HEK293 cells, we show that the suppressive effect of VA RNAI on the interferon-induced PKR pathway is most critical for late gene expression.", "doi": "10.1093/nar/gkt172", "pmid": "23525465", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "gkt172"}, {"db": "pmc", "key": "PMC3643585"}], "notes": [], "created": "2017-05-04T14:58:09.246Z", "modified": "2020-01-21T13:56:00.561Z"}, {"entity": "publication", "iuid": "582a8c67757947af8da206b409f290b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/582a8c67757947af8da206b409f290b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/582a8c67757947af8da206b409f290b2"}}, "title": "Membrane protein shaving with thermolysin can be used to evaluate topology predictors.", "authors": [{"family": "Bendz", "given": "Maria", "initials": "M"}, {"family": "Skwark", "given": "Marcin", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Granholm", "given": "Viktor", "initials": "V"}, {"family": "Cristobal", "given": "Susana", "initials": "S"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "9", "pages": "1467-1480", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Topology analysis of membrane proteins can be obtained by enzymatic shaving in combination with MS identification of peptides. Ideally, such analysis could provide quite detailed information about the membrane spanning regions. Here, we examine the ability of some shaving enzymes to provide large-scale analysis of membrane proteome topologies. To compare different shaving enzymes, we first analyzed the detected peptides from two over-expressed proteins. Second, we analyzed the peptides from non-over-expressed Escherichia coli membrane proteins with known structure to evaluate the shaving methods. Finally, the identified peptides were used to test the accuracy of a number of topology predictors. At the end we suggest that the usage of thermolysin, an enzyme working at the natural pH of the cell for membrane shaving, is superior because: (i) we detect a similar number of peptides and proteins using thermolysin and trypsin; (ii) thermolysin shaving can be run at a natural pH and (iii) the incubation time is quite short. (iv) Fewer detected peptides from thermolysin shaving originate from the transmembrane regions. Using thermolysin shaving we can also provide a clear separation between the best and the less accurate topology predictors, indicating that using data from shaving can provide valuable information when developing new topology predictors.", "doi": "10.1002/pmic.201200517", "pmid": "23512833", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:28.081Z", "modified": "2020-01-21T13:53:20.509Z"}, {"entity": "publication", "iuid": "a011177aefea4d8dbac7e0bc51c6509f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a011177aefea4d8dbac7e0bc51c6509f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a011177aefea4d8dbac7e0bc51c6509f"}}, "title": "Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins.", "authors": [{"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Sagit", "given": "Rauan", "initials": "R"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Elofsson", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "1834", "issn": "0006-3002", "issue": "5", "pages": "890-897", "title": "Biochim. Biophys. Acta", "issn-l": null}, "abstract": "Proteins evolve through point mutations as well as by insertions and deletions (indels). During the last decade it has become apparent that protein regions that do not fold into three-dimensional structures, i.e. intrinsically disordered regions, are quite common. Here, we have studied the relationship between protein disorder and indels using HMM-HMM pairwise alignments in two sets of orthologous eukaryotic protein pairs. First, we show that disordered residues are much more frequent among indel residues than among aligned residues and, also are more prevalent among indels than in coils. Second, we observed that disordered residues are particularly common in longer indels. Disordered indels of short-to-medium size are prevalent in the non-terminal regions of proteins while the longest indels, ordered and disordered alike, occur toward the termini of the proteins where new structural units are comparatively well tolerated. Finally, while disordered regions often evolve faster than ordered regions and disorder is common in indels, there are some previously recognized protein families where the disordered region is more conserved than the ordered region. We find that these rare proteins are often involved in information processes, such as RNA processing and translation. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.", "doi": "10.1016/j.bbapap.2013.01.002", "pmid": "23333420", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S1570-9639(13)00007-1"}], "notes": [], "created": "2017-05-04T14:56:20.632Z", "modified": "2020-01-21T13:53:20.724Z"}, {"entity": "publication", "iuid": "62e30e406b1e47de9751a6a688fe0004", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62e30e406b1e47de9751a6a688fe0004.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62e30e406b1e47de9751a6a688fe0004"}}, "title": "Identification of acetate-oxidizing bacteria in a coastal marine surface sediment by RNA-stable isotope probing in anoxic slurries and intact cores.", "authors": [{"family": "Vandieken", "given": "Verona", "initials": "V"}, {"family": "Thamdrup", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "84", "issn": "1574-6941", "issue": "2", "pages": "373-386", "title": "FEMS Microbiol. Ecol.", "issn-l": "0168-6496"}, "abstract": "We investigated the terminal electron-accepting pathways and the acetate-oxidizing bacteria in surface sediment (0-5 mm depth) of Aarhus Bay, Denmark, in anoxic slurry and intact core incubations. In the intact cores, oxygen, nitrate, oxides of manganese and iron, and sulfate were all available and likely all used as electron acceptors by the microbial community, whereas microbial iron and sulfate reduction dominated in the slurries. The availability of electron acceptors clearly affected which organisms were labeled by 16S rRNA-stable isotope probing (SIP). Members of the Oceanospirillaceae were identified as (13) C-acetate oxidizers in both types of incubations, but bacteria related to Colwellia and Arcobacter oxidized acetate in the intact core, while members of the Desulfuromonadales and Acidithiobacillaceae did so in the slurry incubation. Desulfuromonadales sequences also dominated 16S rRNA gene clone libraries from the highest positive dilution of the acetate-oxidizing most probable number cultures with manganese and iron oxides. Thus, members of Desulfuromonadales are likely important for acetate oxidation coupled to iron and manganese reduction in situ, while the identified Gammaproteobacteria and affiliates of Arcobacter may utilize oxygen, nitrate and manganese oxides. Our study further highlights some of the biases that are associated with the use of RNA-SIP as well as slurry and intact core incubations.", "doi": "10.1111/1574-6941.12069", "pmid": "23289443", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:24.097Z", "modified": "2020-01-21T13:56:02.664Z"}, {"entity": "publication", "iuid": "04c66129954e4ca2a6da42c4278867b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04c66129954e4ca2a6da42c4278867b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04c66129954e4ca2a6da42c4278867b8"}}, "title": "Identification of a functional apolipoprotein E promoter polymorphism regulating plasma apolipoprotein E concentration.", "authors": [{"family": "Mannila", "given": "Maria Nastase", "initials": "MN"}, {"family": "Mahdessian", "given": "Hovsep", "initials": "H"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eggertsen", "given": "G\u00f6sta", "initials": "G"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "van 't Hooft", "given": "Ferdinand M", "initials": "FM"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "33", "issn": "1524-4636", "issue": "5", "pages": "1063-1069", "title": "Arterioscler. Thromb. Vasc. Biol.", "issn-l": "1079-5642"}, "abstract": "There is compelling evidence that the plasma apolipoprotein E (APOE) concentration, in addition to the APOE \u03b52/\u03b53/\u03b54 genotype, influences plasma lipoprotein levels, but the functional genetic variants influencing the plasma APOE concentration have not been identified.\n\nGenome-wide association studies in 2 cohorts of healthy, middle-aged subjects identified the APOE locus as the only genetic locus showing robust associations with the plasma APOE concentration. Fine-mapping of the APOE locus confirmed that the rs7412 \u03b52-allele is the primary genetic variant responsible for the relationship with plasma APOE concentration. Further mapping of the APOE locus uncovered that rs769446 (-427T/C) in the APOE promoter is independently associated with the plasma APOE concentration. Expression studies in 199 human liver samples demonstrated that the rs769446 C-allele is associated with increased APOE mRNA levels (P=0.015). Transient transfection studies and electrophoretic mobility shift assays in human hepatoma HepG2 cells corroborated the role of rs769446 in transcriptional regulation of APOE. However, no relationships were found between rs769446 genotype and plasma lipoprotein levels in 2 cohorts (n=1648 and n=1039) of healthy middle-aged carriers of the APOE \u03b53/\u03b53 genotype.\n\nrs769446 is a functional polymorphism involved in the regulation of the plasma APOE concentration.", "doi": "10.1161/ATVBAHA.112.300353", "pmid": "23430611", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ATVBAHA.112.300353"}], "notes": [], "created": "2017-05-04T15:01:14.470Z", "modified": "2021-07-07T15:11:02.277Z"}, {"entity": "publication", "iuid": "4314e230f7e1454ea5921f5643f9ab2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4314e230f7e1454ea5921f5643f9ab2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4314e230f7e1454ea5921f5643f9ab2a"}}, "title": "Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions.", "authors": [{"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Nitharwal", "given": "Ram G", "initials": "RG"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Behra", "given": "Krishna P R", "initials": "KPR"}, {"family": "Benedik", "given": "Evgen", "initials": "E"}, {"family": "Arasu", "given": "Uma T", "initials": "UT"}, {"family": "Islam", "given": "Nurul M", "initials": "NM"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Bhattacharya", "given": "Alok", "initials": "A"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "342", "issn": "1574-6968", "issue": "2", "pages": "98-105", "title": "FEMS Microbiol. Lett.", "issn-l": "0378-1097"}, "abstract": "Like other bacteria, Mycobacterium spp. have developed different strategies in response to environmental changes such as nutrient limitations and other different stress situations. We have identified candidate genes (rsb genes) from Mycobacterium marinum involved in the regulation of the activity of the alternative sigma factor, \u03c3(F) . This is a homolog of the master regulator of general stress response, \u03c3(B) , and the sporulation-specific sigma factor, \u03c3(F) , in Bacillus subtilis. The organization of these genes in M.\u00a0marinum and B.\u00a0subtilis is similar. Transcriptome and qRT-PCR data show that these genes are indeed expressed in M.\u00a0marinum and that the levels of expression vary with growth phase and exposure to stress. In particular, cold stress caused a significant rise in the expression of all identified rsb and sigF genes. We discuss these data in relation to what is currently known for other Mycobacterium spp.", "doi": "10.1111/1574-6968.12118", "pmid": "23480639", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:54.149Z", "modified": "2021-06-16T14:51:44.583Z"}, {"entity": "publication", "iuid": "257f6952882f44a5b76eeb2f3eccc8a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/257f6952882f44a5b76eeb2f3eccc8a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/257f6952882f44a5b76eeb2f3eccc8a2"}}, "title": "Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.", "authors": [{"family": "Berndt", "given": "Sonja I", "initials": "SI"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Wheeler", "given": "Eleanor", "initials": "E"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Monda", "given": "Keri L", "initials": "KL"}, {"family": "Croteau-Chonka", "given": "Damien C", "initials": "DC"}, {"family": "Day", "given": "Felix R", "initials": "FR"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Ferreira", "given": "Teresa", "initials": "T"}, {"family": "Gentilini", "given": "Davide", "initials": "D"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Randall", "given": "Joshua C", "initials": "JC"}, {"family": "Vedantam", "given": "Sailaja", "initials": "S"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Workalemahu", "given": "Tsegaselassie", "initials": "T"}, {"family": "Hu", "given": "Yi-Juan", "initials": "Y"}, {"family": "Lee", "given": "Sang Hong", "initials": "SH"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Lin", "given": "Dan-Yu", "initials": "D"}, {"family": "Min", "given": "Josine L", "initials": "JL"}, {"family": "Neale", "given": "Benjamin M", "initials": "BM"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Bragg-Gresham", "given": "Jennifer L", "initials": "JL"}, {"family": "Cadby", "given": "Gemma", "initials": "G"}, {"family": "den Heijer", "given": "Martin", "initials": "M"}, {"family": "Eklund", "given": "Niina", "initials": "N"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "J"}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "Jarick", "given": "Ivonne", "initials": "I"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "K\u00f6nig", "given": "Inke R", "initials": "IR"}, {"family": "Kristiansson", "given": "Kati", "initials": "K"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Lamina", "given": "Claudia", "initials": "C"}, {"family": "Lecoeur", "given": "Cecile", "initials": "C"}, {"family": "Li", "given": "Guo", "initials": "G"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "McArdle", "given": "Wendy L", "initials": "WL"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Ngwa", "given": "Julius S", "initials": "JS"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Paternoster", "given": "Lavinia", "initials": "L"}, {"family": "Pechlivanis", "given": "Sonali", "initials": "S"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Peters", "given": "Marjolein J", "initials": "MJ"}, {"family": "Preuss", "given": "Michael", "initials": "M"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Shi", "given": "Jianxin", "initials": "J"}, {"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Trip", "given": "Mieke D", "initials": "MD"}, {"family": "Tyrer", "given": "Jonathan", "initials": "J"}, {"family": "Van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV"}, {"family": "Vandenput", "given": "Liesbeth", "initials": "L"}, {"family": "Waite", "given": "Lindsay L", "initials": "LL"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Atalay", "given": "Mustafa", "initials": "M"}, {"family": "Attwood", "given": "Antony P", "initials": "AP"}, {"family": "Balmforth", "given": "Anthony J", "initials": "AJ"}, {"family": "Basart", "given": "Hanneke", "initials": "H"}, {"family": "Beilby", "given": "John", "initials": "J"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Brambilla", "given": "Paolo", "initials": "P"}, {"family": "Bruinenberg", "given": "Marcel", "initials": "M"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Connell", "given": "John M", "initials": "JM"}, {"family": "Cookson", "given": "William O", "initials": "WO"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "de Vegt", "given": "Femmie", "initials": "F"}, {"family": "Dei", "given": "Mariano", "initials": "M"}, {"family": "Dimitriou", "given": "Maria", "initials": "M"}, {"family": "Edkins", "given": "Sarah", "initials": "S"}, {"family": "Estrada", "given": "Karol", "initials": "K"}, {"family": "Evans", "given": "David M", "initials": "DM"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Ferrario", "given": "Marco M", "initials": "MM"}, {"family": "Ferri\u00e8res", "given": "Jean", "initials": "J"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Frau", "given": "Francesca", "initials": "F"}, {"family": "Gejman", "given": "Pablo V", "initials": "PV"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hall", "given": "Alistair S", "initials": "AS"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Hartikainen", "given": "Anna-Liisa", "initials": "A"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heard-Costa", "given": "Nancy L", "initials": "NL"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Hebebrand", "given": "Johannes", "initials": "J"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Hunt", "given": "Sarah E", "initials": "SE"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}, {"family": "Iribarren", "given": "Carlos", "initials": "C"}, {"family": "Jacobs", "given": "Kevin B", "initials": "KB"}, {"family": "Jansson", "given": "John-Olov", "initials": "J"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Kee", "given": "Frank", "initials": "F"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "K"}, {"family": "Kivim\u00e4ki", "given": "Mika", "initials": "M"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Kraja", "given": "Aldi T", "initials": "AT"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Kuulasmaa", "given": "Kari", "initials": "K"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laitinen", "given": "Jaana H", "initials": "JH"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindstr\u00f6m", "given": "Jaana", "initials": "J"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Liuzzi", "given": "Antonio", "initials": "A"}, {"family": "Lokki", "given": "Marja-Liisa", "initials": "M"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Madden", "given": "Pamela A", "initials": "PA"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK"}, {"family": "Manunta", "given": "Paolo", "initials": "P"}, {"family": "Marek", "given": "Diana", "initials": "D"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Mateo Leach", "given": "Irene", "initials": "I"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "M\u00fchleisen", "given": "Thomas W", "initials": "TW"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Musk", "given": "Arthur W", "initials": "AW"}, {"family": "Narisu", "given": "Narisu", "initials": "N"}, {"family": "Navis", "given": "Gerjan", "initials": "G"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Nohr", "given": "Ellen A", "initials": "EA"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Pedersen", "given": "Nancy", "initials": "N"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "P\u00fctter", "given": "Carolin", "initials": "C"}, {"family": "Radhakrishnan", "given": "Aparna", "initials": "A"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Rendon", "given": "Augusto", "initials": "A"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Saaristo", "given": "Timo E", "initials": "TE"}, {"family": "Sambrook", "given": "Jennifer G", "initials": "JG"}, {"family": "Sanders", "given": "Alan R", "initials": "AR"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Saramies", "given": "Jouko", "initials": "J"}, {"family": "Schipf", "given": "Sabine", "initials": "S"}, {"family": "Schreiber", "given": "Stefan", "initials": "S"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Shin", "given": "So-Youn", "initials": "S"}, {"family": "Signorini", "given": "Stefano", "initials": "S"}, {"family": "Sinisalo", "given": "Juha", "initials": "J"}, {"family": "Skrobek", "given": "Boris", "initials": "B"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Stan\u010d\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Stark", "given": "Klaus", "initials": "K"}, {"family": "Stephens", "given": "Jonathan C", "initials": "JC"}, {"family": "Stirrups", "given": "Kathleen", "initials": "K"}, {"family": "Stolk", "given": "Ronald P", "initials": "RP"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Swift", "given": "Amy J", "initials": "AJ"}, {"family": "Theodoraki", "given": "Eirini V", "initials": "EV"}, {"family": "Thorand", "given": "Barbara", "initials": "B"}, {"family": "Tregouet", "given": "David-Alexandre", "initials": "D"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Van der Klauw", "given": "Melanie M", "initials": "MM"}, {"family": "van Meurs", "given": "Joyce B J", "initials": "JBJ"}, {"family": "Vermeulen", "given": "Sita H", "initials": "SH"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "Virtamo", "given": "Jarmo", "initials": "J"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Waeber", "given": "G\u00e9rard", "initials": "G"}, {"family": "Wang", "given": "Zhaoming", "initials": "Z"}, {"family": "Wid\u00e9n", "given": "Elisabeth", "initials": "E"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Winkelmann", "given": "Bernhard R", "initials": "BR"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JCM"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BHR"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Boehm", "given": "Bernhard O", "initials": "BO"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Chanock", "given": "Stephen J", "initials": "SJ"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hengstenberg", "given": "Christian", "initials": "C"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Hingorani", "given": "Aroon", "initials": "A"}, {"family": "Hinney", "given": "Anke", "initials": "A"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Hovingh", "given": "Kees G", "initials": "KG"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "J\u00f6ckel", "given": "Karl-Heinz", "initials": "K"}, {"family": "Keinanen-Kiukaanniemi", "given": "Sirkka M", "initials": "SM"}, {"family": "Kiemeney", "given": "Lambertus A", "initials": "LA"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Levinson", "given": "Douglas F", "initials": "DF"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Nieminen", "given": "Markku S", "initials": "MS"}, {"family": "Nj\u00f8lstad", "given": "Inger", "initials": "I"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "Ouwehand", "given": "Willem H", "initials": "WH"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Penninx", "given": "Brenda", "initials": "B"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TIA"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Uusitupa", "given": "Matti", "initials": "M"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Wallaschofski", "given": "Henri", "initials": "H"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Wichmann", "given": "H-Erich", "initials": "H"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Abecasis", "given": "Goncalo R", "initials": "GR"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Frayling", "given": "Timothy", "initials": "T"}, {"family": "Groop", "given": "Leif C", "initials": "LC"}, {"family": "Haritunian", "given": "Talin", "initials": "T"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Hunter", "given": "David", "initials": "D"}, {"family": "Kaplan", "given": "Robert C", "initials": "RC"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Moffatt", "given": "Miriam F", "initials": "MF"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Di Blasio", "given": "Anna Maria", "initials": "AM"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Meyre", "given": "David", "initials": "D"}, {"family": "Scherag", "given": "Andr\u00e9", "initials": "A"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Speliotes", "given": "Elizabeth K", "initials": "EK"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}], "type": "comparative study", "published": "2013-05-00", "journal": {"volume": "45", "issn": "1546-1718", "issue": "5", "pages": "501-512", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.", "doi": "10.1038/ng.2606", "pmid": "23563607", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.2606"}, {"db": "pmc", "key": "PMC3973018"}, {"db": "mid", "key": "NIHMS536922"}], "notes": [], "created": "2017-05-04T14:58:05.146Z", "modified": "2020-01-21T13:56:08.682Z"}, {"entity": "publication", "iuid": "64335175e4f742b5812377610f8eb800", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64335175e4f742b5812377610f8eb800.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64335175e4f742b5812377610f8eb800"}}, "title": "Genome-wide analysis in German shepherd dogs reveals association of a locus on CFA 27 with atopic dermatitis.", "authors": [{"family": "Tengvall", "given": "Katarina", "initials": "K"}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Bergvall", "given": "Kerstin", "initials": "K"}, {"family": "Olsson", "given": "Mia", "initials": "M"}, {"family": "Frankowiack", "given": "Marcel", "initials": "M"}, {"family": "Farias", "given": "Fabiana H G", "initials": "FHG"}, {"family": "Pielberg", "given": "Gerli", "initials": "G"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}, {"family": "Leeb", "given": "Tosso", "initials": "T"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "9", "issn": "1553-7404", "issue": "5", "pages": "e1003475", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Humans and dogs are both affected by the allergic skin disease atopic dermatitis (AD), caused by an interaction between genetic and environmental factors. The German shepherd dog (GSD) is a high-risk breed for canine AD (CAD). In this study, we used a Swedish cohort of GSDs as a model for human AD. Serum IgA levels are known to be lower in GSDs compared to other breeds. We detected significantly lower IgA levels in the CAD cases compared to controls (p = 1.1 \u00d7 10(-5)) in our study population. We also detected a separation within the GSD cohort, where dogs could be grouped into two different subpopulations. Disease prevalence differed significantly between the subpopulations contributing to population stratification (\u03bb = 1.3), which was successfully corrected for using a mixed model approach. A genome-wide association analysis of CAD was performed (n cases = 91, n controls = 88). IgA levels were included in the model, due to the high correlation between CAD and low IgA levels. In addition, we detected a correlation between IgA levels and the age at the time of sampling (corr = 0.42, p = 3.0 \u00d7 10(-9)), thus age was included in the model. A genome-wide significant association was detected on chromosome 27 (praw = 3.1 \u00d7 10(-7), pgenome = 0.03). The total associated region was defined as a ~1.5-Mb-long haplotype including eight genes. Through targeted re-sequencing and additional genotyping of a subset of identified SNPs, we defined 11 smaller haplotype blocks within the associated region. Two blocks showed the strongest association to CAD. The ~209-kb region, defined by the two blocks, harbors only the PKP2 gene, encoding Plakophilin 2 expressed in the desmosomes and important for skin structure. Our results may yield further insight into the genetics behind both canine and human AD.", "doi": "10.1371/journal.pgen.1003475", "pmid": "23671420", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-01656"}, {"db": "pmc", "key": "PMC3649999"}], "notes": [], "created": "2017-05-04T14:58:12.404Z", "modified": "2021-06-16T10:19:26.545Z"}, {"entity": "publication", "iuid": "07e1b05f0f354153939cca58f67c6651", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07e1b05f0f354153939cca58f67c6651.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07e1b05f0f354153939cca58f67c6651"}}, "title": "Genetic determinants of mortality. Can findings from genome-wide association studies explain variation in human mortality?", "authors": [{"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "132", "issn": "1432-1203", "issue": "5", "pages": "553-561", "title": "Hum. Genet.", "issn-l": "0340-6717"}, "abstract": "Twin studies have estimated the heritability of longevity to be approximately 20-30 %. Genome-wide association studies (GWAS) have revealed a large number of determinants of morbidity, but so far, no new polymorphisms have been discovered to be associated with longevity per se in GWAS. We aim to determine whether the genetic architecture of mortality can be explained by single nucleotide polymorphisms (SNPs) associated with common traits and diseases related to mortality. By extensive quality control of published GWAS we created a genetic score from 707 common SNPs associated with 125 diseases or risk factors related with overall mortality. We prospectively studied the association of the genetic score with: (1) time-to-death; (2) incidence of the first of nine major diseases (coronary heart disease, stroke, heart failure, diabetes, dementia, lung, breast, colon and prostate cancers) in two population-based cohorts of Dutch and Swedish individuals (N = 15,039; age range 47-99 years). During a median follow-up of 6.3 years (max 22.2 years), we observed 4,318 deaths and 2,132 incident disease events. The genetic score was significantly associated with time-to-death [hazard ratio (HR) per added risk allele = 1.003, P value = 0.006; HR 4th vs. 1st quartile = 1.103]. The association between the genetic score and incidence of major diseases was stronger (HR per added risk allele = 1.004, P value = 0.002; HR 4th vs. 1st quartile = 1.160). Associations were stronger for individuals dying at older ages. Our findings are compatible with the view of mortality as a complex and highly polygenetic trait, not easily explainable by common genetic variants related to diseases and physiological traits.", "doi": "10.1007/s00439-013-1267-6", "pmid": "23354976", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:56.630Z", "modified": "2020-01-21T13:56:08.759Z"}, {"entity": "publication", "iuid": "e2607b9f38fb4dab859b2ad0efb085fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2607b9f38fb4dab859b2ad0efb085fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2607b9f38fb4dab859b2ad0efb085fd"}}, "title": "Comprehensive analysis of copy number variation in monozygotic twins discordant for bipolar disorder or schizophrenia.", "authors": [{"family": "Bloom", "given": "Rachael J", "initials": "RJ"}, {"family": "K\u00e4hler", "given": "Anna K", "initials": "AK"}, {"family": "Collins", "given": "Ann L", "initials": "AL"}, {"family": "Chen", "given": "Guanhua", "initials": "G"}, {"family": "Cannon", "given": "Tyrone D", "initials": "TD"}, {"family": "Hultman", "given": "Christina", "initials": "C"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "146", "issn": "1573-2509", "issue": "1-3", "pages": "289-290", "title": "Schizophr. Res.", "issn-l": "0920-9964"}, "abstract": "Copy number variation plays a clear role in the etiology of many psychiatric disorders, particularly schizophrenia. We performed array-CGH to look for copy number variants between five pairs of monozygotic twins discordant for bipolar disorder or schizophrenia. Our study found no differences in copy number variants between the sets of twins. Although alluring, realistic accounting for heterogeneity and chimerism highlights the technological limitations in studying monozygotic twins discordant for psychiatric disorders.", "doi": "10.1016/j.schres.2013.02.021", "pmid": "23507357", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "S0920-9964(13)00113-8"}, {"db": "pmc", "key": "PMC3650833"}, {"db": "mid", "key": "NIHMS450150"}], "notes": [], "created": "2017-05-04T15:03:38.677Z", "modified": "2017-05-30T12:46:24.977Z"}, {"entity": "publication", "iuid": "401ede1efc9b4c878a4b77f8ca000c4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/401ede1efc9b4c878a4b77f8ca000c4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/401ede1efc9b4c878a4b77f8ca000c4a"}}, "title": "An adaptive alignment algorithm for quality-controlled label-free LC-MS.", "authors": [{"family": "Sandin", "given": "Marianne", "initials": "M"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Hansson", "given": "Karin", "initials": "K"}, {"family": "M\u00e5nsson", "given": "Olle", "initials": "O"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}, {"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}], "type": "comparative study", "published": "2013-05-00", "journal": {"volume": "12", "issn": "1535-9484", "issue": "5", "pages": "1407-1420", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Label-free quantification using precursor-based intensities is a versatile workflow for large-scale proteomics studies. The method however requires extensive computational analysis and is therefore in need of robust quality control during the data mining stage. We present a new label-free data analysis workflow integrated into a multiuser software platform. A novel adaptive alignment algorithm has been developed to minimize the possible systematic bias introduced into the analysis. Parameters are estimated on the fly from the data at hand, producing a user-friendly analysis suite. Quality metrics are output in every step of the analysis as well as actively incorporated into the parameter estimation. We furthermore show the improvement of this system by comprehensive comparison to classical label-free analysis methodology as well as current state-of-the-art software.", "doi": "10.1074/mcp.O112.021907", "pmid": "23306530", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "O112.021907"}, {"db": "pmc", "key": "PMC3650348"}], "notes": [], "created": "2017-05-04T14:56:25.730Z", "modified": "2020-01-21T13:53:20.466Z"}, {"entity": "publication", "iuid": "3ba82d89aad14984be5a0cbac09383b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ba82d89aad14984be5a0cbac09383b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ba82d89aad14984be5a0cbac09383b5"}}, "title": "A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits.", "authors": [{"family": "Hansen", "given": "Karen", "initials": "K"}, {"family": "Perry", "given": "Brian A", "initials": "BA"}, {"family": "Dranginis", "given": "Andrew W", "initials": "AW"}, {"family": "Pfister", "given": "Donald H", "initials": "DH"}], "type": "journal article", "published": "2013-05-00", "journal": {"volume": "67", "issn": "1095-9513", "issue": "2", "pages": "311-335", "title": "Mol. Phylogenet. Evol.", "issn-l": "1055-7903"}, "abstract": "Pyronemataceae is the largest and most heterogeneous family of Pezizomycetes. It is morphologically and ecologically highly diverse, comprising saprobic, ectomycorrhizal, bryosymbiotic and parasitic species, occurring in a broad range of habitats (on soil, burnt ground, debris, wood, dung and inside living bryophytes, plants and lichens). To assess the monophyly of Pyronemataceae and provide a phylogenetic hypothesis of the group, we compiled a four-gene dataset including one nuclear ribosomal and three protein-coding genes for 132 distinct Pezizomycetes species (4437 nucleotides with all markers available for 80% of the total 142 included taxa). This is the most comprehensive molecular phylogeny of Pyronemataceae, and Pezizomycetes, to date. Three hundred ninety-four new sequences were generated during this project, with the following numbers for each gene: RPB1 (124), RPB2 (99), EF-1\u03b1 (120) and LSU rDNA (51). The dataset includes 93 unique species from 40 genera of Pyronemataceae, and 34 species from 25 genera representing an additional 12 families of the class. Parsimony, maximum likelihood and Bayesian analyses suggest that Pyronemataceae is paraphyletic due to the nesting of both Ascodesmidaceae and Glaziellaceae within the family. Four lineages with taxa currently classified in the family, the Boubovia, Geopyxis, Pseudombrophila and Pulvinula lineages, form a monophyletic group with Ascodesmidaceae and Glaziellaceae. We advocate the exclusion of these four lineages in order to recognize a monophyletic Pyronemataceae. The genus Coprotus (Thelebolales, Leotiomycetes) is shown to belong to Pezizomycetes, forming a strongly supported monophyletic group with Boubovia. Ten strongly supported lineages are identified within Pyronemataceae s. str. Of these, the Pyropyxis and Otidea lineages are identified as successive sister lineages to the rest of Pyronemataceae s. str. The highly reduced (gymnohymenial) Monascella is shown to belong to Pezizomycetes and is for the first time suggested to be closely related to the cleistothecial Warcupia, as a sister group to the primarily apothecial Otidea. None of the lineages of pyronemataceous taxa identified here correspond to previous families or subfamily classifications. Ancestral character state reconstructions (ASR) using a Bayesian approach support that the ancestors of Pezizomycetes and Pyronemataceae were soil inhabiting and saprobic. Ectomycorrhizae have arisen within both lineages A, B and C of Pezizomycetes and are suggested to have evolved independently seven to eight times within Pyronemataceae s. l., whereas an obligate bryosymbiotic lifestyle has arisen only twice. No reversals to a free-living, saprobic lifestyle have happened from symbiotic or parasitic Pyronemataceae. Specializations to various substrates (e.g. burnt ground and dung) are suggested to have occurred several times in mainly saprobic lineages. Although carotenoids in the apothecia are shown to have arisen at least four times in Pezizomycetes, the ancestor of Pyronemataceae s. str., excluding the Pyropyxis and Otidea lineages, most likely produced carotenoids, which were then subsequently lost in some clades (- and possibly gained again). Excipular hairs were found with a high probability to be absent from apothecia in the deepest nodes of Pezizomycetes and in the ancestor of Pyronemataceae s. str. True hairs are restricted to the core group of Pyronemataceae s. str., but are also found in Lasiobolus (Ascodesmidaceae), the Pseudombrophila lineage and the clade of Chorioactidaceae, Sarcoscyphaceae and Sarcosomataceae. The number of gains and losses of true hairs within Pyronemataceae s. str., however, remains uncertain. The ASR of ascospore guttulation under binary coding (present or absent) indicates that this character is fast evolving and prone to shifts.", "doi": "10.1016/j.ympev.2013.01.014", "pmid": "23403226", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S1055-7903(13)00051-1"}], "notes": [], "created": "2017-05-04T14:56:26.029Z", "modified": "2020-01-21T13:53:20.458Z"}, {"entity": "publication", "iuid": "6765ee946264418d8cbd29dbbfbf14c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6765ee946264418d8cbd29dbbfbf14c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6765ee946264418d8cbd29dbbfbf14c0"}}, "title": "SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals.", "authors": [{"family": "Oosterveen", "given": "Tony", "initials": "T"}, {"family": "Kurdija", "given": "Sanja", "initials": "S"}, {"family": "Enster\u00f6", "given": "Mats", "initials": "M"}, {"family": "Uhde", "given": "Christopher W", "initials": "CW"}, {"family": "Bergsland", "given": "Maria", "initials": "M"}, {"family": "Sandberg", "given": "Magnus", "initials": "M"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Muhr", "given": "Jonas", "initials": "J"}, {"family": "Ericson", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2013-04-30", "journal": {"volume": "110", "issn": "1091-6490", "issue": "18", "pages": "7330-7335", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The reiterative deployment of a small cadre of morphogen signals underlies patterning and growth of most tissues during embyogenesis, but how such inductive events result in tissue-specific responses remains poorly understood. By characterizing cis-regulatory modules (CRMs) associated with genes regulated by Sonic hedgehog (Shh), retinoids, or bone morphogenetic proteins in the CNS, we provide evidence that the neural-specific interpretation of morphogen signaling reflects a direct integration of these pathways with SoxB1 proteins at the CRM level. Moreover, expression of SoxB1 proteins in the limb bud confers on mesodermal cells the potential to activate neural-specific target genes upon Shh, retinoid, or bone morphogenetic protein signaling, and the collocation of binding sites for SoxB1 and morphogen-mediatory transcription factors in CRMs faithfully predicts neural-specific gene activity. Thus, an unexpectedly simple transcriptional paradigm appears to conceptually explain the neural-specific interpretation of pleiotropic signaling during vertebrate development. Importantly, genes induced in a SoxB1-dependent manner appear to constitute repressive gene regulatory networks that are directly interlinked at the CRM level to constrain the regional expression of patterning genes. Accordingly, not only does the topology of SoxB1-driven gene regulatory networks provide a tissue-specific mode of gene activation, but it also determines the spatial expression pattern of target genes within the developing neural tube.", "doi": "10.1073/pnas.1220010110", "pmid": "23589857", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1220010110"}, {"db": "pmc", "key": "PMC3645538"}], "notes": [], "created": "2017-05-04T14:58:09.856Z", "modified": "2021-07-07T11:46:33.598Z"}, {"entity": "publication", "iuid": "32d051b055a54dd2b0d572969e20db54", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32d051b055a54dd2b0d572969e20db54.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32d051b055a54dd2b0d572969e20db54"}}, "title": "Employment of complementary dissociation techniques for body fluid characterization and biomarker discovery.", "authors": [{"family": "Good", "given": "David M", "initials": "DM"}, {"family": "Rutishauser", "given": "Dorothea", "initials": "D"}], "type": "journal article", "published": "2013-04-30", "journal": {"volume": "1002", "issn": "1940-6029", "issue": null, "pages": "223-232", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Proteomic analysis of biological fluids has become the de facto method for biomarker discovery over the past half decade. Mass spectrometry, in particular, has emerged as the premier technology to perform such analysis. This shift in the prevailing choice of analytical method is primarily due to the rapid evolution of mass spectrometry technology, with advances in acquisition speed, increased resolving power and mass accuracy, and the development of novel fragmentation methods. The benefits of using one of these new fragmentation methods, electron-transfer dissociation, as a complement to the traditional dissociation technique (i.e., collision-activated dissociation) have been thoroughly illustrated. Detailed here is a method for proteomic analysis of a readily obtainable and often investigated biological fluid, blood plasma, which takes advantage of these complementary dissociation techniques and employs the most recent advances in mass spectrometry technology.", "doi": "10.1007/978-1-62703-360-2_18", "pmid": "23625407", "labels": {"Advanced Mass Spectrometry Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:43.372Z", "modified": "2017-05-30T12:33:28.974Z"}, {"entity": "publication", "iuid": "168f78a27d1e42f1ace305c0f5399d47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/168f78a27d1e42f1ace305c0f5399d47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/168f78a27d1e42f1ace305c0f5399d47"}}, "title": "Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model.", "authors": [{"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "O'Hurley", "given": "Gillian", "initials": "G"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Gad", "given": "Annica K B", "initials": "AK"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2013-04-23", "journal": {"volume": "110", "issn": "1091-6490", "issue": "17", "pages": "6853-6858", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The transformation of normal cells to malignant, metastatic tumor cells is a multistep process caused by the sequential acquirement of genetic changes. To identify these changes, we compared the transcriptomes and levels and distribution of proteins in a four-stage cell model of isogenically matched normal, immortalized, transformed, and metastatic human cells, using deep transcriptome sequencing and immunofluorescence microscopy. The data show that \u223c6% (n = 1,357) of the human protein-coding genes are differentially expressed across the stages in the model. Interestingly, the majority of these genes are down-regulated, linking malignant transformation to dedifferentiation. The up-regulated genes are mainly components that control cellular proliferation, whereas the down-regulated genes consist of proteins exposed on or secreted from the cell surface. As many of the identified gene products control basic cellular functions that are defective in cancers, the data provide candidates for follow-up studies to investigate their functional roles in tumor formation. When we further compared the expression levels of four of the identified proteins in clinical cancer cohorts, similar differences were observed between benign and cancer cells, as in the cell model. This shows that this comprehensive demonstration of the molecular changes underlying malignant transformation is a relevant model to study the process of tumor formation.", "doi": "10.1073/pnas.1216436110", "pmid": "23569271", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "1216436110"}, {"db": "pmc", "key": "PMC3637701"}], "notes": [], "created": "2017-05-04T14:55:14.694Z", "modified": "2021-07-08T13:44:33.038Z"}, {"entity": "publication", "iuid": "c18933a273324f8f820b0d8cb51b36eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c18933a273324f8f820b0d8cb51b36eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c18933a273324f8f820b0d8cb51b36eb"}}, "title": "Expression of fusion proteins of Aspergillus terreus reveals a novel allene oxide synthase.", "authors": [{"family": "Hoffmann", "given": "Inga", "initials": "I"}, {"family": "Jerner\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Oliw", "given": "Ernst H", "initials": "EH"}], "type": "journal article", "published": "2013-04-19", "journal": {"volume": "288", "issn": "1083-351X", "issue": "16", "pages": "11459-11469", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "Aspergilli oxidize C18 unsaturated fatty acids by dioxygenase-cytochrome P450 fusion proteins to signal molecules involved in reproduction and host-pathogen interactions. Aspergillus terreus expresses linoleate 9R-dioxygenase (9R-DOX) and allene oxide synthase (AOS) activities in membrane fractions. The genome contains five genes (ATEG), which may code for a 9R-DOX-AOS fusion protein. The genes were cloned and expressed, but none of them oxidized 18:2n-6 to 9R-hydroperoxy-10(E),12(Z)-octadecadienoic acid (9R-HPODE). ATEG_02036 transformed 9R-HPODE to an unstable allene oxide, 9(R),10-epoxy-10,12(Z)-octadecadienoic acid. A substitution in the P450 domain (C1073S) abolished AOS activity. The N964V and N964D mutants both showed markedly reduced AOS activity, suggesting that Asn(964) may facilitate homolytic cleavage of the dioxygen bond of 9R-HPODE with formation of compound II in analogy with plant AOS (CYP74) and prostacyclin synthase (CYP8A1). ATEG_03992 was identified as 5,8-linoleate diol synthase (5,8-LDS). Replacement of Asn(878) in 5,8-LDS with leucine (N878L) mainly shifted ferryl oxygen insertion from C-5 toward C-6, but replacements of Gln(881) markedly affected catalysis. The Q881L mutant virtually abolished the diol synthase activity. Replacement of Gln(881) with Asn, Glu, Asp, or Lys residues augmented the homolytic cleavage of 8R-HPODE with formation of 10-hydroxy-8(9)-epoxy-12(Z)-octadecenoic acid (erythro/threo, 1-4:1) and/or shifted ferryl oxygen insertion from C-5 toward C-11. We conclude that homolysis and heterolysis of the dioxygen bond with formation of compound II in AOS and compound I in 5,8-LDS are influenced by Asn and Gln residues, respectively, of the I-helices. AOS of A. terreus appears to have evolved independently of CYP74 but with an analogous reaction mechanism.", "doi": "10.1074/jbc.M113.458257", "pmid": "23479731", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "M113.458257"}, {"db": "pmc", "key": "PMC3630850"}], "notes": [], "created": "2017-05-04T15:02:27.819Z", "modified": "2020-01-21T13:56:05.025Z"}, {"entity": "publication", "iuid": "3129c8ab37f543fca019e95e1350a0f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3129c8ab37f543fca019e95e1350a0f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3129c8ab37f543fca019e95e1350a0f6"}}, "title": "Renal sensory and sympathetic nerves reinnervate the kidney in a similar time-dependent fashion after renal denervation in rats.", "authors": [{"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Knuepfer", "given": "Mark M", "initials": "MM"}, {"family": "Kopp", "given": "Ulla C", "initials": "UC"}], "type": "journal article", "published": "2013-04-15", "journal": {"volume": "304", "issn": "1522-1490", "issue": "8", "pages": "R675-R682", "title": "Am. J. Physiol. Regul. Integr. Comp. Physiol.", "issn-l": "0363-6119"}, "abstract": "Efferent renal sympathetic nerves reinnervate the kidney after renal denervation in animals and humans. Therefore, the long-term reduction in arterial pressure following renal denervation in drug-resistant hypertensive patients has been attributed to lack of afferent renal sensory reinnervation. However, afferent sensory reinnervation of any organ, including the kidney, is an understudied question. Therefore, we analyzed the time course of sympathetic and sensory reinnervation at multiple time points (1, 4, and 5 days and 1, 2, 3, 4, 6, 9, and 12 wk) after renal denervation in normal Sprague-Dawley rats. Sympathetic and sensory innervation in the innervated and contralateral denervated kidney was determined as optical density (ImageJ) of the sympathetic and sensory nerves identified by immunohistochemistry using antibodies against markers for sympathetic nerves [neuropeptide Y (NPY) and tyrosine hydroxylase (TH)] and sensory nerves [substance P and calcitonin gene-related peptide (CGRP)]. In denervated kidneys, the optical density of NPY-immunoreactive (ir) fibers in the renal cortex and substance P-ir fibers in the pelvic wall was 6, 39, and 100% and 8, 47, and 100%, respectively, of that in the contralateral innervated kidney at 4 days, 4 wk, and 12 wk after denervation. Linear regression analysis of the optical density of the ratio of the denervated/innervated kidney versus time yielded similar intercept and slope values for NPY-ir, TH-ir, substance P-ir, and CGRP-ir fibers (all R(2) > 0.76). In conclusion, in normotensive rats, reinnervation of the renal sensory nerves occurs over the same time course as reinnervation of the renal sympathetic nerves, both being complete at 9 to 12 wk following renal denervation.", "doi": "10.1152/ajpregu.00599.2012", "pmid": "23408032", "labels": {"Fluorescence Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "ajpregu.00599.2012"}, {"db": "pmc", "key": "PMC3627950"}], "notes": [], "created": "2017-05-04T14:55:18.639Z", "modified": "2017-05-30T11:33:44.736Z"}, {"entity": "publication", "iuid": "7f1758660d6743a48e981544ba59095b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f1758660d6743a48e981544ba59095b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f1758660d6743a48e981544ba59095b"}}, "title": "Eating problems and overlap with ADHD and autism spectrum disorders in a nationwide twin study of 9- and 12-year-old children.", "authors": [{"family": "R\u00e5stam", "given": "Maria", "initials": "M"}, {"family": "T\u00e4ljemark", "given": "Jakob", "initials": "J"}, {"family": "Tajnia", "given": "Armin", "initials": "A"}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S"}, {"family": "Gustafsson", "given": "Peik", "initials": "P"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Gillberg", "given": "Christopher", "initials": "C"}, {"family": "Anckars\u00e4ter", "given": "Henrik", "initials": "H"}, {"family": "Kerekes", "given": "N\u00f3ra", "initials": "N"}], "type": "journal article", "published": "2013-04-15", "journal": {"volume": "2013", "issn": "1537-744X", "issue": null, "pages": "315429", "title": "ScientificWorldJournal", "issn-l": null}, "abstract": "AIM. To establish the prevalence of restrictive eating problems, the overlap and association with attention-deficit/hyperactivity disorder (ADHD), and autism spectrum disorders (ASD) and to estimate the heritability of eating problems in a general population sample of twins aged 9 and 12. METHODS. Parents of all Swedish 9- and 12-year-old twin pairs born between 1993 and 1998 (n = 12,366) were interviewed regarding symptoms of ADHD, ASD, and eating problems (EAT-P). Intraclass correlations and structural equation modelling were used for evaluating the influence of genetic and environmental factors. Cross-twin, cross-trait correlations were used to indicate a possible overlap between conditions. RESULTS. The prevalence of eating problems was 0.6% in the study population and was significantly higher in children with ADHD and/or ASD. Among children with eating problems, 40% were screened positive for ADHD and/or ASD. Social interaction problems were strongly associated with EAT-P in girls, and impulsivity and activity problems with EAT-P in boys. The cross-twin, cross-trait correlations suggested low correlations between EAT-P and ADHD or EAT-P and ASD. Genetic effects accounted for 44% of the variation in liability for eating problems. CONCLUSIONS. In the group with eating problems, there was a clear overrepresentation of individuals with ADHD and/or ASD symptoms.", "doi": "10.1155/2013/315429", "pmid": "23690743", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pmc", "key": "PMC3654255"}], "notes": [], "created": "2017-05-04T15:03:38.978Z", "modified": "2017-05-30T14:53:14.388Z"}, {"entity": "publication", "iuid": "c358e5d781c9474ebcfff3b10b97f2ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c358e5d781c9474ebcfff3b10b97f2ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c358e5d781c9474ebcfff3b10b97f2ed"}}, "title": "Viral Metagenomics \u2013 New applications for the broad-range detection of viromes in veterinary and public health settings", "authors": [{"family": "Karlsson", "given": "Oskar Erik", "initials": "OE"}, {"family": "Norling", "given": "Martin", "initials": "M"}, {"family": "Granberg", "given": "Fredrik", "initials": "F"}, {"family": "Bel\u00e1k", "given": "S\u00e1ndor", "initials": "S"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}], "type": "journal-article", "published": "2013-04-08", "journal": {"volume": "19", "issn": "2226-6089", "issue": "A", "pages": "21", "title": "EMBnet j.", "issn-l": "2226-6089"}, "abstract": null, "doi": "10.14806/ej.19.a.631", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:21.939Z", "modified": "2021-06-22T12:04:49.100Z"}, {"entity": "publication", "iuid": "5d143846d1da4a32b8cb78b6613898f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d143846d1da4a32b8cb78b6613898f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d143846d1da4a32b8cb78b6613898f4"}}, "title": "Metagenomics sample preparation and sequencing.", "authors": [{"family": "Karlsson", "given": "Oskar Erik", "initials": "OE"}, {"family": "Norling", "given": "Martin", "initials": "M"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}], "type": "journal-article", "published": "2013-04-08", "journal": {"volume": "19", "issn": "2226-6089", "issue": "A", "pages": "55", "title": "EMBnet j.", "issn-l": "2226-6089"}, "abstract": null, "doi": "10.14806/ej.19.a.662", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:21.447Z", "modified": "2023-06-19T13:53:28.488Z"}, {"entity": "publication", "iuid": "3cc74cb3a03e4dec86159f2612e29bc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3cc74cb3a03e4dec86159f2612e29bc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3cc74cb3a03e4dec86159f2612e29bc9"}}, "title": "Ion Torrent sequencing and pipeline assembly of the first genome sequence of a mesophilic syntrophic acetate oxidizing bacterium (SAOB)", "authors": [{"family": "Manzoor", "given": "Shahid", "initials": "S"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}], "type": "journal-article", "published": "2013-04-08", "journal": {"volume": "19", "issn": "2226-6089", "issue": "A", "pages": "60", "title": "EMBnet j.", "issn-l": "2226-6089"}, "abstract": null, "doi": "10.14806/ej.19.a.665", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:22.468Z", "modified": "2021-06-22T12:05:07.436Z"}, {"entity": "publication", "iuid": "696f021ed9994599882642e60bbce999", "links": {"self": {"href": "https://publications.scilifelab.se/publication/696f021ed9994599882642e60bbce999.json"}, "display": {"href": "https://publications.scilifelab.se/publication/696f021ed9994599882642e60bbce999"}}, "title": "European H16N3 gull influenza virus attaches to the human respiratory tract and eye.", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Ellstr\u00f6m", "given": "Patrik", "initials": "P"}, {"family": "Olsen", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "van Riel", "given": "Debby", "initials": "D"}, {"family": "Munster", "given": "Vincent J", "initials": "VJ"}, {"family": "Gonz\u00e1lez-Acu\u00f1a", "given": "Daniel", "initials": "D"}, {"family": "Kuiken", "given": "Thijs", "initials": "T"}, {"family": "Jourdain", "given": "Elsa", "initials": "E"}], "type": "journal article", "published": "2013-04-08", "journal": {"volume": "8", "issn": "1932-6203", "issue": "4", "pages": "e60757", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "We explored the attachment of an H16N3 influenza virus to human, mallard, and gull tissues using virus histochemistry applied to tissue microarrays and employing human and mallard viruses as references. Of the viruses tested, the H16N3 gull virus most readily attached to the human respiratory tract and eye. These results underscore the need to assess the potential for gull influenza viruses to replicate in human tissues and further investigate the role of gulls in influenza virus ecology.", "doi": "10.1371/journal.pone.0060757", "pmid": "23593303", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-38518"}, {"db": "pmc", "key": "PMC3620227"}], "notes": [], "created": "2017-05-04T14:56:02.386Z", "modified": "2017-05-30T14:55:20.670Z"}, {"entity": "publication", "iuid": "7473beaadbb845b7b6049576cde85ad5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7473beaadbb845b7b6049576cde85ad5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7473beaadbb845b7b6049576cde85ad5"}}, "title": "The molecular genetic architecture of self-employment.", "authors": [{"family": "van der Loos", "given": "Matthijs J H M", "initials": "MJHM"}, {"family": "Rietveld", "given": "Cornelius A", "initials": "CA"}, {"family": "Eklund", "given": "Niina", "initials": "N"}, {"family": "Koellinger", "given": "Philipp D", "initials": "PD"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "Ankra-Badu", "given": "Georgina A", "initials": "GA"}, {"family": "Baumeister", "given": "Sebastian E", "initials": "SE"}, {"family": "Benjamin", "given": "Daniel J", "initials": "DJ"}, {"family": "Biffar", "given": "Reiner", "initials": "R"}, {"family": "Blankenberg", "given": "Stefan", "initials": "S"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Cesarini", "given": "David", "initials": "D"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Dimitriou", "given": "Maria", "initials": "M"}, {"family": "Eiriksdottir", "given": "Gu\u00f0ny", "initials": "G"}, {"family": "Eriksson", "given": "Johan", "initials": "J"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "H\u00f6hne", "given": "Birgit", "initials": "B"}, {"family": "Holle", "given": "Rolf", "initials": "R"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "J"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "Johannesson", "given": "Magnus", "initials": "M"}, {"family": "Kaakinen", "given": "Marika", "initials": "M"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Laaksonen", "given": "Maarit A", "initials": "MA"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Loitfelder", "given": "Marisa", "initials": "M"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Naitza", "given": "Silvia", "initials": "S"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Petrovic", "given": "Katja", "initials": "K"}, {"family": "Quaye", "given": "Lydia", "initials": "L"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Scheet", "given": "Paul", "initials": "P"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Schmidt", "given": "Carsten O", "initials": "CO"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Senft", "given": "Andrea", "initials": "A"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Svento", "given": "Rauli", "initials": "R"}, {"family": "Terracciano", "given": "Antonio", "initials": "A"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wichmann", "given": "H-Erich", "initials": "H"}, {"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "van Rooij", "given": "Frank J A", "initials": "FJA"}, {"family": "Groenen", "given": "Patrick J F", "initials": "PJF"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Thurik", "given": "A Roy", "initials": "AR"}], "type": "journal article", "published": "2013-04-04", "journal": {"volume": "8", "issn": "1932-6203", "issue": "4", "pages": "e60542", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Economic variables such as income, education, and occupation are known to affect mortality and morbidity, such as cardiovascular disease, and have also been shown to be partly heritable. However, very little is known about which genes influence economic variables, although these genes may have both a direct and an indirect effect on health. We report results from the first large-scale collaboration that studies the molecular genetic architecture of an economic variable-entrepreneurship-that was operationalized using self-employment, a widely-available proxy. Our results suggest that common SNPs when considered jointly explain about half of the narrow-sense heritability of self-employment estimated in twin data (\u03c3(g)(2)/\u03c3(P)(2)\u200a=\u200a25%, h(2)\u200a=\u200a55%). However, a meta-analysis of genome-wide association studies across sixteen studies comprising 50,627 participants did not identify genome-wide significant SNPs. 58 SNPs with p<10(-5) were tested in a replication sample (n\u200a=\u200a3,271), but none replicated. Furthermore, a gene-based test shows that none of the genes that were previously suggested in the literature to influence entrepreneurship reveal significant associations. Finally, SNP-based genetic scores that use results from the meta-analysis capture less than 0.2% of the variance in self-employment in an independent sample (p\u22650.039). Our results are consistent with a highly polygenic molecular genetic architecture of self-employment, with many genetic variants of small effect. Although self-employment is a multi-faceted, heavily environmentally influenced, and biologically distal trait, our results are similar to those for other genetically complex and biologically more proximate outcomes, such as height, intelligence, personality, and several diseases.", "doi": "10.1371/journal.pone.0060542", "pmid": "23593239", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-12-39282"}, {"db": "pmc", "key": "PMC3617140"}], "notes": [], "created": "2017-05-04T14:58:17.694Z", "modified": "2020-01-21T13:56:08.623Z"}, {"entity": "publication", "iuid": "f8811c010db549ebaddaf2f594d12dcd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8811c010db549ebaddaf2f594d12dcd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8811c010db549ebaddaf2f594d12dcd"}}, "title": "\u03b2-thymosins and hemocyte homeostasis in a crustacean.", "authors": [{"family": "Saelee", "given": "Netnapa", "initials": "N"}, {"family": "Noonin", "given": "Chadanat", "initials": "C"}, {"family": "Nupan", "given": "Benjamas", "initials": "B"}, {"family": "Junkunlo", "given": "Kingkamon", "initials": "K"}, {"family": "Phongdara", "given": "Amornrat", "initials": "A"}, {"family": "Lin", "given": "Xionghui", "initials": "X"}, {"family": "S\u00f6derh\u00e4ll", "given": "Kenneth", "initials": "K"}, {"family": "S\u00f6derh\u00e4ll", "given": "Irene", "initials": "I"}], "type": "journal article", "published": "2013-04-02", "journal": {"volume": "8", "issn": "1932-6203", "issue": "4", "pages": "e60974", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Thymosin proteins are well known for their actin-binding activity. Thymosin beta 4 (T\u03b24) has been associated with biological activities in tissue repair and cell migration via interaction with ATP-synthase in vertebrates, while the information of similar thymosin functions in invertebrates is limited. We have shown previously that ATP-synthase is present on the surface of crayfish hematopoietic tissue (HPT) cells, and that astakine 1 (Ast1, an invertebrate cytokine) was found to interact with this \u03b2-subunit of ATP synthase. Here, we identified five different \u03b2-thymosins from Pacifastacus leniusculus, designated Pl-\u03b2-thymosin1-5. The two dominant isoforms in brain, HPT and hemocytes, Pl-\u03b2-thymosin1 and 2, were chosen for functional studies. Both isoforms could bind to the \u03b2-subunit of ATP-synthase, and Pl-\u03b2-thymosin1, but not Pl-\u03b2-thymosin2, significantly increased extracellular ATP formation. Moreover, Pl-\u03b2-thymosin1 stimulated HPT cell migration in vitro and Ast1 blocked this effect. Pl-\u03b2-thymosin2 increased the circulating hemocyte number at an early stage after injection. Additionally, in vivo injection of Pl-\u03b2-thymosin1 resulted in significant reduction of reactive oxygen species (ROS) production in crayfish HPT whereas Pl-\u03b2-thymosin2 had a similar but transient effect. Both Pl-\u03b2-thymosins induced the expression of Ast1 and superoxide dismutase (SOD) transcripts, while silencing of endogenous Pl-\u03b2-thymosin 1 and 2 by RNAi resulted in significant reduction of the Ast1 and SOD transcripts. The diverse effects exhibited by Pl-\u03b2-thymosin1 and Pl-\u03b2-thymosin2 indicates that these proteins are involved in a complex interaction that regulates the hematopoietic stem cell proliferation and differentiation.", "doi": "10.1371/journal.pone.0060974", "pmid": "23565293", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-03793"}, {"db": "pmc", "key": "PMC3614969"}], "notes": [], "created": "2017-05-04T14:58:16.459Z", "modified": "2020-01-21T13:56:06.406Z"}, {"entity": "publication", "iuid": "588bcc002c0247a2b0dd46872c4c105b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/588bcc002c0247a2b0dd46872c4c105b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/588bcc002c0247a2b0dd46872c4c105b"}}, "title": "Systematic antibody generation and validation via tissue microarray technology leading to identification of a novel protein prognostic panel in breast cancer.", "authors": [{"family": "O Leary", "given": "Patrick C", "initials": "PC"}, {"family": "Penny", "given": "Sarah A", "initials": "SA"}, {"family": "Dolan", "given": "Roisin T", "initials": "RT"}, {"family": "Kelly", "given": "Catherine M", "initials": "CM"}, {"family": "Madden", "given": "Stephen F", "initials": "SF"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "McCann", "given": "Amanda H", "initials": "AH"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zagozdzon", "given": "Radoslaw", "initials": "R"}, {"family": "Duffy", "given": "Michael J", "initials": "MJ"}, {"family": "Kell", "given": "Malcolm R", "initials": "MR"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Gallagher", "given": "William M", "initials": "WM"}], "type": "journal article", "published": "2013-04-02", "journal": {"volume": "13", "issn": "1471-2407", "issue": null, "pages": "175", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Although omic-based discovery approaches can provide powerful tools for biomarker identification, several reservations have been raised regarding the clinical applicability of gene expression studies, such as their prohibitive cost. However, the limited availability of antibodies is a key barrier to the development of a lower cost alternative, namely a discrete collection of immunohistochemistry (IHC)-based biomarkers. The aim of this study was to use a systematic approach to generate and screen affinity-purified, mono-specific antibodies targeting progression-related biomarkers, with a view towards developing a clinically applicable IHC-based prognostic biomarker panel for breast cancer.\n\nWe examined both in-house and publicly available breast cancer DNA microarray datasets relating to invasion and metastasis, thus identifying a cohort of candidate progression-associated biomarkers. Of these, 18 antibodies were released for extended analysis. Validated antibodies were screened against a tissue microarray (TMA) constructed from a cohort of consecutive breast cancer cases (n\u2009=\u2009512) to test the immunohistochemical surrogate signature.\n\nAntibody screening revealed 3 candidate prognostic markers: the cell cycle regulator, Anillin (ANLN); the mitogen-activated protein kinase, PDZ-Binding Kinase (PBK); and the estrogen response gene, PDZ-Domain Containing 1 (PDZK1). Increased expression of ANLN and PBK was associated with poor prognosis, whilst increased expression of PDZK1 was associated with good prognosis. A 3-marker signature comprised of high PBK, high ANLN and low PDZK1 expression was associated with decreased recurrence-free survival (p\u2009<\u20090.001) and breast cancer-specific survival (BCSS) (p\u2009<\u20090.001). This novel signature was associated with high tumour grade (p\u2009<\u20090.001), positive nodal status (p\u2009=\u20090.029), ER-negativity (p\u2009=\u20090.006), Her2-positivity (p\u2009=\u20090.036) and high Ki67 status (p\u2009<\u20090.001). However, multivariate Cox regression demonstrated that the signature was not a significant predictor of BCSS (HR\u2009=\u20096.38; 95% CI\u2009=\u20090.79-51.26, p\u2009=\u20090.082).\n\nWe have developed a comprehensive biomarker pathway that extends from discovery through to validation on a TMA platform. This proof-of-concept study has resulted in the identification of a novel 3-protein prognostic panel. Additional biochemical markers, interrogated using this high-throughput platform, may further augment the prognostic accuracy of this panel to a point that may allow implementation into routine clinical practice.", "doi": "10.1186/1471-2407-13-175", "pmid": "23547718", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1471-2407-13-175"}, {"db": "pmc", "key": "PMC3668187"}], "notes": [], "created": "2017-05-04T14:55:55.320Z", "modified": "2021-07-08T13:44:33.279Z"}, {"entity": "publication", "iuid": "a17474f027664211870bb01f84c35232", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a17474f027664211870bb01f84c35232.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a17474f027664211870bb01f84c35232"}}, "title": "Interaction between retinoid acid receptor-related orphan receptor alpha (RORA) and neuropeptide S receptor 1 (NPSR1) in asthma.", "authors": [{"family": "Acevedo", "given": "Nathalie", "initials": "N"}, {"family": "S\u00e4\u00e4f", "given": "Annika", "initials": "A"}, {"family": "S\u00f6derh\u00e4ll", "given": "Cilla", "initials": "C"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Mandelin", "given": "Jami", "initials": "J"}, {"family": "Pietras", "given": "Christina Orsmark", "initials": "CO"}, {"family": "Ezer", "given": "Sini", "initials": "S"}, {"family": "Karisola", "given": "Piia", "initials": "P"}, {"family": "Vendelin", "given": "Johanna", "initials": "J"}, {"family": "Genn\u00e4s", "given": "Gustav Boije af", "initials": "GB"}, {"family": "Yli-Kauhaluoma", "given": "Jari", "initials": "J"}, {"family": "Alenius", "given": "Harri", "initials": "H"}, {"family": "von Mutius", "given": "Erika", "initials": "E"}, {"family": "Doekes", "given": "Gert", "initials": "G"}, {"family": "Braun-Fahrl\u00e4nder", "given": "Charlotte", "initials": "C"}, {"family": "Riedler", "given": "Josef", "initials": "J"}, {"family": "van Hage", "given": "Marianne", "initials": "M"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Pulkkinen", "given": "Ville", "initials": "V"}], "type": "journal article", "published": "2013-04-02", "journal": {"volume": "8", "issn": "1932-6203", "issue": "4", "pages": "e60111", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Retinoid acid receptor-related Orphan Receptor Alpha (RORA) was recently identified as a susceptibility gene for asthma in a genome-wide association study. To investigate the impact of RORA on asthma susceptibility, we performed a genetic association study between RORA single nucleotide polymorphisms (SNPs) in the vicinity of the asthma-associated SNP (rs11071559) and asthma-related traits. Because the regulatory region of a previously implicated asthma susceptibility gene, Neuropeptide S receptor 1 (NPSR1), has predicted elements for RORA binding, we hypothesized that RORA may interact biologically and genetically with NPSR1. 37 RORA SNPs and eight NPSR1 SNPs were genotyped in the Swedish birth cohort BAMSE (2033 children) and the European cross-sectional PARSIFAL study (1120 children). Seven RORA SNPs confined into a 49 kb region were significantly associated with physician-diagnosed childhood asthma. The most significant association with rs7164773 (T/C) was driven by the CC genotype in asthma cases (OR\u200a=\u200a2.0, 95%CI 1.36-2.93, p\u200a=\u200a0.0003 in BAMSE; and 1.61, 1.18-2.19, p\u200a=\u200a0.002 in the combined BAMSE-PARSIFAL datasets, respectively), and strikingly, the risk effect was dependent on the Gln344Arg mutation in NPSR1. In cell models, stimulation of NPSR1 activated a pathway including RORA and other circadian clock genes. Over-expression of RORA decreased NPSR1 promoter activity further suggesting a regulatory loop between these genes. In addition, Rora mRNA expression was lower in the lung tissue of Npsr1 deficient mice compared to wildtype littermates during the early hours of the light period. We conclude that RORA SNPs are associated with childhood asthma and show epistasis with NPSR1, and the interaction between RORA and NPSR1 may be of biological relevance. Combinations of common susceptibility alleles and less common functional polymorphisms may modify the joint risk effects on asthma susceptibility.", "doi": "10.1371/journal.pone.0060111", "pmid": "23565190", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-35098"}, {"db": "pmc", "key": "PMC3615072"}], "notes": [], "created": "2017-05-04T15:03:36.845Z", "modified": "2017-05-30T14:52:50.738Z"}, {"entity": "publication", "iuid": "95abadec9dcf4a13b3ae92cd0dadc428", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95abadec9dcf4a13b3ae92cd0dadc428.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95abadec9dcf4a13b3ae92cd0dadc428"}}, "title": "Genetic determinants of dabigatran plasma levels and their relation to bleeding.", "authors": [{"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Lehr", "given": "Thorsten", "initials": "T"}, {"family": "Connolly", "given": "Stuart", "initials": "S"}, {"family": "Eikelboom", "given": "John", "initials": "J"}, {"family": "Ezekowitz", "given": "Michael D", "initials": "MD"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Haertter", "given": "Sebastian", "initials": "S"}, {"family": "Oldgren", "given": "Jonas", "initials": "J"}, {"family": "Reilly", "given": "Paul", "initials": "P"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Syvanen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Zimdahl-Gelling", "given": "Heike", "initials": "H"}, {"family": "Yusuf", "given": "Salim", "initials": "S"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2013-04-02", "journal": {"volume": "127", "issn": "1524-4539", "issue": "13", "pages": "1404-1412", "title": "Circulation", "issn-l": "0009-7322"}, "abstract": "Fixed-dose unmonitored treatment with dabigatran etexilate is effective and has a favorable safety profile in the prevention of stroke in atrial fibrillation patients compared with warfarin. We hypothesized that genetic variants could contribute to interindividual variability in blood concentrations of the active metabolite of dabigatran etexilate and influence the safety and efficacy of dabigatran.\n\nWe successfully conducted a genome-wide association study in 2944 Randomized Evaluation of Long-term Anticoagulation Therapy (RE-LY) participants. The CES1 single-nucleotide polymorphism rs2244613 was associated with trough concentrations, and the ABCB1 single-nucleotide polymorphism rs4148738 and the CES1 single-nucleotide polymorphism rs8192935 were associated with peak concentrations at genome-wide significance (P<9\u00d710(-8)) with a gene-dose effect. Each minor allele of the CES1 single-nucleotide polymorphism rs2244613 was associated with lower trough concentrations (15% decrease per allele; 95% confidence interval, 10-19; P=1.2\u00d710(-8)) and a lower risk of any bleeding (odds ratio, 0.67; 95% confidence interval, 0.55-0.82; P=7\u00d710(-5)) in dabigatran-treated participants, with a consistent but nonsignificant lower risk of major bleeding (odds ratio, 0.66; 95% confidence interval, 0.43-1.01). The interaction between treatment (warfarin versus all dabigatran) and carrier status was statistically significant (P=0.002), with carriers having less bleeding with dabigatran than warfarin (hazard ratio, 0.59; 95% confidence interval, 0.46-0.76; P=5.2\u00d710(-)5) in contrast to no difference in noncarriers (hazard ratio, 0.96; 95% confidence interval, 0.81-1.14; P=0.65). There was no association with ischemic events, and neither rs4148738 nor rs8192935 was associated with bleeding or ischemic events.\n\nGenome-wide association analysis identified that carriage of the CES1 rs2244613 minor allele occurred in 32.8% of patients in RE-LY and was associated with lower exposure to active dabigatran metabolite. The presence of the polymorphism was associated with a lower risk of bleeding.\n\nURL: http://www.clinicaltrials.gov. Unique identifier: NCT00262600.", "doi": "10.1161/CIRCULATIONAHA.112.001233", "pmid": "23467860", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "CIRCULATIONAHA.112.001233"}, {"db": "ClinicalTrials.gov", "key": "NCT00262600"}], "notes": [], "created": "2017-05-04T15:01:15.922Z", "modified": "2021-07-07T15:11:02.603Z"}, {"entity": "publication", "iuid": "1a04315aeec743cfa0478d39b62901a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a04315aeec743cfa0478d39b62901a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a04315aeec743cfa0478d39b62901a6"}}, "title": "RNA-binding protein QKI regulates Glial fibrillary acidic protein expression in human astrocytes.", "authors": [{"family": "Radomska", "given": "Katarzyna J", "initials": "KJ"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Lindholm Carlstr\u00f6m", "given": "Eva", "initials": "E"}, {"family": "Emilsson", "given": "Lina", "initials": "L"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Jazin", "given": "Elena", "initials": "E"}], "type": "journal article", "published": "2013-04-01", "journal": {"volume": "22", "issn": "1460-2083", "issue": "7", "pages": "1373-1382", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Linkage, association and expression studies previously pointed to the human QKI, KH domain containing, RNA-binding (QKI) as a candidate gene for schizophrenia. Functional studies of the mouse orthologue Qk focused mainly on its role in oligodendrocyte development and myelination, while its function in astroglia remained unexplored. Here, we show that QKI is highly expressed in human primary astrocytes and that its splice forms encode proteins targeting different subcellular localizations. Uncovering the role of QKI in astrocytes is of interest in light of growing evidence implicating astrocyte dysfunction in the pathogenesis of several disorders of the central nervous system. We selectively silenced QKI splice variants in human primary astrocytes and used RNA sequencing to identify differential expression and splice variant composition at the genome-wide level. We found that an mRNA expression of Glial fibrillary acidic protein (GFAP), encoding a major component of astrocyte intermediate filaments, was down-regulated after QKI7 splice variant silencing. Moreover, we identified a potential QKI-binding site within the 3' untranslated region of human GFAP. This sequence was not conserved between mice and humans, raising the possibility that GFAP is a target for QKI in humans but not rodents. Haloperidol treatment of primary astrocytes resulted in coordinated increases in QKI7 and GFAP expression. Taken together, our results provide the first link between QKI and GFAP, two genes with alterations previously observed independently in schizophrenic patients. Our findings for QKI, together with its well-known role in myelination, suggest that QKI is a hub regulator of glia function in humans.", "doi": "10.1093/hmg/dds553", "pmid": "23321059", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "dds553"}], "notes": [], "created": "2017-05-04T15:02:25.213Z", "modified": "2021-07-07T14:15:07.503Z"}, {"entity": "publication", "iuid": "f1019b2b1539445d99fb17566d00cb69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1019b2b1539445d99fb17566d00cb69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1019b2b1539445d99fb17566d00cb69"}}, "title": "Welander distal myopathy caused by an ancient founder mutation in TIA1 associated with perturbed splicing.", "authors": [{"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Sobol", "given": "Maria", "initials": "M"}, {"family": "Melberg", "given": "Atle", "initials": "A"}, {"family": "M\u00e4bert", "given": "Katrin", "initials": "K"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Johansson", "given": "Anna C V", "initials": "AC"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Entesarian", "given": "Miriam", "initials": "M"}, {"family": "Orl\u00e9n", "given": "Hanna", "initials": "H"}, {"family": "Casar-Borota", "given": "Olivera", "initials": "O"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2013-04-00", "journal": {"volume": "34", "issn": "1098-1004", "issue": "4", "pages": "572-577", "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "Welander distal myopathy (WDM) is an adult onset autosomal dominant disorder characterized by distal limb weakness, which progresses slowly from the fifth decade. All WDM patients are of Swedish or Finnish descent and share a rare chromosome 2p13 haplotype. We restricted the WDM-associated haplotype followed by whole exome sequencing. Within the conserved haplotype, we identified a single heterozygous mutation c.1150G>A (p.E384K) in T-cell intracellular antigen-1 (TIA1) in all WDM patients investigated (n = 43). The TIA1 protein regulates splicing, and translation through direct interaction with mRNA and the p.E384K mutation is located in the C-terminal Q-rich domain that interacts with the U1-C splicing factor. TIA1 has been shown to prevent skipping of SMN2 exon 7, and we show that WDM patients have increased levels of spliced SMN2 in skeletal muscle cells when compared with controls. Immunostaining of WDM muscle biopsies showed accumulation of TIA1 and stress granulae proteins adjacent to intracellular inclusions, a typical finding in WDM. The combined findings strongly suggest that the TIA1 mutation causes perturbed RNA splicing and cellular stress resulting in WDM. The selection against the mutation is likely to be negligible and the age of the TIA1 founder mutation was calculated to approximately 1,050 years, which coincides with the epoch of early seafaring across the Baltic Sea.", "doi": "10.1002/humu.22282", "pmid": "23348830", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:57.873Z", "modified": "2021-07-07T14:37:06.652Z"}, {"entity": "publication", "iuid": "0fe491db999b416bbbb6d3f0f9ba117e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0fe491db999b416bbbb6d3f0f9ba117e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0fe491db999b416bbbb6d3f0f9ba117e"}}, "title": "The transporter ABCB7 is a mediator of the phenotype of acquired refractory anemia with ring sideroblasts.", "authors": [{"family": "Nikpour", "given": "M", "initials": "M"}, {"family": "Scharenberg", "given": "C", "initials": "C"}, {"family": "Liu", "given": "A", "initials": "A"}, {"family": "Conte", "given": "S", "initials": "S"}, {"family": "Karimi", "given": "M", "initials": "M"}, {"family": "Mortera-Blanco", "given": "T", "initials": "T"}, {"family": "Giai", "given": "V", "initials": "V"}, {"family": "Fernandez-Mercado", "given": "M", "initials": "M"}, {"family": "Papaemmanuil", "given": "E", "initials": "E"}, {"family": "H\u00f6gstrand", "given": "K", "initials": "K"}, {"family": "Jansson", "given": "M", "initials": "M"}, {"family": "Vedin", "given": "I", "initials": "I"}, {"family": "Stephen Wainscoat", "given": "J", "initials": "J"}, {"family": "Campbell", "given": "P", "initials": "P"}, {"family": "Cazzola", "given": "M", "initials": "M"}, {"family": "Boultwood", "given": "J", "initials": "J"}, {"family": "Grandien", "given": "A", "initials": "A"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "E", "initials": "E"}], "type": "journal article", "published": "2013-04-00", "journal": {"volume": "27", "issn": "1476-5551", "issue": "4", "pages": "889-896", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": "Refractory anemia with ring sideroblasts (RARS) is characterized by mitochondrial ferritin (FTMT) accumulation and markedly suppressed expression of the iron transporter ABCB7. To test the hypothesis that ABCB7 is a key mediator of ineffective erythropoiesis of RARS, we modulated its expression in hematopoietic cells. ABCB7 up and downregulation did not influence growth and survival of K562 cells. In normal bone marrow, ABCB7 downregulation reduced erythroid differentiation, growth and colony formation, and resulted in a gene expression pattern similar to that observed in intermediate RARS erythroblasts, and in the accumulation of FTMT. Importantly, forced ABCB7 expression restored erythroid colony growth and decreased FTMT expression level in RARS CD34+ marrow cells. Mutations in the SF3B1 gene, a core component of the RNA splicing machinery, were recently identified in a high proportion of patients with RARS and 11 of the 13 RARS patients in this study carried this mutation. Interestingly, ABCB7 exon usage differed between normal bone marrow and RARS, as well as within the RARS cohort. In addition, SF3B1 silencing resulted in downregulation of ABCB7 in K562 cells undergoing erythroid differentiation. Our findings support that ABCB7 is implicated in the phenotype of acquired RARS and suggest a relation between SF3B1 mutations and ABCB7 downregulation.", "doi": "10.1038/leu.2012.298", "pmid": "23070040", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "leu2012298"}, {"db": "pmc", "key": "PMC3794445"}, {"db": "mid", "key": "EMS53907"}], "notes": [], "created": "2017-05-04T14:58:02.987Z", "modified": "2020-01-21T13:56:00.738Z"}, {"entity": "publication", "iuid": "d1f79dd429bb40c59c2657b442b5b151", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1f79dd429bb40c59c2657b442b5b151.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1f79dd429bb40c59c2657b442b5b151"}}, "title": "The mitochondrial and autosomal mutation landscapes of prostate cancer.", "authors": [{"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Mills", "given": "Ian G", "initials": "IG"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Liu", "given": "Wennuan", "initials": "W"}, {"family": "Neiman", "given": "M\u00e5rten", "initials": "M"}, {"family": "Xu", "given": "Jianfeng", "initials": "J"}, {"family": "Wikstr\u00f6m", "given": "Pernilla", "initials": "P"}, {"family": "Wiklund", "given": "Peter", "initials": "P"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2013-04-00", "journal": {"volume": "63", "issn": "1873-7560", "issue": "4", "pages": "702-708", "title": "Eur. Urol.", "issn-l": "0302-2838"}, "abstract": "Prostate cancer (PCa) is the most common cancer in men. PCa is strongly age associated; low death rates in surveillance cohorts call into question the widespread use of surgery, which leads to overtreatment and a reduction in quality of life. There is a great need to increase the understanding of tumor characteristics in the context of disease progression.\n\nTo perform the first multigenome investigation of PCa through analysis of both autosomal and mitochondrial DNA, and to integrate exome sequencing data, and RNA sequencing and copy-number alteration (CNA) data to investigate how various different tumor characteristics, commonly analyzed separately, are interconnected.\n\nExome sequencing was applied to 64 tumor samples from 55 PCa patients with varying stage and grade. Integrated analysis was performed on a core set of 50 tumors from which exome sequencing, CNA, and RNA sequencing data were available.\n\nGenes, mutated at a significantly higher rate relative to a genomic background, were identified. In addition, mitochondrial and autosomal mutation rates were correlated to CNAs and proliferation, assessed as a cell cycle gene expression signature.\n\nGenes not previously reported to be significantly mutated in PCa, such as cell division cycle 27 homolog (Saccharomyces cerevisiae) (CDC27), myeloid/lymphoid or mixed-lineage leukemia 3 (MLL3), lysine (K)-specific demethylase 6A (KDM6A), and kinesin family member 5A (KIF5A) were identified. The mutation rate in the mitochondrial genome was 55 times higher than that of the autosomes. Multilevel analysis demonstrated a tight correlation between high reactive-oxygen exposure, chromosomal damage, high proliferation, and in parallel, a transition from multiclonal indolent primary PCa to monoclonal aggressive disease. As we only performed targeted sequence analysis; copy-number neutral rearrangements recently described for PCa were not accounted for.\n\nThe mitochondrial genome displays an elevated mutation rate compared to the autosomal chromosomes. By integrated analysis, we demonstrated that different tumor characteristics are interconnected, providing an increased understanding of PCa etiology.", "doi": "10.1016/j.eururo.2012.11.053", "pmid": "23265383", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "Karolinska High Throughput Center (KHTC)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0302-2838(12)01438-8"}], "notes": [], "created": "2017-05-04T14:57:05.981Z", "modified": "2020-01-21T13:56:05.375Z"}, {"entity": "publication", "iuid": "9f101dc1cb324bfc956d1d9d105653f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f101dc1cb324bfc956d1d9d105653f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f101dc1cb324bfc956d1d9d105653f9"}}, "title": "Modelling the effects of dispersal mechanisms and hydrodynamic regimes upon the structure of microbial communities within fluvial biofilms.", "authors": [{"family": "Woodcock", "given": "Stephen", "initials": "S"}, {"family": "Besemer", "given": "Katharina", "initials": "K"}, {"family": "Battin", "given": "Tom J", "initials": "TJ"}, {"family": "Curtis", "given": "Thomas P", "initials": "TP"}, {"family": "Sloan", "given": "William T", "initials": "WT"}], "type": "journal article", "published": "2013-04-00", "journal": {"volume": "15", "issn": "1462-2920", "issue": "4", "pages": "1216-1225", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "The spatial distribution of microbial taxa is determined primarily by physical and chemical environments and by dispersal. In a homogeneous landscape with limited dispersal, the similarity in abundance of taxa in samples declines with separation distance. We present a one-dimensional model for the spatial autocorrelation in abundances arising from immigration from some remote community and dispersal between environmentally similar landscape patches. Spatial correlation in taxa abundances were calculated from biofilms from the beds of two flumes which differed only in their bedform profiles; one flat and the other a periodic sawtooth shape. The hydraulic regime is approximately uniform over the flat bed, whereas the sawtooth induces fast flow over the peaks and recirculation in the troughs. On the flat bed, the correlation decline between samples was reproduced by a model using one biologically reasonable parameter. A decline was apparent in the other flume; however, a better fit was achieved when dispersal was not assumed constant everywhere. However, analysis of finer-resolution data for the heterogeneous flume suggested even this model did not adequately capture the community's complexity. We conclude that hydrodynamics are a strong driver of taxa-abundance patterns in stream biofilms. However, local adaptability must also be considered to build up a complete mechanistic model.", "doi": "10.1111/1462-2920.12055", "pmid": "23240857", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:06.249Z", "modified": "2020-01-21T13:56:04.110Z"}, {"entity": "publication", "iuid": "3d1923ef7920437f9f0725cd22c87a7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d1923ef7920437f9f0725cd22c87a7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d1923ef7920437f9f0725cd22c87a7f"}}, "title": "Lack of dosage compensation accompanies the arrested stage of sex chromosome evolution in ostriches.", "authors": [{"family": "Adolfsson", "given": "Sofia", "initials": "S"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2013-04-00", "journal": {"volume": "30", "issn": "1537-1719", "issue": "4", "pages": "806-810", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Sex chromosome evolution is usually seen as a process that, once initiated, will inevitably progress toward an advanced stage of degeneration of the nonrecombining chromosome. However, despite evidence that avian sex chromosome evolution was initiated >100 Ma, ratite birds have been trapped in an arrested stage of sex chromosome divergence. We performed RNA sequencing of several tissues from male and female ostriches and assembled the transcriptome de novo. A total of 315 Z-linked genes fell into two categories: those that have equal expression level in the two sexes (for which Z-W recombination still occurs) and those that have a 2-fold excess of male expression (for which Z-W recombination has ceased). We suggest that failure to evolve dosage compensation has constrained sex chromosome divergence in this basal avian lineage. Our results indicate that dosage compensation is a prerequisite for, not only a consequence of, sex chromosome evolution.", "doi": "10.1093/molbev/mst009", "pmid": "23329687", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "mst009"}, {"db": "pmc", "key": "PMC3603317"}], "notes": [], "created": "2017-05-04T14:58:04.821Z", "modified": "2020-01-21T13:56:08.510Z"}, {"entity": "publication", "iuid": "d3a818a1f7574d1886530d913b06ad00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3a818a1f7574d1886530d913b06ad00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3a818a1f7574d1886530d913b06ad00"}}, "title": "Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.", "authors": [{"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Singan", "given": "Vasanth R", "initials": "VR"}, {"family": "Murphy", "given": "Robert F", "initials": "RF"}, {"family": "Pepperkok", "given": "Rainer", "initials": "R"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Simpson", "given": "Jeremy C", "initials": "JC"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2013-04-00", "journal": {"volume": "10", "issn": "1548-7105", "issue": "4", "pages": "315-323", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": "Imaging techniques such as immunofluorescence (IF) and the expression of fluorescent protein (FP) fusions are widely used to investigate the subcellular distribution of proteins. Here we report a systematic analysis of >500 human proteins comparing the localizations obtained in live versus fixed cells using FPs and IF, respectively. We identify systematic discrepancies between IF and FPs as well as between FP tagging at the N and C termini. The analysis shows that for 80% of the proteins, IF and FPs yield the same subcellular distribution, and the locations of 250 previously unlocalized proteins were determined by the overlap between the two methods. Approximately 60% of proteins localize to multiple organelles for both methods, indicating a complex subcellular protein organization. These results show that both IF and FP tagging are reliable techniques and demonstrate the usefulness of an integrative approach for a complete investigation of the subcellular human proteome.", "doi": "10.1038/nmeth.2377", "pmid": "23435261", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "nmeth.2377"}], "notes": [], "created": "2017-05-04T14:55:14.395Z", "modified": "2021-07-08T13:44:33.657Z"}, {"entity": "publication", "iuid": "8a51d784aa5746bd8e434e5046159bec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a51d784aa5746bd8e434e5046159bec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a51d784aa5746bd8e434e5046159bec"}}, "title": "Identification of seven loci affecting mean telomere length and their association with disease.", "authors": [{"family": "Codd", "given": "Veryan", "initials": "V"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Deelen", "given": "Joris", "initials": "J"}, {"family": "Buxton", "given": "Jessica L", "initials": "JL"}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "Mateo Leach", "given": "Irene", "initials": "I"}, {"family": "Salo", "given": "Perttu", "initials": "P"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Matthews", "given": "Mary K", "initials": "MK"}, {"family": "Palmen", "given": "Jutta", "initials": "J"}, {"family": "Norata", "given": "Giuseppe D", "initials": "GD"}, {"family": "O'Reilly", "given": "Paul F", "initials": "PF"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Balmforth", "given": "Anthony J", "initials": "AJ"}, {"family": "Beekman", "given": "Marian", "initials": "M"}, {"family": "de Boer", "given": "Rudolf A", "initials": "RA"}, {"family": "B\u00f6hringer", "given": "Stefan", "initials": "S"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Burton", "given": "Paul R", "initials": "PR"}, {"family": "de Craen", "given": "Anton J M", "initials": "AJ"}, {"family": "Denniff", "given": "Matthew", "initials": "M"}, {"family": "Dong", "given": "Yanbin", "initials": "Y"}, {"family": "Douroudis", "given": "Konstantinos", "initials": "K"}, {"family": "Dubinina", "given": "Elena", "initials": "E"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Garlaschelli", "given": "Katia", "initials": "K"}, {"family": "Guo", "given": "Dehuang", "initials": "D"}, {"family": "Hartikainen", "given": "Anna-Liisa", "initials": "AL"}, {"family": "Henders", "given": "Anjali K", "initials": "AK"}, {"family": "Houwing-Duistermaat", "given": "Jeanine J", "initials": "JJ"}, {"family": "Kananen", "given": "Laura", "initials": "L"}, {"family": "Karssen", "given": "Lennart C", "initials": "LC"}, {"family": "Kettunen", "given": "Johannes", "initials": "J"}, {"family": "Klopp", "given": "Norman", "initials": "N"}, {"family": "Lagou", "given": "Vasiliki", "initials": "V"}, {"family": "van Leeuwen", "given": "Elisabeth M", "initials": "EM"}, {"family": "Madden", "given": "Pamela A", "initials": "PA"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "M\u00e4nnist\u00f6", "given": "Satu", "initials": "S"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Pollard", "given": "Helen", "initials": "H"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Suchiman", "given": "H Eka D", "initials": "HE"}, {"family": "Valdes", "given": "Ana M", "initials": "AM"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Vi\u00f1uela", "given": "Ana", "initials": "A"}, {"family": "Wang", "given": "Xiaoling", "initials": "X"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wright", "given": "Margaret J", "initials": "MJ"}, {"family": "Xia", "given": "Kai", "initials": "K"}, {"family": "Xiao", "given": "Xiangjun", "initials": "X"}, {"family": "van Veldhuisen", "given": "Dirk J", "initials": "DJ"}, {"family": "Catapano", "given": "Alberico L", "initials": "AL"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "Hall", "given": "Alistair S", "initials": "AS"}, {"family": "Blakemore", "given": "Alexandra I F", "initials": "AI"}, {"family": "van Gilst", "given": "Wiek H", "initials": "WH"}, {"family": "Zhu", "given": "Haidong", "initials": "H"}, {"family": "CARDIoGRAM consortium", "given": null, "initials": null}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Talmud", "given": "Philippa J", "initials": "PJ"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Ouwehand", "given": "Willem", "initials": "W"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Hovatta", "given": "Iiris", "initials": "I"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Slagboom", "given": "P Eline", "initials": "PE"}, {"family": "Thompson", "given": "John R", "initials": "JR"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}], "type": "journal article", "published": "2013-04-00", "journal": {"volume": "45", "issn": "1546-1718", "issue": "4", "pages": "422-7, 427e1-2", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Interindividual variation in mean leukocyte telomere length (LTL) is associated with cancer and several age-associated diseases. We report here a genome-wide meta-analysis of 37,684 individuals with replication of selected variants in an additional 10,739 individuals. We identified seven loci, including five new loci, associated with mean LTL (P < 5 \u00d7 10(-8)). Five of the loci contain candidate genes (TERC, TERT, NAF1, OBFC1 and RTEL1) that are known to be involved in telomere biology. Lead SNPs at two loci (TERC and TERT) associate with several cancers and other diseases, including idiopathic pulmonary fibrosis. Moreover, a genetic risk score analysis combining lead variants at all 7 loci in 22,233 coronary artery disease cases and 64,762 controls showed an association of the alleles associated with shorter LTL with increased risk of coronary artery disease (21% (95% confidence interval, 5-35%) per standard deviation in LTL, P = 0.014). Our findings support a causal role of telomere-length variation in some age-related diseases.", "doi": "10.1038/ng.2528", "pmid": "23535734", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ng.2528"}, {"db": "pmc", "key": "PMC4006270"}, {"db": "mid", "key": "NIHMS571267"}], "notes": [], "created": "2017-05-04T14:58:05.933Z", "modified": "2020-01-21T13:56:03.532Z"}, {"entity": "publication", "iuid": "6c66b10d92b141998c568f91c4d7685d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c66b10d92b141998c568f91c4d7685d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c66b10d92b141998c568f91c4d7685d"}}, "title": "Hereditary uveal melanoma: a report of a germline mutation in BAP1.", "authors": [{"family": "H\u00f6iom", "given": "Veronica", "initials": "V"}, {"family": "Edsg\u00e4rd", "given": "Daniel", "initials": "D"}, {"family": "Helgadottir", "given": "Hildur", "initials": "H"}, {"family": "Eriksson", "given": "Hanna", "initials": "H"}, {"family": "All-Ericsson", "given": "Charlotta", "initials": "C"}, {"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "Ivanova", "given": "Ivayla", "initials": "I"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Hansson", "given": "Johan", "initials": "J"}], "type": "case reports", "published": "2013-04-00", "journal": {"volume": "52", "issn": "1098-2264", "issue": "4", "pages": "378-384", "title": "Genes Chromosomes Cancer", "issn-l": "1045-2257"}, "abstract": "Melanoma of the eye is a rare and distinct subtype of melanoma, which only rarely are familial. However, cases of uveal melanoma (UM) have been found in families with mixed cancer syndromes. Here, we describe a comprehensive search for inherited genetic variation in a family with multiple cases of UM but no aggregation of other cancer diagnoses. The proband is a woman diagnosed with UM at 16 years who within 6 months developed liver metastases. We also identified two older paternal relatives of the proband who had died from UM. We performed exome sequencing of germline DNA from members of the affected family. Exome-wide analysis identified a novel loss-of-function mutation in the BAP1 gene, previously suggested as a tumor suppressor. The mutation segregated with the UM phenotype in this family, and we detected a loss of the wild-type allele in the UM tumor of the proband, strongly supporting a causative association with UM. Screening of BAP1 germline mutations in families predisposed for UM may be used to identify individuals at increased risk of disease. Such individuals may then be enrolled in preventive programs and regular screenings to facilitate early detection and thereby improve prognosis.", "doi": "10.1002/gcc.22035", "pmid": "23341325", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:54.457Z", "modified": "2021-07-08T13:26:08.207Z"}, {"entity": "publication", "iuid": "44436c5f44d24480a893aa4e2c418894", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44436c5f44d24480a893aa4e2c418894.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44436c5f44d24480a893aa4e2c418894"}}, "title": "Degradation of Scots pine and beech wood exposed in four test fields used for testing of wood preservatives", "authors": [{"family": "R\u00e5berg", "given": "Ulrika", "initials": "U"}, {"family": "Terziev", "given": "Nasko", "initials": "N"}, {"family": "Daniel", "given": "Geoffrey", "initials": "G"}], "type": "journal-article", "published": "2013-04-00", "journal": {"volume": "79", "issn": "0964-8305", "issue": null, "pages": "20-27", "title": "International Biodeterioration & Biodegradation", "issn-l": null}, "abstract": null, "doi": "10.1016/j.ibiod.2012.12.010", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:26.283Z", "modified": "2021-06-22T12:05:15.935Z"}, {"entity": "publication", "iuid": "287b896d8f4c4cde862253b286a58303", "links": {"self": {"href": "https://publications.scilifelab.se/publication/287b896d8f4c4cde862253b286a58303.json"}, "display": {"href": "https://publications.scilifelab.se/publication/287b896d8f4c4cde862253b286a58303"}}, "title": "Comparative genomics of Wolbachia and the bacterial species concept.", "authors": [{"family": "Ellegaard", "given": "Kirsten Maren", "initials": "KM"}, {"family": "Klasson", "given": "Lisa", "initials": "L"}, {"family": "N\u00e4slund", "given": "Kristina", "initials": "K"}, {"family": "Bourtzis", "given": "Kostas", "initials": "K"}, {"family": "Andersson", "given": "Siv G E", "initials": "SG"}], "type": "comparative study", "published": "2013-04-00", "journal": {"volume": "9", "issn": "1553-7404", "issue": "4", "pages": "e1003381", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally transmitted genes.", "doi": "10.1371/journal.pgen.1003381", "pmid": "23593012", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-02380"}, {"db": "pmc", "key": "PMC3616963"}], "notes": [], "created": "2017-05-04T14:58:11.380Z", "modified": "2020-01-21T13:56:01.175Z"}, {"entity": "publication", "iuid": "11fa4908f11749e2a8ed03dbef5a8055", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11fa4908f11749e2a8ed03dbef5a8055.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11fa4908f11749e2a8ed03dbef5a8055"}}, "title": "Automated classification of immunostaining patterns in breast tissue from the human protein atlas.", "authors": [{"family": "Swamidoss", "given": "Issac Niwas", "initials": "IN"}, {"family": "K\u00e5rsn\u00e4s", "given": "Andreas", "initials": "A"}, {"family": "Uhlmann", "given": "Virginie", "initials": "V"}, {"family": "Ponnusamy", "given": "Palanisamy", "initials": "P"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Simonsson", "given": "Martin", "initials": "M"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Strand", "given": "Robin", "initials": "R"}], "type": "journal article", "published": "2013-03-30", "journal": {"volume": "4", "issn": "2229-5089", "issue": "Suppl", "pages": "S14", "title": "J Pathol Inform", "issn-l": "2229-5089"}, "abstract": "The Human Protein Atlas (HPA) is an effort to map the location of all human proteins (http://www.proteinatlas.org/). It contains a large number of histological images of sections from human tissue. Tissue micro arrays (TMA) are imaged by a slide scanning microscope, and each image represents a thin slice of a tissue core with a dark brown antibody specific stain and a blue counter stain. When generating antibodies for protein profiling of the human proteome, an important step in the quality control is to compare staining patterns of different antibodies directed towards the same protein. This comparison is an ultimate control that the antibody recognizes the right protein. In this paper, we propose and evaluate different approaches for classifying sub-cellular antibody staining patterns in breast tissue samples.\r\n\r\nThe proposed methods include the computation of various features including gray level co-occurrence matrix (GLCM) features, complex wavelet co-occurrence matrix (CWCM) features, and weighted neighbor distance using compound hierarchy of algorithms representing morphology (WND-CHARM)-inspired features. The extracted features are used into two different multivariate classifiers (support vector machine (SVM) and linear discriminant analysis (LDA) classifier). Before extracting features, we use color deconvolution to separate different tissue components, such as the brownly stained positive regions and the blue cellular regions, in the immuno-stained TMA images of breast tissue.\r\n\r\nWe present classification results based on combinations of feature measurements. The proposed complex wavelet features and the WND-CHARM features have accuracy similar to that of a human expert.\r\n\r\nBoth human experts and the proposed automated methods have difficulties discriminating between nuclear and cytoplasmic staining patterns. This is to a large extent due to mixed staining of nucleus and cytoplasm. Methods for quantification of staining patterns in histopathology have many applications, ranging from antibody quality control to tumor grading.", "doi": "10.4103/2153-3539.109881", "pmid": "23766936", "labels": {"Tissue Profiling": null, "BioImage Informatics": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "JPI-4-14"}, {"db": "pmc", "key": "PMC3678740"}], "notes": [], "created": "2017-05-04T14:56:00.153Z", "modified": "2021-07-05T14:18:24.301Z"}, {"entity": "publication", "iuid": "56fddc630d6e4ef59e07267939994a3f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56fddc630d6e4ef59e07267939994a3f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56fddc630d6e4ef59e07267939994a3f"}}, "title": "Genetic variants from lipid-related pathways and risk for incident myocardial infarction.", "authors": [{"family": "Song", "given": "Ci", "initials": "C"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Willenborg", "given": "Christina", "initials": "C"}, {"family": "CARDIoGRAMplusC4D Consortium", "given": "None", "initials": "N"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2013-03-29", "journal": {"volume": "8", "issn": "1932-6203", "issue": "3", "pages": "e60454", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Circulating lipids levels, as well as several familial lipid metabolism disorders, are strongly associated with initiation and progression of atherosclerosis and incidence of myocardial infarction (MI).\r\n\r\nWe hypothesized that genetic variants associated with circulating lipid levels would also be associated with MI incidence, and have tested this in three independent samples.\r\n\r\nUsing age- and sex-adjusted additive genetic models, we analyzed 554 single nucleotide polymorphisms (SNPs) in 41 candidate gene regions proposed to be involved in lipid-related pathways potentially predisposing to incidence of MI in 2,602 participants of the Swedish Twin Register (STR; 57% women). All associations with nominal P<0.01 were further investigated in the Uppsala Longitudinal Study of Adult Men (ULSAM; N = 1,142).\r\n\r\nIn the present study, we report associations of lipid-related SNPs with incident MI in two community-based longitudinal studies with in silico replication in a meta-analysis of genome-wide association studies. Overall, there were 9 SNPs in STR with nominal P-value <0.01 that were successfully genotyped in ULSAM. rs4149313 located in ABCA1 was associated with MI incidence in both longitudinal study samples with nominal significance (hazard ratio, 1.36 and 1.40; P-value, 0.004 and 0.015 in STR and ULSAM, respectively). In silico replication supported the association of rs4149313 with coronary artery disease in an independent meta-analysis including 173,975 individuals of European descent from the CARDIoGRAMplusC4D consortium (odds ratio, 1.03; P-value, 0.048).\r\n\r\nrs4149313 is one of the few amino acid changing variants in ABCA1 known to associate with reduced cholesterol efflux. Our results are suggestive of a weak association between this variant and the development of atherosclerosis and MI.", "doi": "10.1371/journal.pone.0060454", "pmid": "23555974", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-11381"}, {"db": "pmc", "key": "PMC3612051"}], "notes": [], "created": "2017-05-04T14:58:16.760Z", "modified": "2021-07-07T15:11:02.172Z"}, {"entity": "publication", "iuid": "4bfa34257a69416590d769c5a7af7e95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4bfa34257a69416590d769c5a7af7e95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4bfa34257a69416590d769c5a7af7e95"}}, "title": "Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.", "authors": [{"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Einarsson", "given": "Elin", "initials": "E"}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}, {"family": "Ferella", "given": "Marcela", "initials": "M"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "journal article", "published": "2013-03-28", "journal": {"volume": "9", "issn": "1553-7358", "issue": "3", "pages": "e1003000", "title": "PLoS Comput. Biol.", "issn-l": "1553-734X"}, "abstract": "Giardia intestinalis is a common cause of diarrheal disease and it consists of eight genetically distinct genotypes or assemblages (A-H). Only assemblages A and B infect humans and are suggested to represent two different Giardia species. Correlations exist between assemblage type and host-specificity and to some extent symptoms. Phenotypical differences have been documented between assemblages and genome sequences are available for A, B and E. We have characterized and compared the polyadenylated transcriptomes of assemblages A, B and E. Four genetically different isolates were studied (WB (AI), AS175 (AII), P15 (E) and GS (B)) using paired-end, strand-specific RNA-seq. Most of the genome was transcribed in trophozoites grown in vitro, but at vastly different levels. RNA-seq confirmed many of the present annotations and refined the current genome annotation. Gene expression divergence was found to recapitulate the known phylogeny, and uncovered lineage-specific differences in expression. Polyadenylation sites were mapped for over 70% of the genes and revealed many examples of conserved and unexpectedly long 3' UTRs. 28 open reading frames were found in a non-transcribed gene cluster on chromosome 5 of the WB isolate. Analysis of allele-specific expression revealed a correlation between allele-dosage and allele expression in the GS isolate. Previously reported cis-splicing events were confirmed and global mapping of cis-splicing identified only one novel intron. These observations can possibly explain differences in host-preference and symptoms, and it will be the basis for further studies of Giardia pathogenesis and biology.", "doi": "10.1371/journal.pcbi.1003000", "pmid": "23555231", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PCOMPBIOL-D-12-01572"}, {"db": "pmc", "key": "PMC3610916"}, {"db": "GEO", "key": "GSE36490"}], "notes": [], "created": "2017-05-04T15:01:26.084Z", "modified": "2021-07-07T13:58:48.946Z"}, {"entity": "publication", "iuid": "a3dac0c39eae4d3da52777c4bfb724d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3dac0c39eae4d3da52777c4bfb724d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3dac0c39eae4d3da52777c4bfb724d6"}}, "title": "Optimizing Solubility and Permeability of a Biopharmaceutics Classification System (BCS) Class 4 Antibiotic Drug Using Lipophilic Fragments Disturbing the Crystal Lattice", "authors": [{"family": "Tehler", "given": "Ulrika", "initials": "U"}, {"family": "Fagerberg", "given": "Jonas H", "initials": "JH"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Larhed", "given": "Mats", "initials": "M"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Bergstr\u00f6m", "given": "Christel A S", "initials": "CAS"}], "type": "journal-article", "published": "2013-03-28", "journal": {"volume": "56", "issn": "1520-4804", "issue": "6", "pages": "2690-2694", "title": "J. Med. Chem.", "issn-l": "0022-2623"}, "abstract": null, "doi": "10.1021/jm301721e", "pmid": "23432334", "labels": {"Chemical Biology Consortium Sweden": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:07:18.066Z", "modified": "2025-10-17T13:04:30.414Z"}, {"entity": "publication", "iuid": "d6ce3456e6b24530998f38d3b86402e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6ce3456e6b24530998f38d3b86402e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6ce3456e6b24530998f38d3b86402e5"}}, "title": "Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.", "authors": [{"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2013-03-25", "journal": {"volume": "14", "issn": "1474-760X", "issue": "3", "pages": "R24", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "Whole-genome sequencing of tumor tissue has the potential to provide comprehensive characterization of genomic alterations in tumor samples. We present Patchwork, a new bioinformatic tool for allele-specific copy number analysis using whole-genome sequencing data. Patchwork can be used to determine the copy number of homologous sequences throughout the genome, even in aneuploid samples with moderate sequence coverage and tumor cell content. No prior knowledge of average ploidy or tumor cell content is required. Patchwork is freely available as an R package, installable via R-Forge (http://patchwork.r-forge.r-project.org/).", "doi": "10.1186/gb-2013-14-3-r24", "pmid": "23531354", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "gb-2013-14-3-r24"}, {"db": "pmc", "key": "PMC4053982"}], "notes": [], "created": "2017-05-04T15:03:01.598Z", "modified": "2017-05-30T14:49:57.083Z"}, {"entity": "publication", "iuid": "84f018b4745147949f5f97c4400174cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84f018b4745147949f5f97c4400174cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84f018b4745147949f5f97c4400174cf"}}, "title": "Offshoots of the ESF functional genomics programme.", "authors": [{"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2013-03-25", "journal": {"volume": "30", "issn": "1876-4347", "issue": "3", "pages": "296-298", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "After the conclusion of the second five-year period of the European Science Foundation (ESF) programme on functional genomics, it is time to take stock and evaluate its accomplishments. The programme networked leading scientists from a large number of European countries for strategy discussions about the promotion of functional genomics research, and to arrange scientific meetings and exchange programmes. In brief, I believe this programme has punched above its weight, and that it has successfully contributed to the overall organisation of molecular biosciences in Europe. With a modest annual budget the programme has created several interesting new opportunities, some of which may have yet to show their full impact. However, these mini-reviews are intended to provide a personal perspective on this functional genomics effort, and accordingly I focus on my personal experiences from the ESF programme.", "doi": "10.1016/j.nbt.2012.12.003", "pmid": "23295551", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(12)00900-4"}], "notes": [], "created": "2017-05-04T14:55:26.764Z", "modified": "2023-04-14T13:56:29.189Z"}, {"entity": "publication", "iuid": "eb20312a0ee745a29ecae39cf2e45d5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb20312a0ee745a29ecae39cf2e45d5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb20312a0ee745a29ecae39cf2e45d5e"}}, "title": "The genomic signature of dog domestication reveals adaptation to a starch-rich diet.", "authors": [{"family": "Axelsson", "given": "Erik", "initials": "E"}, {"family": "Ratnakumar", "given": "Abhirami", "initials": "A"}, {"family": "Arendt", "given": "Maja-Louise", "initials": "M"}, {"family": "Maqbool", "given": "Khurram", "initials": "K"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Perloski", "given": "Michele", "initials": "M"}, {"family": "Liberg", "given": "Olof", "initials": "O"}, {"family": "Arnemo", "given": "Jon M", "initials": "JM"}, {"family": "Hedhammar", "given": "Ake", "initials": "A"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2013-03-21", "journal": {"volume": "495", "issn": "1476-4687", "issue": "7441", "pages": "360-364", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.", "doi": "10.1038/nature11837", "pmid": "23354050", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "nature11837"}], "notes": [], "created": "2017-05-04T14:58:07.802Z", "modified": "2021-06-16T10:19:26.661Z"}, {"entity": "publication", "iuid": "e700dbb99ef54d5d8b85d15655ee5e50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e700dbb99ef54d5d8b85d15655ee5e50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e700dbb99ef54d5d8b85d15655ee5e50"}}, "title": "Integration of clinical data with a genome-scale metabolic model of the human adipocyte.", "authors": [{"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Agren", "given": "Rasmus", "initials": "R"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Jacobson", "given": "Peter", "initials": "P"}, {"family": "Walley", "given": "Andrew J", "initials": "AJ"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Carlsson", "given": "Lena M", "initials": "LM"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2013-03-21", "journal": {"volume": "9", "issn": "1744-4292", "issue": null, "pages": "649", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "We evaluated the presence/absence of proteins encoded by 14\u2009077 genes in adipocytes obtained from different tissue samples using immunohistochemistry. By combining this with previously published adipocyte-specific proteome data, we identified proteins associated with 7340 genes in human adipocytes. This information was used to reconstruct a comprehensive and functional genome-scale metabolic model of adipocyte metabolism. The resulting metabolic model, iAdipocytes1809, enables mechanistic insights into adipocyte metabolism on a genome-wide level, and can serve as a scaffold for integration of omics data to understand the genotype-phenotype relationship in obese subjects. By integrating human transcriptome and fluxome data, we found an increase in the metabolic activity around androsterone, ganglioside GM2 and degradation products of heparan sulfate and keratan sulfate, and a decrease in mitochondrial metabolic activities in obese subjects compared with lean subjects. Our study hereby shows a path to identify new therapeutic targets for treating obesity through combination of high throughput patient data and metabolic modeling.", "doi": "10.1038/msb.2013.5", "pmid": "23511207", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "msb20135"}, {"db": "pmc", "key": "PMC3619940"}], "notes": [], "created": "2017-05-04T14:56:01.784Z", "modified": "2021-07-08T13:44:33.705Z"}, {"entity": "publication", "iuid": "a205fa99b2e547ea8598d73b52ee6c1c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a205fa99b2e547ea8598d73b52ee6c1c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a205fa99b2e547ea8598d73b52ee6c1c"}}, "title": "Genome Sequence of a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036.", "authors": [{"family": "Manzoor", "given": "Shahid", "initials": "S"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Bejai", "given": "Sarosh", "initials": "S"}, {"family": "Meijer", "given": "Johan", "initials": "J"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2013-03-21", "journal": {"volume": "1", "issn": "2169-8287", "issue": "2", "pages": "e0011113", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "We announce here the genome sequence of Bacillus amyloliquefaciens strain UCMB5036, a plant growth-promoting bacterium isolated from a cotton plant. Its genome contains gene clusters involved in nonribosomal synthesis of secondary metabolites known for their antimicrobial activities. The availability of this genome will provide novel insights into plant-bacterium-associated activities.", "doi": "10.1128/genomeA.00111-13", "pmid": "23516223", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1/2/e00111-13"}, {"db": "pmc", "key": "PMC3622975"}], "notes": [], "created": "2017-05-04T15:01:18.784Z", "modified": "2020-01-21T13:56:09.014Z"}, {"entity": "publication", "iuid": "58ed0ad739a241a49d9f9e145c2d5a92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58ed0ad739a241a49d9f9e145c2d5a92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58ed0ad739a241a49d9f9e145c2d5a92"}}, "title": "Identification of genetic variants influencing the human plasma proteome.", "authors": [{"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Palmblad", "given": "Magnus", "initials": "M"}, {"family": "Deelder", "given": "Andr\u00e9 M", "initials": "AM"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "clinical trial", "published": "2013-03-19", "journal": {"volume": "110", "issn": "1091-6490", "issue": "12", "pages": "4673-4678", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Genetic variants influencing the transcriptome have been extensively studied. However, the impact of the genetic factors on the human proteome is largely unexplored, mainly due to lack of suitable high-throughput methods. Here we present unique and comprehensive identification of genetic variants affecting the human plasma protein profile by combining high-throughput and high-resolution mass spectrometry (MS) with genome-wide SNP data. We identified and quantified the abundance of 1,056 tryptic-digested peptides, representing 163 proteins in the plasma of 1,060 individuals from two population-based cohorts. The abundance level of almost one-fifth (19%) of the peptides was found to be heritable, with heritability ranging from 0.08 to 0.43. The levels of 60 peptides from 25 proteins, 15% of the proteins studied, were influenced by cis-acting SNPs. We identified and replicated individual cis-acting SNPs (combined P value ranging from 3.1 \u00d7 10(-52) to 2.9 \u00d7 10(-12)) influencing 11 peptides from 5 individual proteins. These SNPs represent both regulatory SNPs and nonsynonymous changes defining well-studied disease alleles such as the \u03b54 allele of apolipoprotein E (APOE), which has been shown to increase risk of Alzheimer's disease. Our results show that high-throughput mass spectrometry represents a promising method for large-scale characterization of the human proteome, allowing for both quantification and sequencing of individual proteins. Abundance and peptide composition of a protein plays an important role in the etiology, diagnosis, and treatment of a number of diseases. A better understanding of the genetic impact on the plasma proteome is therefore important for evaluating potential biomarkers and therapeutic agents for common diseases.", "doi": "10.1073/pnas.1217238110", "pmid": "23487758", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1217238110"}, {"db": "pmc", "key": "PMC3606982"}], "notes": [], "created": "2017-05-04T14:58:09.554Z", "modified": "2020-01-21T13:56:09.029Z"}, {"entity": "publication", "iuid": "1ffdcc71b4b048d4b6e82279e3a06bca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ffdcc71b4b048d4b6e82279e3a06bca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ffdcc71b4b048d4b6e82279e3a06bca"}}, "title": "Identification and verification of microRNAs by high-throughput sequencing.", "authors": [{"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "Avesson", "given": "Lotta", "initials": "L"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2013-03-16", "journal": {"volume": "983", "issn": "1940-6029", "issue": null, "pages": "125-138", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "High-throughput sequencing methods have become invaluable for detection and analysis of small RNAs. The results are millions of sequences that need to be carefully analyzed by computational methods and preferentially verified by different experimental techniques. Here we describe how to use high-throughput sequencing followed by bioinformatics and northern blot to identify one particular class of small RNA, microRNAs.", "doi": "10.1007/978-1-62703-302-2_7", "pmid": "23494305", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:04.217Z", "modified": "2021-07-07T15:22:42.686Z"}, {"entity": "publication", "iuid": "c6eb858398204b468aba8e2a2590adb3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6eb858398204b468aba8e2a2590adb3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6eb858398204b468aba8e2a2590adb3"}}, "title": "DNA topoisomerase III localizes to centromeres and affects centromeric CENP-A levels in fission yeast.", "authors": [{"family": "Norman-Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Durand-Dubief", "given": "Micka\u00ebl", "initials": "M"}, {"family": "Prasad", "given": "Punit", "initials": "P"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2013-03-14", "journal": {"volume": "9", "issn": "1553-7404", "issue": "3", "pages": "e1003371", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Centromeres are specialized chromatin regions marked by the presence of nucleosomes containing the centromere-specific histone H3 variant CENP-A, which is essential for chromosome segregation. Assembly and disassembly of nucleosomes is intimately linked to DNA topology, and DNA topoisomerases have previously been implicated in the dynamics of canonical H3 nucleosomes. Here we show that Schizosaccharomyces pombe Top3 and its partner Rqh1 are involved in controlling the levels of CENP-A(Cnp1) at centromeres. Both top3 and rqh1 mutants display defects in chromosome segregation. Using chromatin immunoprecipitation and tiling microarrays, we show that Top3, unlike Top1 and Top2, is highly enriched at centromeric central domains, demonstrating that Top3 is the major topoisomerase in this region. Moreover, centromeric Top3 occupancy positively correlates with CENP-A(Cnp1) occupancy. Intriguingly, both top3 and rqh1 mutants display increased relative enrichment of CENP-A(Cnp1) at centromeric central domains. Thus, Top3 and Rqh1 normally limit the levels of CENP-A(Cnp1) in this region. This new role is independent of the established function of Top3 and Rqh1 in homologous recombination downstream of Rad51. Therefore, we hypothesize that the Top3-Rqh1 complex has an important role in controlling centromere DNA topology, which in turn affects the dynamics of CENP-A(Cnp1) nucleosomes.", "doi": "10.1371/journal.pgen.1003371", "pmid": "23516381", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-01254"}, {"db": "pmc", "key": "PMC3597498"}], "notes": [], "created": "2017-05-04T15:03:16.012Z", "modified": "2017-05-30T14:51:25.853Z"}, {"entity": "publication", "iuid": "1fb3bf573bb84fa5b35f277e5e69c233", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fb3bf573bb84fa5b35f277e5e69c233.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fb3bf573bb84fa5b35f277e5e69c233"}}, "title": "Transcriptome of the alternative ethanol production strain Dekkera bruxellensis CBS 11270 in sugar limited, low oxygen cultivation.", "authors": [{"family": "Tiukova", "given": "Ievgeniia A", "initials": "IA"}, {"family": "Petterson", "given": "Mats E", "initials": "ME"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Eberhard", "given": "Thomas", "initials": "T"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}], "type": "journal article", "published": "2013-03-13", "journal": {"volume": "8", "issn": "1932-6203", "issue": "3", "pages": "e58455", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Dekkera bruxellensis can outcompete Saccharomyces cerevisiae in environments with low sugar concentrations. It is usually regarded as a spoilage yeast but has lately been identified as an alternative ethanol production organism. In this study, global gene expression in the industrial isolate D. bruxellensis CBS 11270 under oxygen and glucose limitation was investigated by whole transcriptome sequencing using the AB SOLiD technology. Among other observations, we noted expression of respiratory complex I NADH-ubiquinone reductase although D. bruxellensis is a Crabtree positive yeast. The observed higher expression of NADH-generating enzymes compared to NAD(+)-generating enzymes might be the reason for the previously observed NADH imbalance and resulting Custer effect in D. bruxellensis. Low expression of genes involved in glycerol production is probably the molecular basis for high efficiency of D. bruxellensis metabolism under nutrient limitation. No D. bruxellensis homologs to the genes involved in the final reactions of glycerol biosynthesis were detected. A high number of expressed sugar transporter genes is consistent with the hypothesis that the competitiveness of D. bruxellensis is due to a higher affinity for the limiting substrate.", "doi": "10.1371/journal.pone.0058455", "pmid": "23516483", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-35813"}, {"db": "pmc", "key": "PMC3596373"}], "notes": [], "created": "2017-05-04T15:02:30.677Z", "modified": "2020-01-21T13:56:01.032Z"}, {"entity": "publication", "iuid": "84a80a4059fd4217ba39d3a1321ed220", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84a80a4059fd4217ba39d3a1321ed220.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84a80a4059fd4217ba39d3a1321ed220"}}, "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.", "authors": [{"family": "Mayer", "given": "Gerhard", "initials": "G"}, {"family": "Montecchi-Palazzi", "given": "Luisa", "initials": "L"}, {"family": "Ovelleiro", "given": "David", "initials": "D"}, {"family": "Jones", "given": "Andrew R", "initials": "AR"}, {"family": "Binz", "given": "Pierre-Alain", "initials": "PA"}, {"family": "Deutsch", "given": "Eric W", "initials": "EW"}, {"family": "Chambers", "given": "Matthew", "initials": "M"}, {"family": "Kallhardt", "given": "Marius", "initials": "M"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Shofstahl", "given": "James", "initials": "J"}, {"family": "Orchard", "given": "Sandra", "initials": "S"}, {"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA"}, {"family": "Hermjakob", "given": "Henning", "initials": "H"}, {"family": "Stephan", "given": "Christian", "initials": "C"}, {"family": "Meyer", "given": "Helmut E", "initials": "HE"}, {"family": "Eisenacher", "given": "Martin", "initials": "M"}, {"family": "HUPO-PSI Group", "given": null, "initials": null}], "type": "journal article", "published": "2013-03-12", "journal": {"volume": "2013", "issn": "1758-0463", "issue": null, "pages": "bat009", "title": "Database (Oxford)", "issn-l": "1758-0463"}, "abstract": "Controlled vocabularies (CVs), i.e. a collection of predefined terms describing a modeling domain, used for the semantic annotation of data, and ontologies are used in structured data formats and databases to avoid inconsistencies in annotation, to have a unique (and preferably short) accession number and to give researchers and computer algorithms the possibility for more expressive semantic annotation of data. The Human Proteome Organization (HUPO)-Proteomics Standards Initiative (PSI) makes extensive use of ontologies/CVs in their data formats. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary. In this article, we describe the overall structure of the CV, the process by which it has been developed and is maintained and the dependencies on other ontologies. Database URL: http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo.", "doi": "10.1093/database/bat009", "pmid": "23482073", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "bat009"}, {"db": "pmc", "key": "PMC3594986"}], "notes": [], "created": "2017-05-04T14:56:23.051Z", "modified": "2020-01-21T13:53:20.615Z"}, {"entity": "publication", "iuid": "755fd30de33c4815b37355906e7fd5f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/755fd30de33c4815b37355906e7fd5f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/755fd30de33c4815b37355906e7fd5f8"}}, "title": "Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing.", "authors": [{"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Hooper", "given": "Sean D", "initials": "SD"}, {"family": "Djureinovic", "given": "Tatjana", "initials": "T"}, {"family": "Larsson", "given": "Chatarina", "initials": "C"}, {"family": "W\u00e4rnberg", "given": "Fredrik", "initials": "F"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2013-03-12", "journal": {"volume": "14", "issn": "1471-2164", "issue": null, "pages": "165", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Chromosomal rearrangements in the form of deletions, insertions, inversions and translocations are frequently observed in breast cancer genomes, and a subset of these rearrangements may play a crucial role in tumorigenesis. To identify novel somatic chromosomal rearrangements, we determined the genome structures of 15 hormone-receptor negative breast tumors by long-insert mate pair massively parallel sequencing.\n\nWe identified and validated 40 somatic structural alterations, including the recurring fusion between genes DDX10 and SKA3 and translocations involving the EPHA5 gene. Other rearrangements were found to affect genes in pathways involved in epigenetic regulation, mitosis and signal transduction, underscoring their potential role in breast tumorigenesis. RNA interference-mediated suppression of five candidate genes (DDX10, SKA3, EPHA5, CLTC and TNIK) led to inhibition of breast cancer cell growth. Moreover, downregulation of DDX10 in breast cancer cells lead to an increased frequency of apoptotic nuclear morphology.\n\nUsing whole genome mate pair sequencing and RNA interference assays, we have discovered a number of novel gene rearrangements in breast cancer genomes and identified DDX10, SKA3, EPHA5, CLTC and TNIK as potential cancer genes with impact on the growth and proliferation of breast cancer cells.", "doi": "10.1186/1471-2164-14-165", "pmid": "23496902", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-14-165"}, {"db": "pmc", "key": "PMC3600027"}], "notes": [], "created": "2017-05-04T15:02:19.774Z", "modified": "2020-01-21T13:56:03.052Z"}, {"entity": "publication", "iuid": "bb9b79fb1a9f423892352a8eb8c5a56d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb9b79fb1a9f423892352a8eb8c5a56d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb9b79fb1a9f423892352a8eb8c5a56d"}}, "title": "Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.", "authors": [{"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Lexow", "given": "Preben", "initials": "P"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2013-03-09", "journal": {"volume": "3", "issn": "2045-2322", "issue": null, "pages": "1186", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Here we demonstrate the use of short-read massive sequencing systems to in effect achieve longer read lengths through hierarchical molecular tagging. We show how indexed and PCR-amplified targeted libraries are degraded, sub-sampled and arrested at timed intervals to achieve pools of differing average length, each of which is indexed with a new tag. By this process, indices of sample origin, molecular origin, and degree of degradation is incorporated in order to achieve a nested hierarchical structure, later to be utilized in the data processing to order the reads over a longer distance than the sequencing system originally allows. With this protocol we show how continuous regions beyond 3000 bp can be decoded by an Illumina sequencing system, and we illustrate the potential applications by calling variants of the lambda genome, analysing TP53 in cancer cell lines, and targeting a variable canine mitochondrial region.", "doi": "10.1038/srep01186", "pmid": "23470464", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep01186"}, {"db": "pmc", "key": "PMC3592332"}], "notes": [], "created": "2017-05-04T14:58:18.306Z", "modified": "2021-07-08T13:26:08.313Z"}, {"entity": "publication", "iuid": "e8b7a12d5c304bb4bc87cc945f7ed1b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e8b7a12d5c304bb4bc87cc945f7ed1b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e8b7a12d5c304bb4bc87cc945f7ed1b1"}}, "title": "Recognition of mono-ADP-ribosylated ARTD10 substrates by ARTD8 macrodomains.", "authors": [{"family": "Forst", "given": "Alexandra H", "initials": "AH"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Herzog", "given": "Nicolas", "initials": "N"}, {"family": "Thorsell", "given": "Ann-Gerd", "initials": "AG"}, {"family": "Gross", "given": "Annika", "initials": "A"}, {"family": "Feijs", "given": "Karla L H", "initials": "KL"}, {"family": "Verheugd", "given": "Patricia", "initials": "P"}, {"family": "Kursula", "given": "Petri", "initials": "P"}, {"family": "Nijmeijer", "given": "Bianca", "initials": "B"}, {"family": "Kremmer", "given": "Elisabeth", "initials": "E"}, {"family": "Kleine", "given": "Henning", "initials": "H"}, {"family": "Ladurner", "given": "Andreas G", "initials": "AG"}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H"}, {"family": "L\u00fcscher", "given": "Bernhard", "initials": "B"}], "type": "journal article", "published": "2013-03-05", "journal": {"volume": "21", "issn": "1878-4186", "issue": "3", "pages": "462-475", "title": "Structure", "issn-l": "0969-2126"}, "abstract": "ADP-ribosyltransferases (ARTs) catalyze the transfer of ADP-ribose from NAD(+) onto substrates. Some ARTs generate in an iterative process ADP-ribose polymers that serve as adaptors for distinct protein domains. Other ARTs, exemplified by ARTD10, function as mono-ADP-ribosyltransferases, but it has been unclear whether this modification occurs in cells and how it is read. We observed that ARTD10 colocalized with ARTD8 and defined its macrodomains 2 and 3 as readers of mono-ADP-ribosylation both in\u00a0vitro and in cells. The crystal structures of these two ARTD8 macrodomains and isothermal titration calorimetry confirmed their interaction with\u00a0ADP-ribose. These macrodomains recognized mono-ADP-ribosylated ARTD10, but not poly-ADP-ribosylated ARTD1. This distinguished them from the macrodomain of macroH2A1.1, which interacted with poly- but not mono-ADP-ribosylated substrates. Moreover, Ran, an ARTD10 substrate, was also read by ARTD8 macrodomains. This identifies readers of mono-ADP-ribosylated proteins, defines their structures, and demonstrates the presence of this modification in cells.", "doi": "10.1016/j.str.2012.12.019", "pmid": "23473667", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "S0969-2126(13)00019-1"}, {"db": "PDB", "key": "3Q6Z"}, {"db": "PDB", "key": "3Q71"}, {"db": "PDB", "key": "3V2B"}, {"db": "PDB", "key": "3VFQ"}, {"db": "PDB", "key": "4ABK"}, {"db": "PDB", "key": "4ABL"}, {"db": "PDB", "key": "4D86"}], "notes": [], "created": "2017-05-04T15:03:50.870Z", "modified": "2017-09-06T11:42:09.447Z"}, {"entity": "publication", "iuid": "35afd44f0879482fa0fed1029c62fc6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35afd44f0879482fa0fed1029c62fc6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35afd44f0879482fa0fed1029c62fc6a"}}, "title": "TagGD: fast and accurate software for DNA Tag generation and demultiplexing.", "authors": [{"family": "Costea", "given": "Paul Igor", "initials": "PI"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Akan", "given": "Pelin", "initials": "P"}], "type": "journal article", "published": "2013-03-04", "journal": {"volume": "8", "issn": "1932-6203", "issue": "3", "pages": "e57521", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Multiplexing is of vital importance for utilizing the full potential of next generation sequencing technologies. We here report TagGD (DNA-based Tag Generator and Demultiplexor), a fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy. The barcodes are designed to minimise their interference with the experiment. Insertion, deletion and substitution events are considered when designing and demultiplexing barcodes. 20,000 barcodes of length 18 were designed in 5 minutes and 2 million barcoded Illumina HiSeq-like reads generated with an error rate of 2% were demultiplexed with full accuracy in 5 minutes. We believe that our software meets a central demand in the current high-throughput biology and can be utilised in any field with ample sample abundance. The software is available on GitHub (https://github.com/pelinakan/UBD.git).", "doi": "10.1371/journal.pone.0057521", "pmid": "23469199", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-34651"}, {"db": "pmc", "key": "PMC3587622"}], "notes": [], "created": "2017-05-04T14:58:14.041Z", "modified": "2021-07-08T13:26:08.137Z"}, {"entity": "publication", "iuid": "5f0845b0df504bca81b169af4038d592", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f0845b0df504bca81b169af4038d592.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f0845b0df504bca81b169af4038d592"}}, "title": "The genetic structure of the Lithuanian wolf population", "authors": [{"family": "Baltr\u016bnait\u0117", "given": "Laima", "initials": "L"}, {"family": "Bal\u010diauskas", "given": "Linas", "initials": "L"}, {"family": "\u00c5kesson", "given": "Mikael", "initials": "M"}], "type": "journal-article", "published": "2013-03-01", "journal": {"volume": "8", "issn": "2391-5412", "issue": "5", "pages": "440-447", "title": "Open Life Sci", "issn-l": "2391-5412"}, "abstract": null, "doi": "10.2478/s11535-013-0154-9", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:20.630Z", "modified": "2021-06-22T12:05:44.083Z"}, {"entity": "publication", "iuid": "825681d762574757ac627e2c5d4f1b3f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/825681d762574757ac627e2c5d4f1b3f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/825681d762574757ac627e2c5d4f1b3f"}}, "title": "The effect of substrate and operational parameters on the abundance of sulphate-reducing bacteria in industrial anaerobic biogas digesters.", "authors": [{"family": "Moestedt", "given": "Jan", "initials": "J"}, {"family": "Nilsson P\u00e5ledal", "given": "S\u00f6ren", "initials": "S"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "132", "issn": "1873-2976", "issue": null, "pages": "327-332", "title": "Bioresour. Technol.", "issn-l": "0960-8524"}, "abstract": "This study evaluated the effects of operational parameters and type of substrate on the abundance of sulphate-reducing bacteria in 25 industrial biogas digesters using qPCR targeting the functional dissimilatory sulphite reductase gene. The aim was to find clues for operational strategies minimizing the production of H2S. The results showed that the operation, considering strategies evaluated, only had scarce effect on the abundance, varying between 10(5) and 10(7) gene copies per ml. However, high ammonia levels and increasing concentration of sulphate resulted in significantly lower and higher levels of sulphate-reducing bacteria, respectively.", "doi": "10.1016/j.biortech.2013.01.043", "pmid": "23416620", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0960-8524(13)00066-7"}], "notes": [], "created": "2017-05-04T14:57:48.777Z", "modified": "2020-01-21T13:56:10.661Z"}, {"entity": "publication", "iuid": "5791ac4d361a44cb9b2356f22cc812d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5791ac4d361a44cb9b2356f22cc812d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5791ac4d361a44cb9b2356f22cc812d2"}}, "title": "Structure of LdtMt2, an L,D-transpeptidase from Mycobacterium tuberculosis.", "authors": [{"family": "B\u00f6th", "given": "Dominic", "initials": "D"}, {"family": "Steiner", "given": "Eva Maria", "initials": "EM"}, {"family": "Stadler", "given": "Daniela", "initials": "D"}, {"family": "Lindqvist", "given": "Ylva", "initials": "Y"}, {"family": "Schnell", "given": "Robert", "initials": "R"}, {"family": "Schneider", "given": "Gunter", "initials": "G"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "69", "issn": "1399-0047", "issue": "Pt 3", "pages": "432-441", "title": "Acta Crystallogr. D Biol. Crystallogr.", "issn-l": "0907-4449"}, "abstract": "The transpeptidase LtdMt2 catalyzes the formation of the (3-3) cross-links characteristic of the peptidoglycan layer in the Mycobacterium tuberculosis cell wall. Bioinformatics analysis suggests that the extramembrane part of the enzyme consists of three domains: two smaller domains (denoted as A and B domains) and a transpeptidase domain (the C domain) at the C-terminus. The crystal structures of two fragments comprising the AB domains and the BC domains have been determined. The structure of the BC module, which was determined to 1.86\u2005\u00c5 resolution using Se-SAD phasing, consists of the B domain with an immunoglobulin-related fold and the catalytic domain belonging to the ErfK/YbiS/YbnG fold family. The structure of the AB-domain fragment, which was solved by molecular replacement to 1.45\u2005\u00c5 resolution, reveals that despite a lack of overall sequence identity the A domain is structurally very similar to the B domain. Combining the structures of the two fragments provides a view of the complete three-domain extramembrane part of LdtMt2 and shows that the protein extends at least 80-100\u2005\u00c5 from the plasma membrane into the peptidoglycan layer and thus defines the maximal distance at which cross-links are formed by this enzyme. The LdtMt-related transpeptidases contain one or two immunoglobulin domains, which suggests that these might serve as extender units to position the catalytic domain at an appropriate distance from the membrane in the peptidoglycan layer.", "doi": "10.1107/S0907444912049268", "pmid": "23519418", "labels": {"Protein Science Facility (PSF)": null}, "xrefs": [{"db": "pii", "key": "S0907444912049268"}, {"db": "pmc", "key": "PMC3605044"}, {"db": "PDB", "key": "4HU2"}, {"db": "PDB", "key": "4HUC"}], "notes": [], "created": "2017-05-04T15:03:46.991Z", "modified": "2017-09-06T11:42:09.118Z"}, {"entity": "publication", "iuid": "0c2f343b703d49b0976b7d8b363e95aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c2f343b703d49b0976b7d8b363e95aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c2f343b703d49b0976b7d8b363e95aa"}}, "title": "Secretion of two novel enzymes, manganese 9S-lipoxygenase and epoxy alcohol synthase, by the rice pathogen Magnaporthe salvinii.", "authors": [{"family": "Wennman", "given": "Anneli", "initials": "A"}, {"family": "Oliw", "given": "Ernst H", "initials": "EH"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "54", "issn": "1539-7262", "issue": "3", "pages": "762-775", "title": "J. Lipid Res.", "issn-l": "0022-2275"}, "abstract": "The mycelium of the rice stem pathogen, Magnaporthe salvinii, secreted linoleate 9S-lipoxygenase (9S-LOX) and epoxy alcohol synthase (EAS). The EAS rapidly transformed 9S-hydroperoxy-octadeca-10E,12Z-dienoic acid (9S-HPODE) to threo 10 (11)-epoxy-9S-hydroxy-12Z-octadecenoic acid, but other hydroperoxy FAs were poor substrates. 9S-LOX was expressed in Pichia pastoris. Recombinant 9S-LOX oxidized 18:2n-6 directly to 9S-HPODE, the end product, and also to two intermediates, 11S-hydroperoxy-9Z,12Z-octadecenoic acid (11S-HPODE; \u223c5%) and 13R-hydroperoxy-9Z,11E-octadecadienoic acid (13R-HPODE; \u223c1%). 11S- and 13R-HPODE were isomerized to 9S-HPODE, probably after oxidation to peroxyl radicals, \u03b2-fragmentation, and oxygen insertion at C-9. The 18:3n-3 was oxidized at C-9, C-11, and C-13, and to 9,16-dihydroxy-10E,12,14E-octadecatrienoic acid. 9S-LOX contained catalytic manganese (Mn:protein \u223c0.2:1; Mn/Fe, 1:0.05), and its sequence could be aligned with 77% identity to 13R-LOX with catalytic manganese lipoxygenase (13R-MnLOX) of the Take-all fungus. The Leu350Met mutant of 9S-LOX shifted oxidation of 18:2n-6 from C-9 to C-13, and the Phe347Leu, Phe347Val, and Phe347Ala mutants of 13R-MnLOX from C-13 to C-9. In conclusion, M. salvinii secretes 9S-LOX with catalytic manganese along with a specific EAS. Alterations in the Sloane determinant of 9S-LOX and 13R-MnLOX with larger and smaller hydrophobic residues interconverted the regiospecific oxidation of 18:2n-6, presumably by altering the substrate position in relation to oxygen insertion.", "doi": "10.1194/jlr.M033787", "pmid": "23233731", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "jlr.M033787"}, {"db": "pmc", "key": "PMC3617950"}], "notes": [], "created": "2017-05-04T14:58:00.302Z", "modified": "2020-01-21T13:56:10.609Z"}, {"entity": "publication", "iuid": "904973ae938946f6854c12586cd67ce9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/904973ae938946f6854c12586cd67ce9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/904973ae938946f6854c12586cd67ce9"}}, "title": "Oral rehydration solution with glycerol to dairy calves: Effects on fluid balance, metabolism, and intestinal microbiota", "authors": [{"family": "Omazic", "given": "A Werner", "initials": "AW"}, {"family": "Tr\u00e5v\u00e9n", "given": "M", "initials": "M"}, {"family": "Roos", "given": "S", "initials": "S"}, {"family": "Mellgren", "given": "E", "initials": "E"}, {"family": "Holtenius", "given": "K", "initials": "K"}], "type": "journal-article", "published": "2013-03-00", "journal": {"volume": "63", "issn": "0906-4702", "issue": "1", "pages": "47-56", "title": "Acta Agriculturae Scandinavica, Section A - Animal Science", "issn-l": null}, "abstract": null, "doi": "10.1080/09064702.2013.785585", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:17.669Z", "modified": "2021-06-22T12:05:27.669Z"}, {"entity": "publication", "iuid": "e1c39bbdf73e495e99c0bc38ef6a1c1c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1c39bbdf73e495e99c0bc38ef6a1c1c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1c39bbdf73e495e99c0bc38ef6a1c1c"}}, "title": "Higher magnesium intake is associated with lower fasting glucose and insulin, with no evidence of interaction with select genetic loci, in a meta-analysis of 15 CHARGE Consortium Studies.", "authors": [{"family": "Hruby", "given": "Adela", "initials": "A"}, {"family": "Ngwa", "given": "Julius S", "initials": "JS"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Wojczynski", "given": "Mary K", "initials": "MK"}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Houston", "given": "Denise K", "initials": "DK"}, {"family": "Jacques", "given": "Paul F", "initials": "PF"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lemaitre", "given": "Rozenn N", "initials": "RN"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Sonestedt", "given": "Emily", "initials": "E"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "van Rooij", "given": "Frank J A", "initials": "FJA"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Djouss\u00e9", "given": "Luc", "initials": "L"}, {"family": "Grigoriou", "given": "Efi", "initials": "E"}, {"family": "Johansson", "given": "Ingegerd", "initials": "I"}, {"family": "Lohman", "given": "Kurt K", "initials": "KK"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Riserus", "given": "Ulf", "initials": "U"}, {"family": "Yannakoulia", "given": "Mary", "initials": "M"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Hassanali", "given": "Neelam", "initials": "N"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Mozaffarian", "given": "Dariush", "initials": "D"}, {"family": "Papoutsakis", "given": "Constantina", "initials": "C"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "Groves", "given": "Christopher J", "initials": "CJ"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Mikkil\u00e4", "given": "Vera", "initials": "V"}, {"family": "Mukamal", "given": "Kenneth", "initials": "K"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kao", "given": "W H Linda", "initials": "WHL"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JCM"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "McKeown", "given": "Nicola M", "initials": "NM"}, {"family": "Nettleton", "given": "Jennifer A", "initials": "JA"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "143", "issn": "1541-6100", "issue": "3", "pages": "345-353", "title": "J. Nutr.", "issn-l": "0022-3166"}, "abstract": "Favorable associations between magnesium intake and glycemic traits, such as fasting glucose and insulin, are observed in observational and clinical studies, but whether genetic variation affects these associations is largely unknown. We hypothesized that single nucleotide polymorphisms (SNPs) associated with either glycemic traits or magnesium metabolism affect the association between magnesium intake and fasting glucose and insulin. Fifteen studies from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium provided data from up to 52,684 participants of European descent without known diabetes. In fixed-effects meta-analyses, we quantified 1) cross-sectional associations of dietary magnesium intake with fasting glucose (mmol/L) and insulin (ln-pmol/L) and 2) interactions between magnesium intake and SNPs related to fasting glucose (16 SNPs), insulin (2 SNPs), or magnesium (8 SNPs) on fasting glucose and insulin. After adjustment for age, sex, energy intake, BMI, and behavioral risk factors, magnesium (per 50-mg/d increment) was inversely associated with fasting glucose [\u03b2 = -0.009 mmol/L (95% CI: -0.013, -0.005), P < 0.0001] and insulin [-0.020 ln-pmol/L (95% CI: -0.024, -0.017), P < 0.0001]. No magnesium-related SNP or interaction between any SNP and magnesium reached significance after correction for multiple testing. However, rs2274924 in magnesium transporter-encoding TRPM6 showed a nominal association (uncorrected P = 0.03) with glucose, and rs11558471 in SLC30A8 and rs3740393 near CNNM2 showed a nominal interaction (uncorrected, both P = 0.02) with magnesium on glucose. Consistent with other studies, a higher magnesium intake was associated with lower fasting glucose and insulin. Nominal evidence of TRPM6 influence and magnesium interaction with select loci suggests that further investigation is warranted.", "doi": "10.3945/jn.112.172049", "pmid": "23343670", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "jn.112.172049"}, {"db": "pmc", "key": "PMC3713023"}], "notes": [], "created": "2017-05-04T14:58:01.515Z", "modified": "2021-07-07T15:11:02.227Z"}, {"entity": "publication", "iuid": "1bffc75b0b2b45f5984c82529687bb44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1bffc75b0b2b45f5984c82529687bb44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1bffc75b0b2b45f5984c82529687bb44"}}, "title": "Genetic effects on old-age cognitive functioning: a population-based study.", "authors": [{"family": "Laukka", "given": "Erika J", "initials": "EJ"}, {"family": "L\u00f6vd\u00e9n", "given": "Martin", "initials": "M"}, {"family": "Herlitz", "given": "Agneta", "initials": "A"}, {"family": "Karlsson", "given": "Sari", "initials": "S"}, {"family": "Ferencz", "given": "Beata", "initials": "B"}, {"family": "Pantzar", "given": "Alexandra", "initials": "A"}, {"family": "Keller", "given": "Lina", "initials": "L"}, {"family": "Graff", "given": "Caroline", "initials": "C"}, {"family": "Fratiglioni", "given": "Laura", "initials": "L"}, {"family": "B\u00e4ckman", "given": "Lars", "initials": "L"}], "type": "comparative study", "published": "2013-03-00", "journal": {"volume": "28", "issn": "1939-1498", "issue": "1", "pages": "262-274", "title": "Psychol Aging", "issn-l": "0882-7974"}, "abstract": "Associations between genotypes and cognitive outcomes may provide clues as to which mechanisms cause individual differences in old-age cognitive performance. We investigated the effects of five polymorphisms on cognitive functioning in a population-based sample of 2,694 persons without dementia (60-102 years). A structural equation model (SEM) was fit to the cognitive data, yielding five specific latent factors (perceptual speed, episodic memory, semantic memory, category fluency, and letter fluency), as well as a global cognitive factor. These factors showed the expected associations with chronological age. Genotyping was performed for five single-nucleotide polymorphisms that have been associated with cognitive performance: APOE (rs429358), COMT (rs4680), BDNF (rs6265), KIBRA (rs17070145), and CLSTN2 (rs6439886). After controlling for age, gender, and education, as well as correcting for multiple comparisons, we observed negative effects of being an APOE \u03b54 carrier on episodic memory and perceptual speed. Furthermore, being a CLSTN2 TT carrier was associated with poorer semantic memory. For the global factor, the same pattern of results was observed. In addition, being a BDNF any A carrier was associated with better cognitive performance. Also, older age was associated with stronger genetic effects of APOE on global cognition. However, this interaction effect was partly driven by the presence of preclinical dementia cases in our sample. Similarly, excluding future dementia cases attenuated the effects of APOE on episodic memory and global cognition, suggesting that part of the effects of APOE on old-age cognitive performance may be driven by dementia-related processes.", "doi": "10.1037/a0030829", "pmid": "23276211", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "2012-34905-001"}], "notes": [], "created": "2017-05-04T15:03:38.370Z", "modified": "2017-05-30T12:46:20.244Z"}, {"entity": "publication", "iuid": "2aad8a9c846643b3abfd4862174e86aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2aad8a9c846643b3abfd4862174e86aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2aad8a9c846643b3abfd4862174e86aa"}}, "title": "Genetic determinants of plasma \u03b2\u2082-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain.", "authors": [{"family": "Athanasiadis", "given": "G", "initials": "G"}, {"family": "Sabater-Lleal", "given": "M", "initials": "M"}, {"family": "Buil", "given": "A", "initials": "A"}, {"family": "Souto", "given": "J C", "initials": "JC"}, {"family": "Borrell", "given": "M", "initials": "M"}, {"family": "Lathrop", "given": "M", "initials": "M"}, {"family": "Watkins", "given": "H", "initials": "H"}, {"family": "Almasy", "given": "L", "initials": "L"}, {"family": "Hamsten", "given": "A", "initials": "A"}, {"family": "Soria", "given": "J M", "initials": "JM"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "11", "issn": "1538-7836", "issue": "3", "pages": "521-528", "title": "J. Thromb. Haemost.", "issn-l": null}, "abstract": "\u03b22 -Glycoprotein I (\u03b22 -GPI), also designated apolipoprotein H, is a 50-kDa protein that circulates in blood at high concentrations, playing important roles in autoimmune diseases, hemostasis, atherogenesis, and angiogenesis, as well as in host defense against bacteria and in protein/cellular waste removal. Plasma \u03b22 -GPI levels have a significant genetic component (heritability of ~ 80%).\n\nTo present the results of a genome-wide association study for plasma \u03b22 -GPI levels in a set of extended pedigrees from the Genetic Analysis of Idiopathic Thrombophilia (GAIT) Project.\n\nA total of 306 individuals for whom \u03b22 -GPI plasma measurements were available were typed for 307,984 single-nucleotide polymorphisms (SNPs) with the Infinium 317k Beadchip (Illumina). Association with the \u03b22 -GPI phenotype was investigated through variance component analysis, and the most significant results were followed up for association with coronary artery disease (CAD) in an independent in silico analysis involving 5765 CAD cases from the PROCARDIS Project and 7264 controls from the PROCARDIS Project and the Wellcome Trust Case Control Consortium (WTCCC) collection.\n\nAfter correction for multiple testing, three SNPs located in/around two genes (ELF5 and SCUBE2) reached genome-wide significance. Moreover, an SNP in the APOH gene showed suggestive association with the \u03b22 -GPI phenotype. Some of the identified genes are plausible biological candidates, as they are actually or potentially involved in inflammatory processes.\n\nOur results represent a first step towards identifying common variants reflecting the genetic architecture influencing plasma \u03b22 -GPI levels, and warrant further validation by functional experiments, as the functions of some of the discovered loci are still unknown.", "doi": "10.1111/jth.12120", "pmid": "23279374", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:02.078Z", "modified": "2020-01-21T13:56:01.221Z"}, {"entity": "publication", "iuid": "f007db0ad6f0442f887cf6d7b998147c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f007db0ad6f0442f887cf6d7b998147c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f007db0ad6f0442f887cf6d7b998147c"}}, "title": "Fine-mapping of restless legs locus 4 (RLS4) identifies a haplotype over the SPATS2L and KCTD18 genes.", "authors": [{"family": "Pichler", "given": "Irene", "initials": "I"}, {"family": "Schwienbacher", "given": "Christine", "initials": "C"}, {"family": "Zanon", "given": "Alessandra", "initials": "A"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Serafin", "given": "Alice", "initials": "A"}, {"family": "Facheris", "given": "Maurizio F", "initials": "MF"}, {"family": "Marroni", "given": "Fabio", "initials": "F"}, {"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "Shen", "given": "Yiping", "initials": "Y"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Gusella", "given": "James F", "initials": "JF"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "49", "issn": "1559-1166", "issue": "3", "pages": "600-605", "title": "J. Mol. Neurosci.", "issn-l": "0895-8696"}, "abstract": "Restless legs syndrome (RLS) is a sleep-related movement disorder that affects up to 15 % of the population. Linkage studies have identified several genomic loci in single families (12q, 14q, 9p, 2q, 20p and 16p, respectively). However, confirmation of these loci has not always been achieved, and causative mutations have not yet been identified. The locus on chromosome 2q33 (RLS4) was identified in two South Tyrolean families who shared a haplotype of microsatellite marker alleles across an 8.2-cM region. To pinpoint the gene localisation within RLS4, additional families from the same geographic region were evaluated, and linkage was replicated in one family. Within the candidate region, we initially found a haplotype of 23 single nucleotide polymorphism markers spanning 131.6 Kb shared by all affected members of the three linked families. Using a next generation sequencing approach, we further restricted the shared candidate region to 46.9 Kb over the potassium channel-related gene KCTD18 and exons 10-13 of SPATS2L.", "doi": "10.1007/s12031-012-9891-5", "pmid": "23054586", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:01.202Z", "modified": "2020-01-21T13:56:10.426Z"}, {"entity": "publication", "iuid": "5c2b6ea77b4743da82063c2c4f7a0b30", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c2b6ea77b4743da82063c2c4f7a0b30.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c2b6ea77b4743da82063c2c4f7a0b30"}}, "title": "Determination of the obesity-associated gene variants within the entire FTO gene by ultra-deep targeted sequencing in obese and lean children.", "authors": [{"family": "S\u00e4llman Alm\u00e9n", "given": "M", "initials": "M"}, {"family": "Rask-Andersen", "given": "M", "initials": "M"}, {"family": "Jacobsson", "given": "J A", "initials": "JA"}, {"family": "Ameur", "given": "A", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Kalnina", "given": "I", "initials": "I"}, {"family": "Moschonis", "given": "G", "initials": "G"}, {"family": "Juhlin", "given": "S", "initials": "S"}, {"family": "Bringeland", "given": "N", "initials": "N"}, {"family": "Hedberg", "given": "L A", "initials": "LA"}, {"family": "Ignatovica", "given": "V", "initials": "V"}, {"family": "Chrousos", "given": "G P", "initials": "GP"}, {"family": "Manios", "given": "Y", "initials": "Y"}, {"family": "Klovins", "given": "J", "initials": "J"}, {"family": "Marcus", "given": "C", "initials": "C"}, {"family": "Gyllensten", "given": "U", "initials": "U"}, {"family": "Fredriksson", "given": "R", "initials": "R"}, {"family": "Schi\u00f6th", "given": "H B", "initials": "HB"}], "type": "comparative study", "published": "2013-03-00", "journal": {"volume": "37", "issn": "1476-5497", "issue": "3", "pages": "424-431", "title": "Int J Obes (Lond)", "issn-l": "0307-0565"}, "abstract": "The Fat mass and obesity-associated gene (FTO) was the first gene reliably associated with body mass index in genome-wide association studies on a population level. At present, the genetic variations within the FTO gene are still the common variants that have the largest influence on body mass index.\n\nIn the current study, we amplified the entire FTO gene, in total 412 Kbp, in over 200 long-range PCR fragments from each individual, from 524 severely obese and 527 lean Swedish children, and sequenced the products as two DNA pools using massive parallel sequencing (SOLiD).\n\nThe sequencing achieved very high coverage (median 18 000 reads) and we detected and estimated allele frequencies for 705 single nucleotide polymorphisms (SNPs) (19 novel) and 40 indels (24 novel) using a sophisticated statistical approach to remove false-positive SNPs. We identified 19 obesity-associated SNPs within intron one of the FTO gene, and validated our findings with genotyping. Ten of the validated obesity-associated SNPs have a stronger obesity association (P<0.007) than the commonly studied rs9939609 SNP (P<0.012).\n\nThis study provides a comprehensive obesity-associated variation map of FTO, identifies novel lead SNPs and evaluates putative causative variants. We conclude that intron one is the only region within the FTO gene associated with obesity, and finally, we establish next generation sequencing of pooled DNA as a powerful method to investigate genetic association with complex diseases and traits.", "doi": "10.1038/ijo.2012.57", "pmid": "22531089", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ijo201257"}, {"db": "pmc", "key": "PMC3595467"}], "notes": [], "created": "2017-05-04T14:57:58.779Z", "modified": "2021-07-07T14:37:06.459Z"}, {"entity": "publication", "iuid": "cd503c88e4774b5e85b3eddf807bbdd6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd503c88e4774b5e85b3eddf807bbdd6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd503c88e4774b5e85b3eddf807bbdd6"}}, "title": "Brain gene expression differences are associated with abnormal tail biting behavior in pigs.", "authors": [{"family": "Brunberg", "given": "E", "initials": "E"}, {"family": "Jensen", "given": "P", "initials": "P"}, {"family": "Isaksson", "given": "A", "initials": "A"}, {"family": "Keeling", "given": "L J", "initials": "LJ"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "12", "issn": "1601-183X", "issue": "2", "pages": "275-281", "title": "Genes Brain Behav.", "issn-l": null}, "abstract": "Knowledge about gene expression in animals involved in abnormal behaviors can contribute to the understanding of underlying biological mechanisms. This study aimed to explore the motivational background to tail biting, an abnormal injurious behavior and severe welfare problem in pig production. Affymetrix microarrays were used to investigate gene expression differences in the hypothalamus and prefrontal cortex of pigs performing tail biting, pigs receiving bites to the tail and neutral pigs who were not involved in the behavior. In the hypothalamus, 32 transcripts were differentially expressed (P < 0.05) when tail biters were compared with neutral pigs, 130 when comparing receiver pigs with neutrals, and two when tail biters were compared with receivers. In the prefrontal cortex, seven transcripts were differently expressed in tail biters when compared with neutrals, seven in receivers vs. neutrals and none in the tail biters vs. receivers. In total, 19 genes showed a different expression pattern in neutral pigs when compared with both performers and receivers. This implies that the functions of these may provide knowledge about why the neutral pigs are not involved in tail biting behavior as performers or receivers. Among these 19 transcripts were genes associated with production traits in pigs (PDK4), sociality in humans and mice (GTF2I) and novelty seeking in humans (EGF). These are in line with hypotheses linking tail biting with reduced back fat thickness and explorative behavior.", "doi": "10.1111/gbb.12002", "pmid": "23146156", "labels": {"Array and Analysis Facility": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:01.297Z", "modified": "2017-05-30T12:37:55.391Z"}, {"entity": "publication", "iuid": "c6b3f1aedd074ffca4966f1d6d54d5e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6b3f1aedd074ffca4966f1d6d54d5e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6b3f1aedd074ffca4966f1d6d54d5e3"}}, "title": "Astakine 2--the dark knight linking melatonin to circadian regulation in crustaceans.", "authors": [{"family": "Watthanasurorot", "given": "Apiruck", "initials": "A"}, {"family": "Saelee", "given": "Netnapa", "initials": "N"}, {"family": "Phongdara", "given": "Amornrat", "initials": "A"}, {"family": "Roytrakul", "given": "Sittiruk", "initials": "S"}, {"family": "Jiravanichpaisal", "given": "Pikul", "initials": "P"}, {"family": "S\u00f6derh\u00e4ll", "given": "Kenneth", "initials": "K"}, {"family": "S\u00f6derh\u00e4ll", "given": "Irene", "initials": "I"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "9", "issn": "1553-7404", "issue": "3", "pages": "e1003361", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Daily, circadian rhythms influence essentially all living organisms and affect many physiological processes from sleep and nutrition to immunity. This ability to respond to environmental daily rhythms has been conserved along evolution, and it is found among species from bacteria to mammals. The hematopoietic process of the crayfish Pacifastacus leniusculus is under circadian control and is tightly regulated by astakines, a new family of cytokines sharing a prokineticin (PROK) domain. The expression of AST1 and AST2 are light-dependent, and this suggests an evolutionarily conserved function for PROK domain proteins in mediating circadian rhythms. Vertebrate PROKs are transmitters of circadian rhythms of the suprachiasmatic nucleus (SCN) in the brain of mammals, but the mechanism by which they function is unknown. Here we demonstrate that high AST2 expression is induced by melatonin in the brain. We identify RACK1 as a binding protein of AST2 and further provide evidence that a complex between AST2 and RACK1 functions as a negative-feedback regulator of the circadian clock. By DNA mobility shift assay, we showed that the AST2-RACK1 complex will interfere with the binding between BMAL1 and CLK and inhibit the E-box binding activity of the complex BMAL1-CLK. Finally, we demonstrate by gene knockdown that AST2 is necessary for melatonin-induced inhibition of the complex formation between BMAL1 and CLK during the dark period. In summary, we provide evidence that melatonin regulates AST2 expression and thereby affects the core clock of the crustacean brain. This process may be very important in all animals that have AST2 molecules, i.e. spiders, ticks, crustaceans, scorpions, several insect groups such as Hymenoptera, Hemiptera, and Blattodea, but not Diptera and Coleoptera. Our findings further reveal an ancient evolutionary role for the prokineticin superfamily protein that links melatonin to direct regulation of the core clock gene feedback loops.", "doi": "10.1371/journal.pgen.1003361", "pmid": "23555281", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-01816"}, {"db": "pmc", "key": "PMC3605217"}], "notes": [], "created": "2017-05-04T14:58:12.725Z", "modified": "2020-01-21T13:56:05.124Z"}, {"entity": "publication", "iuid": "7c4249fa03d543eb963d322a8842ba24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c4249fa03d543eb963d322a8842ba24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c4249fa03d543eb963d322a8842ba24"}}, "title": "A modified Glenn shunt improves haemodynamics in acute right ventricular failure in an experimental model.", "authors": [{"family": "Vikholm", "given": "Per", "initials": "P"}, {"family": "Schiller", "given": "Petter", "initials": "P"}, {"family": "Johansson", "given": "Jakob", "initials": "J"}, {"family": "Hellgren", "given": "Laila", "initials": "L"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "43", "issn": "1873-734X", "issue": "3", "pages": "612-618", "title": "Eur J Cardiothorac Surg", "issn-l": "1010-7940"}, "abstract": "Right heart failure is a major cause of morbidity and mortality after left ventricular assist device implantation and is still hard to predict. This study investigated the haemodynamic effect of a modified Glenn shunt on induced right ventricular (RV) failure.\n\nIsolated RV failure was induced by coronary ligation in 11 pigs. A modified Glenn shunt was established by a superior vena cava to pulmonary artery connection. Haemodynamic data were obtained at baseline, RV failure, and RV failure and open shunt. Myocardial biopsies were taken to ascertain established heart failure.\n\nRV failure defined as right atrial pressure \u226520 mmHg was achieved in all 11 animals. A reduction in cardiac output (CO) from 3.7 (3.5-4.2) to 2.3 l/min (2.0-2.6) and mean arterial pressure (MAP) from median 72.7 (70.1-82.2) to 55.9 mmHg (52.6-59.8) was seen during heart failure. The median flow in the shunt was 681 ml. Right atrial pressures decreased from 20.3 (19.6-21.1) to 13.4 mmHg (12.7-14.0), and RV pressures decreased from 18.1 (16.4-20.1) to 13.6 mmHg (13.5-14.2) with open shunt (P = 0.001 for both). CO increased to 2.9 l/min (2.4-3.3) when the shunt was in use. Mixed venous oxygen saturation increased with the shunt from 32 (27-38) to 49% (45-56), P = 0.001. Genes associated with heart failure were upregulated during heart failure.\n\nA modified Glenn shunt improved haemodynamics by reduced right atrial pressure, increased CO, MAP and mixed venous oxygen saturation in an experimental model of induced RV failure.", "doi": "10.1093/ejcts/ezs386", "pmid": "22761503", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "ezs386"}], "notes": [], "created": "2017-05-04T15:02:57.786Z", "modified": "2017-05-30T12:37:08.560Z"}, {"entity": "publication", "iuid": "12710516f0314d4ab08f35c83a061fe9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12710516f0314d4ab08f35c83a061fe9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12710516f0314d4ab08f35c83a061fe9"}}, "title": "A genome-wide assessment of variability in human serum metabolism.", "authors": [{"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Lewis", "given": "Matthew R", "initials": "MR"}, {"family": "Isaacs", "given": "William", "initials": "W"}, {"family": "Zheng", "given": "Lilly S", "initials": "LS"}, {"family": "Xu", "given": "Jianfeng", "initials": "J"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Broeckling", "given": "Corey", "initials": "C"}, {"family": "Prenni", "given": "Jessica E", "initials": "JE"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "34", "issn": "1098-1004", "issue": "3", "pages": "515-524", "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "The study of the genetic regulation of metabolism in human serum samples can contribute to a better understanding of the intermediate biological steps that lead from polymorphism to disease. Here, we conducted a genome-wide association study (GWAS) to discover metabolic quantitative trait loci (mQTLs) utilizing samples from a study of prostate cancer in Swedish men, consisting of 402 individuals (214 cases and 188 controls) in a discovery set and 489 case-only samples in a replication set. A global nontargeted metabolite profiling approach was utilized resulting in the detection of 6,138 molecular features followed by targeted identification of associated metabolites. Seven replicating loci were identified (PYROXD2, FADS1, PON1, CYP4F2, UGT1A8, ACADL, and LIPC) with associated sequence variants contributing significantly to trait variance for one or more metabolites (P = 10(-13) -10(-91)). Regional mQTL enrichment analyses implicated two loci that included FADS1 and a novel locus near PDGFC. Biological pathway analysis implicated ACADM, ACADS, ACAD8, ACAD10, ACAD11, and ACOXL, reflecting significant enrichment of genes with acyl-CoA dehydrogenase activity. mQTL SNPs and mQTL-harboring genes were over-represented across GWASs conducted to date, suggesting that these data may have utility in tracing the molecular basis of some complex disease associations.", "doi": "10.1002/humu.22267", "pmid": "23281178", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:57.574Z", "modified": "2020-01-21T13:56:00.794Z"}, {"entity": "publication", "iuid": "7a7a5b10ce274384a2d4acba2432303b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a7a5b10ce274384a2d4acba2432303b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a7a5b10ce274384a2d4acba2432303b"}}, "title": "A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella.", "authors": [{"family": "Guy", "given": "Lionel", "initials": "L"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Toft", "given": "Christina", "initials": "C"}, {"family": "Zaremba-Niedzwiedzka", "given": "Katarzyna", "initials": "K"}, {"family": "Berglund", "given": "Eva C", "initials": "EC"}, {"family": "Granberg", "given": "Fredrik", "initials": "F"}, {"family": "N\u00e4slund", "given": "Kristina", "initials": "K"}, {"family": "Eriksson", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Andersson", "given": "Siv G E", "initials": "SG"}], "type": "journal article", "published": "2013-03-00", "journal": {"volume": "9", "issn": "1553-7404", "issue": "3", "pages": "e1003393", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Gene transfer agents (GTAs) randomly transfer short fragments of a bacterial genome. A novel putative GTA was recently discovered in the mouse-infecting bacterium Bartonella grahamii. Although GTAs are widespread in phylogenetically diverse bacteria, their role in evolution is largely unknown. Here, we present a comparative analysis of 16 Bartonella genomes ranging from 1.4 to 2.6 Mb in size, including six novel genomes from Bartonella isolated from a cow, two moose, two dogs, and a kangaroo. A phylogenetic tree inferred from 428 orthologous core genes indicates that the deadly human pathogen B. bacilliformis is related to the ruminant-adapted clade, rather than being the earliest diverging species in the genus as previously thought. A gene flux analysis identified 12 genes for a GTA and a phage-derived origin of replication as the most conserved innovations. These are located in a region of a few hundred kb that also contains 8 insertions of gene clusters for type III, IV, and V secretion systems, and genes for putatively secreted molecules such as cholera-like toxins. The phylogenies indicate a recent transfer of seven genes in the virB gene cluster for a type IV secretion system from a cat-adapted B. henselae to a dog-adapted B. vinsonii strain. We show that the B. henselae GTA is functional and can transfer genes in vitro. We suggest that the maintenance of the GTA is driven by selection to increase the likelihood of horizontal gene transfer and argue that this process is beneficial at the population level, by facilitating adaptive evolution of the host-adaptation systems and thereby expansion of the host range size. The process counters gene loss and forces all cells to contribute to the production of the GTA and the secreted molecules. The results advance our understanding of the role that GTAs play for the evolution of bacterial genomes.", "doi": "10.1371/journal.pgen.1003393", "pmid": "23555299", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-12-01962"}, {"db": "pmc", "key": "PMC3610622"}], "notes": [], "created": "2017-05-04T14:58:11.685Z", "modified": "2021-06-16T15:15:11.757Z"}, {"entity": "publication", "iuid": "4757933eb5e04a869a182478dd622a04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4757933eb5e04a869a182478dd622a04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4757933eb5e04a869a182478dd622a04"}}, "title": "Metagenomic detection of viral pathogens in Spanish honeybees: co-infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses.", "authors": [{"family": "Granberg", "given": "Fredrik", "initials": "F"}, {"family": "Vicente-Rubiano", "given": "Marina", "initials": "M"}, {"family": "Rubio-Guerri", "given": "Consuelo", "initials": "C"}, {"family": "Karlsson", "given": "Oskar E", "initials": "OE"}, {"family": "Kukielka", "given": "Deborah", "initials": "D"}, {"family": "Bel\u00e1k", "given": "S\u00e1ndor", "initials": "S"}, {"family": "S\u00e1nchez-Vizca\u00edno", "given": "Jos\u00e9 Manuel", "initials": "JM"}], "type": "journal article", "published": "2013-02-27", "journal": {"volume": "8", "issn": "1932-6203", "issue": "2", "pages": "e57459", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The situation in Europe concerning honeybees has in recent years become increasingly aggravated with steady decline in populations and/or catastrophic winter losses. This has largely been attributed to the occurrence of a variety of known and \"unknown\", emerging novel diseases. Previous studies have demonstrated that colonies often can harbour more than one pathogen, making identification of etiological agents with classical methods difficult. By employing an unbiased metagenomic approach, which allows the detection of both unexpected and previously unknown infectious agents, the detection of three viruses, Aphid Lethal Paralysis Virus (ALPV), Israel Acute Paralysis Virus (IAPV), and Lake Sinai Virus (LSV), in honeybees from Spain is reported in this article. The existence of a subgroup of ALPV with the ability to infect bees was only recently reported and this is the first identification of such a strain in Europe. Similarly, LSV appear to be a still unclassified group of viruses with unclear impact on colony health and these viruses have not previously been identified outside of the United States. Furthermore, our study also reveals that these bees carried a plant virus, Turnip Ringspot Virus (TuRSV), potentially serving as important vector organisms. Taken together, these results demonstrate the new possibilities opened up by high-throughput sequencing and metagenomic analysis to study emerging new diseases in domestic and wild animal populations, including honeybees.", "doi": "10.1371/journal.pone.0057459", "pmid": "23460860", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-15653"}, {"db": "pmc", "key": "PMC3583878"}], "notes": [], "created": "2017-05-04T15:01:28.810Z", "modified": "2020-01-21T13:56:02.049Z"}, {"entity": "publication", "iuid": "60def3883784449d9884f29e78eccdc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60def3883784449d9884f29e78eccdc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60def3883784449d9884f29e78eccdc6"}}, "title": "Origin and evolution of medium chain alcohol dehydrogenases.", "authors": [{"family": "J\u00f6rnvall", "given": "Hans", "initials": "H"}, {"family": "Hedlund", "given": "Joel", "initials": "J"}, {"family": "Bergman", "given": "Tomas", "initials": "T"}, {"family": "Kallberg", "given": "Yvonne", "initials": "Y"}, {"family": "Cederlund", "given": "Ella", "initials": "E"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}], "type": "journal article", "published": "2013-02-25", "journal": {"volume": "202", "issn": "1872-7786", "issue": "1-3", "pages": "91-96", "title": "Chem. Biol. Interact.", "issn-l": "0009-2797"}, "abstract": "Different lines of alcohol dehydrogenases (ADHs) have separate superfamily origins, already recognized but now extended and re-evaluated by re-screening of the latest databank update. The short-chain form (SDR) is still the superfamily with most abundant occurrence, most multiple divergence, most prokaryotic emphasis, and most non-complicated architecture. This pattern is compatible with an early appearance at the time of the emergence of prokaryotic cellular life. The medium-chain form (MDR) is also old but second in terms of all the parameters above, and therefore compatible with a second emergence. However, this step appears seemingly earlier than previously considered, and may indicate sub-stages of early emergences at the increased resolution available from the now greater number of data entries. The Zn-MDR origin constitutes a third stage, possibly compatible with the transition to oxidative conditions on earth. Within all these three lines, repeated enzymogeneses gave the present divergence. MDR-ADH origin(s), at a fourth stage, may also be further resolved in multiple or extended modes, but the classical liver MDR-ADH of the liver type can still be traced to a gene duplication ~550 MYA (million years ago), at the early vertebrate radiation, compatible with the post-eon-shift, \"Cambrian explosion\". Classes and isozymes correspond to subsequent and recent duplicatory events, respectively. They illustrate a peculiar pattern with functional and emerging evolutionary distinctions between parent and emerging lines, suggesting a parallelism between duplicatory and mutational events, now also visible at separate sub-stages. Combined, all forms show distinctive patterns at different levels and illustrate correlations with global events. They further show that simple molecular observations on patterns, multiplicities and occurrence give much information, suggesting common divergence rules not much disturbed by horizontal gene transfers after the initial origins.", "doi": "10.1016/j.cbi.2012.11.008", "pmid": "23200944", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "S0009-2797(12)00252-9"}], "notes": [], "created": "2017-05-04T14:56:22.149Z", "modified": "2021-07-05T12:34:46.003Z"}, {"entity": "publication", "iuid": "90ae156bc11f447fb7decb8223931d4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90ae156bc11f447fb7decb8223931d4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90ae156bc11f447fb7decb8223931d4f"}}, "title": "Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs).", "authors": [{"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Kallberg", "given": "Yvonne", "initials": "Y"}], "type": "journal article", "published": "2013-02-25", "journal": {"volume": "202", "issn": "1872-7786", "issue": "1-3", "pages": "111-115", "title": "Chem. Biol. Interact.", "issn-l": "0009-2797"}, "abstract": "The short-chain dehydrogenases/reductases (SDRs) constitute one of the largest protein superfamilies known today. The members are distantly related with typically 20-30% residue identity in pair-wise comparisons. Still, all hitherto structurally known SDRs present a common three-dimensional structure consisting of a Rossmann fold with a parallel beta sheet flanked by three helices on each side. Using hidden Markov models (HMMs), we have developed a semi-automated subclassification system for this huge family. Currently, 75% of all SDR forms have been assigned to one of the 464 families totalling 122,940 proteins. There are 47 human SDR families, corresponding to 75 genes. Most human SDR families (35 families) have only one gene, while 12 have between 2 and 8 genes. For more than half of the human SDR families, the three-dimensional fold is known. The number of SDR members increases considerably every year, but the number of SDR families now starts to converge. The classification method has paved the ground for a sustainable and expandable nomenclature system. Information on the SDR superfamily is continuously updated at http://sdr-enzymes.org/.", "doi": "10.1016/j.cbi.2012.11.009", "pmid": "23200746", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "S0009-2797(12)00253-0"}], "notes": [], "created": "2017-05-04T14:56:22.458Z", "modified": "2021-07-05T12:34:46.037Z"}, {"entity": "publication", "iuid": "82d52b73bd3b4b62839f8b5f7a6d957f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82d52b73bd3b4b62839f8b5f7a6d957f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82d52b73bd3b4b62839f8b5f7a6d957f"}}, "title": "Evolution of sperm structure and energetics in passerine birds.", "authors": [{"family": "Rowe", "given": "Melissah", "initials": "M"}, {"family": "Laskemoen", "given": "Terje", "initials": "T"}, {"family": "Johnsen", "given": "Arild", "initials": "A"}, {"family": "Lifjeld", "given": "Jan T", "initials": "JT"}], "type": "journal article", "published": "2013-02-22", "journal": {"volume": "280", "issn": "1471-2954", "issue": "1753", "pages": "20122616", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "Spermatozoa exhibit considerable interspecific variability in size and shape. Our understanding of the adaptive significance of this diversity, however, remains limited. Determining how variation in sperm structure translates into variation in sperm performance will contribute to our understanding of the evolutionary diversification of sperm form. Here, using data from passerine birds, we test the hypothesis that longer sperm swim faster because they have more available energy. We found that sperm with longer midpieces have higher levels of intracellular adenosine triphosphate (ATP), but that greater energy reserves do not translate into faster-swimming sperm. Additionally, we found that interspecific variation in sperm ATP concentration is not associated with the level of sperm competition faced by males. Finally, using Bayesian methods, we compared the evolutionary trajectories of sperm morphology and ATP content, and show that both traits have undergone directional evolutionary change. However, in contrast to recent suggestions in other taxa, we show that changes in ATP are unlikely to have preceded changes in morphology in passerine sperm. These results suggest that variable selective pressures are likely to have driven the evolution of sperm traits in different taxa, and highlight fundamental biological differences between taxa with internal and external fertilization, as well as those with and without sperm storage.", "doi": "10.1098/rspb.2012.2616", "pmid": "23282997", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "rspb.2012.2616"}, {"db": "pmc", "key": "PMC3574354"}], "notes": [], "created": "2017-05-04T14:56:26.554Z", "modified": "2020-01-21T13:53:20.608Z"}, {"entity": "publication", "iuid": "8cf94c2161ba4ace877f492726dce9bd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cf94c2161ba4ace877f492726dce9bd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cf94c2161ba4ace877f492726dce9bd"}}, "title": "Imatinib ameliorates neuroinflammation in a rat model of multiple sclerosis by enhancing blood-brain barrier integrity and by modulating the peripheral immune response.", "authors": [{"family": "Adzemovic", "given": "Milena V", "initials": "MV"}, {"family": "Adzemovic", "given": "Milena Z", "initials": "MZ"}, {"family": "Zeitelhofer", "given": "Manuel", "initials": "M"}, {"family": "Eriksson", "given": "Ulf", "initials": "U"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Nilsson", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2013-02-20", "journal": {"volume": "8", "issn": "1932-6203", "issue": "2", "pages": "e56586", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Central nervous system (CNS) disorders such as ischemic stroke, multiple sclerosis (MS) or Alzheimers disease are characterized by the loss of blood-brain barrier (BBB) integrity. Here we demonstrate that the small tyrosine kinase inhibitor imatinib enhances BBB integrity in experimental autoimmune encephalomyelitis, an animal model of multiple sclerosis (MS). Treatment was accompanied by decreased CNS inflammation and demyelination and especially reduced T-cell recruitment. This was supported by downregulation of the chemokine receptor (CCR) 2 in CNS and lymph nodes, and by modulation of the peripheral immune response towards an anti-inflammatory phenotype. Interestingly, imatinib ameliorated neuroinflammation, even when the treatment was initiated after the clinical manifestation of the disease. We have previously shown that imatinib reduces BBB disruption and stroke volume after experimentally induced ischemic stroke by targeting platelet-derived growth factor receptor -\u03b1 (PDGFR-\u03b1) signaling. Here we demonstrate that PDGFR-\u03b1 signaling is a central regulator of BBB integrity during neuroinflammation and therefore imatinib should be considered as a potentially effective treatment for MS.", "doi": "10.1371/journal.pone.0056586", "pmid": "23437178", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-27544"}, {"db": "pmc", "key": "PMC3577871"}], "notes": [], "created": "2017-05-04T15:03:16.331Z", "modified": "2017-05-30T14:51:30.487Z"}, {"entity": "publication", "iuid": "3e3990c8c3dc4cb79371f46b1a6681f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e3990c8c3dc4cb79371f46b1a6681f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e3990c8c3dc4cb79371f46b1a6681f7"}}, "title": "The synthetic progestin levonorgestrel is a potent androgen in the three-spined stickleback (Gasterosteus aculeatus).", "authors": [{"family": "Svensson", "given": "Johan", "initials": "J"}, {"family": "Fick", "given": "Jerker", "initials": "J"}, {"family": "Brandt", "given": "Ingvar", "initials": "I"}, {"family": "Brunstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2013-02-19", "journal": {"volume": "47", "issn": "1520-5851", "issue": "4", "pages": "2043-2051", "title": "Environ. Sci. Technol.", "issn-l": "0013-936X"}, "abstract": "The use of progestins has resulted in contamination of aquatic environments and some progestins have in experimental studies been shown to impair reproduction in fish and amphibians at low ng L(-1) concentrations. The mechanisms underlying their reproductive toxicity are largely unknown. Some progestins, such as levonorgestrel (LNG), exert androgenic effects in mammals by activating the androgen receptor (AR). Male three-spined stickleback (Gasterosteus aculeatus) kidneys produce spiggin, a gluelike glycoprotein used in nest building, and its production is directly governed by androgens. Spiggin is normally absent in females but its production in female kidneys can be induced by AR agonists. Spiggin serves as the best known biomarker for androgens in fish. We exposed adult female sticklebacks to LNG at 5.5, 40, and 358 ng L(-1) for 21 days. Androgenic effects were found at LNG concentrations \u226540 ng L(-1) including induction of spiggin transcription, kidney hypertrophy, and suppressed liver vitellogenin transcription. These are the first in vivo quantitative data showing that LNG is a potent androgen in fish supporting the contention that androgenic effects of certain progestins contribute to their reproductive toxicity.", "doi": "10.1021/es304305k", "pmid": "23362984", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Uppsala (Uppsala Genome Center)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:52.516Z", "modified": "2020-01-21T13:56:01.785Z"}, {"entity": "publication", "iuid": "02e1f5c00470444babe5e686e12f9819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02e1f5c00470444babe5e686e12f9819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02e1f5c00470444babe5e686e12f9819"}}, "title": "STC1 expression by cancer-associated fibroblasts drives metastasis of colorectal cancer.", "authors": [{"family": "Pe\u00f1a", "given": "Cristina", "initials": "C"}, {"family": "C\u00e9spedes", "given": "Mar\u00eda Virtudes", "initials": "MV"}, {"family": "Lindh", "given": "Maja Bradic", "initials": "MB"}, {"family": "Kiflemariam", "given": "Sara", "initials": "S"}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "H\u00e4ggl\u00f6f", "given": "Christina", "initials": "C"}, {"family": "Birgisson", "given": "Helgi", "initials": "H"}, {"family": "Bojmar", "given": "Linda", "initials": "L"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Sandstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Olsson", "given": "Eleonor", "initials": "E"}, {"family": "Veerla", "given": "Srinivas", "initials": "S"}, {"family": "Gallardo", "given": "Alberto", "initials": "A"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}, {"family": "Chang", "given": "Andy C-M", "initials": "AC"}, {"family": "Reddel", "given": "Roger R", "initials": "RR"}, {"family": "Mangues", "given": "Ram\u00f3n", "initials": "R"}, {"family": "Augsten", "given": "Martin", "initials": "M"}, {"family": "Ostman", "given": "Arne", "initials": "A"}], "type": "journal article", "published": "2013-02-15", "journal": {"volume": "73", "issn": "1538-7445", "issue": "4", "pages": "1287-1297", "title": "Cancer Res.", "issn-l": "0008-5472"}, "abstract": "Platelet-derived growth factor (PDGF) receptor signaling is a major functional determinant of cancer-associated fibroblasts (CAF). Elevated expression of PDGF receptors on stromal CAFs is associated with metastasis and poor prognosis, but mechanism(s) that underlie these connections are not understood. Here, we report the identification of the secreted glycoprotein stanniocalcin-1 (STC1) as a mediator of metastasis by PDGF receptor function in the setting of colorectal cancer. PDGF-stimulated fibroblasts increased migration and invasion of cocultured colorectal cancer cells in an STC1-dependent manner. Analyses of human colorectal cancers revealed significant associations between stromal PDGF receptor and STC1 expression. In an orthotopic mouse model of colorectal cancer, tumors formed in the presence of STC1-deficient fibroblasts displayed reduced intravasation of tumor cells along with fewer and smaller distant metastases formed. Our results reveal a mechanistic basis for understanding the contribution of PDGF-activated CAFs to cancer metastasis.", "doi": "10.1158/0008-5472.CAN-12-1875", "pmid": "23243022", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "0008-5472.CAN-12-1875"}], "notes": [], "created": "2017-05-04T14:55:55.926Z", "modified": "2017-05-30T12:51:06.500Z"}, {"entity": "publication", "iuid": "ac2d4ddb0e494689b337cee0a2f79304", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac2d4ddb0e494689b337cee0a2f79304.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac2d4ddb0e494689b337cee0a2f79304"}}, "title": "Coastal bacterioplankton community dynamics in response to a natural disturbance.", "authors": [{"family": "Yeo", "given": "Sara K", "initials": "SK"}, {"family": "Huggett", "given": "Megan J", "initials": "MJ"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Rapp\u00e9", "given": "Michael S", "initials": "MS"}], "type": "journal article", "published": "2013-02-07", "journal": {"volume": "8", "issn": "1932-6203", "issue": "2", "pages": "e56207", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of Gammaproteobacteria, Betaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition.", "doi": "10.1371/journal.pone.0056207", "pmid": "23409156", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-27911"}, {"db": "pmc", "key": "PMC3567041"}], "notes": [], "created": "2017-05-04T14:58:18.006Z", "modified": "2020-01-21T13:56:04.522Z"}, {"entity": "publication", "iuid": "fa89c116fc284ce78b1b366d1dc7d97f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa89c116fc284ce78b1b366d1dc7d97f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa89c116fc284ce78b1b366d1dc7d97f"}}, "title": "Causal relationship between obesity and vitamin D status: bi-directional Mendelian randomization analysis of multiple cohorts.", "authors": [{"family": "Vimaleswaran", "given": "Karani S", "initials": "KS"}, {"family": "Berry", "given": "Diane J", "initials": "DJ"}, {"family": "Lu", "given": "Chen", "initials": "C"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Pilz", "given": "Stefan", "initials": "S"}, {"family": "Hiraki", "given": "Linda T", "initials": "LT"}, {"family": "Cooper", "given": "Jason D", "initials": "JD"}, {"family": "Dastani", "given": "Zari", "initials": "Z"}, {"family": "Li", "given": "Rui", "initials": "R"}, {"family": "Houston", "given": "Denise K", "initials": "DK"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Vandenput", "given": "Liesbeth", "initials": "L"}, {"family": "Zgaga", "given": "Lina", "initials": "L"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Kaakinen", "given": "Marika", "initials": "M"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Jameson", "given": "Karen", "initials": "K"}, {"family": "Arden", "given": "Nigel", "initials": "N"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "Lohman", "given": "Kurt K", "initials": "KK"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Byberg", "given": "Liisa", "initials": "L"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Dunlop", "given": "Malcolm", "initials": "M"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Herzig", "given": "Karl-Heinz", "initials": "KH"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Hartikainen", "given": "Anna-Liisa", "initials": "AL"}, {"family": "Genetic Investigation of Anthropometric Traits-GIANT Consortium", "given": null, "initials": null}, {"family": "Streeten", "given": "Elizabeth A", "initials": "EA"}, {"family": "Theodoratou", "given": "Evropi", "initials": "E"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Richards", "given": "J Brent", "initials": "JB"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Ouwehand", "given": "Willem H", "initials": "WH"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Cooper", "given": "Cyrus", "initials": "C"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Wang", "given": "Thomas J", "initials": "TJ"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Whittaker", "given": "John C", "initials": "JC"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}], "type": "journal article", "published": "2013-02-05", "journal": {"volume": "10", "issn": "1549-1676", "issue": "2", "pages": "e1001383", "title": "PLoS Med.", "issn-l": "1549-1277"}, "abstract": "Obesity is associated with vitamin D deficiency, and both are areas of active public health concern. We explored the causality and direction of the relationship between body mass index (BMI) and 25-hydroxyvitamin D [25(OH)D] using genetic markers as instrumental variables (IVs) in bi-directional Mendelian randomization (MR) analysis.\n\nWe used information from 21 adult cohorts (up to 42,024 participants) with 12 BMI-related SNPs (combined in an allelic score) to produce an instrument for BMI and four SNPs associated with 25(OH)D (combined in two allelic scores, separately for genes encoding its synthesis or metabolism) as an instrument for vitamin D. Regression estimates for the IVs (allele scores) were generated within-study and pooled by meta-analysis to generate summary effects. Associations between vitamin D scores and BMI were confirmed in the Genetic Investigation of Anthropometric Traits (GIANT) consortium (n\u200a=\u200a123,864). Each 1 kg/m(2) higher BMI was associated with 1.15% lower 25(OH)D (p\u200a=\u200a6.52\u00d710\u207b\u00b2\u2077). The BMI allele score was associated both with BMI (p\u200a=\u200a6.30\u00d710\u207b\u2076\u00b2) and 25(OH)D (-0.06% [95% CI -0.10 to -0.02], p\u200a=\u200a0.004) in the cohorts that underwent meta-analysis. The two vitamin D allele scores were strongly associated with 25(OH)D (p\u22648.07\u00d710\u207b\u2075\u2077 for both scores) but not with BMI (synthesis score, p\u200a=\u200a0.88; metabolism score, p\u200a=\u200a0.08) in the meta-analysis. A 10% higher genetically instrumented BMI was associated with 4.2% lower 25(OH)D concentrations (IV ratio: -4.2 [95% CI -7.1 to -1.3], p\u200a=\u200a0.005). No association was seen for genetically instrumented 25(OH)D with BMI, a finding that was confirmed using data from the GIANT consortium (p\u22650.57 for both vitamin D scores).\n\nOn the basis of a bi-directional genetic approach that limits confounding, our study suggests that a higher BMI leads to lower 25(OH)D, while any effects of lower 25(OH)D increasing BMI are likely to be small. Population level interventions to reduce BMI are expected to decrease the prevalence of vitamin D deficiency.", "doi": "10.1371/journal.pmed.1001383", "pmid": "23393431", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PMEDICINE-D-12-01552"}, {"db": "pmc", "key": "PMC3564800"}], "notes": [], "created": "2017-05-04T14:58:13.410Z", "modified": "2020-01-21T13:56:06.434Z"}, {"entity": "publication", "iuid": "b49daef208484f799d58336b9e5235cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b49daef208484f799d58336b9e5235cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b49daef208484f799d58336b9e5235cb"}}, "title": "FANTOM: Functional and taxonomic analysis of metagenomes.", "authors": [{"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "Karlsson", "given": "Fredrik H", "initials": "FH"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2013-02-01", "journal": {"volume": "14", "issn": "1471-2105", "issue": null, "pages": "38", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context.\n\nHere we introduce FANTOM, a tool that allows for exploratory and comparative analysis of metagenomics abundance data integrated with metadata information and biological databases. Importantly, FANTOM can make use of any hierarchical database and it comes supplied with NCBI taxonomic hierarchies as well as KEGG Orthology, COG, PFAM and TIGRFAM databases.\n\nThe software is implemented in Python, is platform independent, and is available at http://www.sysbio.se/Fantom.", "doi": "10.1186/1471-2105-14-38", "pmid": "23375020", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2105-14-38"}, {"db": "pmc", "key": "PMC3566963"}], "notes": [], "created": "2017-05-04T14:56:21.245Z", "modified": "2021-07-05T13:05:37.732Z"}, {"entity": "publication", "iuid": "ac0708bc0161400a80b688b9ae4e6f82", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac0708bc0161400a80b688b9ae4e6f82.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac0708bc0161400a80b688b9ae4e6f82"}}, "title": "The phylogeographic pattern of Francisella tularensis in Sweden indicates a Scandinavian origin of Eurosiberian tularaemia.", "authors": [{"family": "Karlsson", "given": "Edvin", "initials": "E"}, {"family": "Svensson", "given": "Kerstin", "initials": "K"}, {"family": "Lindgren", "given": "Petter", "initials": "P"}, {"family": "Bystr\u00f6m", "given": "Mona", "initials": "M"}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A"}, {"family": "Forsman", "given": "Mats", "initials": "M"}, {"family": "Johansson", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "15", "issn": "1462-2920", "issue": "2", "pages": "634-645", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "Previous studies of the causative agent of tularaemia, Francisella tularensis have identified phylogeographic patterns suggestive of environmental maintenance reservoirs. To investigate the phylogeography of tularaemia in Sweden, we selected 163 clinical isolates obtained during 1995-2009 in 10 counties and sequenced one isolate's genome to identify new genetic markers. An improved typing scheme based on two indels and nine SNPs was developed using hydrolysis or TaqMan MGB probe assays. The results showed that much of the known global genetic diversity of F. tularensis subsp. holarctica is present in Sweden. Thirteen of the 163 isolates belonged to a new genetic group that is basal to all other known members of the major genetic clade B.I, which is spread across the Eurosiberian region. One hundred and twenty-five of the 163 Swedish isolates belonged to B.I, but individual clades' frequencies differed from county to county (P < 0.001). Subsequent analyses revealed a correlation between genotype variation over time and recurrent outbreaks at specific places, supporting the 'maintenance reservoir' environmental maintenance hypothesis. Most importantly, the findings reveal the presence of diverse source populations of F. tularensis subsp. holarctica in Sweden and suggest a historical spread of the disease from Scandinavia to other parts of Eurosiberia.", "doi": "10.1111/1462-2920.12052", "pmid": "23253075", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:52.199Z", "modified": "2023-06-19T11:58:47.581Z"}, {"entity": "publication", "iuid": "10d33ae5d0ac4b878aeb6157d686d0de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10d33ae5d0ac4b878aeb6157d686d0de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10d33ae5d0ac4b878aeb6157d686d0de"}}, "title": "The Swedish Twin Registry: establishment of a biobank and other recent developments.", "authors": [{"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Rahman", "given": "Iffat", "initials": "I"}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Viktorin", "given": "Alexander", "initials": "A"}, {"family": "Walum", "given": "Hasse", "initials": "H"}, {"family": "Halldner", "given": "Linda", "initials": "L"}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S"}, {"family": "Ull\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "L\u00e5ngstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Larsson", "given": "Henrik", "initials": "H"}, {"family": "Nyman", "given": "Anastasia", "initials": "A"}, {"family": "Gumpert", "given": "Clara Hellner", "initials": "CH"}, {"family": "R\u00e5stam", "given": "Maria", "initials": "M"}, {"family": "Anckars\u00e4ter", "given": "Henrik", "initials": "H"}, {"family": "Cnattingius", "given": "Sven", "initials": "S"}, {"family": "Johannesson", "given": "Magnus", "initials": "M"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "16", "issn": "1832-4274", "issue": "1", "pages": "317-329", "title": "Twin Res Hum Genet", "issn-l": null}, "abstract": "The Swedish Twin Registry (STR) today contains more than 194,000 twins and more than 75,000 pairs have zygosity determined by an intra-pair similarity algorithm, DNA, or by being of opposite sex. Of these, approximately 20,000, 25,000, and 30,000 pairs are monozygotic, same-sex dizygotic, and opposite-sex dizygotic pairs, respectively. Since its establishment in the late 1950s, the STR has been an important epidemiological resource for the study of genetic and environmental influences on a multitude of traits, behaviors, and diseases. Following large investments in the collection of biological specimens in the past 10 years we have now established a Swedish twin biobank with DNA from 45,000 twins and blood serum from 15,000 twins, which effectively has also transformed the registry into a powerful resource for molecular studies. We here describe the main projects within which the new collections of both biological samples as well as phenotypic measures have been collected. Coverage by year of birth, zygosity determination, ethnic heterogeneity, and influences of in vitro fertilization are also described.", "doi": "10.1017/thg.2012.104", "pmid": "23137839", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S1832427412001041"}], "notes": [], "created": "2017-05-04T14:58:18.971Z", "modified": "2020-01-21T13:56:08.590Z"}, {"entity": "publication", "iuid": "1b6a0bb2b85c45858c576ab5cd0e2ed7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b6a0bb2b85c45858c576ab5cd0e2ed7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b6a0bb2b85c45858c576ab5cd0e2ed7"}}, "title": "Sequence variation in mitochondrialATPsynthase subunit 6 & 8and nuclear genesITS1andITS2in 17 cyprinid species", "authors": [{"family": "Demandt", "given": "M H", "initials": "MH"}], "type": "journal-article", "published": "2013-02-00", "journal": {"volume": "29", "issn": "0175-8659", "issue": "1", "pages": "278-280", "title": "J. Appl. Ichthyol.", "issn-l": null}, "abstract": null, "doi": "10.1111/j.1439-0426.2012.02035.x", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:27.555Z", "modified": "2021-06-22T12:05:35.879Z"}, {"entity": "publication", "iuid": "b380f7e136c54c1fba2524c096768e77", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b380f7e136c54c1fba2524c096768e77.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b380f7e136c54c1fba2524c096768e77"}}, "title": "Population pharmacokinetic modeling and deconvolution of enantioselective absorption of eflornithine in the rat", "authors": [{"family": "Johansson", "given": "Carl Christer", "initials": "CC"}, {"family": "Gennemark", "given": "Peter", "initials": "P"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "\u00c4bel\u00f6", "given": "Angela", "initials": "A"}, {"family": "Ashton", "given": "Michael", "initials": "M"}, {"family": "Jansson-L\u00f6fmark", "given": "Rasmus", "initials": "R"}], "type": "journal-article", "published": "2013-02-00", "journal": {"volume": "40", "issn": "1567-567X", "issue": "1", "pages": "117-128", "title": "J Pharmacokinet Pharmacodyn", "issn-l": null}, "abstract": null, "doi": "10.1007/s10928-012-9293-x", "pmid": "23307171", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-31T12:05:05.043Z", "modified": "2025-10-17T13:04:30.425Z"}, {"entity": "publication", "iuid": "055175ed7e5148528aff7cce6e57f6d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/055175ed7e5148528aff7cce6e57f6d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/055175ed7e5148528aff7cce6e57f6d9"}}, "title": "Olfactory receptor 51E1 protein as a potential novel tissue biomarker for small intestine neuroendocrine carcinomas.", "authors": [{"family": "Cui", "given": "Tao", "initials": "T"}, {"family": "Tsolakis", "given": "Apostolos V", "initials": "AV"}, {"family": "Li", "given": "Su-Chen", "initials": "S"}, {"family": "Cunningham", "given": "Janet L", "initials": "JL"}, {"family": "Lind", "given": "Thomas", "initials": "T"}, {"family": "\u00d6berg", "given": "Kjell", "initials": "K"}, {"family": "Giandomenico", "given": "Valeria", "initials": "V"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "168", "issn": "1479-683X", "issue": "2", "pages": "253-261", "title": "Eur. J. Endocrinol.", "issn-l": "0804-4643"}, "abstract": "Late diagnosis hinders proper management of small intestine neuroendocrine carcinoma (SI-NEC) patients. The olfactory receptor, family 51, subfamily E, member 1 (OR51E1) has been reported as a potential novel SI-NEC marker, without protein expression recognition. Thus, we further studied whether the encoded protein may be a novel SI-NEC clinical biomarker.\r\n\r\nOR51E1 coding sequence was cloned using total RNA from SI-NEC patient specimens. Quantitative real-time PCR analysis explored OR51E1 expression in laser capture microdissected SI-NEC cells and adjacent microenvironment cells. Moreover, immunohistochemistry investigated OR51E1 protein expression on operation and biopsy material from primary SI-NECs, mesentery, and liver metastases from 70 patients. Furthermore, double immunofluorescence studies explored the potential co-localization of the vesicular monoamine transporter 1 (SLC18A1, generally referred to as VMAT1) and OR51E1 in the neoplastic cells and in the intestinal mucosa adjacent to the tumor.\r\n\r\nOR51E1 coding sequence analysis showed absence of mutation in SI-NEC patients at different stages of disease. OR51E1 expression was higher in microdissected SI-NEC cells than in the adjacent microenvironment cells. Furthermore, both membranous and cytoplasmic OR51E1 immunostaining patterns were detected in both primary SI-NECs and metastases. Briefly, 18/43 primary tumors, 7/28 mesentery metastases, and 6/18 liver metastases were 'positive' for OR51E1 in more than 50% of the tumor cells. In addition, co-localization studies showed that OR51E1 was expressed in >50% of the VMAT1 immunoreactive tumor cells and of the enterochromaffin cells in the intestinal mucosa adjacent to the tumor.\r\n\r\nOR51E1 protein is a potential novel clinical tissue biomarker for SI-NECs. Moreover, we suggest its potential therapeutic molecular target development using solid tumor radioimmunotherapy.", "doi": "10.1530/EJE-12-0814", "pmid": "23184910", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "EJE-12-0814"}], "notes": [], "created": "2017-05-04T14:57:52.817Z", "modified": "2020-01-21T13:56:10.552Z"}, {"entity": "publication", "iuid": "13eb2eee89584305aab1e955570e23b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13eb2eee89584305aab1e955570e23b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13eb2eee89584305aab1e955570e23b3"}}, "title": "In vitro and in vivo activities of 2-aminopyrazines and 2-aminopyridines in experimental models of human African trypanosomiasis.", "authors": [{"family": "Vodnala", "given": "Suman K", "initials": "SK"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Sj\u00f6berg", "given": "Birger", "initials": "B"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Rottenberg", "given": "Martin E", "initials": "ME"}, {"family": "Hammarstr\u00f6m", "given": "Lars G J", "initials": "LGJ"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "57", "issn": "1098-6596", "issue": "2", "pages": "1012-1018", "title": "Antimicrob. Agents Chemother.", "issn-l": "0066-4804"}, "abstract": "New drugs for the treatment of human African trypanosomiasis are urgently needed. A number of 2-aminopyrazines/2-aminopyridines were identified as promising leads following a focused screen of 5,500 compounds for Trypanosoma brucei subsp. brucei viability. Described compounds are trypanotoxic in the submicromolar range and show comparably low cytotoxicity on representative mammalian cell lines. Specifically, 6-([6-fluoro-3,4-dihydro-2H-1-benzopyran-4-yl)]oxy)-N-(piperidin-4-yl)pyrazin-2-amine (CBK201352) is trypanotoxic for T. brucei subsp. brucei, T. brucei subsp. gambiense, and T. brucei subsp. rhodesiense and is nontoxic to mammalian cell lines, and in vitro preclinical assays predict promising pharmacokinetic parameters. Mice inoculated intraperitoneally (i.p.) with 25 mg/kg CBK201352 twice daily for 10 days, starting on the day of infection with T. brucei subsp. brucei, show complete clearance of parasites for more than 90 days. Thus, CBK201352 and related analogs are promising leads for the development of novel treatments for human African trypanosomiasis.", "doi": "10.1128/AAC.01870-12", "pmid": "23254423", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "AAC.01870-12"}, {"db": "pmc", "key": "PMC3553678"}], "notes": "Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)\r\nADME of Therapeutics (UDOPP)", "created": "2017-05-04T14:56:46.506Z", "modified": "2025-10-17T13:04:30.435Z"}, {"entity": "publication", "iuid": "f05ab5b610ee4bf89dc0eb508779ef00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f05ab5b610ee4bf89dc0eb508779ef00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f05ab5b610ee4bf89dc0eb508779ef00"}}, "title": "Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.", "authors": [{"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Krumsiek", "given": "Jan", "initials": "J"}, {"family": "Hundertmark", "given": "Claudia", "initials": "C"}, {"family": "Pistis", "given": "Giorgio", "initials": "G"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "O'Seaghdha", "given": "Conall M", "initials": "CM"}, {"family": "Haller", "given": "Toomas", "initials": "T"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Shi", "given": "Julia", "initials": "J"}, {"family": "Struchalin", "given": "Maksim", "initials": "M"}, {"family": "Middelberg", "given": "Rita P S", "initials": "RP"}, {"family": "Brown", "given": "Morris J", "initials": "MJ"}, {"family": "Gaffo", "given": "Angelo L", "initials": "AL"}, {"family": "Pirastu", "given": "Nicola", "initials": "N"}, {"family": "Li", "given": "Guo", "initials": "G"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Huffman", "given": "Jennifer", "initials": "J"}, {"family": "Yengo", "given": "Loic", "initials": "L"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Demirkan", "given": "Ayse", "initials": "A"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Liu", "given": "Xuan", "initials": "X"}, {"family": "Malerba", "given": "Giovanni", "initials": "G"}, {"family": "Lopez", "given": "Lorna M", "initials": "LM"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Li", "given": "Xinzhong", "initials": "X"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Murgia", "given": "Federico", "initials": "F"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJ"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Steri", "given": "Maristella", "initials": "M"}, {"family": "Tenesa", "given": "Albert", "initials": "A"}, {"family": "Lagou", "given": "Vasiliki", "initials": "V"}, {"family": "Salo", "given": "Perttu", "initials": "P"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Woodward", "given": "Owen M", "initials": "OM"}, {"family": "Okada", "given": "Yukinori", "initials": "Y"}, {"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "M\u00fcller", "given": "Christian", "initials": "C"}, {"family": "Oldmeadow", "given": "Christopher", "initials": "C"}, {"family": "Putku", "given": "Margus", "initials": "M"}, {"family": "Czamara", "given": "Darina", "initials": "D"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Frogheri", "given": "Laura", "initials": "L"}, {"family": "Thun", "given": "Gian Andri", "initials": "GA"}, {"family": "Grotevendt", "given": "Anne", "initials": "A"}, {"family": "Gislason", "given": "Gauti Kjartan", "initials": "GK"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "McArdle", "given": "Patrick", "initials": "P"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Coresh", "given": "Josef", "initials": "J"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Schallert", "given": "Michael", "initials": "M"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Kubo", "given": "Michiaki", "initials": "M"}, {"family": "Nakamura", "given": "Yusuke", "initials": "Y"}, {"family": "Tanaka", "given": "Toshihiro", "initials": "T"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Jacobs", "given": "David R", "initials": "DR"}, {"family": "Liu", "given": "Kiang", "initials": "K"}, {"family": "D'Adamo", "given": "Pio", "initials": "P"}, {"family": "Ulivi", "given": "Sheila", "initials": "S"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Waeber", "given": "Gerard", "initials": "G"}, {"family": "Campbell", "given": "Susan", "initials": "S"}, {"family": "Devuyst", "given": "Olivier", "initials": "O"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Hastie", "given": "Nicholas", "initials": "N"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Salumets", "given": "Andres", "initials": "A"}, {"family": "Khaw", "given": "Kay Tee", "initials": "KT"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Kraja", "given": "Aldi", "initials": "A"}, {"family": "Zhang", "given": "Qunyuan", "initials": "Q"}, {"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Scott", "given": "Rodney J", "initials": "RJ"}, {"family": "Holliday", "given": "Elizabeth G", "initials": "EG"}, {"family": "Org", "given": "Elin", "initials": "E"}, {"family": "Viigimaa", "given": "Margus", "initials": "M"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Metter", "given": "Jeffrey E", "initials": "JE"}, {"family": "Lupo", "given": "Antonio", "initials": "A"}, {"family": "Trabetti", "given": "Elisabetta", "initials": "E"}, {"family": "Sorice", "given": "Rossella", "initials": "R"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "Lattka", "given": "Eva", "initials": "E"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Theis", "given": "Fabian", "initials": "F"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "Gow", "given": "Alan J", "initials": "AJ"}, {"family": "Bruinenberg", "given": "Marcel", "initials": "M"}, {"family": "LifeLines Cohort Study", "given": null, "initials": null}, {"family": "Stolk", "given": "Ronald P", "initials": "RP"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Winkelmann", "given": "Bernhard R", "initials": "BR"}, {"family": "Boehm", "given": "Bernhard O", "initials": "BO"}, {"family": "Lucae", "given": "Susanne", "initials": "S"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Curhan", "given": "Gary", "initials": "G"}, {"family": "Mudgal", "given": "Poorva", "initials": "P"}, {"family": "Plenge", "given": "Robert M", "initials": "RM"}, {"family": "Portas", "given": "Laura", "initials": "L"}, {"family": "Persico", "given": "Ivana", "initials": "I"}, {"family": "Kirin", "given": "Mirna", "initials": "M"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Mateo Leach", "given": "Irene", "initials": "I"}, {"family": "van Gilst", "given": "Wiek H", "initials": "WH"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Ongen", "given": "Halit", "initials": "H"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Imboden", "given": "Medea", "initials": "M"}, {"family": "von Eckardstein", "given": "Arnold", "initials": "A"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "Nagaraja", "given": "Ramaiah", "initials": "R"}, {"family": "Piras", "given": "Maria Grazia", "initials": "MG"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Schurmann", "given": "Claudia", "initials": "C"}, {"family": "Budde", "given": "Kathrin", "initials": "K"}, {"family": "Ernst", "given": "Florian", "initials": "F"}, {"family": "Farrington", "given": "Susan M", "initials": "SM"}, {"family": "Theodoratou", "given": "Evropi", "initials": "E"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Shin", "given": "So-Youn", "initials": "SY"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Sala", "given": "Cinzia", "initials": "C"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "Hengstenberg", "given": "Christian", "initials": "C"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "CARDIoGRAM Consortium", "given": null, "initials": null}, {"family": "DIAGRAM Consortium", "given": null, "initials": null}, {"family": "ICBP Consortium", "given": null, "initials": null}, {"family": "MAGIC Consortium", "given": null, "initials": null}, {"family": "Meschia", "given": "James F", "initials": "JF"}, {"family": "Nalls", "given": "Michael A", "initials": "MA"}, {"family": "Sharma", "given": "Pankaj", "initials": "P"}, {"family": "Singleton", "given": "Andrew B", "initials": "AB"}, {"family": "Kamatani", "given": "Naoyuki", "initials": "N"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Burnier", "given": "Michel", "initials": "M"}, {"family": "Attia", "given": "John", "initials": "J"}, {"family": "Laan", "given": "Maris", "initials": "M"}, {"family": "Klopp", "given": "Norman", "initials": "N"}, {"family": "Hillege", "given": "Hans L", "initials": "HL"}, {"family": "Kloiber", "given": "Stefan", "initials": "S"}, {"family": "Choi", "given": "Hyon", "initials": "H"}, {"family": "Pirastu", "given": "Mario", "initials": "M"}, {"family": "Tore", "given": "Silvia", "initials": "S"}, {"family": "Probst-Hensch", "given": "Nicole M", "initials": "NM"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Parsa", "given": "Afshin", "initials": "A"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Pola\u0161ek", "given": "Ozren", "initials": "O"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Gambaro", "given": "Giovanni", "initials": "G"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BH"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Navis", "given": "Gerjan", "initials": "G"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Schipf", "given": "Sabine", "initials": "S"}, {"family": "Dunlop", "given": "Malcolm G", "initials": "MG"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Kao", "given": "W H Linda", "initials": "WH"}, {"family": "Ciullo", "given": "Marina", "initials": "M"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Caulfield", "given": "Mark", "initials": "M"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Gieger", "given": "Christian", "initials": "C"}], "type": "comparative study", "published": "2013-02-00", "journal": {"volume": "45", "issn": "1546-1718", "issue": "2", "pages": "145-154", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Elevated serum urate concentrations can cause gout, a prevalent and painful inflammatory arthritis. By combining data from >140,000 individuals of European ancestry within the Global Urate Genetics Consortium (GUGC), we identified and replicated 28 genome-wide significant loci in association with serum urate concentrations (18 new regions in or near TRIM46, INHBB, SFMBT1, TMEM171, VEGFA, BAZ1B, PRKAG2, STC1, HNF4G, A1CF, ATXN2, UBE2Q2, IGF1R, NFAT5, MAF, HLF, ACVR1B-ACVRL1 and B3GNT4). Associations for many of the loci were of similar magnitude in individuals of non-European ancestry. We further characterized these loci for associations with gout, transcript expression and the fractional excretion of urate. Network analyses implicate the inhibins-activins signaling pathways and glucose metabolism in systemic urate control. New candidate genes for serum urate concentration highlight the importance of metabolic control of urate production and excretion, which may have implications for the treatment and prevention of gout.", "doi": "10.1038/ng.2500", "pmid": "23263486", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.2500"}, {"db": "pmc", "key": "PMC3663712"}, {"db": "mid", "key": "NIHMS458823"}], "notes": [], "created": "2017-05-04T15:01:23.524Z", "modified": "2020-01-21T13:56:06.174Z"}, {"entity": "publication", "iuid": "b1621f7bf26746fab16285c1800c8476", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1621f7bf26746fab16285c1800c8476.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1621f7bf26746fab16285c1800c8476"}}, "title": "First insights into the syntrophic acetate-oxidizing bacteria--a genetic study.", "authors": [{"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "2", "issn": "2045-8827", "issue": "1", "pages": "35-53", "title": "Microbiologyopen", "issn-l": "2045-8827"}, "abstract": "Syntrophic acetate-oxidizing bacteria have been identified as key organisms for efficient biogas production from protein-rich materials. They normally grow as lithotrophs or heterotrophs, producing acetate through the Wood-Ljungdahl pathway, but when growing in syntrophy with methanogens, they reportedly reverse this pathway and oxidize acetate to hydrogen and carbon dioxide. However, the biochemical and regulatory mechanisms behind the shift and the way in which the bacteria regain energy remain unknown. In a genome-walking approach, starting with degenerated primers, we identified those gene clusters in Syntrophaceticus schinkii, Clostridium ultunense, and Tepidanaerobacter acetatoxydans that comprise the formyltetrahydrofolate synthetase gene (fhs), encoding a key enzyme of the Wood-Ljungdahl pathway. We also discovered that the latter two harbor two fhs alleles. The fhs genes are phylogenetically separated and in the case of S. schinkii functionally linked to sulfate reducers. The T. acetatoxydans fhs1 cluster combines features of acetogens, sulfate reducers, and carbon monoxide oxidizers and is organized as a putative operon. The T. acetatoxydans fhs2 cluster encodes Wood-Ljungdahl pathway enzymes, which are also known to be involved in C1 carbon metabolism. Isolation of the enzymes illustrated that both formyltetrahydrofolate synthetases of T. acetatoxydans were functionally active. However, only fhs1 was expressed, confirming bidirectional usage of the pathway.", "doi": "10.1002/mbo3.50", "pmid": "23239474", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pmc", "key": "PMC3584212"}, {"db": "GENBANK", "key": "JQ979072"}, {"db": "GENBANK", "key": "JQ979073"}, {"db": "GENBANK", "key": "JQ979074"}, {"db": "GENBANK", "key": "JQ979075"}, {"db": "GENBANK", "key": "JQ979076"}, {"db": "GENBANK", "key": "JQ979077"}], "notes": [], "created": "2017-05-04T14:58:04.514Z", "modified": "2020-01-21T13:56:10.434Z"}, {"entity": "publication", "iuid": "522305b2ffdc45d89bbb7b488c012459", "links": {"self": {"href": "https://publications.scilifelab.se/publication/522305b2ffdc45d89bbb7b488c012459.json"}, "display": {"href": "https://publications.scilifelab.se/publication/522305b2ffdc45d89bbb7b488c012459"}}, "title": "Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins.", "authors": [{"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Liu", "given": "Wennuan", "initials": "W"}, {"family": "Neiman", "given": "M\u00e5rten", "initials": "M"}, {"family": "Xu", "given": "Jianfeng", "initials": "J"}, {"family": "Wiklund", "given": "Peter", "initials": "P"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Mills", "given": "Ian G", "initials": "IG"}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "63", "issn": "1873-7560", "issue": "2", "pages": "347-353", "title": "Eur. Urol.", "issn-l": "0302-2838"}, "abstract": "Prostate cancer (PCa) is a clinically and pathologically heterogeneous disease. The rapid development of sequencing technology has the potential to deliver new biomarkers with emphasis on aggressive disease and to revolutionise personalised cancer treatment. However, a prostate harbouring cancer commonly contains multiple separate tumour foci, with the potential to aggravate tumour sampling. The level of intraprostatic tumour heterogeneity remains to be determined.\n\nTo determine the level of intraprostatic tumour heterogeneity through genome-wide, high-resolution profiling of multiple tumour samples from the same individual.\n\nMultiple tumour samples were obtained from four individuals following radical prostatectomy. One individual (SWE-1) contained >70% cancer cells in all tumour samples, whereas the other three (SWE-2 to SWE-4) required the use of laser capture microdissection for tumour cell enrichment. Subsequently, DNA was extracted from all tissue samples, and exome sequencing was performed. All tumour foci of SWE-1 were also profiled using a high-resolution array for the identification of copy number alterations (CNA).\n\nShared somatic high-frequency single nucleotide variants (SNV) and CNAs were used to infer the level of intraprostatic tumour heterogeneity.\n\nNo high-frequency mutations, common for the three tumour samples of SWE-1, were identified. Ten randomly chosen positions were validated with Sanger sequencing in all foci, which verified the exome data. The high level of intraprostatic heterogeneity was consistent in all individuals. In total, three out of four individuals harboured tumours without an apparent common somatic denominator. Although we cannot exclude the presence of common structural rearrangements, a high-density array was used for the detection of deletions and amplifications in SWE-1, which agreed with the exome data.\n\nWe present evidence for the presence of somatically independent tumours within the same prostate. This finding will have implications for personalised cancer treatment and biomarker discovery.", "doi": "10.1016/j.eururo.2012.03.050", "pmid": "22502944", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "Karolinska High Throughput Center (KHTC)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0302-2838(12)00402-2"}], "notes": [], "created": "2017-05-04T14:57:05.469Z", "modified": "2020-01-21T13:56:02.307Z"}, {"entity": "publication", "iuid": "097b7e8a789744aeb60d443c4756baee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/097b7e8a789744aeb60d443c4756baee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/097b7e8a789744aeb60d443c4756baee"}}, "title": "Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis.", "authors": [{"family": "Liu", "given": "Yun", "initials": "Y"}, {"family": "Aryee", "given": "Martin J", "initials": "MJ"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Fallin", "given": "M Daniele", "initials": "MD"}, {"family": "Hesselberg", "given": "Espen", "initials": "E"}, {"family": "Runarsson", "given": "Arni", "initials": "A"}, {"family": "Reinius", "given": "Lovisa", "initials": "L"}, {"family": "Acevedo", "given": "Nathalie", "initials": "N"}, {"family": "Taub", "given": "Margaret", "initials": "M"}, {"family": "Ronninger", "given": "Marcus", "initials": "M"}, {"family": "Shchetynsky", "given": "Klementy", "initials": "K"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}, {"family": "Feinberg", "given": "Andrew P", "initials": "AP"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "31", "issn": "1546-1696", "issue": "2", "pages": "142-147", "title": "Nat. Biotechnol.", "issn-l": "1087-0156"}, "abstract": "Epigenetic mechanisms integrate genetic and environmental causes of disease, but comprehensive genome-wide analyses of epigenetic modifications have not yet demonstrated robust association with common diseases. Using Illumina HumanMethylation450 arrays on 354 anti-citrullinated protein antibody-associated rheumatoid arthritis cases and 337 controls, we identified two clusters within the major histocompatibility complex (MHC) region whose differential methylation potentially mediates genetic risk for rheumatoid arthritis. To reduce confounding factors that have hampered previous epigenome-wide studies, we corrected for cellular heterogeneity by estimating and adjusting for cell-type proportions in our blood-derived DNA samples and used mediation analysis to filter out associations likely to be a consequence of disease. Four CpGs also showed an association between genotype and variance of methylation. The associations for both clusters replicated at least one CpG (P < 0.01), with the rest showing suggestive association, in monocyte cell fractions in an independent cohort of 12 cases and 12 controls. Thus, DNA methylation is a potential mediator of genetic risk.", "doi": "10.1038/nbt.2487", "pmid": "23334450", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "nbt.2487"}, {"db": "pmc", "key": "PMC3598632"}, {"db": "mid", "key": "NIHMS430504"}, {"db": "GEO", "key": "GSE42861"}], "notes": [], "created": "2017-05-04T15:03:36.223Z", "modified": "2017-05-30T12:45:47.718Z"}, {"entity": "publication", "iuid": "7b3f0f1b36884b6c835a6faf0ce43884", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b3f0f1b36884b6c835a6faf0ce43884.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b3f0f1b36884b6c835a6faf0ce43884"}}, "title": "Early-phase GVHD gene expression profile in target versus non-target tissues: kidney, a possible target?", "authors": [{"family": "Sadeghi", "given": "B", "initials": "B"}, {"family": "Al-Chaqmaqchi", "given": "H", "initials": "H"}, {"family": "Al-Hashmi", "given": "S", "initials": "S"}, {"family": "Brodin", "given": "D", "initials": "D"}, {"family": "Hassan", "given": "Z", "initials": "Z"}, {"family": "Abedi-Valugerdi", "given": "M", "initials": "M"}, {"family": "Moshfegh", "given": "A", "initials": "A"}, {"family": "Hassan", "given": "M", "initials": "M"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "48", "issn": "1476-5365", "issue": "2", "pages": "284-293", "title": "Bone Marrow Transplant.", "issn-l": "0268-3369"}, "abstract": "GVHD is a major complication after allo-SCT. In GVHD, some tissues like liver, intestine and skin are infiltrated by donor T cells while others like muscle are not. The mechanism underlying targeted tropism of donor T cells is not fully understood. In the present study, we aim to explore differences in gene expression profile among target versus non-target tissues in a mouse model of GVHD based on chemotherapy conditioning. Expression levels of JAK-signal transducers and activators of transcription (STAT), CXCL1, ICAM1 and STAT3 were increased in the liver and remained unchanged (or decreased) in the muscle and kidney after conditioning. At the start of GVHD the expression levels of CXCL9, ITGb2, SAA3, MARCO, TLR and VCAM1 were significantly higher in the liver or kidney compared with the muscle of GVHD animals. Moreover, biological processes of inflammatory reactions, leukocyte migration, response to bacterium and chemotaxis followed the same pattern. Our data show that both chemotherapy and allogenicity exclusively induce expression of inflammatory genes in target tissues. Moreover, gene expression profile and histopathological findings in the kidney are similar to those observed in the liver of GVHD mice.", "doi": "10.1038/bmt.2012.120", "pmid": "22825425", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "bmt2012120"}], "notes": [], "created": "2017-05-04T15:03:11.638Z", "modified": "2017-05-30T12:40:30.518Z"}, {"entity": "publication", "iuid": "0f314be789404dc994a04feee374a04f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f314be789404dc994a04feee374a04f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f314be789404dc994a04feee374a04f"}}, "title": "Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor.", "authors": [{"family": "Uddenberg", "given": "Daniel", "initials": "D"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Clapham", "given": "David", "initials": "D"}, {"family": "Almqvist", "given": "Curt", "initials": "C"}, {"family": "von Arnold", "given": "Sara", "initials": "S"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "161", "issn": "1532-2548", "issue": "2", "pages": "813-823", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": "Conifers normally go through a long juvenile period, for Norway spruce (Picea abies) around 20 to 25 years, before developing male and female cones. We have grown plants from inbred crosses of a naturally occurring spruce mutant (acrocona). One-fourth of the segregating acrocona plants initiate cones already in their second growth cycle, suggesting control by a single locus. The early cone-setting properties of the acrocona mutant were utilized to identify candidate genes involved in vegetative-to-reproductive phase change in Norway spruce. Poly(A(+)) RNA samples from apical and basal shoots of cone-setting and non-cone-setting plants were subjected to high-throughput sequencing (RNA-seq). We assembled and investigated 33,383 expressed putative protein-coding acrocona transcripts. Eight transcripts were differentially expressed between selected sample pairs. One of these (Acr42124_1) was significantly up-regulated in apical shoot samples from cone-setting acrocona plants, and the encoded protein belongs to the MADS box gene family of transcription factors. Using quantitative real-time polymerase chain reaction with independently derived plant material, we confirmed that the MADS box gene is up-regulated in both needles and buds of cone-inducing shoots when reproductive identity is determined. Our results constitute important steps for the development of a rapid cycling model system that can be used to study gene function in conifers. In addition, our data suggest the involvement of a MADS box transcription factor in the vegetative-to-reproductive phase change in Norway spruce.", "doi": "10.1104/pp.112.207746", "pmid": "23221834", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "pp.112.207746"}, {"db": "pmc", "key": "PMC3561021"}], "notes": [], "created": "2017-05-04T14:58:10.754Z", "modified": "2020-01-21T13:56:00.718Z"}, {"entity": "publication", "iuid": "598fbcca822f435b8d94bbd4034c2660", "links": {"self": {"href": "https://publications.scilifelab.se/publication/598fbcca822f435b8d94bbd4034c2660.json"}, "display": {"href": "https://publications.scilifelab.se/publication/598fbcca822f435b8d94bbd4034c2660"}}, "title": "An MBL-like protein may interfere with the activation of the proPO-system, an important innate immune reaction in invertebrates.", "authors": [{"family": "Wu", "given": "Chenglin", "initials": "C"}, {"family": "Charoensapsri", "given": "Walaiporn", "initials": "W"}, {"family": "Nakamura", "given": "Seiko", "initials": "S"}, {"family": "Tassanakajon", "given": "Anchalee", "initials": "A"}, {"family": "S\u00f6derh\u00e4ll", "given": "Irene", "initials": "I"}, {"family": "S\u00f6derh\u00e4ll", "given": "Kenneth", "initials": "K"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "218", "issn": "1878-3279", "issue": "2", "pages": "159-168", "title": "Immunobiology", "issn-l": "0171-2985"}, "abstract": "An important characteristic of the innate immune systems of crayfish and other arthropods is the activation of a serine proteinase cascade in the hemolymph, which results in the activation of prophenoloxidase and subsequently leading to the formation of toxic quinones and melanin. Although no true complement homologues have been detected in crayfish or crustaceans, several proteins with similarities to vertebrate pattern recognition receptors (PRRs), which are involved in the lectin pathway of complement activation in vertebrates, are present. One is a C-type lectin, a mannose-binding lectin (Pl-MBL), which is secreted from granular hemocytes. Here we report that Pl-MBL has LPS-binding capacity and is dependent upon high Ca(2+) for its solubility and Pl-MBL interferes with proPO activation in vitro when HLS is prepared at high Ca(2+). The proPO-activating system is efficiently activated by microbial polysaccharides and it has to be neatly regulated to avoid activation in places where it is inappropriate and the active enzyme PO should be prevented from spreading throughout the body of the animal. This may be particularly important during molting when proPO is involved in hardening of a new cuticle and the animal is vulnerable to microbes. The presence of high amount of Pl-MBL in the granular hemocytes may play a role in this process. Since a hemocyte lysate supernatant (HLS) prepared at 100 mM Ca(2+) could become activated when the concentration of LPS was increased up to 3 mg/ml, this may indicate that Pl-MBL acts as a scavenger for LPS to prevent spreading of LPS in the hemolymph to avoid further activation of the proPO-system.", "doi": "10.1016/j.imbio.2012.02.011", "pmid": "22459272", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0171-2985(12)00056-3"}], "notes": [], "created": "2017-05-04T14:57:58.177Z", "modified": "2020-01-21T13:56:02.442Z"}, {"entity": "publication", "iuid": "752ae511ee974720af3eb8a3ba277f87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/752ae511ee974720af3eb8a3ba277f87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/752ae511ee974720af3eb8a3ba277f87"}}, "title": "Adipose tissue resting energy expenditure and expression of genes involved in mitochondrial function are higher in women than in men.", "authors": [{"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Svensson", "given": "Per-Arne", "initials": "PA"}, {"family": "Jacobson", "given": "Peter", "initials": "P"}, {"family": "Jern\u00e5s", "given": "Margareta", "initials": "M"}, {"family": "Taube", "given": "Magdalena", "initials": "M"}, {"family": "Larsson", "given": "Ingrid", "initials": "I"}, {"family": "Andersson-Assarsson", "given": "Johanna C", "initials": "JC"}, {"family": "Sj\u00f6str\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Walley", "given": "Andrew", "initials": "A"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Carlsson", "given": "Lena M S", "initials": "LM"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "98", "issn": "1945-7197", "issue": "2", "pages": "E370-E378", "title": "J. Clin. Endocrinol. Metab.", "issn-l": "0021-972X"}, "abstract": "Men and women differ in body fat distribution and adipose tissue metabolism as well as in obesity comorbidities and their response to obesity treatment.\n\nThe objective of the study was a search for sex differences in adipose tissue function.\n\nThis was an exploratory study performed at a university hospital.\n\nResting metabolic rate (RMR), body composition, and sc adipose tissue genome-wide expression were measured in the SOS Sib Pair study (n = 732).\n\nThe relative contribution of fat mass to RMR and the metabolic rate per kilogram adipose tissue was higher in women than in men (P value for sex by fat mass interaction = .0019). Women had increased expression of genes involved in mitochondrial function, here referred to as a mitochondrial gene signature. Analysis of liver, muscle, and blood showed that the pronounced mitochondrial gene signature in women was specific for adipose tissue. Brown adipocytes are dense in mitochondria, and the expression of the brown adipocyte marker uncoupling protein 1 was 5-fold higher in women compared with men in the SOS Sib Pair Study (P = 7.43 \u00d7 10(-7)), and this was confirmed in a cross-sectional, population-based study (n = 83, 6-fold higher in women, P = .00256).\n\nThe increased expression of the brown adipocyte marker uncoupling protein 1 in women indicates that the higher relative contribution of the fat mass to RMR in women is in part explained by an increased number of brown adipocytes.", "doi": "10.1210/jc.2012-2764", "pmid": "23264395", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "jc.2012-2764"}, {"db": "pmc", "key": "PMC3633773"}], "notes": [], "created": "2017-05-04T14:56:24.579Z", "modified": "2021-07-05T13:05:37.674Z"}, {"entity": "publication", "iuid": "2416138eb5a54271ae6314e25d470b7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2416138eb5a54271ae6314e25d470b7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2416138eb5a54271ae6314e25d470b7e"}}, "title": "A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.", "authors": [{"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Teytelman", "given": "Leonid", "initials": "L"}, {"family": "Klemm", "given": "Sandy", "initials": "S"}, {"family": "Itzkovitz", "given": "Shalev", "initials": "S"}, {"family": "van Oudenaarden", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "10", "issn": "1548-7105", "issue": "2", "pages": "122-124", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": "We developed a cost-effective genome-scale PCR-based method for high-definition DNA FISH (HD-FISH). We visualized gene loci with diffraction-limited resolution, chromosomes as spot clusters and single genes together with transcripts by combining HD-FISH with single-molecule RNA FISH. We provide a database of over 4.3 million primer pairs targeting the human and mouse genomes that is readily usable for rapid and flexible generation of probes.", "doi": "10.1038/nmeth.2306", "pmid": "23263692", "labels": {"Advanced FISH Technologies": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC3735345"}, {"db": "mid", "key": "NIHMS500266"}], "notes": [], "created": "2020-01-21T12:36:13.660Z", "modified": "2020-02-12T15:17:32.435Z"}, {"entity": "publication", "iuid": "d345c48669194332892dfdd108d3e525", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d345c48669194332892dfdd108d3e525.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d345c48669194332892dfdd108d3e525"}}, "title": "A gene-centric study of common carotid artery remodelling.", "authors": [{"family": "Harrison", "given": "Seamus C", "initials": "SC"}, {"family": "Zabaneh", "given": "Delilah", "initials": "D"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Drenos", "given": "Fotios", "initials": "F"}, {"family": "Jones", "given": "Gregory T", "initials": "GT"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "Gertow", "given": "Karl", "initials": "K"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Holewijn", "given": "Suzanne", "initials": "S"}, {"family": "De Graaf", "given": "Jacqueline", "initials": "J"}, {"family": "Vermeulen", "given": "Sita", "initials": "S"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "van Rij", "given": "Andre M", "initials": "AM"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Talmud", "given": "Philippa J", "initials": "PJ"}, {"family": "Deanfield", "given": "John E", "initials": "JE"}, {"family": "Agu", "given": "Obi", "initials": "O"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Bown", "given": "Matthew J", "initials": "MJ"}, {"family": "Nyyss\u00f6nen", "given": "Kristiina", "initials": "K"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Mannarino", "given": "Elmo", "initials": "E"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "de Borst", "given": "Gert J", "initials": "GJ"}, {"family": "van der Graaf", "given": "Yolanda", "initials": "Y"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Baas", "given": "Annette F", "initials": "AF"}, {"family": "Blankensteijn", "given": "Jan D", "initials": "JD"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Fowkes", "given": "Gerry", "initials": "G"}, {"family": "Tzoulaki", "given": "Ionna", "initials": "I"}, {"family": "Price", "given": "Jacqueline F", "initials": "JF"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}], "type": "journal article", "published": "2013-02-00", "journal": {"volume": "226", "issn": "1879-1484", "issue": "2", "pages": "440-446", "title": "Atherosclerosis", "issn-l": "0021-9150"}, "abstract": "Expansive remodelling is the process of compensatory arterial enlargement in response to atherosclerotic stimuli. The genetic determinants of this process are poorly characterized.\n\nGenetic association analyses of inter-adventitial common carotid artery diameter (ICCAD) in the IMPROVE study (n\u00a0=\u00a03427) using the Illumina 200k Metabochip was performed. Single nucleotide polymorphisms (SNPs) that met array-wide significance were taken forward for analysis in three further studies (n\u00a0=\u00a05704), and tested for association with Abdominal Aortic Aneurysm (AAA).\n\nrs3768445 on Chromosome 1q24.3, in a cluster of protein coding genes (DNM3, PIGC, C1orf105) was associated with larger ICCAD in the IMPROVE study. For each copy of the rare allele carried, ICCAD was on average 0.13\u00a0mm greater (95% CI 0.08-0.18\u00a0mm, P\u00a0=\u00a08.2\u00a0\u00d7\u00a010(-8)). A proxy SNP (rs4916251, R(2)\u00a0=\u00a00.99) did not, however, show association with ICCAD in three follow-up studies (P for replication\u00a0=\u00a00.29). There was evidence of interaction between carotid intima-media thickness (CIMT) and rs4916251 on ICCAD in two of the cohorts studies suggesting that it plays a role in the remodelling response to atherosclerosis. In meta-analysis of 5 case-control studies pooling data from 5007 cases and 43,630 controls, rs4916251 was associated with presence of AAA 1.10, 95% CI 1.03-1.17, p\u00a0=\u00a02.8\u00a0\u00d7\u00a010(-3), I(2)\u00a0=\u00a018.8, Q\u00a0=\u00a00.30). A proxy SNP, rs4916251 was also associated with increased expression of PIGC in aortic tissue, suggesting that this may the mechanism by which this locus affects vascular remodelling.\n\nCommon variation at 1q24.3 is associated with expansive vascular remodelling and risk of AAA. These findings support a hypothesis that pathways involved in systemic vascular remodelling play a role in AAA development.", "doi": "10.1016/j.atherosclerosis.2012.11.002", "pmid": "23246012", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0021-9150(12)00797-6"}, {"db": "pmc", "key": "PMC3573227"}], "notes": [], "created": "2017-05-04T15:01:14.776Z", "modified": "2021-07-07T15:11:02.748Z"}, {"entity": "publication", "iuid": "7b5bddd8bc1c4c31a6a8f62a59e234ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b5bddd8bc1c4c31a6a8f62a59e234ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b5bddd8bc1c4c31a6a8f62a59e234ac"}}, "title": "Workshop on laboratory protocol standards for the Molecular Methods Database.", "authors": [{"family": "Klingstr\u00f6m", "given": "Tomas", "initials": "T"}, {"family": "Soldatova", "given": "Larissa", "initials": "L"}, {"family": "Stevens", "given": "Robert", "initials": "R"}, {"family": "Roos", "given": "T Erik", "initials": "TE"}, {"family": "Swertz", "given": "Morris A", "initials": "MA"}, {"family": "M\u00fcller", "given": "Kristian M", "initials": "KM"}, {"family": "Kala\u0161", "given": "Mat\u00fa\u0161", "initials": "M"}, {"family": "Lambrix", "given": "Patrick", "initials": "P"}, {"family": "Taussig", "given": "Michael J", "initials": "MJ"}, {"family": "Litton", "given": "Jan-Eric", "initials": "JE"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}], "type": "congress", "published": "2013-01-25", "journal": {"volume": "30", "issn": "1876-4347", "issue": "2", "pages": "109-113", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.", "doi": "10.1016/j.nbt.2012.05.019", "pmid": "22687389", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(12)00121-5"}], "notes": [], "created": "2017-05-04T14:55:26.465Z", "modified": "2023-04-14T13:56:29.338Z"}, {"entity": "publication", "iuid": "9c786f1bc8bb4c8c8d8de227ac395e4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c786f1bc8bb4c8c8d8de227ac395e4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c786f1bc8bb4c8c8d8de227ac395e4f"}}, "title": "Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation.", "authors": [{"family": "Gu", "given": "Gucci Jijuan", "initials": "GJ"}, {"family": "Friedman", "given": "Mikaela", "initials": "M"}, {"family": "Jost", "given": "Christian", "initials": "C"}, {"family": "Johnsson", "given": "Kai", "initials": "K"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Pl\u00fcckthun", "given": "Andreas", "initials": "A"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2013-01-25", "journal": {"volume": "30", "issn": "1876-4347", "issue": "2", "pages": "144-152", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "While antibodies currently play a dominant role as affinity reagents in biological research and for diagnostics, a broad range of recombinant proteins are emerging as promising alternative affinity reagents in detection assays and quantification. DNA-mediated affinity-based assays, such as immuno-PCR and proximity ligation assays (PLA), use oligonucleotides attached to affinity reagents as reporter molecules. Conjugation of oligonucleotides to affinity reagents generally employs chemistries that target primary amines or cysteines. Because of the random nature of these processes neither the number of oligonucleotides conjugated per molecule nor their sites of attachment can be accurately controlled for affinity reagents with several available amines and cysteines. Here, we present a straightforward and convenient approach to functionalize recombinant affinity reagents for PLA by expressing the reagents as fusion partners with SNAP protein tags. This allowed us to conjugate oligonucleotides in a site-specific fashion, yielding precisely one oligonucleotide per affinity reagent. We demonstrate this method using designed ankyrin repeat proteins (DARPins) recognizing the tumor antigen HER2 and we apply the conjugates in different assay formats. We also show that SNAP or CLIP tags, expressed as fusion partners of transfected genes, allow oligonucleotide conjugations to be performed in fixed cells, with no need for specific affinity reagents. The approach is used to demonstrate induced interactions between the fusion proteins FKBP and FRB by allowing the in situ conjugated oligonucleotides to direct the production of templates for localized rolling circle amplification reactions.", "doi": "10.1016/j.nbt.2012.05.005", "pmid": "22664266", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(12)00107-0"}], "notes": [], "created": "2017-05-04T14:55:25.861Z", "modified": "2023-04-14T13:56:29.545Z"}, {"entity": "publication", "iuid": "dd2df100118046b5bd0e391d60c77107", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd2df100118046b5bd0e391d60c77107.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd2df100118046b5bd0e391d60c77107"}}, "title": "Multiplex protein detection with DNA readout via mass spectrometry.", "authors": [{"family": "Flanigon", "given": "James", "initials": "J"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Burbulis", "given": "Ian", "initials": "I"}, {"family": "Annink", "given": "Carla", "initials": "C"}, {"family": "Steffen", "given": "Martin", "initials": "M"}, {"family": "Oeth", "given": "Paul", "initials": "P"}, {"family": "Brent", "given": "Roger", "initials": "R"}, {"family": "van den Boom", "given": "Dirk", "initials": "D"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Cantor", "given": "Charles", "initials": "C"}], "type": "journal article", "published": "2013-01-25", "journal": {"volume": "30", "issn": "1876-4347", "issue": "2", "pages": "153-158", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "Multiplex protein quantification has been constrained by issues of assay specificity, sensitivity and throughput. This research presents a novel approach that overcomes these limitations using antibody-oligonucleotide conjugates for immuno-polymerase chain reaction (immuno-PCR) or proximity ligation, coupled with competitive PCR and MALDI-TOF mass spectrometry. Employing these combinations of technologies, we demonstrate multiplex detection and quantification of up to eight proteins, spanning wide dynamic ranges from femtomolar concentrations, using only microliter sample volumes.", "doi": "10.1016/j.nbt.2012.11.003", "pmid": "23201185", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(12)00860-6"}, {"db": "pmc", "key": "PMC3616745"}, {"db": "mid", "key": "NIHMS425130"}], "notes": [], "created": "2017-05-04T14:55:26.162Z", "modified": "2023-04-14T13:56:29.711Z"}, {"entity": "publication", "iuid": "c241a08918ae412aa88963b509d13d63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c241a08918ae412aa88963b509d13d63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c241a08918ae412aa88963b509d13d63"}}, "title": "DNA methylation in the Neuropeptide S Receptor 1 (NPSR1) promoter in relation to asthma and environmental factors.", "authors": [{"family": "Reinius", "given": "Lovisa E", "initials": "LE"}, {"family": "Gref", "given": "Anna", "initials": "A"}, {"family": "S\u00e4\u00e4f", "given": "Annika", "initials": "A"}, {"family": "Acevedo", "given": "Nathalie", "initials": "N"}, {"family": "Joerink", "given": "Maaike", "initials": "M"}, {"family": "Kupczyk", "given": "Maciej", "initials": "M"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}, {"family": "Dahl\u00e9n", "given": "Sven-Erik", "initials": "SE"}, {"family": "BIOAIR Study Group", "given": null, "initials": null}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G"}, {"family": "S\u00f6derh\u00e4ll", "given": "Cilla", "initials": "C"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2013-01-23", "journal": {"volume": "8", "issn": "1932-6203", "issue": "1", "pages": "e53877", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Asthma and allergy are complex disorders influenced by both inheritance and environment, a relationship that might be further clarified by epigenetics. Neuropeptide S Receptor 1 (NPSR1) has been associated with asthma and allergy and a study suggested modulation of the genetic risk by environmental factors. We aimed to study DNA methylation in the promoter region of NPSR1 in relation to asthma and environmental exposures. Electrophoretic Mobility Shift Assay (EMSA) was used to investigate potential functional roles of both genotypes and methylation status in the NPSR1 promoter. DNA methylation was analysed using EpiTYPER in blood samples from two well-characterized cohorts; the BIOAIR study of severe asthma in adults and the Swedish birth cohort BAMSE. We observed that DNA methylation and genetic variants in the promoter influenced the binding of nuclear proteins to DNA, suggesting functional relevance. Significant, although small, differences in methylation were related to both adult severe asthma (p\u200a=\u200a0.0001) and childhood allergic asthma (p\u200a=\u200a0.01). Furthermore, DNA methylation was associated with exposures such as current smoking in adults for two CpG sites (p\u200a=\u200a0.005 and 0.04), parental smoking during infancy in the children (p\u200a=\u200a0.02) and in which month the sample was taken (p\u200a=\u200a0.01). In summary, DNA methylation levels in the promoter of NPSR1 showed small but significant associations with asthma, both in adults and in children, and to related traits such as allergy and certain environmental exposures. Both genetic variation and the methylated state of CpG sites seem to have an effect on the binding of nuclear proteins in the regulatory region of NPSR1 suggesting complex regulation of this gene in asthma and allergy.", "doi": "10.1371/journal.pone.0053877", "pmid": "23372674", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-14529"}, {"db": "pmc", "key": "PMC3553086"}], "notes": [], "created": "2017-05-04T15:03:38.060Z", "modified": "2017-05-30T14:53:09.670Z"}, {"entity": "publication", "iuid": "39fee09c147549d49b073f4fa59ac00b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39fee09c147549d49b073f4fa59ac00b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39fee09c147549d49b073f4fa59ac00b"}}, "title": "Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach.", "authors": [{"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Drakare", "given": "Stina", "initials": "S"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Pernthaler", "given": "Jakob", "initials": "J"}, {"family": "Peura", "given": "Sari", "initials": "S"}, {"family": "Rofner", "given": "Carina", "initials": "C"}, {"family": "Simek", "given": "Karel", "initials": "K"}, {"family": "Yang", "given": "Yang", "initials": "Y"}, {"family": "Znachor", "given": "Petr", "initials": "P"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}], "type": "journal article", "published": "2013-01-22", "journal": {"volume": "8", "issn": "1932-6203", "issue": "1", "pages": "e53516", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The recognition and discrimination of phytoplankton species is one of the foundations of freshwater biodiversity research and environmental monitoring. This step is frequently a bottleneck in the analytical chain from sampling to data analysis and subsequent environmental status evaluation. Here we present phytoplankton diversity data from 49 lakes including three seasonal surveys assessed by next generation sequencing (NGS) of 16S ribosomal RNA chloroplast and cyanobacterial gene amplicons and also compare part of these datasets with identification based on morphology. Direct comparison of NGS to microscopic data from three time-series showed that NGS was able to capture the seasonality in phytoplankton succession as observed by microscopy. Still, the PCR-based approach was only semi-quantitative, and detailed NGS and microscopy taxa lists had only low taxonomic correspondence. This is probably due to, both, methodological constraints and current discrepancies in taxonomic frameworks. Discrepancies included Euglenophyta and Heterokonta that were scarce in the NGS but frequently detected by microscopy and Cyanobacteria that were in general more abundant and classified with high resolution by NGS. A deep-branching taxonomically unclassified cluster was frequently detected by NGS but could not be linked to any group identified by microscopy. NGS derived phytoplankton composition differed significantly among lakes with different trophic status, showing that our approach can resolve phytoplankton communities at a level relevant for ecosystem management. The high reproducibility and potential for standardization and parallelization makes our NGS approach an excellent candidate for simultaneous monitoring of prokaryotic and eukaryotic phytoplankton in inland waters.", "doi": "10.1371/journal.pone.0053516", "pmid": "23349714", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-28577"}, {"db": "pmc", "key": "PMC3551911"}], "notes": [], "created": "2017-05-04T14:58:14.642Z", "modified": "2020-01-21T13:56:01.627Z"}, {"entity": "publication", "iuid": "d8f759d520a4451786bdaf27f5d04886", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d8f759d520a4451786bdaf27f5d04886.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d8f759d520a4451786bdaf27f5d04886"}}, "title": "Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis.", "authors": [{"family": "Gioti", "given": "Anastasia", "initials": "A"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Li", "given": "Wenjun", "initials": "W"}, {"family": "Xu", "given": "Jun", "initials": "J"}, {"family": "Andersson", "given": "Anna", "initials": "A"}, {"family": "Averette", "given": "Anna F", "initials": "AF"}, {"family": "M\u00fcnch", "given": "Karin", "initials": "K"}, {"family": "Wang", "given": "Xuying", "initials": "X"}, {"family": "Kappauf", "given": "Catharine", "initials": "C"}, {"family": "Kingsbury", "given": "Joanne M", "initials": "JM"}, {"family": "Kraak", "given": "Bart", "initials": "B"}, {"family": "Walker", "given": "Louise A", "initials": "LA"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ"}, {"family": "Holm", "given": "Tina", "initials": "T"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Stajich", "given": "Jason E", "initials": "JE"}, {"family": "Mieczkowski", "given": "Piotr", "initials": "P"}, {"family": "Kahmann", "given": "Regine", "initials": "R"}, {"family": "Kennell", "given": "John C", "initials": "JC"}, {"family": "Cardenas", "given": "Maria E", "initials": "ME"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Saunders", "given": "Charles W", "initials": "CW"}, {"family": "Boekhout", "given": "Teun", "initials": "T"}, {"family": "Dawson", "given": "Thomas L", "initials": "TL"}, {"family": "Munro", "given": "Carol A", "initials": "CA"}, {"family": "de Groot", "given": "Piet W J", "initials": "PW"}, {"family": "Butler", "given": "Geraldine", "initials": "G"}, {"family": "Heitman", "given": "Joseph", "initials": "J"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}], "type": "comparative study", "published": "2013-01-22", "journal": {"volume": "4", "issn": "2150-7511", "issue": "1", "pages": "e00572-e00512", "title": "MBio", "issn-l": null}, "abstract": "Malassezia commensal yeasts are associated with a number of skin disorders, such as atopic eczema/dermatitis and dandruff, and they also can cause systemic infections. Here we describe the 7.67-Mbp genome of Malassezia sympodialis, a species associated with atopic eczema, and contrast its genome repertoire with that of Malassezia globosa, associated with dandruff, as well as those of other closely related fungi. Ninety percent of the predicted M. sympodialis protein coding genes were experimentally verified by mass spectrometry at the protein level. We identified a relatively limited number of genes related to lipid biosynthesis, and both species lack the fatty acid synthase gene, in line with the known requirement of these yeasts to assimilate lipids from the host. Malassezia species do not appear to have many cell wall-localized glycosylphosphatidylinositol (GPI) proteins and lack other cell wall proteins previously identified in other fungi. This is surprising given that in other fungi these proteins have been shown to mediate interactions (e.g., adhesion and biofilm formation) with the host. The genome revealed a complex evolutionary history for an allergen of unknown function, Mala s 7, shown to be encoded by a member of an amplified gene family of secreted proteins. Based on genetic and biochemical studies with the basidiomycete human fungal pathogen Cryptococcus neoformans, we characterized the allergen Mala s 6 as the cytoplasmic cyclophilin A. We further present evidence that M. sympodialis may have the capacity to undergo sexual reproduction and present a model for a pseudobipolar mating system that allows limited recombination between two linked MAT loci.\n\nMalassezia commensal yeasts are associated with a number of skin disorders. The previously published genome of M. globosa provided some of the first insights into Malassezia biology and its involvement in dandruff. Here, we present the genome of M. sympodialis, frequently isolated from patients with atopic eczema and healthy individuals. We combined comparative genomics with sequencing and functional characterization of specific genes in a population of clinical isolates and in closely related model systems. Our analyses provide insights into the evolution of allergens related to atopic eczema and the evolutionary trajectory of the machinery for sexual reproduction and meiosis. We hypothesize that M. sympodialis may undergo sexual reproduction, which has important implications for the understanding of the life cycle and virulence potential of this medically important yeast. Our findings provide a foundation for the development of genetic and genomic tools to elucidate host-microbe interactions that occur on the skin and to identify potential therapeutic targets.", "doi": "10.1128/mBio.00572-12", "pmid": "23341551", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "mBio.00572-12"}, {"db": "pmc", "key": "PMC3560662"}, {"db": "GENBANK", "key": "HE999549"}, {"db": "GENBANK", "key": "HE999550"}, {"db": "GENBANK", "key": "HE999551"}, {"db": "GENBANK", "key": "HE999552"}, {"db": "GENBANK", "key": "HE999553"}, {"db": "GENBANK", "key": "HE999554"}, {"db": "GENBANK", "key": "HE999555"}, {"db": "GENBANK", "key": "HE999556"}, {"db": "GENBANK", "key": "HE999557"}, {"db": "GENBANK", "key": "HE999558"}, {"db": "GENBANK", "key": "HE999559"}, {"db": "GENBANK", "key": "HE999560"}, {"db": "GENBANK", "key": "HE999561"}, {"db": "GENBANK", "key": "HE999562"}, {"db": "GENBANK", "key": "HE999563"}, {"db": "GENBANK", "key": "HE999564"}, {"db": "GENBANK", "key": "HE999565"}, {"db": "GENBANK", "key": "HE999566"}, {"db": "GENBANK", "key": "HE999567"}, {"db": "GENBANK", "key": "HE999568"}, {"db": "GENBANK", "key": "HE999569"}, {"db": "GENBANK", "key": "HE999570"}, {"db": "GENBANK", "key": "HE999571"}, {"db": "GENBANK", "key": "HE999572"}, {"db": "GENBANK", "key": "HE999573"}, {"db": "GENBANK", "key": "HE999574"}, {"db": "GENBANK", "key": "HE999575"}, {"db": "GENBANK", "key": "HE999576"}, {"db": "GENBANK", "key": "HE999577"}, {"db": "GENBANK", "key": "HE999578"}, {"db": "GENBANK", "key": "HE999579"}, {"db": "GENBANK", "key": "HE999580"}, {"db": "GENBANK", "key": "HE999581"}, {"db": "GENBANK", "key": "HE999582"}, {"db": "GENBANK", "key": "HE999583"}, {"db": "GENBANK", "key": "HE999584"}, {"db": "GENBANK", "key": "HE999585"}, {"db": "GENBANK", "key": "HE999586"}, {"db": "GENBANK", "key": "HE999587"}, {"db": "GENBANK", "key": "HE999588"}, {"db": "GENBANK", "key": "HE999589"}, {"db": "GENBANK", "key": "HE999590"}, {"db": "GENBANK", "key": "HE999591"}, {"db": "GENBANK", "key": "HE999592"}, {"db": "GENBANK", "key": "HE999593"}, {"db": "GENBANK", "key": "HE999594"}, {"db": "GENBANK", "key": "HE999595"}, {"db": "GENBANK", "key": "HE999596"}, {"db": "GENBANK", "key": "HE999597"}, {"db": "GENBANK", "key": "HE999598"}, {"db": "GENBANK", "key": "HE999599"}, {"db": "GENBANK", "key": "HE999600"}, {"db": "GENBANK", "key": "HE999601"}, {"db": "GENBANK", "key": "HE999602"}, {"db": "GENBANK", "key": "HE999603"}, {"db": "GENBANK", "key": "HE999604"}, {"db": "GENBANK", "key": "HE999605"}, {"db": "GENBANK", "key": "HE999606"}, {"db": "GENBANK", "key": "HE999607"}, {"db": "GENBANK", "key": "HE999608"}, {"db": "GENBANK", "key": "HE999609"}, {"db": "GENBANK", "key": "HE999610"}, {"db": "GENBANK", "key": "HE999611"}, {"db": "GENBANK", "key": "HE999612"}, {"db": "GENBANK", "key": "HE999613"}, {"db": "GENBANK", "key": "HF558646"}, {"db": "GENBANK", "key": "JX964800"}, {"db": "GENBANK", "key": "JX964801"}, {"db": "GENBANK", "key": "JX964802"}, {"db": "GENBANK", "key": "JX964840"}, {"db": "GENBANK", "key": "JX964841"}, {"db": "GENBANK", "key": "JX964842"}, {"db": "GENBANK", "key": "JX964843"}, {"db": "GENBANK", "key": "JX964844"}, {"db": "GENBANK", "key": "JX964845"}, {"db": "GENBANK", "key": "JX964846"}, {"db": "GENBANK", "key": "JX964847"}, {"db": "GENBANK", "key": "JX964848"}, {"db": "GENBANK", "key": "JX964849"}, {"db": "GENBANK", "key": "JX964850"}], "notes": [], "created": "2017-05-04T14:58:03.302Z", "modified": "2021-07-08T13:26:08.367Z"}, {"entity": "publication", "iuid": "8eea4041c6b445b58bb04c77b59cbe11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8eea4041c6b445b58bb04c77b59cbe11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8eea4041c6b445b58bb04c77b59cbe11"}}, "title": "DNA-binding specificities of human transcription factors.", "authors": [{"family": "Jolma", "given": "Arttu", "initials": "A"}, {"family": "Yan", "given": "Jian", "initials": "J"}, {"family": "Whitington", "given": "Thomas", "initials": "T"}, {"family": "Toivonen", "given": "Jarkko", "initials": "J"}, {"family": "Nitta", "given": "Kazuhiro R", "initials": "KR"}, {"family": "Rastas", "given": "Pasi", "initials": "P"}, {"family": "Morgunova", "given": "Ekaterina", "initials": "E"}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Taipale", "given": "Mikko", "initials": "M"}, {"family": "Wei", "given": "Gonghong", "initials": "G"}, {"family": "Palin", "given": "Kimmo", "initials": "K"}, {"family": "Vaquerizas", "given": "Juan M", "initials": "JM"}, {"family": "Vincentelli", "given": "Renaud", "initials": "R"}, {"family": "Luscombe", "given": "Nicholas M", "initials": "NM"}, {"family": "Hughes", "given": "Timothy R", "initials": "TR"}, {"family": "Lemaire", "given": "Patrick", "initials": "P"}, {"family": "Ukkonen", "given": "Esko", "initials": "E"}, {"family": "Kivioja", "given": "Teemu", "initials": "T"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2013-01-17", "journal": {"volume": "152", "issn": "1097-4172", "issue": "1-2", "pages": "327-339", "title": "Cell", "issn-l": "0092-8674"}, "abstract": "Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed the sequence-specific binding of human TFs using high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificities. The models represent the majority of human TFs, approximately doubling the coverage compared to existing systematic studies. Our results reveal additional specificity determinants for a large number of factors for which a partial specificity was known, including a commonly observed A- or T-rich stretch that flanks the core motifs. Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated. We further describe a binding model incorporating these features that is required to understand binding of TFs to DNA.", "doi": "10.1016/j.cell.2012.12.009", "pmid": "23332764", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "S0092-8674(12)01496-1"}], "notes": [], "created": "2017-05-04T14:57:04.866Z", "modified": "2017-05-31T08:13:20.430Z"}, {"entity": "publication", "iuid": "5a64498b168244c5ae9d722fbce39952", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a64498b168244c5ae9d722fbce39952.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a64498b168244c5ae9d722fbce39952"}}, "title": "A genome-wide association study identifies genomic regions for virulence in the non-model organism Heterobasidion annosum s.s.", "authors": [{"family": "Dalman", "given": "Kerstin", "initials": "K"}, {"family": "Himmelstrand", "given": "Kajsa", "initials": "K"}, {"family": "Olson", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Lind", "given": "M\u00e5rten", "initials": "M"}, {"family": "Brandstr\u00f6m-Durling", "given": "Mikael", "initials": "M"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2013-01-16", "journal": {"volume": "8", "issn": "1932-6203", "issue": "1", "pages": "e53525", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The dense single nucleotide polymorphisms (SNP) panels needed for genome wide association (GWA) studies have hitherto been expensive to establish and use on non-model organisms. To overcome this, we used a next generation sequencing approach to both establish SNPs and to determine genotypes. We conducted a GWA study on a fungal species, analysing the virulence of Heterobasidion annosum s.s., a necrotrophic pathogen, on its hosts Picea abies and Pinus sylvestris. From a set of 33,018 single nucleotide polymorphisms (SNP) in 23 haploid isolates, twelve SNP markers distributed on seven contigs were associated with virulence (P<0.0001). Four of the contigs harbour known virulence genes from other fungal pathogens and the remaining three harbour novel candidate genes. Two contigs link closely to virulence regions recognized previously by QTL mapping in the congeneric hybrid H. irregulare \u00d7 H. occidentale. Our study demonstrates the efficiency of GWA studies for dissecting important complex traits of small populations of non-model haploid organisms with small genomes.", "doi": "10.1371/journal.pone.0053525", "pmid": "23341945", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-26429"}, {"db": "pmc", "key": "PMC3547014"}], "notes": [], "created": "2017-05-04T15:01:28.291Z", "modified": "2020-01-21T13:56:02.470Z"}, {"entity": "publication", "iuid": "1208d0060f064ad5b8eed96dcd21e652", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1208d0060f064ad5b8eed96dcd21e652.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1208d0060f064ad5b8eed96dcd21e652"}}, "title": "Meta-analysis investigating associations between healthy diet and fasting glucose and insulin levels and modification by loci associated with glucose homeostasis in data from 15 cohorts.", "authors": [{"family": "Nettleton", "given": "Jennifer A", "initials": "JA"}, {"family": "Hivert", "given": "Marie-France", "initials": "MF"}, {"family": "Lemaitre", "given": "Rozenn N", "initials": "RN"}, {"family": "McKeown", "given": "Nicola M", "initials": "NM"}, {"family": "Mozaffarian", "given": "Dariush", "initials": "D"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Wojczynski", "given": "Mary K", "initials": "MK"}, {"family": "Hruby", "given": "Adela", "initials": "A"}, {"family": "Djouss\u00e9", "given": "Luc", "initials": "L"}, {"family": "Ngwa", "given": "Julius S", "initials": "JS"}, {"family": "Follis", "given": "Jack L", "initials": "JL"}, {"family": "Dimitriou", "given": "Maria", "initials": "M"}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Houston", "given": "Denise K", "initials": "DK"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Mikkil\u00e4", "given": "Vera", "initials": "V"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Sonestedt", "given": "Emily", "initials": "E"}, {"family": "van Rooij", "given": "Frank J A", "initials": "FJ"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "de Koning", "given": "Lawrence", "initials": "L"}, {"family": "Ericson", "given": "Ulrika", "initials": "U"}, {"family": "Hassanali", "given": "Neelam", "initials": "N"}, {"family": "Kiefte-de Jong", "given": "Jessica C", "initials": "JC"}, {"family": "Lohman", "given": "Kurt K", "initials": "KK"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Papoutsakis", "given": "Constantina", "initials": "C"}, {"family": "Sjogren", "given": "Per", "initials": "P"}, {"family": "Stirrups", "given": "Kathleen", "initials": "K"}, {"family": "Ax", "given": "Erika", "initials": "E"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Groves", "given": "Christopher J", "initials": "CJ"}, {"family": "Jacques", "given": "Paul F", "initials": "PF"}, {"family": "Johansson", "given": "Ingegerd", "initials": "I"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "North", "given": "Kari", "initials": "K"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Kolovou", "given": "Genovefa", "initials": "G"}, {"family": "Mukamal", "given": "Kenneth", "initials": "K"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Rolandsson", "given": "Olov", "initials": "O"}, {"family": "Sepp\u00e4l\u00e4", "given": "Ilkka", "initials": "I"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Jacobs", "given": "David R", "initials": "DR"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}], "type": "journal article", "published": "2013-01-15", "journal": {"volume": "177", "issn": "1476-6256", "issue": "2", "pages": "103-115", "title": "Am. J. Epidemiol.", "issn-l": "0002-9262"}, "abstract": "Whether loci that influence fasting glucose (FG) and fasting insulin (FI) levels, as identified by genome-wide association studies, modify associations of diet with FG or FI is unknown. We utilized data from 15 U.S. and European cohort studies comprising 51,289 persons without diabetes to test whether genotype and diet interact to influence FG or FI concentration. We constructed a diet score using study-specific quartile rankings for intakes of whole grains, fish, fruits, vegetables, and nuts/seeds (favorable) and red/processed meats, sweets, sugared beverages, and fried potatoes (unfavorable). We used linear regression within studies, followed by inverse-variance-weighted meta-analysis, to quantify 1) associations of diet score with FG and FI levels and 2) interactions of diet score with 16 FG-associated loci and 2 FI-associated loci. Diet score (per unit increase) was inversely associated with FG (\u03b2 = -0.004 mmol/L, 95% confidence interval: -0.005, -0.003) and FI (\u03b2 = -0.008 ln-pmol/L, 95% confidence interval: -0.009, -0.007) levels after adjustment for demographic factors, lifestyle, and body mass index. Genotype variation at the studied loci did not modify these associations. Healthier diets were associated with lower FG and FI concentrations regardless of genotype at previously replicated FG- and FI-associated loci. Studies focusing on genomic regions that do not yield highly statistically significant associations from main-effect genome-wide association studies may be more fruitful in identifying diet-gene interactions.", "doi": "10.1093/aje/kws297", "pmid": "23255780", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "kws297"}, {"db": "pmc", "key": "PMC3707424"}], "notes": [], "created": "2017-05-04T14:57:47.240Z", "modified": "2020-01-21T13:56:00.780Z"}, {"entity": "publication", "iuid": "8612a29d126645759788621e019e0ea4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8612a29d126645759788621e019e0ea4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8612a29d126645759788621e019e0ea4"}}, "title": "A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.", "authors": [{"family": "Teschendorff", "given": "Andrew E", "initials": "AE"}, {"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "Lechner", "given": "Matthias", "initials": "M"}, {"family": "Bartlett", "given": "Thomas", "initials": "T"}, {"family": "Tegner", "given": "Jesper", "initials": "J"}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D"}, {"family": "Beck", "given": "Stephan", "initials": "S"}], "type": "journal article", "published": "2013-01-15", "journal": {"volume": "29", "issn": "1367-4811", "issue": "2", "pages": "189-196", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "The Illumina Infinium 450 k DNA Methylation Beadchip is a prime candidate technology for Epigenome-Wide Association Studies (EWAS). However, a difficulty associated with these beadarrays is that probes come in two different designs, characterized by widely different DNA methylation distributions and dynamic range, which may bias downstream analyses. A key statistical issue is therefore how best to adjust for the two different probe designs.\n\nHere we propose a novel model-based intra-array normalization strategy for 450 k data, called BMIQ (Beta MIxture Quantile dilation), to adjust the beta-values of type2 design probes into a statistical distribution characteristic of type1 probes. The strategy involves application of a three-state beta-mixture model to assign probes to methylation states, subsequent transformation of probabilities into quantiles and finally a methylation-dependent dilation transformation to preserve the monotonicity and continuity of the data. We validate our method on cell-line data, fresh frozen and paraffin-embedded tumour tissue samples and demonstrate that BMIQ compares favourably with two competing methods. Specifically, we show that BMIQ improves the robustness of the normalization procedure, reduces the technical variation and bias of type2 probe values and successfully eliminates the type1 enrichment bias caused by the lower dynamic range of type2 probes. BMIQ will be useful as a preprocessing step for any study using the Illumina Infinium 450 k platform.\n\nBMIQ is freely available from http://code.google.com/p/bmiq/.\n\na.teschendorff@ucl.ac.uk\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/bts680", "pmid": "23175756", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "bts680"}, {"db": "pmc", "key": "PMC3546795"}], "notes": [], "created": "2017-05-04T14:56:20.940Z", "modified": "2020-01-21T13:53:20.630Z"}, {"entity": "publication", "iuid": "baa73d4e57d84fffa56934c8956bf61b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/baa73d4e57d84fffa56934c8956bf61b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/baa73d4e57d84fffa56934c8956bf61b"}}, "title": "Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells.", "authors": [{"family": "Paredes", "given": "Jo\u00e3o A", "initials": "JA"}, {"family": "Zhou", "given": "Xiaoshan", "initials": "X"}, {"family": "H\u00f6glund", "given": "Stefan", "initials": "S"}, {"family": "Karlsson", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2013-01-14", "journal": {"volume": "8", "issn": "1932-6203", "issue": "1", "pages": "e53698", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Loss of thymidine kinase 2 (TK2) causes a heterogeneous myopathic form of mitochondrial DNA (mtDNA) depletion syndrome (MDS) in humans that predominantly affects skeletal muscle tissue. In mice, TK2 deficiency also affects several tissues in addition to skeletal muscle, including brain, heart, adipose tissue, kidneys and causes death about 3 weeks after birth. We analysed skeletal muscle and heart muscle tissues of Tk2 knockout mice at postnatal development phase and observed that TK2 deficient pups grew slower and their skeletal muscles appeared significantly underdeveloped, whereas heart was close to normal in size. Both tissues showed mtDNA depletion and mitochondria with altered ultrastructure, as revealed by transmission electron microscopy. Gene expression microarray analysis showed a strong down-regulation of genes involved in cell cycle and cell proliferation in both tissues, suggesting a lower pool of undifferentiated proliferating cells. Analysis of isolated primary myoblasts from Tk2 knockout mice showed slow proliferation, less ability to differentiate and signs of premature senescence, even in absence of mtDNA depletion. Our data demonstrate that TK2 deficiency disturbs myogenic progenitor cells function in postnatal skeletal muscle and we propose this as one of the causes of underdeveloped phenotype and myopathic characteristic of the TK2 deficient mice, in addition to the progressive mtDNA depletion, mitochondrial damage and respiratory chain deficiency in post-mitotic differentiated tissue.", "doi": "10.1371/journal.pone.0053698", "pmid": "23341978", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-23752"}, {"db": "pmc", "key": "PMC3544874"}], "notes": [], "created": "2017-05-04T15:03:16.658Z", "modified": "2017-05-30T14:51:35.132Z"}, {"entity": "publication", "iuid": "32222c65cf914e8ba642562dc9c16b20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32222c65cf914e8ba642562dc9c16b20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32222c65cf914e8ba642562dc9c16b20"}}, "title": "Exome RNA sequencing reveals rare and novel alternative transcripts.", "authors": [{"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2013-01-07", "journal": {"volume": "41", "issn": "1362-4962", "issue": "1", "pages": "e6", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "RNA sequencing has become an important method to perform hypothesis-free characterization of global gene expression. One of the limitations of RNA sequencing is that most sequence reads represent highly expressed transcripts, whereas low level transcripts are challenging to detect. To combine the benefits of traditional expression arrays with the advantages of RNA sequencing, we have used whole exome enrichment prior to sequencing of total RNA. We show that whole exome capture can be successfully applied to cDNA to study the transcriptional landscape in human tissues. By introducing the exome enrichment step, we are able to identify transcripts present at very low levels, which are below the level of detection in conventional RNA sequencing. Although the enrichment increases the ability to detect presence of transcripts, it also lowers the accuracy of quantification of expression levels. Our results yield a large number of novel exons and splice isoforms, suggesting that conventional RNA sequencing methods only detect a small fraction of the full transcript diversity. We propose that whole exome enrichment of RNA is a suitable strategy for genome-wide discovery of novel transcripts, alternative splice variants and fusion genes.", "doi": "10.1093/nar/gks816", "pmid": "22941640", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "gks816"}, {"db": "pmc", "key": "PMC3592422"}], "notes": [], "created": "2017-05-04T14:58:08.941Z", "modified": "2021-07-07T14:15:07.525Z"}, {"entity": "publication", "iuid": "a897a3ab2afe4d01bcf41c0404b265d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a897a3ab2afe4d01bcf41c0404b265d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a897a3ab2afe4d01bcf41c0404b265d0"}}, "title": "RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.", "authors": [{"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Wiking", "given": "Mikaela", "initials": "M"}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Ait Blal", "given": "Hammou", "initials": "H"}, {"family": "Hjelmare", "given": "Martin", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2013-01-04", "journal": {"volume": "12", "issn": "1535-3907", "issue": "1", "pages": "299-307", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "One of the major challenges of a chromosome-centric proteome project is to explore in a systematic manner the potential proteins identified from the chromosomal genome sequence, but not yet characterized on a protein level. Here, we describe the use of RNA deep sequencing to screen human cell lines for RNA profiles and to use this information to select cell lines suitable for characterization of the corresponding gene product. In this manner, the subcellular localization of proteins can be analyzed systematically using antibody-based confocal microscopy. We demonstrate the usefulness of selecting cell lines with high expression levels of RNA transcripts to increase the likelihood of high quality immunofluorescence staining and subsequent successful subcellular localization of the corresponding protein. The results show a path to combine transcriptomics with affinity proteomics to characterize the proteins in a gene- or chromosome-centric manner.", "doi": "10.1021/pr3009308", "pmid": "23227862", "labels": {"Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:13.177Z", "modified": "2021-07-08T13:44:33.502Z"}, {"entity": "publication", "iuid": "97551f87fce64e9ea072d060659c720c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97551f87fce64e9ea072d060659c720c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97551f87fce64e9ea072d060659c720c"}}, "title": "A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.", "authors": [{"family": "Liu", "given": "Suli", "initials": "S"}, {"family": "Im", "given": "Hogune", "initials": "H"}, {"family": "Bairoch", "given": "Amos", "initials": "A"}, {"family": "Cristofanilli", "given": "Massimo", "initials": "M"}, {"family": "Chen", "given": "Rui", "initials": "R"}, {"family": "Deutsch", "given": "Eric W", "initials": "EW"}, {"family": "Dalton", "given": "Stephen", "initials": "S"}, {"family": "Fenyo", "given": "David", "initials": "D"}, {"family": "Fanayan", "given": "Susan", "initials": "S"}, {"family": "Gates", "given": "Chris", "initials": "C"}, {"family": "Gaudet", "given": "Pascale", "initials": "P"}, {"family": "Hincapie", "given": "Marina", "initials": "M"}, {"family": "Hanash", "given": "Samir", "initials": "S"}, {"family": "Kim", "given": "Hoguen", "initials": "H"}, {"family": "Jeong", "given": "Seul-Ki", "initials": "SK"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Mias", "given": "George", "initials": "G"}, {"family": "Menon", "given": "Rajasree", "initials": "R"}, {"family": "Mu", "given": "Zhaomei", "initials": "Z"}, {"family": "Nice", "given": "Edouard", "initials": "E"}, {"family": "Paik", "given": "Young-Ki", "initials": "YK"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Wells", "given": "Lance", "initials": "L"}, {"family": "Wu", "given": "Shiaw-Lin", "initials": "SL"}, {"family": "Yan", "given": "Fangfei", "initials": "F"}, {"family": "Zhang", "given": "Fan", "initials": "F"}, {"family": "Zhang", "given": "Yue", "initials": "Y"}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS"}, {"family": "Beavis", "given": "Ronald C", "initials": "RC"}, {"family": "Hancock", "given": "William S", "initials": "WS"}], "type": "journal article", "published": "2013-01-04", "journal": {"volume": "12", "issn": "1535-3907", "issue": "1", "pages": "45-57", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "We report progress assembling the parts list for chromosome 17 and illustrate the various processes that we have developed to integrate available data from diverse genomic and proteomic knowledge bases. As primary resources, we have used GPMDB, neXtProt, PeptideAtlas, Human Protein Atlas (HPA), and GeneCards. All sites share the common resource of Ensembl for the genome modeling information. We have defined the chromosome 17 parts list with the following information: 1169 protein-coding genes, the numbers of proteins confidently identified by various experimental approaches as documented in GPMDB, neXtProt, PeptideAtlas, and HPA, examples of typical data sets obtained by RNASeq and proteomic studies of epithelial derived tumor cell lines (disease proteome) and a normal proteome (peripheral mononuclear cells), reported evidence of post-translational modifications, and examples of alternative splice variants (ASVs). We have constructed a list of the 59 \"missing\" proteins as well as 201 proteins that have inconclusive mass spectrometric (MS) identifications. In this report we have defined a process to establish a baseline for the incorporation of new evidence on protein identification and characterization as well as related information from transcriptome analyses. This initial list of \"missing\" proteins that will guide the selection of appropriate samples for discovery studies as well as antibody reagents. Also we have illustrated the significant diversity of protein variants (including post-translational modifications, PTMs) using regions on chromosome 17 that contain important oncogenes. We emphasize the need for mandated deposition of proteomics data in public databases, the further development of improved PTM, ASV, and single nucleotide variant (SNV) databases, and the construction of Web sites that can integrate and regularly update such information. In addition, we describe the distribution of both clustered and scattered sets of protein families on the chromosome. Since chromosome 17 is rich in cancer-associated genes, we have focused the clustering of cancer-associated genes in such genomic regions and have used the ERBB2 amplicon as an example of the value of a proteogenomic approach in which one integrates transcriptomic with proteomic information and captures evidence of coexpression through coordinated regulation.", "doi": "10.1021/pr300985j", "pmid": "23259914", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pmc", "key": "PMC4142220"}, {"db": "mid", "key": "NIHMS431316"}], "notes": [], "created": "2017-05-04T14:55:13.784Z", "modified": "2021-07-08T13:44:33.454Z"}, {"entity": "publication", "iuid": "3c825df5e171438792031ef930fdba9a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c825df5e171438792031ef930fdba9a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c825df5e171438792031ef930fdba9a"}}, "title": "Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation.", "authors": [{"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Lohr", "given": "Miriam", "initials": "M"}, {"family": "Hellwig", "given": "Birte", "initials": "B"}, {"family": "Holmberg", "given": "Lars", "initials": "L"}, {"family": "Lambe", "given": "Mats", "initials": "M"}, {"family": "Berglund", "given": "Anders", "initials": "A"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "K\u00f6nig", "given": "Andr\u00e9", "initials": "A"}, {"family": "Fernandes", "given": "Oswaldo", "initials": "O"}, {"family": "Karlsson", "given": "Mats", "initials": "M"}, {"family": "Helenius", "given": "Gisela", "initials": "G", "orcid": "0000-0003-2317-5738", "researcher": {"href": "https://publications.scilifelab.se/researcher/2994acfdacff45ceb9c6b29aae2148c7.json"}}, {"family": "Karlsson", "given": "Christina", "initials": "C"}, {"family": "Rahnenf\u00fchrer", "given": "J\u00f6rg", "initials": "J"}, {"family": "Hengstler", "given": "Jan G", "initials": "JG"}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2013-01-01", "journal": {"volume": "19", "issn": "1557-3265", "issue": "1", "pages": "194-204", "title": "Clin. Cancer Res.", "issn-l": "1078-0432"}, "abstract": "Global gene expression profiling has been widely used in lung cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis and therapy response. So far, the value of these multigene signatures in clinical practice is unclear, and the biologic importance of individual genes is difficult to assess, as the published signatures virtually do not overlap.\n\nHere, we describe a novel single institute cohort, including 196 non-small lung cancers (NSCLC) with clinical information and long-term follow-up. Gene expression array data were used as a training set to screen for single genes with prognostic impact. The top 450 probe sets identified using a univariate Cox regression model (significance level P < 0.01) were tested in a meta-analysis including five publicly available independent lung cancer cohorts (n = 860).\n\nThe meta-analysis revealed 14 genes that were significantly associated with survival (P < 0.001) with a false discovery rate <1%. The prognostic impact of one of these genes, the cell adhesion molecule 1 (CADM1), was confirmed by use of immunohistochemistry on tissue microarrays from 2 independent NSCLC cohorts, altogether including 617 NSCLC samples. Low CADM1 protein expression was significantly associated with shorter survival, with particular influence in the adenocarcinoma patient subgroup.\n\nUsing a novel NSCLC cohort together with a meta-analysis validation approach, we have identified a set of single genes with independent prognostic impact. One of these genes, CADM1, was further established as an immunohistochemical marker with a potential application in clinical diagnostics.", "doi": "10.1158/1078-0432.CCR-12-1139", "pmid": "23032747", "labels": {"Array and Analysis Facility": null, "Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1078-0432.CCR-12-1139"}], "notes": [], "created": "2017-05-04T14:55:56.842Z", "modified": "2021-07-06T16:29:23.776Z"}, {"entity": "publication", "iuid": "16838ea4f35f48159159929c6f33659c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16838ea4f35f48159159929c6f33659c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16838ea4f35f48159159929c6f33659c"}}, "title": "Proceedings of the 15th International Congress on Circumpolar Health", "authors": [], "type": "journal-article", "published": "2013-01-00", "journal": {"volume": "72", "issn": "2242-3982", "issue": "1", "pages": "22447", "title": "International Journal of Circumpolar Health", "issn-l": "1239-9736"}, "abstract": null, "doi": "10.3402/ijch.v72i0.22447", "pmid": "28156288", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:26.814Z", "modified": "2020-01-21T13:56:09.952Z"}, {"entity": "publication", "iuid": "5c5adba54ca245a89e135b8b6bb343d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c5adba54ca245a89e135b8b6bb343d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c5adba54ca245a89e135b8b6bb343d7"}}, "title": "Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime.", "authors": [{"family": "Forsberg", "given": "Lars Anders", "initials": "LA"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Dumanski", "given": "Jan Piotr", "initials": "JP"}], "type": "journal article", "published": "2013-01-00", "journal": {"volume": "50", "issn": "1468-6244", "issue": "1", "pages": "1-10", "title": "J. Med. Genet.", "issn-l": "0022-2593"}, "abstract": "The heritability of most common, multifactorial diseases is rather modest and known genetic effects account for a small part of it. The remaining portion of disease aetiology has been conventionally ascribed to environmental effects, with an unknown part being stochastic. This review focuses on recent studies highlighting stochastic events of potentially great importance in human disease-the accumulation of post-zygotic structural aberrations with age in phenotypically normal humans. These findings are in agreement with a substantial mutational load predicted to occur during lifetime within the human soma. A major consequence of these results is that the genetic profile of a single tissue collected at one time point should be used with caution as a faithful portrait of other tissues from the same subject or the same tissue throughout life. Thus, the design of studies in human genetics interrogating a single sample per subject or applying lymphoblastoid cell lines may come into question. Sporadic disorders are common in medicine. We wish to stress the non-heritable genetic variation as a potentially important factor behind the development of sporadic diseases. Moreover, associations between post-zygotic mutations, clonal cell expansions and their relation to cancer predisposition are central in this context. Post-zygotic mutations are amenable to robust examination and are likely to explain a sizable part of non-heritable disease causality, which has routinely been thought of as synonymous with environmental factors. In view of the widespread accumulation of genetic aberrations with age and strong predictions of disease risk from such analyses, studies of post-zygotic mutations may be a fruitful approach for delineation of variants that are causative for common human disorders.", "doi": "10.1136/jmedgenet-2012-101322", "pmid": "23172682", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "jmedgenet-2012-101322"}, {"db": "pmc", "key": "PMC3534255"}], "notes": [], "created": "2017-05-04T14:58:00.599Z", "modified": "2020-01-21T13:56:08.738Z"}, {"entity": "publication", "iuid": "2736819dd2974cf7ae1ed7a88f420b76", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2736819dd2974cf7ae1ed7a88f420b76.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2736819dd2974cf7ae1ed7a88f420b76"}}, "title": "Large-scale association analysis identifies new risk loci for coronary artery disease.", "authors": [{"family": "CARDIoGRAMplusC4D Consortium", "given": "None", "initials": "N"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Willenborg", "given": "Christina", "initials": "C"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Thompson", "given": "John R", "initials": "JR"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Goldstein", "given": "Benjamin A", "initials": "BA"}, {"family": "Stirrups", "given": "Kathleen", "initials": "K"}, {"family": "K\u00f6nig", "given": "Inke R", "initials": "IR"}, {"family": "Cazier", "given": "Jean-Baptiste", "initials": "J"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Hall", "given": "Alistair S", "initials": "AS"}, {"family": "Lee", "given": "Jong-Young", "initials": "J"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Grundberg", "given": "Elin", "initials": "E"}, {"family": "Havulinna", "given": "Aki S", "initials": "AS"}, {"family": "Ho", "given": "Weang K", "initials": "WK"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Kristiansson", "given": "Kati", "initials": "K"}, {"family": "Lundmark", "given": "Per", "initials": "P"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "L"}, {"family": "Rafelt", "given": "Suzanne", "initials": "S"}, {"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Van Zuydam", "given": "Natalie", "initials": "N"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Waite", "given": "Lindsay L", "initials": "LL"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Ziegler", "given": "Andreas", "initials": "A"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Balmforth", "given": "Anthony J", "initials": "AJ"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Burgdorf", "given": "Christof", "initials": "C"}, {"family": "Claudi-Boehm", "given": "Simone", "initials": "S"}, {"family": "Cox", "given": "David", "initials": "D"}, {"family": "Dimitriou", "given": "Maria", "initials": "M"}, {"family": "Do", "given": "Ron", "initials": "R"}, {"family": "DIAGRAM Consortium", "given": "None", "initials": "N"}, {"family": "CARDIOGENICS Consortium", "given": "None", "initials": "N"}, {"family": "Doney", "given": "Alex S F", "initials": "ASF"}, {"family": "El Mokhtari", "given": "NourEddine", "initials": "N"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Fontanillas", "given": "Pierre", "initials": "P"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Hager", "given": "J\u00f6rg", "initials": "J"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Han", "given": "Bok-Ghee", "initials": "B"}, {"family": "Hunt", "given": "Sarah E", "initials": "SE"}, {"family": "Kang", "given": "Hyun M", "initials": "HM"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Kessler", "given": "Thorsten", "initials": "T"}, {"family": "Knowles", "given": "Joshua W", "initials": "JW"}, {"family": "Kolovou", "given": "Genovefa", "initials": "G"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Langford", "given": "Cordelia", "initials": "C"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Lokki", "given": "Marja-Liisa", "initials": "M"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Maouche", "given": "Seraya", "initials": "S"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "MuTHER Consortium", "given": "None", "initials": "N"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Rayner", "given": "N William", "initials": "NW"}, {"family": "Rasheed", "given": "Asif", "initials": "A"}, {"family": "Rosinger", "given": "Silke", "initials": "S"}, {"family": "Rubin", "given": "Diana", "initials": "D"}, {"family": "Rumpf", "given": "Moritz P", "initials": "MP"}, {"family": "Sch\u00e4fer", "given": "Arne", "initials": "A"}, {"family": "Sivananthan", "given": "Mohan", "initials": "M"}, {"family": "Song", "given": "Ci", "initials": "C"}, {"family": "Stewart", "given": "Alexandre F R", "initials": "AFR"}, {"family": "Tan", "given": "Sian-Tsung", "initials": "S"}, {"family": "Thorgeirsson", "given": "Gudmundur", "initials": "G"}, {"family": "van der Schoot", "given": "C Ellen", "initials": "CE"}, {"family": "Wagner", "given": "Peter J", "initials": "PJ"}, {"family": "Wellcome Trust Case Control Consortium", "given": "None", "initials": "N"}, {"family": "Wells", "given": "George A", "initials": "GA"}, {"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Yang", "given": "Tsun-Po", "initials": "T"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Arveiler", "given": "Dominique", "initials": "D"}, {"family": "Basart", "given": "Hanneke", "initials": "H"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Brambilla", "given": "Paolo", "initials": "P"}, {"family": "Cambien", "given": "Francois", "initials": "F"}, {"family": "Cupples", "given": "Adrienne L", "initials": "AL"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Diemert", "given": "Patrick", "initials": "P"}, {"family": "Epstein", "given": "Stephen E", "initials": "SE"}, {"family": "Evans", "given": "Alun", "initials": "A"}, {"family": "Ferrario", "given": "Marco M", "initials": "MM"}, {"family": "Ferri\u00e8res", "given": "Jean", "initials": "J"}, {"family": "Gauguier", "given": "Dominique", "initials": "D"}, {"family": "Go", "given": "Alan S", "initials": "AS"}, {"family": "Goodall", "given": "Alison H", "initials": "AH"}, {"family": "Gudnason", "given": "Villi", "initials": "V"}, {"family": "Hazen", "given": "Stanley L", "initials": "SL"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Iribarren", "given": "Carlos", "initials": "C"}, {"family": "Jang", "given": "Yangsoo", "initials": "Y"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kee", "given": "Frank", "initials": "F"}, {"family": "Kim", "given": "Hyo-Soo", "initials": "H"}, {"family": "Klopp", "given": "Norman", "initials": "N"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Kratzer", "given": "Wolfgang", "initials": "W"}, {"family": "Kuulasmaa", "given": "Kari", "initials": "K"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Laaksonen", "given": "Reijo", "initials": "R"}, {"family": "Lee", "given": "Ji-Young", "initials": "J"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ouwehand", "given": "Willem H", "initials": "WH"}, {"family": "Parish", "given": "Sarah", "initials": "S"}, {"family": "Park", "given": "Jeong E", "initials": "JE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Quertermous", "given": "Thomas", "initials": "T"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Schadt", "given": "Eric", "initials": "E"}, {"family": "Shah", "given": "Svati H", "initials": "SH"}, {"family": "Sinisalo", "given": "Juha", "initials": "J"}, {"family": "Stark", "given": "Klaus", "initials": "K"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Tr\u00e9gou\u00ebt", "given": "David-Alexandre", "initials": "D"}, {"family": "Virtamo", "given": "Jarmo", "initials": "J"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Wareham", "given": "Nicholas", "initials": "N"}, {"family": "Zimmermann", "given": "Martina E", "initials": "ME"}, {"family": "Nieminen", "given": "Markku S", "initials": "MS"}, {"family": "Hengstenberg", "given": "Christian", "initials": "C"}, {"family": "Sandhu", "given": "Manjinder S", "initials": "MS"}, {"family": "Pastinen", "given": "Tomi", "initials": "T"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Zalloua", "given": "Pierre A", "initials": "PA"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Schreiber", "given": "Stefan", "initials": "S"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Blankenberg", "given": "Stefan S", "initials": "SS"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Boehm", "given": "Bernhard O", "initials": "BO"}, {"family": "O'Donnell", "given": "Christopher", "initials": "C"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Collins", "given": "Rory", "initials": "R"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Roberts", "given": "Robert", "initials": "R"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}], "type": "journal article", "published": "2013-01-00", "journal": {"volume": "45", "issn": "1546-1718", "issue": "1", "pages": "25-33", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Coronary artery disease (CAD) is the commonest cause of death. Here, we report an association analysis in 63,746 CAD cases and 130,681 controls identifying 15 loci reaching genome-wide significance, taking the number of susceptibility loci for CAD to 46, and a further 104 independent variants (r(2) < 0.2) strongly associated with CAD at a 5% false discovery rate (FDR). Together, these variants explain approximately 10.6% of CAD heritability. Of the 46 genome-wide significant lead SNPs, 12 show a significant association with a lipid trait, and 5 show a significant association with blood pressure, but none is significantly associated with diabetes. Network analysis with 233 candidate genes (loci at 10% FDR) generated 5 interaction networks comprising 85% of these putative genes involved in CAD. The four most significant pathways mapping to these networks are linked to lipid metabolism and inflammation, underscoring the causal role of these activities in the genetic etiology of CAD. Our study provides insights into the genetic basis of CAD and identifies key biological pathways.", "doi": "10.1038/ng.2480", "pmid": "23202125", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.2480"}, {"db": "pmc", "key": "PMC3679547"}, {"db": "mid", "key": "NIHMS468575"}], "notes": [], "created": "2017-05-04T14:58:05.536Z", "modified": "2021-07-07T15:11:02.159Z"}, {"entity": "publication", "iuid": "c3f96c94d1b34e9bbc91a346e4a18cf2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3f96c94d1b34e9bbc91a346e4a18cf2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3f96c94d1b34e9bbc91a346e4a18cf2"}}, "title": "Genome-wide profiling of target genes for the systemic lupus erythematosus-associated transcription factors IRF5 and STAT4.", "authors": [{"family": "Wang", "given": "Chuan", "initials": "C"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Hagberg", "given": "Niklas", "initials": "N"}, {"family": "Berggren", "given": "Olof", "initials": "O"}, {"family": "Sigurdsson", "given": "Snaevar", "initials": "S"}, {"family": "Karlberg", "given": "Olof", "initials": "O"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2013-01-00", "journal": {"volume": "72", "issn": "1468-2060", "issue": "1", "pages": "96-103", "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": "The transcription factors interferon regulatory factor 5 (IRF5) and signal transducer and activator of transcription 4 (STAT4) are encoded by two of the strongest susceptibility genes for systemic lupus erythematosus (SLE).\n\nTo investigate the target genes and functional roles of IRF5 and STAT4 in human peripheral blood mononuclear cells (PBMCs).\n\nChromatin immunoprecipitation-sequencing (ChIP-seq) was performed in PBMCs stimulated to activate IRF5 and STAT4. The expression of the target genes of IRF5 and STAT4 was investigated in a publicly available dataset generated from PBMCs from patients with SLE and healthy controls. The genomic regions bound by the transcription complexes mediated by IRF5 and STAT4 were examined for transcription factor binding motifs and SLE-associated sequence variants.\n\nMore than 7000 target genes for IRF5 and STAT4 were identified in stimulated PBMCs. These genes were enriched to functional pathways in the type I interferon system, and have key roles in the inflammatory response. The expression patterns of the target genes were characteristic for patients with SLE. The transcription factors high mobility group-I/Y, specificity protein 1, and paired box 4 may function cooperatively with IRF5 and STAT4 in transcriptional regulation. Eight of the target regions for IRF5 and STAT4 contain SLE-associated sequence variants.\n\nBy participating in transcription complex with other co-factors, IRF5 and STAT4 harbour the potential of regulating a large number of target genes, which may contribute to their strong association with SLE.", "doi": "10.1136/annrheumdis-2012-201364", "pmid": "22730365", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "annrheumdis-2012-201364"}], "notes": [], "created": "2017-05-04T15:01:13.945Z", "modified": "2021-07-07T15:11:02.722Z"}, {"entity": "publication", "iuid": "bc889656aee749f4b8890968a40491f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc889656aee749f4b8890968a40491f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc889656aee749f4b8890968a40491f7"}}, "title": "First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1.", "authors": [{"family": "Manzoor", "given": "Shahid", "initials": "S"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}], "type": "journal article", "published": "2013-01-00", "journal": {"volume": "1", "issn": "2169-8287", "issue": "1", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "Syntrophic acetate-oxidizing bacteria (SAOB) have been identified as key organisms for efficient biogas production from protein-rich materials. Tepidanaerobacter acetatoxydans is the first reported SAOB for which the genome has been sequenced. Genome analysis will aid us in understanding the mechanisms regulating syntrophy, particularly energy-conserving and electron transfer mechanisms.", "doi": "10.1128/genomeA.00213-12", "pmid": "23469343", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "genomeA00213-12"}, {"db": "pmc", "key": "PMC3587937"}], "notes": [], "created": "2017-05-04T15:02:24.697Z", "modified": "2020-01-21T13:56:04.929Z"}, {"entity": "publication", "iuid": "46a18a9c8aaf4db1b6effc79fdc3f06a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46a18a9c8aaf4db1b6effc79fdc3f06a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46a18a9c8aaf4db1b6effc79fdc3f06a"}}, "title": "450K-array analysis of chronic lymphocytic leukemia cells reveals global DNA methylation to be relatively stable over time and similar in resting and proliferative compartments.", "authors": [{"family": "Cahill", "given": "N", "initials": "N"}, {"family": "Bergh", "given": "A-C", "initials": "AC"}, {"family": "Kanduri", "given": "M", "initials": "M"}, {"family": "G\u00f6ransson-Kultima", "given": "H", "initials": "H"}, {"family": "Mansouri", "given": "L", "initials": "L"}, {"family": "Isaksson", "given": "A", "initials": "A"}, {"family": "Ryan", "given": "F", "initials": "F"}, {"family": "Smedby", "given": "K E", "initials": "KE"}, {"family": "Juliusson", "given": "G", "initials": "G"}, {"family": "Sundstr\u00f6m", "given": "C", "initials": "C"}, {"family": "Ros\u00e9n", "given": "A", "initials": "A"}, {"family": "Rosenquist", "given": "R", "initials": "R"}], "type": "comparative study", "published": "2013-01-00", "journal": {"volume": "27", "issn": "1476-5551", "issue": "1", "pages": "150-158", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": "In chronic lymphocytic leukemia (CLL), the microenvironment influences gene expression patterns; however, knowledge is limited regarding the extent to which methylation changes with time and exposure to specific microenvironments. Using high-resolution 450K arrays, we provide the most comprehensive DNA methylation study of CLL to date, analyzing paired diagnostic/follow-up samples from IGHV-mutated/untreated and IGHV-unmutated/treated patients (n=36) and patient-matched peripheral blood and lymph node samples (n=20). On an unprecedented scale, we revealed 2239 differentially methylated CpG sites between IGHV-mutated and unmutated patients, with the majority of sites positioned outside annotated CpG islands. Intriguingly, CLL prognostic genes (for example, CLLU1, LPL, ZAP70 and NOTCH1), epigenetic regulator (for example, HDAC9, HDAC4 and DNMT3B), B-cell signaling (for example, IBTK) and numerous TGF-\u03b2 and NF-\u03baB/TNF pathway genes were alternatively methylated between subgroups. Contrary, DNA methylation over time was deemed rather stable with few recurrent changes noted within subgroups. Although a larger number of non-recurrent changes were identified among IGHV-unmutated relative to mutated cases over time, these equated to a low global change. Similarly, few changes were identified between compartment cases. Altogether, we reveal CLL subgroups to display unique methylation profiles and unveil methylation as relatively stable over time and similar within different CLL compartments, implying aberrant methylation as an early leukemogenic event.", "doi": "10.1038/leu.2012.245", "pmid": "22922567", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "leu2012245"}], "notes": [], "created": "2017-05-04T15:01:21.005Z", "modified": "2020-01-21T13:56:01.993Z"}, {"entity": "publication", "iuid": "c282a323456c429f85c223e3604521ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c282a323456c429f85c223e3604521ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c282a323456c429f85c223e3604521ac"}}, "title": "The A-CD analogue of 16\u03b2,17\u03b1-estriol is a potent and highly selective estrogen receptor \u03b2 agonist", "authors": [{"family": "Sauv\u00e9e", "given": "Claire", "initials": "C"}, {"family": "Sch\u00e4fer", "given": "Anja", "initials": "A"}, {"family": "Sund\u00e9n", "given": "Henrik", "initials": "H"}, {"family": "Ma", "given": "Jian Nong", "initials": "JN"}, {"family": "Gustavsson", "given": "Anna Lena", "initials": "AL", "orcid": "0000-0003-4332-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b014ef7ea0d461b8e2ddb87506b1252.json"}}, {"family": "Burstein", "given": "Ethan S", "initials": "ES"}, {"family": "Olsson", "given": "Roger", "initials": "R"}], "type": "journal-article", "published": "2013-00-00", "journal": {"volume": "4", "issn": "2040-2503", "issue": "11", "pages": "1439", "title": "Med. Chem. Commun.", "issn-l": null}, "abstract": null, "doi": "10.1039/c3md00194f", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-20T14:58:21.405Z", "modified": "2025-10-17T13:04:30.475Z"}, {"entity": "publication", "iuid": "22c3192dbe7446889d727c0d81025c27", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22c3192dbe7446889d727c0d81025c27.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22c3192dbe7446889d727c0d81025c27"}}, "title": "Nanoscale elucidation of Na,K-ATPase isoforms in dendritic spines", "authors": [{"family": "Liebmann", "given": "Thomas", "initials": "T"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Aperia", "given": "Anita", "initials": "A"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}], "type": "journal-article", "published": "2013-00-00", "journal": {"volume": "2", "issn": "2192-2853", "issue": "1", "pages": "6", "title": "Optical Nanoscopy Opt Nanoscopy", "issn-l": "2192-2853"}, "abstract": null, "doi": "10.1186/2192-2853-2-6", "pmid": null, "labels": {"Integrated Microscopy Technologies Stockholm": "Technology development"}, "xrefs": [], "notes": "We have utilized PALM for dissection of nanoscale localization in mature cultured neurons and demonstrated similar topology and quantification estimates with PAGFP and mEos. PALM topology assessments of the sodium pump appeared similar to previous STED studies, though quantification estimates varied, implying that labeling strategies, sample analysis and choice of nanoscopic imaging method can be critical factors for correct molecular quantification.", "created": "2018-04-27T08:30:22.114Z", "modified": "2021-06-22T12:06:16.540Z"}]}