Publications 2013

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Publications

2021 (1)

2020 (314)

2019 (741)

2018 (663)

2017 (698)

2016 (671)

2015 (432)

2014 (376)

2013 (320)

2012 (243)

2011 (163)

2010 (139)

All (4761)


Facilities

Journals

320 publications

PubMed DOI Crossref
Association of STAT4 polymorphism with severe renal insufficiency in lupus nephritis.
Bolin K, Sandling JK, Zickert A, ..., Gunnarsson I, Nordmark G
pii: PONE-D-13-14730 pmc: PMC3873995
PLoS ONE 8 (12) e84450 [2013-12-27; online 2013-12-27]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Structure-activity relationships of synthetic cordycepin analogues as experimental therapeutics for African trypanosomiasis.
Vodnala SK, Lundbäck T, Yeheskieli E, ..., Hammarström LGJ, Rottenberg ME
J. Med. Chem. 56 (24) 9861-9873 [2013-12-27; online 2013-11-29]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
PubMed DOI Crossref
Plasma and erythrocyte glutathione peroxidase activity, serum selenium concentration, and plasma total antioxidant capacity in cats with IRIS stages I-IV chronic kidney disease.
Krofič Žel M, Tozon N, Nemec Svete A
pmc: PMC4895542
J. Vet. Intern. Med. 28 (1) 130-136 [2013-12-16; online 2013-12-16]
Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Automated quality control system for LC-SRM setups.
Teleman J, Waldemarson S, Malmström J, Levander F
pii: S1874-3919(13)00176-0
J Proteomics 95 (-) 77-83 [2013-12-16; online 2013-04-16]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Profiling post-centrifugation delay of serum and plasma with antibody bead arrays.
Qundos U, Hong M, Tybring G, ..., Nilsson P, Schwenk JM
pii: S1874-3919(13)00209-1
J Proteomics 95 (-) 46-54 [2013-12-16; online 2013-05-02]
Plasma Profiling [Collaborative]
PubMed DOI Crossref
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.
Thessen Hedreul M, Möller S, Stridh P, ..., Olsson T, Jagodic M
pii: ddt343 pmc: PMC3836475
Hum. Mol. Genet. 22 (24) 4952-4966 [2013-12-15; online 2013-08-01]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
Chemical probes to study ADP-ribosylation: synthesis and biochemical evaluation of inhibitors of the human ADP-ribosyltransferase ARTD3/PARP3.
Lindgren AE, Karlberg T, Ekblad T, ..., Schüler H, Elofsson M
PDB: 4L6Z PDB: 4L70 PDB: 4L7L PDB: 4L7N PDB: 4L7O PDB: 4L7P PDB: 4L7R PDB: 4L7U
J. Med. Chem. 56 (23) 9556-9568 [2013-12-12; online 2013-11-06]
Protein Science Facility (PSF)
PubMed DOI Crossref
Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B.
Karlsson EK, Sigurdsson S, Ivansson E, ..., Breen M, Lindblad-Toh K
pii: gb-2013-14-12-r132 pmc: PMC4053774 GEO: GSE52147
Genome Biol. 14 (12) R132 [2013-12-12; online 2013-12-12]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Linkage analysis in familial non-Lynch syndrome colorectal cancer families from Sweden.
Kontham V, von Holst S, Lindblom A
pii: PONE-D-13-40988 pmc: PMC3859667
PLoS ONE 8 (12) e83936 [2013-12-11; online 2013-12-11]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Utilizing twins as controls for non-twin case-materials in genome wide association studies.
Ganna A, Ortega-Alonso A, Havulinna A, ..., Hultman CM, Magnusson PKE
pii: PONE-D-13-27564 pmc: PMC3858365
PLoS ONE 8 (12) e83101 [2013-12-10; online 2013-12-10]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Statistical molecular design: a tool to follow up hits from small-molecule screening.
Lindgren AE, Larsson A, Linusson A, Elofsson M
Methods Mol. Biol. 1056 (-) 169-188 [2013-12-07; online 2013-12-07]
Chemical Biology Consortium Sweden (CBCS) [Technology development]
PubMed DOI Crossref
Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment.
Berglund EC, Lindqvist CM, Hayat S, ..., Lönnerholm G, Syvänen A
pii: 1471-2164-14-856 pmc: PMC4046713
BMC Genomics 14 (-) 856 [2013-12-05; online 2013-12-05]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Urinary prognostic biomarkers and classification of IgA nephropathy by high resolution mass spectrometry coupled with liquid chromatography.
Kalantari S, Rutishauser D, Samavat S, ..., Rezaei-Tavirani M, Zubarev RA
pii: PONE-D-13-33465 pmc: PMC3855054
PLoS ONE 8 (12) e80830 [2013-12-05; online 2013-12-05]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
The resveratrol tetramer (-)-hopeaphenol inhibits type III secretion in the gram-negative pathogens Yersinia pseudotuberculosis and Pseudomonas aeruginosa.
Zetterström CE, Hasselgren J, Salin O, ..., Sundin C, Elofsson M
pii: PONE-D-13-39735 pmc: PMC3853165
PLoS ONE 8 (12) e81969 [2013-12-04; online 2013-12-04]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
PubMed DOI Crossref
Integrated molecular portrait of non-small cell lung cancers.
Lazar V, Suo C, Orear C, ..., Hansson J, Pawitan Y
pii: 1755-8794-6-53 pmc: PMC4222074
BMC Med Genomics 6 (-) 53 [2013-12-03; online 2013-12-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis.
Weidinger S, Willis-Owen SA, Kamatani Y, ..., Irvine AD, Moffatt MF
pii: ddt317 pmc: PMC3820131
Hum. Mol. Genet. 22 (23) 4841-4856 [2013-12-01; online 2013-07-28]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Evaluation of real-time immunohistochemistry and interaction map as an alternative objective assessment of HER2 expression in human breast cancer tissue.
Gedda L, Björkelund H, Lebel L, ..., Malmqvist M, Andersson K
Appl. Immunohistochem. Mol. Morphol. 21 (6) 497-505 [2013-12-00; online 2013-03-05]
Tissue Profiling
PubMed DOI Crossref
The association between plasma homocysteine and coronary heart disease is modified by the MTHFR 677C>T polymorphism.
Mehlig K, Leander K, de Faire U, ..., Lissner L, Thelle D
pii: heartjnl-2013-304460
Heart 99 (23) 1761-1765 [2013-12-00; online 2013-09-10]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Distinct loci in the CHRNA5/CHRNA3/CHRNB4 gene cluster are associated with onset of regular smoking.
Stephens SH, Hartz SM, Hoft NR, ..., Bierut LJ, Ehringer MA
pmc: PMC3947535 mid: NIHMS538239
Genet. Epidemiol. 37 (8) 846-859 [2013-12-00; online 2013-11-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genetic variation at the IGF1 locus shows association with post-stroke outcome and to circulating IGF1.
Aberg ND, Olsson S, Aberg D, ..., Isgaard J, Jern C
pii: EJE-13-0486
Eur. J. Endocrinol. 169 (6) 759-765 [2013-12-00; online 2013-09-06]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Selectivity analysis of single binder assays used in plasma protein profiling.
Neiman M, Fredolini C, Johansson H, ..., Nilsson P, Schwenk JM
pmc: PMC4265267
Proteomics 13 (23-24) 3406-3410 [2013-12-00; online 2013-10-24]
Plasma Profiling [Technology development]
PubMed DOI Crossref
Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803.
Anfelt J, Hallström B, Nielsen J, Uhlén M, Hudson EP
pii: AEM.02694-13 pmc: PMC3837751
Appl. Environ. Microbiol. 79 (23) 7419-7427 [2013-12-00; online 2013-09-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
DNA damage leads to progressive replicative decline but extends the life span of long-lived mutant animals.
Lans H, Lindvall JM, Thijssen K, ..., Nilsen H, Vermeulen W
pii: cdd2013126 pmc: PMC3824592
Cell Death Differ. 20 (12) 1709-1718 [2013-12-00; online 2013-09-10]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
Protein expansion is primarily due to indels in intrinsically disordered regions.
Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A
pii: mst157
Mol. Biol. Evol. 30 (12) 2645-2653 [2013-12-00; online 2013-09-17]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
High expression of glycolytic and pigment proteins is associated with worse clinical outcome in stage III melanoma.
Falkenius J, Lundeberg J, Johansson H, ..., Hansson J, Egyhazi Brage S
Melanoma Res. 23 (6) 452-460 [2013-12-00; online 2013-10-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade.
Zaremba-Niedzwiedzka K, Viklund J, Zhao W, ..., Stepanauskas R, Andersson SG
pii: gb-2013-14-11-r130 pmc: PMC4053759
Genome Biol. 14 (11) R130 [2013-11-28; online 2013-11-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Identification of candidate serum proteins for classifying well-differentiated small intestinal neuroendocrine tumors.
Darmanis S, Cui T, Drobin K, ..., Schwenk JM, Giandomenico V
pii: PONE-D-13-03665 pmc: PMC3839889
PLoS ONE 8 (11) e81712 [2013-11-25; online 2013-11-25]
Plasma Profiling [Collaborative]
PubMed DOI Crossref
Germline genetic contributions to risk for esophageal adenocarcinoma, Barrett's esophagus, and gastroesophageal reflux.
Ek WE, Levine DM, D'Amato M, ..., MacGregor S, BEACON study investigators
pii: djt303 pmc: PMC3833931
J. Natl. Cancer Inst. 105 (22) 1711-1718 [2013-11-20; online 2013-10-29]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Rule-based models of the interplay between genetic and environmental factors in childhood allergy.
Bornelöv S, Sääf A, Melén E, ..., Pershagen G, Komorowski J
pii: PONE-D-13-20229 pmc: PMC3833974
PLoS ONE 8 (11) e80080 [2013-11-19; online 2013-11-19]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).
Norman AJ, Street NR, Spong G
pii: PONE-D-13-25655 pmc: PMC3832409
PLoS ONE 8 (11) e81012 [2013-11-18; online 2013-11-18]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner.
Åhsberg J, Ungerbäck J, Strid T, ..., Qian H, Sigvardsson M
pii: M113.506261 pmc: PMC3829190
J. Biol. Chem. 288 (46) 33449-33461 [2013-11-15; online 2013-10-01]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Substrate specificity and oligomerization of human GMP synthetase.
Welin M, Lehtiö L, Johansson A, ..., Gräslund S, Nordlund P
pii: S0022-2836(13)00427-0 PDB: 2VXO
J. Mol. Biol. 425 (22) 4323-4333 [2013-11-15; online 2013-07-03]
Protein Science Facility (PSF)
PubMed DOI Crossref
miR-128 regulates non-myocyte hyperplasia, deposition of extracellular matrix and Islet1 expression during newt cardiac regeneration.
Witman N, Heigwer J, Thaler B, Lui WO, Morrison JI
pii: S0012-1606(13)00485-5
Dev. Biol. 383 (2) 253-263 [2013-11-15; online 2013-09-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Discovery of an allosteric inhibitor binding site in 3-Oxo-acyl-ACP reductase from Pseudomonas aeruginosa.
Cukier CD, Hope AG, Elamin AA, ..., Gray DW, Schneider G
pmc: PMC3833349
ACS Chem. Biol. 8 (11) 2518-2527 [2013-11-15; online 2013-09-11]
Protein Science Facility (PSF)
DOI Crossref
Polymer–Pendant Interactions in Poly(pyrrol-3-ylhydroquinone): A Solution for the Use of Conducting Polymers at Stable Conditions
Karlsson C, Huang H, Strømme M, Gogoll A, Sjödin M
J. Phys. Chem. C 117 (45) 23558-23567 [2013-11-14; online 2013-11-05]
Swedish NMR Centre (SNC) [Service]
PubMed DOI Crossref
Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.
Zaghlool A, Ameur A, Nyberg L, ..., Cavelier L, Feuk L
pii: 1472-6750-13-99 pmc: PMC3833653
BMC Biotechnol. 13 (-) 99 [2013-11-13; online 2013-11-13]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Disturbance induced decoupling between host genetics and composition of the associated microbiome.
Wegner KM, Volkenborn N, Peter H, Eiler A
pii: 1471-2180-13-252 pmc: PMC3840651
BMC Microbiol. 13 (-) 252 [2013-11-09; online 2013-11-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer.
Bysani M, Wallerman O, Bornelöv S, ..., Komorowski J, Wadelius C
pii: 1755-8794-6-50 pmc: PMC3831757 SRA: SRA066400
BMC Med Genomics 6 (-) 50 [2013-11-08; online 2013-11-08]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Inference of the genetic architecture underlying BMI and height with the use of 20,240 sibling pairs.
Hemani G, Yang J, Vinkhuyzen A, ..., Martin NG, Visscher PM
pii: S0002-9297(13)00462-X pmc: PMC3965855
Am. J. Hum. Genet. 93 (5) 865-875 [2013-11-07; online 2013-10-31]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data.
Ahsan M, Li X, Lundberg AE, ..., Carlborg O, Marklund S
pmc: PMC3817360
Front Genet 4 (-) 226 [2013-11-05; online 2013-11-05]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Combined in vitro-in vivo approach to assess the hepatobiliary disposition of a novel oral thrombin inhibitor.
Matsson EM, Eriksson UG, Palm JE, ..., Schützer K, Lennernäs H
Mol. Pharm. 10 (11) 4252-4262 [2013-11-04; online 2013-10-02]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
PubMed DOI Crossref
In vitro and in vivo evaluation of osteoporosis therapeutic peptide PTH 1-34 loaded pegylated chitosan nanoparticles.
Narayanan D, Anitha A, Jayakumar R, Chennazhi KP
Mol. Pharm. 10 (11) 4159-4167 [2013-11-04; online 2013-09-07]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
7,8- and 5,8-Linoleate diol synthases support the heterolytic scission of oxygen-oxygen bonds by different amide residues.
Hoffmann I, Oliw EH
pii: S0003-9861(13)00286-5
Arch. Biochem. Biophys. 539 (1) 87-91 [2013-11-01; online 2013-09-26]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide DNA methylation assay reveals novel candidate biomarker genes in cervical cancer.
Farkas SA, Milutin-Gašperov N, Grce M, Nilsson TK
pii: 26346
Epigenetics 8 (11) 1213-1225 [2013-11-00; online 2013-09-14]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Association of genes in the NF-κB pathway with antibody-positive primary Sjögren's syndrome.
Nordmark G, Wang C, Vasaitis L, ..., Syvänen AC, UK Primary Sjögren’s Syndrome Registry
Scand. J. Immunol. 78 (5) 447-454 [2013-11-00; online 2013-08-16]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Common variants associated with plasma triglycerides and risk for coronary artery disease.
Do R, Willer CJ, Schmidt EM, ..., Neale BM, Kathiresan S
pii: ng.2795 pmc: PMC3904346 mid: NIHMS524704
Nat. Genet. 45 (11) 1345-1352 [2013-11-00; online 2013-10-08]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Metal-mediated crystallization of the xylose transporter XylE from Escherichia coli in three different crystal forms.
Quistgaard EM, Löw C, Moberg P, Nordlund P
pii: S1047-8477(13)00239-6
J. Struct. Biol. 184 (2) 375-378 [2013-11-00; online 2013-09-26]
Protein Science Facility (PSF)
PubMed DOI Crossref
Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome.
Lessard CJ, Li H, Adrianto I, ..., Harley JB, Sivils KL
pii: ng.2792 pmc: PMC3867192 mid: EMS54762
Nat. Genet. 45 (11) 1284-1292 [2013-11-00; online 2013-10-08]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Wobble decoding by the Escherichia coli selenocysteine insertion machinery.
Xu J, Croitoru V, Rutishauser D, Cheng Q, Arnér ES
pii: gkt764 pmc: PMC3834832
Nucleic Acids Res. 41 (21) 9800-9811 [2013-11-00; online 2013-08-29]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi.
Meerupati T, Andersson KM, Friman E, ..., Tunlid A, Ahrén D
pii: PGENETICS-D-13-01003 pmc: PMC3828140
PLoS Genet. 9 (11) e1003909 [2013-11-00; online 2013-11-14]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Antibodies biotinylated using a synthetic Z-domain from protein A provide stringent in situ protein detection.
Andersson S, Konrad A, Ashok N, ..., Hober S, Asplund A
pii: 0022155413502360 pmc: PMC3808578
J. Histochem. Cytochem. 61 (11) 773-784 [2013-11-00; online 2013-08-08]
Tissue Profiling
PubMed DOI Crossref
Discovery and refinement of loci associated with lipid levels.
Global Lipids Genetics Consortium N, Willer CJ, Schmidt EM, ..., Ingelsson E, Abecasis GR
pii: ng.2797 pmc: PMC3838666 mid: NIHMS524703
Nat. Genet. 45 (11) 1274-1283 [2013-11-00; online 2013-10-08]
NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Comparative drug pair screening across multiple glioblastoma cell lines reveals novel drug-drug interactions.
Schmidt L, Kling T, Monsefi N, ..., Gerlee P, Nelander S
pii: not111 pmc: PMC3813417
Neuro-oncology 15 (11) 1469-1478 [2013-11-00; online 2013-10-06]
Drug Discovery and Development (DDD) [Collaborative]
PubMed DOI Crossref
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, ..., Dermitzakis ET, Lappalainen T
pii: nbt.2702
Nat. Biotechnol. 31 (11) 1015-1022 [2013-11-00; online 2013-09-17]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
In situ Protein Detection for Companion Diagnostics.
Gremel G, Grannas K, Sutton LA, Pontén F, Zieba A
pmc: PMC3814083
Front Oncol 3 (-) 271 [2013-10-31; online 2013-10-31]
Tissue Profiling
PubMed DOI Crossref
Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress.
Butler È, Alsterfjord M, Olofsson TC, ..., Malmström J, Vásquez A
pii: 1471-2180-13-235 pmc: PMC4015849 GENBANK: KC776061 GENBANK: KC776062 GENBANK: KC776063 GENBANK: KC776064 GENBANK: KC776065 GENBANK: KC776066 GENBANK: KC776067 GENBANK: KC776068 GENBANK: KC776069 GENBANK: KC776070 GENBANK: KC776071 GENBANK: KC776073 GENBANK: KC776074 GENBANK: KC776075 GENBANK: KC776076 GENBANK: KC776077 GENBANK: KC776078 GENBANK: KC776079 GENBANK: KC776080 GENBANK: KC776081 GENBANK: KC776082 GENBANK: KC776083 GENBANK: KC776084 GENBANK: KC776085 GENBANK: KC776086 GENBANK: KC776087 GENBANK: KC776088 GENBANK: KC776089 GENBANK: KC776090 GENBANK: KC776091 GENBANK: KC776092 GENBANK: KC776093 GENBANK: KC776094 GENBANK: KC776095 GENBANK: KC776096 GENBANK: KC776097 GENBANK: KC776098 GENBANK: KC776099 GENBANK: KC776100 GENBANK: KC776101 GENBANK: KC776102 GENBANK: KC776103 GENBANK: KC776104 GENBANK: KC776105 GENBANK: KC776106 GENBANK: KC776107 GENBANK: KC776108 GENBANK: KC776109 GENBANK: KC776110 GENBANK: KC776111 GENBANK: KC789963 GENBANK: KC789964 GENBANK: KC789965 GENBANK: KC789966 GENBANK: KC789967 GENBANK: KC789968 GENBANK: KC789969 GENBANK: KC789970 GENBANK: KC789971 GENBANK: KC789972 GENBANK: KC789973 GENBANK: KC789974 GENBANK: KC789975 GENBANK: KC789976 GENBANK: KC789977 GENBANK: KC789978 GENBANK: KC789979 GENBANK: KC789980 GENBANK: KC789981 GENBANK: KC789982 GENBANK: KC789983 GENBANK: KC789984 GENBANK: KC789985 GENBANK: KC789986 GENBANK: KC789987 GENBANK: KC789988 GENBANK: KC789989 GENBANK: KC789990 GENBANK: KC789991 GENBANK: KC789992 GENBANK: KC789993 GENBANK: KC789994 GENBANK: KC789995 GENBANK: KC789996 GENBANK: KC789997 GENBANK: KC789998 GENBANK: KC789999 GENBANK: KC790000 GENBANK: KC790001 GENBANK: KC790002 GENBANK: KC790003 GENBANK: KC790004 GENBANK: KC790005 GENBANK: KC790006 GENBANK: KC790007 GENBANK: KC790008 GENBANK: KC790009 GENBANK: KC790010 GENBANK: KC790011 GENBANK: KC790012 GENBANK: KC790013 GENBANK: KC790014 GENBANK: KC790015 GENBANK: KC790016 GENBANK: KC790017 GENBANK: KC790018 GENBANK: KC801035
BMC Microbiol. 13 (-) 235 [2013-10-22; online 2013-10-22]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Nanobody mediated crystallization of an archeal mechanosensitive channel.
Löw C, Yau YH, Pardon E, ..., Steyaert J, Nordlund P
pii: PONE-D-13-33201 pmc: PMC3804602
PLoS ONE 8 (10) e77984 [2013-10-21; online 2013-10-21]
Protein Science Facility (PSF)
PubMed DOI Crossref
Eleven candidate susceptibility genes for common familial colorectal cancer.
Gylfe AE, Katainen R, Kondelin J, ..., Karhu A, Aaltonen LA
pii: PGENETICS-D-13-01401 pmc: PMC3798264
PLoS Genet. 9 (10) e1003876 [2013-10-17; online 2013-10-17]
Karolinska High Throughput Center (KHTC)
PubMed DOI Crossref
Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker.
Nookaew I, Thorell K, Worah K, ..., Nielsen J, Lundin SB
pii: 1755-8794-6-41 pmc: PMC4015281
BMC Med Genomics 6 (-) 41 [2013-10-11; online 2013-10-11]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Chemical fragmentation for massively parallel sequencing library preparation.
Gyarmati P, Song Y, Hällman J, Käller M
pii: S0168-1656(13)00365-9
J. Biotechnol. 168 (1) 95-100 [2013-10-10; online 2013-09-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Divergent structure-activity relationships of structurally similar acetylcholinesterase inhibitors.
Andersson CD, Forsgren N, Akfur C, ..., Ekström F, Linusson A
J. Med. Chem. 56 (19) 7615-7624 [2013-10-10; online 2013-08-30]
Chemical Biology Consortium Sweden (CBCS) [Service]
PubMed DOI Crossref
Molecular characterization of the α-subunit of Na⁺/K⁺ ATPase from the euryhaline barnacle Balanus improvisus reveals multiple genes and differential expression of alternative splice variants.
Lind U, Alm Rosenblad M, Wrange AL, ..., Havenhand J, Blomberg A
pii: PONE-D-12-40484 pmc: PMC3793950 GENBANK: KC357568 GENBANK: KC357569 GENBANK: KC357570
PLoS ONE 8 (10) e77069 [2013-10-09; online 2013-10-09]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Brain proteomics supports the role of glutamate metabolism and suggests other metabolic alterations in protein l-isoaspartyl methyltransferase (PIMT)-knockout mice.
Yang H, Lowenson JD, Clarke S, Zubarev RA
pmc: PMC3818641 mid: NIHMS523577
J. Proteome Res. 12 (10) 4566-4576 [2013-10-04; online 2013-08-21]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
Aneuploidy in neuroblastoma tumors is not associated with inactivating point mutations in the STAG2 gene.
Djos A, Fransson S, Kogner P, Martinsson T
pii: 1471-2350-14-102 pmc: PMC3853135
BMC Med. Genet. 14 (-) 102 [2013-10-02; online 2013-10-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells.
Wang X, Jiang L, Wallerman O, ..., Andersson L, Welsh N
pii: 1303625110 pmc: PMC3791784
Proc. Natl. Acad. Sci. U.S.A. 110 (40) 15997-16002 [2013-10-01; online 2013-09-18]
NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
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Profiling of atherosclerotic lesions by gene and tissue microarrays reveals PCSK6 as a novel protease in unstable carotid atherosclerosis.
Perisic L, Hedin E, Razuvaev A, ..., Odeberg J, Hedin U
pii: ATVBAHA.113.301743
Arterioscler. Thromb. Vasc. Biol. 33 (10) 2432-2443 [2013-10-00; online 2013-08-03]
Tissue Profiling
PubMed DOI Crossref
Recent advances in crayfish hematopoietic stem cell culture: a model for studies of hemocyte differentiation and immunity.
Söderhäll I
pmc: PMC3967606
Cytotechnology 65 (5) 691-695 [2013-10-00; online 2013-05-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Structural diversity of signal recognition particle RNAs in plastids.
Rosenblad MA, Träger C, Schünemann D
Plant Signal Behav 8 (10) doi: 10.4161/psb.26848 [2013-10-00; online 2014-02-05]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.
Fortunato CS, Eiler A, Herfort L, ..., Peterson TD, Crump BC
pii: ismej201379 pmc: PMC3965310 SRA: SRA058065 SRA: SRP006412
ISME J 7 (10) 1899-1911 [2013-10-00; online 2013-05-31]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Heart research advances using database search engines, Human Protein Atlas and the Sydney Heart Bank.
Li A, Estigoy C, Raftery M, ..., Lal S, Dos Remedios CG
pii: S1443-9506(13)01036-6
Heart Lung Circ 22 (10) 819-826 [2013-10-00; online 2013-07-17]
Tissue Profiling
PubMed DOI Crossref
Comprehensive genetic analysis identifies a pathognomonic NAB2/STAT6 fusion gene, nonrandom secondary genomic imbalances, and a characteristic gene expression profile in solitary fibrous tumor.
Mohajeri A, Tayebwa J, Collin A, ..., Nord KH, Mertens F
Genes Chromosomes Cancer 52 (10) 873-886 [2013-10-00; online 2013-06-14]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, ..., Estivill X, Dermitzakis ET
pii: nature12531 pmc: PMC3918453 mid: NIHMS512974
Nature 501 (7468) 506-511 [2013-09-26; online 2013-09-17]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
FHOD1, a formin upregulated in epithelial-mesenchymal transition, participates in cancer cell migration and invasion.
Gardberg M, Kaipio K, Lehtinen L, ..., Koivisto M, Carpén O
pii: PONE-D-13-15073 pmc: PMC3784416
PLoS ONE 8 (9) e74923 [2013-09-26; online 2013-09-26]
Tissue Profiling
PubMed DOI Crossref
Genetic variants of coagulation factor XI show association with ischemic stroke up to 70 years of age.
Hanson E, Nilsson S, Jood K, ..., Melander O, Jern C
pii: PONE-D-13-15903 pmc: PMC3783404
PLoS ONE 8 (9) e75286 [2013-09-25; online 2013-09-25]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Spinal deformity in aged zebrafish is accompanied by degenerative changes to their vertebrae that resemble osteoarthritis.
Hayes AJ, Reynolds S, Nowell MA, ..., Caterson B, Hammond CL
pii: PONE-D-13-26599 pmc: PMC3782452
PLoS ONE 8 (9) e75787 [2013-09-24; online 2013-09-24]
Genome Engineering Zebrafish
PubMed DOI Crossref
Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia.
Nordlund J, Bäcklin CL, Wahlberg P, ..., Lönnerholm G, Syvänen A
pii: gb-2013-14-9-r105 pmc: PMC4014804
Genome Biol. 14 (9) r105 [2013-09-24; online 2013-09-24]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Equine multiple congenital ocular anomalies and silver coat colour result from the pleiotropic effects of mutant PMEL.
Andersson LS, Wilbe M, Viluma A, ..., Ewart S, Lindgren G
pii: PONE-D-13-06293 pmc: PMC3781063
PLoS ONE 8 (9) e75639 [2013-09-23; online 2013-09-23]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities.
Thureborn P, Lundin D, Plathan J, ..., Sjöberg BM, Sjöling S
pii: PONE-D-13-23027 pmc: PMC3781128
PLoS ONE 8 (9) e74983 [2013-09-23; online 2013-09-23]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Ebsulfur Is a Benzisothiazolone Cytocidal Inhibitor Targeting the Trypanothione Reductase ofTrypanosoma brucei
Lu J, Vodnala SK, Gustavsson AL, ..., Rottenberg ME, Holmgren A
J. Biol. Chem. 288 (38) 27456-27468 [2013-09-20; online 2013-07-29]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
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Hydrogenosomes in the diplomonad Spironucleus salmonicida.
Jerlström-Hultqvist J, Einarsson E, Xu F, ..., Andersson JO, Svärd SG
pii: ncomms3493 pmc: PMC3778541
Nat Commun 4 (-) 2493 [2013-09-18; online 2013-09-18]
Mass Spectrometry-based Proteomics, Uppsala
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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.
Sabater-Lleal M, Huang J, Chasman D, ..., Hamsten A, O'Donnell CJ
pii: CIRCULATIONAHA.113.002251 pmc: PMC3842025 mid: NIHMS518819
Circulation 128 (12) 1310-1324 [2013-09-17; online 2013-08-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Blood plasma IgG Fc glycans are significantly altered in Alzheimer's disease and progressive mild cognitive impairment.
Lundström SL, Yang H, Lyutvinskiy Y, ..., Soininen H, Zubarev RA
pii: D06G67816GG7R671
J. Alzheimers Dis. 38 (3) 567-579 [2013-09-14; online 2013-09-14]
Advanced Mass Spectrometry Proteomics
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Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis.
Beaudoin M, Goyette P, Boucher G, ..., Daly MJ, Rioux JD
pii: PGENETICS-D-13-00555 pmc: PMC3772057
PLoS Genet. 9 (9) e1003723 [2013-09-12; online 2013-09-12]
Mutation Analysis Facility (MAF)
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A tosyl-activated magnetic bead cellulose as solid support for sensitive protein detection.
Yan J, Horák D, Lenfeld J, Hammond M, Kamali-Moghaddam M
pii: S0168-1656(13)00266-6
J. Biotechnol. 167 (3) 235-240 [2013-09-10; online 2013-07-03]
PLA and Single Cell Proteomics
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The Oct1 homolog Nubbin is a repressor of NF-κB-dependent immune gene expression that increases the tolerance to gut microbiota.
Dantoft W, Davis MM, Lindvall JM, ..., Beskow A, Engström Y
pii: 1741-7007-11-99 pmc: PMC3849502
BMC Biol. 11 (-) 99 [2013-09-06; online 2013-09-06]
Bioinformatics and Expression Analysis (BEA)
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Post-zygotic and inter-individual structural genetic variation in a presumptive enhancer element of the locus between the IL10Rβ and IFNAR1 genes.
Razzaghian HR, Forsberg LA, Prakash KR, ..., Absher D, Dumanski JP
pii: PONE-D-13-04402 pmc: PMC3762855
PLoS ONE 8 (9) e67752 [2013-09-04; online 2013-09-04]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Progesterone receptor negativity is an independent risk factor for relapse in patients with early stage endometrioid endometrial adenocarcinoma.
Huvila J, Talve L, Carpén O, ..., Grénman S, Auranen A
pii: S0090-8258(13)00848-2
Gynecol. Oncol. 130 (3) 463-469 [2013-09-00; online 2013-06-20]
Tissue Profiling
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Autoantibody profiling in multiple sclerosis using arrays of human protein fragments.
Ayoglu B, Häggmark A, Khademi M, ..., Schwenk JM, Nilsson P
pii: M112.026757 pmc: PMC3769337
Mol. Cell Proteomics 12 (9) 2657-2672 [2013-09-00; online 2013-06-05]
Autoimmunity Profiling [Technology development]
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Structural insights into substrate recognition in proton-dependent oligopeptide transporters.
Guettou F, Quistgaard EM, Trésaugues L, ..., Nordlund P, Löw C
pii: embor2013107 pmc: PMC3790050 PDB: 4LEP
EMBO Rep. 14 (9) 804-810 [2013-09-00; online 2013-07-23]
Protein Science Facility (PSF)
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Role of individual MARK isoforms in phosphorylation of tau at Ser²⁶² in Alzheimer's disease.
Gu GJ, Lund H, Wu D, ..., Sunnemark D, Kamali-Moghaddam M
Neuromolecular Med. 15 (3) 458-469 [2013-09-00; online 2013-05-15]
Clinical Biomarkers PLA and Single Cell Proteomics
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Genes identified in Asian SLE GWASs are also associated with SLE in Caucasian populations.
Wang C, Ahlford A, Järvinen TM, ..., Syvänen AC, Sandling JK
pii: ejhg2012277 pmc: PMC3746253
Eur. J. Hum. Genet. 21 (9) 994-999 [2013-09-00; online 2012-12-20]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Multilocus genetic risk scores for coronary heart disease prediction.
Ganna A, Magnusson PKE, Pedersen NL, ..., Hamsten A, Ingelsson E
pii: ATVBAHA.113.301218
Arterioscler. Thromb. Vasc. Biol. 33 (9) 2267-2272 [2013-09-00; online 2013-05-21]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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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.
Paulsson K, Forestier E, Andersen MK, ..., Swedish Cytogenetic Leukemia Study Group (SCLSG) , NOPHO Leukemia Cytogenetic Study Group (NLCSG)
pii: haematol.2013.085852 pmc: PMC3762100
Haematologica 98 (9) 1424-1432 [2013-09-00; online 2013-05-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Identification of candidate oncogenes in human colorectal cancers with microsatellite instability.
Gylfe AE, Kondelin J, Turunen M, ..., Vahteristo P, Aaltonen LA
pii: S0016-5085(13)00747-6
Gastroenterology 145 (3) 540-3.e22 [2013-09-00; online 2013-05-21]
Karolinska High Throughput Center (KHTC)
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Genome-wide analysis shows association of epigenetic changes in regulators of Rab and Rho GTPases with spinal muscular atrophy severity.
Zheleznyakova GY, Voisin S, Kiselev AV, ..., Baranov VS, Schiöth HB
pii: ejhg2012293 pmc: PMC3746269
Eur. J. Hum. Genet. 21 (9) 988-993 [2013-09-00; online 2013-01-10]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
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Phylogeography of willow grouse (Lagopus lagopus) in the Arctic: taxonomic discordance as inferred from molecular data
Höglund J, Wang B, Axelsson T, Quintela M
Biol J Linn Soc Lond 110 (1) 77-90 [2013-09-00; online 2013-05-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.
Cross-Disorder Group of the Psychiatric Genomics Consortium N, Lee SH, Ripke S, ..., Wray NR, International Inflammatory Bowel Disease Genetics Consortium (IIBDGC) N
pii: ng.2711 pmc: PMC3800159 mid: NIHMS516146
Nat. Genet. 45 (9) 984-994 [2013-09-00; online 2013-08-13]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Glutamatergic GRIN2B and polyaminergic ODC1 genes in suicide attempts: associations and gene-environment interactions with childhood/adolescent physical assault.
Sokolowski M, Ben-Efraim YJ, Wasserman J, Wasserman D
pii: mp2012112
Mol. Psychiatry 18 (9) 985-992 [2013-09-00; online 2012-08-02]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Global DNA hypermethylation is associated with high serum levels of persistent organic pollutants in an elderly population.
Lind L, Penell J, Luttropp K, ..., Ingelsson E, Lind PM
pii: S0160-4120(13)00152-9
Environ Int 59 (-) 456-461 [2013-09-00; online 2013-08-13]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins.
Demina IV, Persson T, Santos P, Plaszczyca M, Pawlowski K
pii: PONE-D-13-21713 pmc: PMC3756986
PLoS ONE 8 (8) e72442 [2013-08-29; online 2013-08-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Genome-wide transcriptional analysis of Drosophila larvae infected by entomopathogenic nematodes shows involvement of complement, recognition and extracellular matrix proteins.
Arefin B, Kucerova L, Dobes P, ..., Zurovec M, Theopold U
pii: 000353734
J Innate Immun 6 (2) 192-204 [2013-08-27; online 2013-08-27]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Structure-Guided Design of Novel Thiazolidine Inhibitors ofO-Acetyl Serine Sulfhydrylase from Mycobacterium tuberculosis
Poyraz Ö, Jeankumar VU, Saxena S, ..., Sriram D, Schneider G
J. Med. Chem. 56 (16) 6457-6466 [2013-08-22; online 2013-08-22]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
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Genome-wide relatedness of Treponema pedis, from gingiva and necrotic skin lesions of pigs, with the human oral pathogen Treponema denticola.
Svartström O, Mushtaq M, Pringle M, Segerman B
pii: PONE-D-13-11951 pmc: PMC3747143
PLoS ONE 8 (8) e71281 [2013-08-19; online 2013-08-19]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Automated serial extraction of DNA and RNA from biobanked tissue specimens.
Mathot L, Wallin M, Sjöblom T
pii: 1472-6750-13-66 pmc: PMC3751724
BMC Biotechnol. 13 (-) 66 [2013-08-19; online 2013-08-19]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
PARP inhibitor with selectivity toward ADP-ribosyltransferase ARTD3/PARP3.
Lindgren AE, Karlberg T, Thorsell AG, ..., Elofsson M, Schüler H
PDB: 4GV0 PDB: 4GV2 PDB: 4GV4 PDB: 4GV7
ACS Chem. Biol. 8 (8) 1698-1703 [2013-08-16; online 2013-06-08]
Protein Science Facility (PSF)
PubMed DOI Crossref
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites.
Yan J, Enge M, Whitington T, ..., Taipale M, Taipale J
pii: S0092-8674(13)00942-2 GEO: GSE48448 GEO: GSE49402
Cell 154 (4) 801-813 [2013-08-15; online 2013-08-21]
Bioinformatics and Expression Analysis (BEA) Karolinska High Throughput Center (KHTC)
PubMed DOI Crossref
Investigation of six testicular germ cell tumor susceptibility genes suggests a parent-of-origin effect in SPRY4.
Karlsson R, Andreassen KE, Kristiansen W, ..., Grotmol T, Wiklund F
pii: ddt188
Hum. Mol. Genet. 22 (16) 3373-3380 [2013-08-15; online 2013-05-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The STK33-linked SNP rs4929949 is associated with obesity and BMI in two independent cohorts of Swedish and Greek children.
Rask-Andersen M, Moschonis G, Chrousos GP, ..., Fredriksson R, Schiöth HB
pii: PONE-D-13-07092 pmc: PMC3744548
PLoS ONE 8 (8) e71353 [2013-08-15; online 2013-08-15]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Structural and biophysical characterization of the cytoplasmic domains of human BAP29 and BAP31.
Quistgaard EM, Löw C, Moberg P, ..., Maddi K, Nordlund P
pii: PONE-D-13-14318 pmc: PMC3742741 PDB: 4JZL PDB: 4JZP
PLoS ONE 8 (8) e71111 [2013-08-13; online 2013-08-13]
Advanced Mass Spectrometry Proteomics Protein Science Facility (PSF)
PubMed DOI Crossref
Meta-analysis of gene-level associations for rare variants based on single-variant statistics.
Hu Y, Berndt SI, Gustafsson S, ..., Ingelsson E, Lin D
pii: S0002-9297(13)00280-2 pmc: PMC3738834
Am. J. Hum. Genet. 93 (2) 236-248 [2013-08-08; online 2013-07-31]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Temperament and character in the Child and Adolescent Twin Study in Sweden (CATSS): comparison to the general population, and genetic structure analysis.
Garcia D, Lundström S, Brändström S, ..., Nilsson T, Anckarsäter H
pii: PONE-D-13-13063 pmc: PMC3734246
PLoS ONE 8 (8) e70475 [2013-08-05; online 2013-08-05]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
An Integratedin VitroModel for Simultaneous Assessment of Drug Uptake, Metabolism, and Efflux
Neve EPA, Artursson P, Ingelman-Sundberg M, Karlgren M
Mol. Pharmaceutics 10 (8) 3152-3163 [2013-08-05; online 2013-08-05]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
PubMed DOI Crossref
Improved production of membrane proteins in Escherichia coli by selective codon substitutions.
Nørholm MH, Toddo S, Virkki MT, ..., von Heijne G, Daley DO
pii: S0014-5793(13)00442-0
FEBS Lett. 587 (15) 2352-2358 [2013-08-02; online 2013-06-19]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Chronic airway-induced allergy in mice modifies gene expression in the brain toward insulin resistance and inflammatory responses.
Sarlus H, Wang X, Cedazo-Minguez A, Schultzberg M, Oprica M
pii: 1742-2094-10-99 pmc: PMC3750454
J Neuroinflammation 10 (-) 99 [2013-08-01; online 2013-08-01]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
Identification of adenovirus-encoded small RNAs by deep RNA sequencing.
Zhao H, Chen M, Pettersson U
pii: S0042-6822(13)00200-6
Virology 442 (2) 148-155 [2013-08-01; online 2013-05-11]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Antibody-based profiling of cerebrospinal fluid within multiple sclerosis.
Häggmark A, Byström S, Ayoglu B, ..., Schwenk JM, Nilsson P
Proteomics 13 (15) 2256-2267 [2013-08-00; online 2013-05-23]
Plasma Profiling [Collaborative]
DOI Crossref
Molecular identification and phylogenic analysis by sequencing the rDNA of copper-tolerant soft-rot Phialophora spp.
Karunasekera H, Daniel G
International Biodeterioration & Biodegradation 82 (-) 45-52 [2013-08-00; online 2013-08-00]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Genetic variation in the dimethylarginine dimethylaminohydrolase 1 gene (DDAH1) is related to asymmetric dimethylarginine (ADMA) levels, but not to endothelium-dependent vasodilation.
Lind L, Ingelsson E, Kumar J, ..., Axelsson T, Teerlink T
pii: 1358863X13496488
Vasc Med 18 (4) 192-199 [2013-08-00; online 2013-07-31]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
DOI Crossref
Design of a Highly Selective and Potent Class of Non-planar Estrogen Receptor β Agonists
Sundén H, Ma JN, Hansen LK, ..., Burstein ES, Olsson R
ChemMedChem 8 (8) 1283-1294 [2013-08-00; online 2013-06-19]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
PubMed DOI Crossref
Expression of chondroitin/dermatan sulfate glycosyltransferases during early zebrafish development.
Filipek-Górniok B, Holmborn K, Haitina T, ..., Kreuger J, Ledin J
Dev. Dyn. 242 (8) 964-975 [2013-08-00; online 2013-05-25]
Genome Engineering Zebrafish
PubMed DOI Crossref
Synergistic interactions between camptothecin and EGFR or RAC1 inhibitors and between imatinib and Notch signaling or RAC1 inhibitors in glioblastoma cell lines.
Sooman L, Ekman S, Andersson C, ..., Lennartsson J, Gullbo J
Cancer Chemother. Pharmacol. 72 (2) 329-340 [2013-08-00; online 2013-06-06]
Array and Analysis Facility
PubMed DOI Crossref
High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation.
Anandapadamanaban M, Andresen C, Helander S, ..., Moche M, Sunnerhagen M
pii: nsmb.2611 pmc: PMC4972576 mid: CAMS4086 PDB: 4B0A
Nat. Struct. Mol. Biol. 20 (8) 1008-1014 [2013-08-00; online 2013-07-16]
Protein Science Facility (PSF)
PubMed DOI Crossref
A novel intellectual disability syndrome caused by GPI anchor deficiency due to homozygous mutations in PIGT.
Kvarnung M, Nilsson D, Lindstrand A, ..., Nordenskjöld M, Nordgren A
pii: jmedgenet-2013-101654
J. Med. Genet. 50 (8) 521-528 [2013-08-00; online 2013-05-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Tumour expression of bladder cancer-associated urinary proteins.
Lindén M, Segersten U, Runeson M, ..., Lind SB, Malmström PU
BJU Int. 112 (3) 407-415 [2013-08-00; online 2013-03-09]
Tissue Profiling
PubMed DOI Crossref
In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models.
Lyutvinskiy Y, Yang H, Rutishauser D, Zubarev RA
pii: O112.023804 pmc: PMC3734588
Mol. Cell Proteomics 12 (8) 2324-2331 [2013-08-00; online 2013-04-17]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.
Andersson KM, Meerupati T, Levander F, ..., Ahrén D, Tunlid A
pii: AEM.01390-13 pmc: PMC3754708
Appl. Environ. Microbiol. 79 (16) 4993-5004 [2013-08-00; online 2013-06-19]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
New viruses in veterinary medicine, detected by metagenomic approaches.
Belák S, Karlsson OE, Blomström AL, Berg M, Granberg F
pii: S0378-1135(13)00074-6
Vet. Microbiol. 165 (1-2) 95-101 [2013-07-26; online 2013-02-23]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Gene × physical activity interactions in obesity: combined analysis of 111,421 individuals of European ancestry.
Ahmad S, Rukh G, Varga TV, ..., Orho-Melander M, Franks PW
pii: PGENETICS-D-12-03208 pmc: PMC3723486
PLoS Genet. 9 (7) e1003607 [2013-07-25; online 2013-07-25]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
NCR3/NKp30 contributes to pathogenesis in primary Sjogren's syndrome.
Rusakiewicz S, Nocturne G, Lazure T, ..., Zitvogel L, Mariette X
pii: 5/195/195ra96 pmc: PMC4237161 mid: NIHMS638202
Sci Transl Med 5 (195) 195ra96 [2013-07-24; online 2013-07-26]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer.
Johansson HJ, Sanchez BC, Mundt F, ..., Linderholm BK, Lehtiö J
pii: ncomms3175 pmc: PMC3759040
Nat Commun 4 (-) 2175 [2013-07-23; online 2013-07-23]
Drug Discovery and Development (DDD) [Collaborative]
PubMed DOI Crossref
Genetic variants in hormone-related genes and risk of breast cancer.
Clendenen T, Zeleniuch-Jacquotte A, Wirgin I, ..., Shore RE, Chen Y
pii: PONE-D-13-05381 pmc: PMC3720532
PLoS ONE 8 (7) e69367 [2013-07-23; online 2013-07-23]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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SNP in TXNRD2 associated with radiation-induced fibrosis: a study of genetic variation in reactive oxygen species metabolism and signaling.
Edvardsen H, Landmark-Høyvik H, Reinertsen KV, ..., Fosså SD, Kristensen VN
pii: S0360-3016(13)00217-4
Int. J. Radiat. Oncol. Biol. Phys. 86 (4) 791-799 [2013-07-15; online 2013-04-20]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Novel signatures of cancer-associated fibroblasts.
Bozóky B, Savchenko A, Csermely P, ..., Székely L, Klein G
Int. J. Cancer 133 (2) 286-293 [2013-07-15; online 2013-01-16]
Tissue Profiling
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Prevalence, comorbidity and heritability of hoarding symptoms in adolescence: a population based twin study in 15-year olds.
Ivanov VZ, Mataix-Cols D, Serlachius E, ..., Långström N, Rück C
pii: PONE-D-13-13943 pmc: PMC3707873
PLoS ONE 8 (7) e69140 [2013-07-10; online 2013-07-10]
Mutation Analysis Facility (MAF)
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Amyloid-β protofibrils: size, morphology and synaptotoxicity of an engineered mimic.
Dubnovitsky A, Sandberg A, Rahman MM, ..., Lendel C, Härd T
pii: PONE-D-13-01978 pmc: PMC3699592
PLoS ONE 8 (7) e66101 [2013-07-02; online 2013-07-02]
Mass Spectrometry-based Proteomics, Uppsala
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Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.
Cousminer DL, Berry DJ, Timpson NJ, ..., Widén E, Early Growth Genetics (EGG) Consortium
pii: ddt104 pmc: PMC3674797
Hum. Mol. Genet. 22 (13) 2735-2747 [2013-07-01; online 2013-02-27]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Active nitrogen-fixing heterotrophic bacteria at and below the chemocline of the central Baltic Sea.
Farnelid H, Bentzon-Tilia M, Andersson AF, ..., Jürgens K, Riemann L
pii: ismej201326 pmc: PMC3695292
ISME J 7 (7) 1413-1423 [2013-07-00; online 2013-03-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Family-based study of HTR2A in suicide attempts: observed gene, gene × environment and parent-of-origin associations.
Ben-Efraim YJ, Wasserman D, Wasserman J, Sokolowski M
pii: mp201286
Mol. Psychiatry 18 (7) 758-766 [2013-07-00; online 2012-07-04]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Republished: Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime.
Forsberg LA, Absher D, Dumanski JP
pii: postgradmedj-2012-101322rep pmc: PMC3711362
Postgrad Med J 89 (1053) 417-426 [2013-07-00; online 2013-06-20]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Computational Prospecting for Drug–Transporter Interactions
Matsson P, Artursson P
Clin Pharmacol Ther 94 (1) 30-32 [2013-07-00; online 2013-04-02]
Chemical Biology Consortium Sweden (CBCS) [Technology development]
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Massive functional mapping of a 5'-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing.
Holmqvist E, Reimegård J, Wagner EG
pii: gkt267 pmc: PMC3695526
Nucleic Acids Res. 41 (12) e122 [2013-07-00; online 2013-04-24]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Somatic mutations in H-RAS in sporadic pheochromocytoma and paraganglioma identified by exome sequencing.
Crona J, Delgado Verdugo A, Maharjan R, ..., Hellman P, Björklund P
pii: jc.2012-4257
J. Clin. Endocrinol. Metab. 98 (7) E1266-E1271 [2013-07-00; online 2013-05-04]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Estrogen receptor β expression induces changes in the microRNA pool in human colon cancer cells.
Edvardsson K, Nguyen-Vu T, Kalasekar SM, ..., Gustafsson JÅ, Williams C
pii: bgt067
Carcinogenesis 34 (7) 1431-1441 [2013-07-00; online 2013-02-26]
Tissue Profiling
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Implications of baseline polymorphisms for potential resistance to NS3 protease inhibitors in Hepatitis C virus genotypes 1a, 2b and 3a.
Palanisamy N, Danielsson A, Kokkula C, ..., Duberg AS, Lennerstrand J
pii: S0166-3542(13)00117-4
Antiviral Res. 99 (1) 12-17 [2013-07-00; online 2013-05-08]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
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Response of Acidithiobacillus caldus toward suboptimal pH conditions.
Mangold S, Rao Jonna V, Dopson M
Extremophiles 17 (4) 689-696 [2013-07-00; online 2013-05-29]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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Family-based study of AVPR1B association and interaction with stressful life events on depression and anxiety in suicide attempts.
Ben-Efraim YJ, Wasserman D, Wasserman J, Sokolowski M
pii: npp201349 pmc: PMC3682145
Neuropsychopharmacology 38 (8) 1504-1511 [2013-07-00; online 2013-02-21]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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CDK-mediated activation of the SCF(FBXO) (28) ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer.
Cepeda D, Ng HF, Sharifi HR, ..., Larsson LG, Sangfelt O
pmc: PMC3721474
EMBO Mol Med 5 (7) 1067-1086 [2013-07-00; online 2013-06-19]
Tissue Profiling
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Clinical depression, antidepressant use and risk of future cardiovascular disease.
Rahman I, Humphreys K, Bennet AM, ..., Pedersen NL, Magnusson PK
Eur. J. Epidemiol. 28 (7) 589-595 [2013-07-00; online 2013-07-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Cenani-Lenz syndrome restricted to limb and kidney anomalies associated with a novel LRP4 missense mutation.
Khan TN, Klar J, Ali Z, ..., Baig SM, Dahl N
pii: S1769-7212(13)00091-8
Eur J Med Genet 56 (7) 371-374 [2013-07-00; online 2013-05-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides.
Ducani C, Kaul C, Moche M, Shih WM, Högberg B
pii: nmeth.2503 pmc: PMC3843646 mid: NIHMS528250 PDB: 4B8D
Nat. Methods 10 (7) 647-652 [2013-07-00; online 2013-06-04]
Protein Science Facility (PSF)
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Unbiased approach for virus detection in skin lesions.
Bzhalava D, Johansson H, Ekström J, ..., Forslund O, Dillner J
pii: PONE-D-12-36687 pmc: PMC3696016
PLoS ONE 8 (6) e65953 [2013-06-28; online 2013-06-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan.
Johansson A, Enroth S, Gyllensten U
pii: PONE-D-13-02458 pmc: PMC3695075
PLoS ONE 8 (6) e67378 [2013-06-27; online 2013-06-27]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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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.
Fransson R, Sköld C, Kratz JM, ..., Hallberg M, Sandström A
J. Med. Chem. 56 (12) 4953-4965 [2013-06-27; online 2013-06-06]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
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The crystal structure of the lumenal domain of Erv41p, a protein involved in transport between the endoplasmic reticulum and Golgi apparatus.
Biterova EI, Svärd M, Possner DD, Guy JE
pii: S0022-2836(13)00173-3 PDB: 3ZLC
J. Mol. Biol. 425 (12) 2208-2218 [2013-06-26; online 2013-03-26]
Protein Science Facility (PSF)
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The role of adiposity in cardiometabolic traits: a Mendelian randomization analysis.
Fall T, Hägg S, Mägi R, ..., Prokopenko I, European Network for Genetic and Genomic Epidemiology (ENGAGE) consortium N
pii: PMEDICINE-D-12-03573 pmc: PMC3692470
PLoS Med. 10 (6) e1001474 [2013-06-25; online 2013-06-25]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data.
Lampa S, Dahlö M, Olason PI, Hagberg J, Spjuth O
pii: 2047-217X-2-9 pmc: PMC3704847
Gigascience 2 (1) 9 [2013-06-25; online 2013-06-25]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates.
Chen MW, Lohkamp B, Schnell R, Lescar J, Schneider G
pii: PONE-D-13-09972 pmc: PMC3689657
PLoS ONE 8 (6) e66936 [2013-06-21; online 2013-06-21]
Protein Science Facility (PSF)
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GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.
Rietveld CA, Medland SE, Derringer J, ..., Cesarini D, Koellinger PD
pii: science.1235488 pmc: PMC3751588 mid: NIHMS495960
Science 340 (6139) 1467-1471 [2013-06-21; online 2013-06-01]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Vandetanib combined with a p38 MAPK inhibitor synergistically reduces glioblastoma cell survival.
Sooman L, Lennartsson J, Gullbo J, ..., Blomquist E, Ekman S
Med. Oncol. 30 (3) 638 [2013-06-20; online 2013-06-20]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Tissue Profiling
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Behavioural and Brain Gene Expression Profiling in Pigs during Tail Biting Outbreaks - Evidence of a Tail Biting Resistant Phenotype.
Brunberg E, Jensen P, Isaksson A, Keeling LJ
pii: PONE-D-12-16862 pmc: PMC3688911
PLoS ONE 8 (6) e66513 [2013-06-18; online 2013-06-18]
Array and Analysis Facility
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Stable isotope labeling methods in protein profiling.
Lengqvist J, Sandberg A
Methods Mol. Biol. 1023 (-) 21-51 [2013-06-15; online 2013-06-15]
Clinical Proteomics Mass spectrometry
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Narrow-range peptide isoelectric focusing as peptide prefractionation method prior to tandem mass spectrometry analysis.
Pernemalm M
Methods Mol. Biol. 1023 (-) 3-11 [2013-06-15; online 2013-06-15]
Clinical Proteomics Mass spectrometry
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Protein quantification by peptide quality control (PQPQ) of shotgun proteomics data.
Forshed J
Methods Mol. Biol. 1023 (-) 149-158 [2013-06-15; online 2013-06-15]
Clinical Proteomics Mass spectrometry
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Comprehensive analysis of MHC ligands in clinical material by immunoaffinity-mass spectrometry.
Kasuga K
Methods Mol. Biol. 1023 (-) 203-218 [2013-06-15; online 2013-06-15]
Clinical Proteomics Mass spectrometry
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Highly multiplexed antibody suspension bead arrays for plasma protein profiling.
Drobin K, Nilsson P, Schwenk JM
Methods Mol. Biol. 1023 (-) 137-145 [2013-06-15; online 2013-06-15]
Plasma Profiling [Technology development]
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Molecular genetics and subjective well-being.
Rietveld CA, Cesarini D, Benjamin DJ, ..., Krueger RF, Bartels M
pii: 1222171110 pmc: PMC3683731
Proc. Natl. Acad. Sci. U.S.A. 110 (24) 9692-9697 [2013-06-11; online 2013-05-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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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.
Lohr M, Edlund K, Botling J, ..., Rahnenführer J, Micke P
pii: S0304-3835(13)00080-3
Cancer Lett. 333 (2) 222-228 [2013-06-10; online 2013-02-02]
Tissue Profiling
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Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP).
Fagerberg L, Oksvold P, Skogs M, ..., von Feilitzen K, Uhlén M
J. Proteome Res. 12 (6) 2439-2448 [2013-06-07; online 2013-01-02]
Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling
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Promoter DNA methylation pattern identifies prognostic subgroups in childhood T-cell acute lymphoblastic leukemia.
Borssén M, Palmqvist L, Karrman K, ..., Roos G, Degerman S
pii: PONE-D-12-31749 pmc: PMC3675104
PLoS ONE 8 (6) e65373 [2013-06-06; online 2013-06-06]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Rapid Measurement of Intracellular Unbound Drug Concentrations
Mateus A, Matsson P, Artursson P
Mol. Pharmaceutics 10 (6) 2467-2478 [2013-06-03; online 2013-06-03]
Chemical Biology Consortium Sweden (CBCS) [Technology development]
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Next-generation sequencing in the clinical genetic screening of patients with pheochromocytoma and paraganglioma.
Crona J, Verdugo AD, Granberg D, ..., Hellman P, Björklund P
pii: EC130009 pmc: PMC3682230
Endocr Connect 2 (2) 104-111 [2013-06-01; online 2013-05-28]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Parallel visualization of multiple protein complexes in individual cells in tumor tissue.
Leuchowius KJ, Clausson CM, Grannas K, ..., Landegren U, Söderberg O
pii: O112.023374 pmc: PMC3675814
Mol. Cell Proteomics 12 (6) 1563-1571 [2013-06-00; online 2013-02-26]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure PLA and Single Cell Proteomics
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Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.
den Hoed M, Eijgelsheim M, Esko T, ..., Samani NJ, Loos RJF
pii: ng.2610 pmc: PMC3696959 mid: NIHMS473857
Nat. Genet. 45 (6) 621-631 [2013-06-00; online 2013-04-16]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Coronary heart disease in systemic lupus erythematosus is associated with interferon regulatory factor-8 gene variants.
Leonard D, Svenungsson E, Sandling JK, ..., Syvänen AC, Rönnblom L
pii: CIRCGENETICS.113.000044
Circ Cardiovasc Genet 6 (3) 255-263 [2013-06-00; online 2013-05-11]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species.
Källman T, Chen J, Gyllenstrand N, Lagercrantz U
pii: pp.113.214643 pmc: PMC3668067 GENBANK: ACN49932 GENBANK: TC161203 GEO: GSE28755
Plant Physiol. 162 (2) 741-754 [2013-06-00; online 2013-04-13]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.
Geiger T, Velic A, Macek B, ..., Cox J, Mann M
pii: M112.024919 pmc: PMC3675825
Mol. Cell Proteomics 12 (6) 1709-1722 [2013-06-00; online 2013-02-26]
Cell Profiling Tissue Profiling
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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.
Prieto P, Kinsner-Ovaskainen A, Stanzel S, ..., Zurbano MJ, Kopp-Schneider A
pii: S0887-2333(12)00217-2
Toxicol In Vitro 27 (4) 1357-1376 [2013-06-00; online 2012-08-28]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
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Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing.
Nong RY, Wu D, Yan J, ..., Landegren U, Darmanis S
pii: nprot.2013.070
Nat Protoc 8 (6) 1234-1248 [2013-06-00; online 2013-05-30]
PLA and Single Cell Proteomics
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Contribution of IKBKE and IFIH1 gene variants to SLE susceptibility.
Wang C, Ahlford A, Laxman N, ..., Rönnblom L, Syvänen AC
pii: gene20139
Genes Immun. 14 (4) 217-222 [2013-06-00; online 2013-03-29]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Stepping-stone expansion and habitat loss explain a peculiar genetic structure and distribution of a forest insect.
Cassel-Lundhagen A, Ronnås C, Battisti A, Wallén J, Larsson S
GENBANK: JX243015 GENBANK: JX243021
Mol. Ecol. 22 (12) 3362-3375 [2013-06-00; online 2013-05-31]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
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Sortilin receptor 1 predicts longitudinal cognitive change.
Reynolds CA, Zavala C, Gatz M, ..., Prince JA, Pedersen NL
pii: S0197-4580(12)00621-5 pmc: PMC3839667 mid: NIHMS435934
Neurobiol. Aging 34 (6) 1710.e11-1710.e18 [2013-06-00; online 2013-01-16]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Gambogic acid is cytotoxic to cancer cells through inhibition of the ubiquitin-proteasome system.
Felth J, Lesiak-Mieczkowska K, D'Arcy P, ..., Fryknäs M, Rickardson L
Invest New Drugs 31 (3) 587-598 [2013-06-00; online 2012-11-28]
Array and Analysis Facility
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Exome sequencing in diagnostic evaluation of colorectal cancer predisposition in young patients.
Tanskanen T, Gylfe AE, Katainen R, ..., Vahteristo P, Aaltonen LA
Scand. J. Gastroenterol. 48 (6) 672-678 [2013-06-00; online 2013-04-03]
Karolinska High Throughput Center (KHTC)
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Circadian regulation of melanization and prokineticin homologues is conserved in the brain of freshwater crayfish and zebrafish.
Noonin C, Watthanasurorot A, Winberg S, Söderhäll I
pii: S0145-305X(13)00057-8
Dev. Comp. Immunol. 40 (2) 218-226 [2013-06-00; online 2013-03-19]
Genome Engineering Zebrafish NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase.
Lim SM, Chen D, Teo H, ..., Pervushin K, Nordlund P
pii: jlr.M035410 pmc: PMC3646464
J. Lipid Res. 54 (6) 1630-1643 [2013-06-00; online 2013-03-26]
Protein Science Facility (PSF)
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Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits.
Randall JC, Winkler TW, Kutalik Z, ..., North KE, Heid IM
pii: PGENETICS-D-12-01098 pmc: PMC3674993
PLoS Genet. 9 (6) e1003500 [2013-06-00; online 2013-06-06]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Structural basis for substrate transport in the GLUT-homology family of monosaccharide transporters.
Quistgaard EM, Löw C, Moberg P, Trésaugues L, Nordlund P
pii: nsmb.2569 PDB: 4JA3 PDB: 4JA4
Nat. Struct. Mol. Biol. 20 (6) 766-768 [2013-06-00; online 2013-04-30]
Protein Science Facility (PSF)
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The impact of splicing on protein domain architecture.
Light S, Elofsson A
pii: S0959-440X(13)00043-2
Curr. Opin. Struct. Biol. 23 (3) 451-458 [2013-06-00; online 2013-04-09]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
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Prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in healthy Swedish preschool children.
Kaarme J, Molin Y, Olsen B, Melhus A
Acta Paediatr. 102 (6) 655-660 [2013-06-00; online 2013-02-20]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
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No association of primary Sjögren's syndrome with Fcγ receptor gene variants.
Haldorsen K, Appel S, Le Hellard S, ..., Jonsson R, Bolstad AI
pii: gene201312
Genes Immun. 14 (4) 234-237 [2013-06-00; online 2013-04-05]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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The Norway spruce genome sequence and conifer genome evolution.
Nystedt B, Street NR, Wetterbom A, ..., Lundeberg J, Jansson S
pii: nature12211
Nature 497 (7451) 579-584 [2013-05-30; online 2013-05-24]
Bioinformatics Compute and Storage Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria.
Herlemann DP, Lundin D, Labrenz M, ..., Aspeborg H, Andersson AF
pii: mBio.00569-12 pmc: PMC3663571 GENBANK: ADX05696 GENBANK: AF217460 GENBANK: AF217461 GENBANK: AF217462
MBio 4 (3) e00569-e00512 [2013-05-28; online 2013-05-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Dynamic gradients of an intermediate filament-like cytoskeleton are recruited by a polarity landmark during apical growth.
Fuchino K, Bagchi S, Cantlay S, ..., Flärdh K, Ausmees N
pii: 1305358110 pmc: PMC3666699
Proc. Natl. Acad. Sci. U.S.A. 110 (21) E1889-E1897 [2013-05-21; online 2013-05-04]
PLA and Single Cell Proteomics
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A texture based pattern recognition approach to distinguish melanoma from non-melanoma cells in histopathological tissue microarray sections.
Rexhepaj E, Agnarsdóttir M, Bergman J, ..., Lundberg E, Ponten F
pii: PONE-D-12-33946 pmc: PMC3656869
PLoS ONE 8 (5) e62070 [2013-05-17; online 2013-05-17]
Cell Profiling Tissue Profiling
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Adaptive mutations and replacements of virulence traits in the Escherichia coli O104:H4 outbreak population.
Guy L, Jernberg C, Arvén Norling J, ..., Engstrand L, Andersson SGE
pii: PONE-D-13-05699 pmc: PMC3651199
PLoS ONE 8 (5) e63027 [2013-05-10; online 2013-05-10]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Age dependence of tumor genetics in unfavorable neuroblastoma: arrayCGH profiles of 34 consecutive cases, using a Swedish 25-year neuroblastoma cohort for validation.
Cetinkaya C, Martinsson T, Sandgren J, ..., Díaz de Ståhl T, Hedborg F
pii: 1471-2407-13-231 pmc: PMC3664071
BMC Cancer 13 (-) 231 [2013-05-09; online 2013-05-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1.
Arczewska KD, Tomazella GG, Lindvall JM, ..., Thiede B, Nilsen H
pii: gkt225 pmc: PMC3664812
Nucleic Acids Res. 41 (10) 5368-5381 [2013-05-01; online 2013-04-13]
Bioinformatics and Expression Analysis (BEA)
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Genome-wide association study of susceptibility loci for cervical cancer.
Chen D, Juko-Pecirep I, Hammer J, ..., Wilander E, Gyllensten U
pii: djt051
J. Natl. Cancer Inst. 105 (9) 624-633 [2013-05-01; online 2013-03-14]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
The adenovirus VA RNA-derived miRNAs are not essential for lytic virus growth in tissue culture cells.
Kamel W, Segerman B, Öberg D, Punga T, Akusjärvi G
pii: gkt172 pmc: PMC3643585
Nucleic Acids Res. 41 (9) 4802-4812 [2013-05-00; online 2013-03-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Identification of a functional apolipoprotein E promoter polymorphism regulating plasma apolipoprotein E concentration.
Mannila MN, Mahdessian H, Franco-Cereceda A, ..., Hamsten A, van 't Hooft FM
pii: ATVBAHA.112.300353
Arterioscler. Thromb. Vasc. Biol. 33 (5) 1063-1069 [2013-05-00; online 2013-02-23]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Genetic determinants of mortality. Can findings from genome-wide association studies explain variation in human mortality?
Ganna A, Rivadeneira F, Hofman A, ..., Ingelsson E, Tiemeier H
Hum. Genet. 132 (5) 553-561 [2013-05-00; online 2013-01-29]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
Berndt SI, Gustafsson S, Mägi R, ..., Loos RJF, Ingelsson E
pii: ng.2606 pmc: PMC3973018 mid: NIHMS536922
Nat. Genet. 45 (5) 501-512 [2013-05-00; online 2013-04-09]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits.
Hansen K, Perry BA, Dranginis AW, Pfister DH
pii: S1055-7903(13)00051-1
Mol. Phylogenet. Evol. 67 (2) 311-335 [2013-05-00; online 2013-02-14]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
An adaptive alignment algorithm for quality-controlled label-free LC-MS.
Sandin M, Ali A, Hansson K, ..., Resjö S, Levander F
pii: O112.021907 pmc: PMC3650348
Mol. Cell Proteomics 12 (5) 1407-1420 [2013-05-00; online 2013-01-12]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions.
Pettersson BMF, Nitharwal RG, Das S, ..., Bhattacharya A, Kirsebom LA
FEMS Microbiol. Lett. 342 (2) 98-105 [2013-05-00; online 2013-03-14]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Membrane protein shaving with thermolysin can be used to evaluate topology predictors.
Bendz M, Skwark M, Nilsson D, ..., Käll L, Elofsson A
Proteomics 13 (9) 1467-1480 [2013-05-00; online 2013-03-21]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Identification of acetate-oxidizing bacteria in a coastal marine surface sediment by RNA-stable isotope probing in anoxic slurries and intact cores.
Vandieken V, Thamdrup B
FEMS Microbiol. Ecol. 84 (2) 373-386 [2013-05-00; online 2013-01-08]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide analysis in German shepherd dogs reveals association of a locus on CFA 27 with atopic dermatitis.
Tengvall K, Kierczak M, Bergvall K, ..., Hedhammar Å, Lindblad-Toh K
pii: PGENETICS-D-12-01656 pmc: PMC3649999
PLoS Genet. 9 (5) e1003475 [2013-05-00; online 2013-05-09]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
The combined effects of single-nucleotide polymorphisms, tobacco products, and ethanol on normal resting blood mononuclear cells.
Cederblad L, Thunberg U, Engström M, ..., Rutqvist LE, Laytragoon-Lewin N
pii: nts207
Nicotine Tob. Res. 15 (5) 890-895 [2013-05-00; online 2012-10-09]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins.
Light S, Sagit R, Ekman D, Elofsson A
pii: S1570-9639(13)00007-1
Biochim. Biophys. Acta 1834 (5) 890-897 [2013-05-00; online 2013-01-22]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Variation in genes in the endothelin pathway and endothelium-dependent and endothelium-independent vasodilation in an elderly population.
Lind L, Syvänen AC, Axelsson T, ..., Hägg S, Larsson A
Acta Physiol (Oxf) 208 (1) 88-94 [2013-05-00; online 2013-01-23]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Comprehensive analysis of copy number variation in monozygotic twins discordant for bipolar disorder or schizophrenia.
Bloom RJ, Kähler AK, Collins AL, ..., Hultman C, Sullivan PF
pii: S0920-9964(13)00113-8 pmc: PMC3650833 mid: NIHMS450150
Schizophr. Res. 146 (1-3) 289-290 [2013-05-00; online 2013-03-20]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Employment of complementary dissociation techniques for body fluid characterization and biomarker discovery.
Good DM, Rutishauser D
Methods Mol. Biol. 1002 (-) 223-232 [2013-04-30; online 2013-04-30]
Advanced Mass Spectrometry Proteomics
PubMed DOI Crossref
SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals.
Oosterveen T, Kurdija S, Ensterö M, ..., Muhr J, Ericson J
pii: 1220010110 pmc: PMC3645538
Proc. Natl. Acad. Sci. U.S.A. 110 (18) 7330-7335 [2013-04-30; online 2013-04-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model.
Danielsson F, Skogs M, Huss M, ..., Uhlén M, Lundberg E
pii: 1216436110 pmc: PMC3637701
Proc. Natl. Acad. Sci. U.S.A. 110 (17) 6853-6858 [2013-04-23; online 2013-04-10]
Cell Profiling
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Expression of fusion proteins of Aspergillus terreus reveals a novel allene oxide synthase.
Hoffmann I, Jernerén F, Oliw EH
pii: M113.458257 pmc: PMC3630850
J. Biol. Chem. 288 (16) 11459-11469 [2013-04-19; online 2013-03-13]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Renal sensory and sympathetic nerves reinnervate the kidney in a similar time-dependent fashion after renal denervation in rats.
Mulder J, Hökfelt T, Knuepfer MM, Kopp UC
pii: ajpregu.00599.2012 pmc: PMC3627950
Am. J. Physiol. Regul. Integr. Comp. Physiol. 304 (8) R675-R682 [2013-04-15; online 2013-02-15]
Fluorescence Tissue Profiling
PubMed DOI Crossref
Eating problems and overlap with ADHD and autism spectrum disorders in a nationwide twin study of 9- and 12-year-old children.
Råstam M, Täljemark J, Tajnia A, ..., Anckarsäter H, Kerekes N
pmc: PMC3654255
ScientificWorldJournal 2013 (-) 315429 [2013-04-15; online 2013-04-15]
Mutation Analysis Facility (MAF)
DOI Crossref
Ion Torrent sequencing and pipeline assembly of the first genome sequence of a mesophilic syntrophic acetate oxidizing bacterium (SAOB)
Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B
EMBnet j. 19 (A) 60 [2013-04-08; online 2013-04-08]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
DOI Crossref
Metagenomics sample preparation and sequencing.
Karlsson OE, Norling M, Bongcam-Rudloff E
EMBnet j. 19 (A) 55 [2013-04-08; online 2013-04-08]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
European H16N3 gull influenza virus attaches to the human respiratory tract and eye.
Lindskog C, Ellström P, Olsen B, ..., Kuiken T, Jourdain E
pii: PONE-D-12-38518 pmc: PMC3620227
PLoS ONE 8 (4) e60757 [2013-04-08; online 2013-04-08]
Tissue Profiling
DOI Crossref
Viral Metagenomics – New applications for the broad-range detection of viromes in veterinary and public health settings
Karlsson OE, Norling M, Granberg F, Belák S, Bongcam-Rudloff E
EMBnet j. 19 (A) 21 [2013-04-08; online 2013-04-08]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
The molecular genetic architecture of self-employment.
van der Loos MJHM, Rietveld CA, Eklund N, ..., Hofman A, Thurik AR
pii: PONE-D-12-39282 pmc: PMC3617140
PLoS ONE 8 (4) e60542 [2013-04-04; online 2013-04-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Systematic antibody generation and validation via tissue microarray technology leading to identification of a novel protein prognostic panel in breast cancer.
O Leary PC, Penny SA, Dolan RT, ..., Jirström K, Gallagher WM
pii: 1471-2407-13-175 pmc: PMC3668187
BMC Cancer 13 (-) 175 [2013-04-02; online 2013-04-02]
Tissue Profiling
PubMed DOI Crossref
Genetic determinants of dabigatran plasma levels and their relation to bleeding.
Paré G, Eriksson N, Lehr T, ..., Yusuf S, Wallentin L
pii: CIRCULATIONAHA.112.001233 ClinicalTrials.gov: NCT00262600
Circulation 127 (13) 1404-1412 [2013-04-02; online 2013-03-08]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Interaction between retinoid acid receptor-related orphan receptor alpha (RORA) and neuropeptide S receptor 1 (NPSR1) in asthma.
Acevedo N, Sääf A, Söderhäll C, ..., Kere J, Pulkkinen V
pii: PONE-D-12-35098 pmc: PMC3615072
PLoS ONE 8 (4) e60111 [2013-04-02; online 2013-04-02]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
β-thymosins and hemocyte homeostasis in a crustacean.
Saelee N, Noonin C, Nupan B, ..., Söderhäll K, Söderhäll I
pii: PONE-D-13-03793 pmc: PMC3614969
PLoS ONE 8 (4) e60974 [2013-04-02; online 2013-04-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
RNA-binding protein QKI regulates Glial fibrillary acidic protein expression in human astrocytes.
Radomska KJ, Halvardson J, Reinius B, ..., Feuk L, Jazin E
pii: dds553
Hum. Mol. Genet. 22 (7) 1373-1382 [2013-04-01; online 2013-01-17]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
The transporter ABCB7 is a mediator of the phenotype of acquired refractory anemia with ring sideroblasts.
Nikpour M, Scharenberg C, Liu A, ..., Grandien A, Hellström-Lindberg E
pii: leu2012298 pmc: PMC3794445 mid: EMS53907
Leukemia 27 (4) 889-896 [2013-04-00; online 2012-10-17]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Comparative genomics of Wolbachia and the bacterial species concept.
Ellegaard KM, Klasson L, Näslund K, Bourtzis K, Andersson SG
pii: PGENETICS-D-12-02380 pmc: PMC3616963
PLoS Genet. 9 (4) e1003381 [2013-04-00; online 2013-04-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Lack of dosage compensation accompanies the arrested stage of sex chromosome evolution in ostriches.
Adolfsson S, Ellegren H
pii: mst009 pmc: PMC3603317
Mol. Biol. Evol. 30 (4) 806-810 [2013-04-00; online 2013-01-19]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
DOI Crossref
Degradation of Scots pine and beech wood exposed in four test fields used for testing of wood preservatives
Råberg U, Terziev N, Daniel G
International Biodeterioration & Biodegradation 79 (-) 20-27 [2013-04-00; online 2013-04-00]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Hereditary uveal melanoma: a report of a germline mutation in BAP1.
Höiom V, Edsgärd D, Helgadottir H, ..., Emanuelsson O, Hansson J
Genes Chromosomes Cancer 52 (4) 378-384 [2013-04-00; online 2013-01-24]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Identification of seven loci affecting mean telomere length and their association with disease.
Codd V, Nelson CP, Albrecht E, ..., van der Harst P, Samani NJ
pii: ng.2528 pmc: PMC4006270 mid: NIHMS571267
Nat. Genet. 45 (4) 422-7, 427e1-2 [2013-04-00; online 2013-03-29]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Modelling the effects of dispersal mechanisms and hydrodynamic regimes upon the structure of microbial communities within fluvial biofilms.
Woodcock S, Besemer K, Battin TJ, Curtis TP, Sloan WT
Environ. Microbiol. 15 (4) 1216-1225 [2013-04-00; online 2012-12-18]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
The mitochondrial and autosomal mutation landscapes of prostate cancer.
Lindberg J, Mills IG, Klevebring D, ..., Egevad L, Grönberg H
pii: S0302-2838(12)01438-8
Eur. Urol. 63 (4) 702-708 [2013-04-00; online 2012-12-26]
Karolinska High Throughput Center (KHTC) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.
Stadler C, Rexhepaj E, Singan VR, ..., Simpson JC, Lundberg E
pii: nmeth.2377
Nat. Methods 10 (4) 315-323 [2013-04-00; online 2013-02-26]
Cell Profiling
PubMed DOI Crossref
Welander distal myopathy caused by an ancient founder mutation in TIA1 associated with perturbed splicing.
Klar J, Sobol M, Melberg A, ..., Casar-Borota O, Dahl N
Hum. Mutat. 34 (4) 572-577 [2013-04-00; online 2013-01-26]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Automated classification of immunostaining patterns in breast tissue from the human protein atlas.
Swamidoss IN, Kårsnäs A, Uhlmann V, ..., Wählby C, Strand R
pii: JPI-4-14 pmc: PMC3678740
J Pathol Inform 4 (Suppl) S14 [2013-03-30; online 2013-03-30]
BioImage Informatics [Technology development] Tissue Profiling
PubMed DOI Crossref
Genetic variants from lipid-related pathways and risk for incident myocardial infarction.
Song C, Pedersen NL, Reynolds CA, ..., Prince JA, Ingelsson E
pii: PONE-D-12-11381 pmc: PMC3612051
PLoS ONE 8 (3) e60454 [2013-03-29; online 2013-03-29]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
Franzén O, Jerlström-Hultqvist J, Einarsson E, ..., Andersson B, Svärd SG
pii: PCOMPBIOL-D-12-01572 pmc: PMC3610916 GEO: GSE36490
PLoS Comput. Biol. 9 (3) e1003000 [2013-03-28; online 2013-03-28]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Optimizing Solubility and Permeability of a Biopharmaceutics Classification System (BCS) Class 4 Antibiotic Drug Using Lipophilic Fragments Disturbing the Crystal Lattice
Tehler U, Fagerberg JH, Svensson R, ..., Artursson P, Bergström CAS
J. Med. Chem. 56 (6) 2690-2694 [2013-03-28; online 2013-03-28]
Chemical Biology Consortium Sweden (CBCS) [Technology development]
PubMed DOI Crossref
Offshoots of the ESF functional genomics programme.
Landegren U
pii: S1871-6784(12)00900-4
N Biotechnol 30 (3) 296-298 [2013-03-25; online 2013-01-09]
PLA and Single Cell Proteomics
PubMed DOI Crossref
Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.
Mayrhofer M, DiLorenzo S, Isaksson A
pii: gb-2013-14-3-r24 pmc: PMC4053982
Genome Biol. 14 (3) R24 [2013-03-25; online 2013-03-25]
Array and Analysis Facility
PubMed DOI Crossref
Genome Sequence of a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036.
Manzoor S, Niazi A, Bejai S, Meijer J, Bongcam-Rudloff E
pii: 1/2/e00111-13 pmc: PMC3622975
Genome Announc 1 (2) e0011113 [2013-03-21; online 2013-03-21]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Integration of clinical data with a genome-scale metabolic model of the human adipocyte.
Mardinoglu A, Agren R, Kampf C, ..., Uhlen M, Nielsen J
pii: msb20135 pmc: PMC3619940
Mol. Syst. Biol. 9 (-) 649 [2013-03-21; online 2013-03-21]
Tissue Profiling
PubMed DOI Crossref
The genomic signature of dog domestication reveals adaptation to a starch-rich diet.
Axelsson E, Ratnakumar A, Arendt M, ..., Hedhammar A, Lindblad-Toh K
pii: nature11837
Nature 495 (7441) 360-364 [2013-03-21; online 2013-01-29]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Identification of genetic variants influencing the human plasma proteome.
Johansson Å, Enroth S, Palmblad M, ..., Bergquist J, Gyllensten U
pii: 1217238110 pmc: PMC3606982
Proc. Natl. Acad. Sci. U.S.A. 110 (12) 4673-4678 [2013-03-19; online 2013-03-15]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Identification and verification of microRNAs by high-throughput sequencing.
Hällman J, Avesson L, Reimegård J, Käller M, Söderbom F
Methods Mol. Biol. 983 (-) 125-138 [2013-03-16; online 2013-03-16]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
DNA topoisomerase III localizes to centromeres and affects centromeric CENP-A levels in fission yeast.
Norman-Axelsson U, Durand-Dubief M, Prasad P, Ekwall K
pii: PGENETICS-D-12-01254 pmc: PMC3597498
PLoS Genet. 9 (3) e1003371 [2013-03-14; online 2013-03-14]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
Transcriptome of the alternative ethanol production strain Dekkera bruxellensis CBS 11270 in sugar limited, low oxygen cultivation.
Tiukova IA, Petterson ME, Tellgren-Roth C, ..., Pettersson OV, Passoth V
pii: PONE-D-12-35813 pmc: PMC3596373
PLoS ONE 8 (3) e58455 [2013-03-13; online 2013-03-13]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing.
Jiao X, Hooper SD, Djureinovic T, ..., Botling J, Sjöblom T
pii: 1471-2164-14-165 pmc: PMC3600027
BMC Genomics 14 (-) 165 [2013-03-12; online 2013-03-12]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
Mayer G, Montecchi-Palazzi L, Ovelleiro D, ..., Eisenacher M, HUPO-PSI Group
pii: bat009 pmc: PMC3594986
Database (Oxford) 2013 (-) bat009 [2013-03-12; online 2013-03-12]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.
Lundin S, Gruselius J, Nystedt B, ..., Käller M, Lundeberg J
pii: srep01186 pmc: PMC3592332
Sci Rep 3 (-) 1186 [2013-03-09; online 2013-03-09]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Recognition of mono-ADP-ribosylated ARTD10 substrates by ARTD8 macrodomains.
Forst AH, Karlberg T, Herzog N, ..., Schüler H, Lüscher B
pii: S0969-2126(13)00019-1 PDB: 3Q6Z PDB: 3Q71 PDB: 3V2B PDB: 3VFQ PDB: 4ABK PDB: 4ABL PDB: 4D86
Structure 21 (3) 462-475 [2013-03-05; online 2013-03-12]
Protein Science Facility (PSF)
PubMed DOI Crossref
TagGD: fast and accurate software for DNA Tag generation and demultiplexing.
Costea PI, Lundeberg J, Akan P
pii: PONE-D-12-34651 pmc: PMC3587622
PLoS ONE 8 (3) e57521 [2013-03-04; online 2013-03-04]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Secretion of two novel enzymes, manganese 9S-lipoxygenase and epoxy alcohol synthase, by the rice pathogen Magnaporthe salvinii.
Wennman A, Oliw EH
pii: jlr.M033787 pmc: PMC3617950
J. Lipid Res. 54 (3) 762-775 [2013-03-00; online 2012-12-13]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
A genome-wide assessment of variability in human serum metabolism.
Hong MG, Karlsson R, Magnusson PK, ..., Wiklund F, Prince JA
Hum. Mutat. 34 (3) 515-524 [2013-03-00; online 2013-01-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genetic effects on old-age cognitive functioning: a population-based study.
Laukka EJ, Lövdén M, Herlitz A, ..., Fratiglioni L, Bäckman L
pii: 2012-34905-001
Psychol Aging 28 (1) 262-274 [2013-03-00; online 2013-01-02]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Genetic determinants of plasma β₂-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain.
Athanasiadis G, Sabater-Lleal M, Buil A, ..., Hamsten A, Soria JM
J. Thromb. Haemost. 11 (3) 521-528 [2013-03-00; online 2013-01-03]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Structure of LdtMt2, an L,D-transpeptidase from Mycobacterium tuberculosis.
Böth D, Steiner EM, Stadler D, ..., Schnell R, Schneider G
pii: S0907444912049268 pmc: PMC3605044 PDB: 4HU2 PDB: 4HUC
Acta Crystallogr. D Biol. Crystallogr. 69 (Pt 3) 432-441 [2013-03-00; online 2013-02-16]
Protein Science Facility (PSF)
PubMed DOI Crossref
Determination of the obesity-associated gene variants within the entire FTO gene by ultra-deep targeted sequencing in obese and lean children.
Sällman Almén M, Rask-Andersen M, Jacobsson JA, ..., Fredriksson R, Schiöth HB
pii: ijo201257 pmc: PMC3595467
Int J Obes (Lond) 37 (3) 424-431 [2013-03-00; online 2012-04-26]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella.
Guy L, Nystedt B, Toft C, ..., Eriksson AS, Andersson SG
pii: PGENETICS-D-12-01962 pmc: PMC3610622
PLoS Genet. 9 (3) e1003393 [2013-03-00; online 2013-03-28]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A modified Glenn shunt improves haemodynamics in acute right ventricular failure in an experimental model.
Vikholm P, Schiller P, Johansson J, Hellgren L
pii: ezs386
Eur J Cardiothorac Surg 43 (3) 612-618 [2013-03-00; online 2012-07-05]
Array and Analysis Facility
PubMed DOI Crossref
The effect of substrate and operational parameters on the abundance of sulphate-reducing bacteria in industrial anaerobic biogas digesters.
Moestedt J, Nilsson Påledal S, Schnürer A
pii: S0960-8524(13)00066-7
Bioresour. Technol. 132 (-) 327-332 [2013-03-00; online 2013-02-19]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
DOI Crossref
Oral rehydration solution with glycerol to dairy calves: Effects on fluid balance, metabolism, and intestinal microbiota
Omazic AW, Tråvén M, Roos S, Mellgren E, Holtenius K
Acta Agriculturae Scandinavica, Section A - Animal Science 63 (1) 47-56 [2013-03-00; online 2013-03-00]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Astakine 2--the dark knight linking melatonin to circadian regulation in crustaceans.
Watthanasurorot A, Saelee N, Phongdara A, ..., Söderhäll K, Söderhäll I
pii: PGENETICS-D-12-01816 pmc: PMC3605217
PLoS Genet. 9 (3) e1003361 [2013-03-00; online 2013-03-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Brain gene expression differences are associated with abnormal tail biting behavior in pigs.
Brunberg E, Jensen P, Isaksson A, Keeling LJ
Genes Brain Behav. 12 (2) 275-281 [2013-03-00; online 2012-11-14]
Array and Analysis Facility
PubMed DOI Crossref
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.
Hruby A, Ngwa JS, Renström F, ..., McKeown NM, Nettleton JA
pii: jn.112.172049 pmc: PMC3713023
J. Nutr. 143 (3) 345-353 [2013-03-00; online 2013-01-25]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Fine-mapping of restless legs locus 4 (RLS4) identifies a haplotype over the SPATS2L and KCTD18 genes.
Pichler I, Schwienbacher C, Zanon A, ..., Hicks AA, Pramstaller PP
J. Mol. Neurosci. 49 (3) 600-605 [2013-03-00; online 2012-10-12]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Metagenomic detection of viral pathogens in Spanish honeybees: co-infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses.
Granberg F, Vicente-Rubiano M, Rubio-Guerri C, ..., Belák S, Sánchez-Vizcaíno JM
pii: PONE-D-12-15653 pmc: PMC3583878
PLoS ONE 8 (2) e57459 [2013-02-27; online 2013-02-27]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Origin and evolution of medium chain alcohol dehydrogenases.
Jörnvall H, Hedlund J, Bergman T, ..., Cederlund E, Persson B
pii: S0009-2797(12)00252-9
Chem. Biol. Interact. 202 (1-3) 91-96 [2013-02-25; online 2012-12-04]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs).
Persson B, Kallberg Y
pii: S0009-2797(12)00253-0
Chem. Biol. Interact. 202 (1-3) 111-115 [2013-02-25; online 2012-12-04]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Evolution of sperm structure and energetics in passerine birds.
Rowe M, Laskemoen T, Johnsen A, Lifjeld JT
pii: rspb.2012.2616 pmc: PMC3574354
Proc. Biol. Sci. 280 (1753) 20122616 [2013-02-22; online 2013-01-04]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Imatinib ameliorates neuroinflammation in a rat model of multiple sclerosis by enhancing blood-brain barrier integrity and by modulating the peripheral immune response.
Adzemovic MV, Adzemovic MZ, Zeitelhofer M, ..., Olsson T, Nilsson I
pii: PONE-D-12-27544 pmc: PMC3577871
PLoS ONE 8 (2) e56586 [2013-02-20; online 2013-02-20]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
The synthetic progestin levonorgestrel is a potent androgen in the three-spined stickleback (Gasterosteus aculeatus).
Svensson J, Fick J, Brandt I, Brunström B
Environ. Sci. Technol. 47 (4) 2043-2051 [2013-02-19; online 2013-02-01]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
STC1 expression by cancer-associated fibroblasts drives metastasis of colorectal cancer.
Peña C, Céspedes MV, Lindh MB, ..., Augsten M, Ostman A
pii: 0008-5472.CAN-12-1875
Cancer Res. 73 (4) 1287-1297 [2013-02-15; online 2012-12-18]
Tissue Profiling
PubMed DOI Crossref
Coastal bacterioplankton community dynamics in response to a natural disturbance.
Yeo SK, Huggett MJ, Eiler A, Rappé MS
pii: PONE-D-12-27911 pmc: PMC3567041
PLoS ONE 8 (2) e56207 [2013-02-07; online 2013-02-07]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Causal relationship between obesity and vitamin D status: bi-directional Mendelian randomization analysis of multiple cohorts.
Vimaleswaran KS, Berry DJ, Lu C, ..., Hingorani AD, Hyppönen E
pii: PMEDICINE-D-12-01552 pmc: PMC3564800
PLoS Med. 10 (2) e1001383 [2013-02-05; online 2013-02-05]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
FANTOM: Functional and taxonomic analysis of metagenomes.
Sanli K, Karlsson FH, Nookaew I, Nielsen J
pii: 1471-2105-14-38 pmc: PMC3566963
BMC Bioinformatics 14 (-) 38 [2013-02-01; online 2013-02-01]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Olfactory receptor 51E1 protein as a potential novel tissue biomarker for small intestine neuroendocrine carcinomas.
Cui T, Tsolakis AV, Li S, ..., Öberg K, Giandomenico V
pii: EJE-12-0814
Eur. J. Endocrinol. 168 (2) 253-261 [2013-02-00; online 2012-11-28]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis.
Liu Y, Aryee MJ, Padyukov L, ..., Ekström TJ, Feinberg AP
pii: nbt.2487 pmc: PMC3598632 mid: NIHMS430504 GEO: GSE42861
Nat. Biotechnol. 31 (2) 142-147 [2013-02-00; online 2013-01-22]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor.
Uddenberg D, Reimegård J, Clapham D, ..., Emanuelsson O, Sundström JF
pii: pp.112.207746 pmc: PMC3561021
Plant Physiol. 161 (2) 813-823 [2013-02-00; online 2012-12-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The Swedish Twin Registry: establishment of a biobank and other recent developments.
Magnusson PKE, Almqvist C, Rahman I, ..., Pedersen NL, Lichtenstein P
pii: S1832427412001041
Twin Res Hum Genet 16 (1) 317-329 [2013-02-00; online 2012-11-10]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
In vitro and in vivo activities of 2-aminopyrazines and 2-aminopyridines in experimental models of human African trypanosomiasis.
Vodnala SK, Lundbäck T, Sjöberg B, ..., Rottenberg ME, Hammarström LGJ
pii: AAC.01870-12 pmc: PMC3553678
Antimicrob. Agents Chemother. 57 (2) 1012-1018 [2013-02-00; online 2012-12-21]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
DOI Crossref
Sequence variation in mitochondrial ATP synthase subunit 6 & 8 and nuclear genes ITS1 and ITS2 in 17 cyprinid species
Demandt MH
J. Appl. Ichthyol. 29 (1) 278-280 [2013-02-00; online 2012-06-22]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.
Bienko M, Crosetto N, Teytelman L, ..., Itzkovitz S, van Oudenaarden A
pmc: PMC3735345 mid: NIHMS500266
Nat. Methods 10 (2) 122-124 [2013-02-00; online 2012-12-23]
Advanced FISH Technologies [Technology development]
PubMed DOI Crossref
Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins.
Lindberg J, Klevebring D, Liu W, ..., Egevad L, Grönberg H
pii: S0302-2838(12)00402-2
Eur. Urol. 63 (2) 347-353 [2013-02-00; online 2012-04-17]
Karolinska High Throughput Center (KHTC) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
An MBL-like protein may interfere with the activation of the proPO-system, an important innate immune reaction in invertebrates.
Wu C, Charoensapsri W, Nakamura S, ..., Söderhäll I, Söderhäll K
pii: S0171-2985(12)00056-3
Immunobiology 218 (2) 159-168 [2013-02-00; online 2012-03-31]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Adipose tissue resting energy expenditure and expression of genes involved in mitochondrial function are higher in women than in men.
Nookaew I, Svensson PA, Jacobson P, ..., Nielsen J, Carlsson LM
pii: jc.2012-2764 pmc: PMC3633773
J. Clin. Endocrinol. Metab. 98 (2) E370-E378 [2013-02-00; online 2012-12-25]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Early-phase GVHD gene expression profile in target versus non-target tissues: kidney, a possible target?
Sadeghi B, Al-Chaqmaqchi H, Al-Hashmi S, ..., Moshfegh A, Hassan M
pii: bmt2012120
Bone Marrow Transplant. 48 (2) 284-293 [2013-02-00; online 2012-07-25]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
The phylogeographic pattern of Francisella tularensis in Sweden indicates a Scandinavian origin of Eurosiberian tularaemia.
Karlsson E, Svensson K, Lindgren P, ..., Forsman M, Johansson A
Environ. Microbiol. 15 (2) 634-645 [2013-02-00; online 2012-12-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
First insights into the syntrophic acetate-oxidizing bacteria--a genetic study.
Müller B, Sun L, Schnürer A
pmc: PMC3584212 GENBANK: JQ979072 GENBANK: JQ979073 GENBANK: JQ979074 GENBANK: JQ979075 GENBANK: JQ979076 GENBANK: JQ979077
Microbiologyopen 2 (1) 35-53 [2013-02-00; online 2012-12-15]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Population pharmacokinetic modeling and deconvolution of enantioselective absorption of eflornithine in the rat
Johansson CC, Gennemark P, Artursson P, ..., Ashton M, Jansson-Löfmark R
J Pharmacokinet Pharmacodyn 40 (1) 117-128 [2013-02-00; online 2013-01-10]
Chemical Biology Consortium Sweden (CBCS) [Service]
PubMed DOI Crossref
A gene-centric study of common carotid artery remodelling.
Harrison SC, Zabaneh D, Asselbergs FW, ..., Hamsten A, Humphries SE
pii: S0021-9150(12)00797-6 pmc: PMC3573227
Atherosclerosis 226 (2) 440-446 [2013-02-00; online 2012-12-19]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.
Köttgen A, Albrecht E, Teumer A, ..., Bochud M, Gieger C
pii: ng.2500 pmc: PMC3663712 mid: NIHMS458823
Nat. Genet. 45 (2) 145-154 [2013-02-00; online 2012-12-25]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Workshop on laboratory protocol standards for the Molecular Methods Database.
Klingström T, Soldatova L, Stevens R, ..., Landegren U, Bongcam-Rudloff E
pii: S1871-6784(12)00121-5
N Biotechnol 30 (2) 109-113 [2013-01-25; online 2012-06-13]
PLA and Single Cell Proteomics
PubMed DOI Crossref
Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation.
Gu GJ, Friedman M, Jost C, ..., Landegren U, Söderberg O
pii: S1871-6784(12)00107-0
N Biotechnol 30 (2) 144-152 [2013-01-25; online 2012-06-06]
PLA and Single Cell Proteomics
PubMed DOI Crossref
Multiplex protein detection with DNA readout via mass spectrometry.
Flanigon J, Kamali-Moghaddam M, Burbulis I, ..., Landegren U, Cantor C
pii: S1871-6784(12)00860-6 pmc: PMC3616745 mid: NIHMS425130
N Biotechnol 30 (2) 153-158 [2013-01-25; online 2012-12-04]
PLA and Single Cell Proteomics
PubMed DOI Crossref
DNA methylation in the Neuropeptide S Receptor 1 (NPSR1) promoter in relation to asthma and environmental factors.
Reinius LE, Gref A, Sääf A, ..., Söderhäll C, Kere J
pii: PONE-D-12-14529 pmc: PMC3553086
PLoS ONE 8 (1) e53877 [2013-01-23; online 2013-01-23]
Mutation Analysis Facility (MAF)
PubMed DOI Crossref
Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach.
Eiler A, Drakare S, Bertilsson S, ..., Znachor P, Lindström ES
pii: PONE-D-12-28577 pmc: PMC3551911
PLoS ONE 8 (1) e53516 [2013-01-22; online 2013-01-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis.
Gioti A, Nystedt B, Li W, ..., Heitman J, Scheynius A
pii: mBio.00572-12 pmc: PMC3560662 GENBANK: HE999549 GENBANK: HE999550 GENBANK: HE999551 GENBANK: HE999552 GENBANK: HE999553 GENBANK: HE999554 GENBANK: HE999555 GENBANK: HE999556 GENBANK: HE999557 GENBANK: HE999558 GENBANK: HE999559 GENBANK: HE999560 GENBANK: HE999561 GENBANK: HE999562 GENBANK: HE999563 GENBANK: HE999564 GENBANK: HE999565 GENBANK: HE999566 GENBANK: HE999567 GENBANK: HE999568 GENBANK: HE999569 GENBANK: HE999570 GENBANK: HE999571 GENBANK: HE999572 GENBANK: HE999573 GENBANK: HE999574 GENBANK: HE999575 GENBANK: HE999576 GENBANK: HE999577 GENBANK: HE999578 GENBANK: HE999579 GENBANK: HE999580 GENBANK: HE999581 GENBANK: HE999582 GENBANK: HE999583 GENBANK: HE999584 GENBANK: HE999585 GENBANK: HE999586 GENBANK: HE999587 GENBANK: HE999588 GENBANK: HE999589 GENBANK: HE999590 GENBANK: HE999591 GENBANK: HE999592 GENBANK: HE999593 GENBANK: HE999594 GENBANK: HE999595 GENBANK: HE999596 GENBANK: HE999597 GENBANK: HE999598 GENBANK: HE999599 GENBANK: HE999600 GENBANK: HE999601 GENBANK: HE999602 GENBANK: HE999603 GENBANK: HE999604 GENBANK: HE999605 GENBANK: HE999606 GENBANK: HE999607 GENBANK: HE999608 GENBANK: HE999609 GENBANK: HE999610 GENBANK: HE999611 GENBANK: HE999612 GENBANK: HE999613 GENBANK: HF558646 GENBANK: JX964800 GENBANK: JX964801 GENBANK: JX964802 GENBANK: JX964840 GENBANK: JX964841 GENBANK: JX964842 GENBANK: JX964843 GENBANK: JX964844 GENBANK: JX964845 GENBANK: JX964846 GENBANK: JX964847 GENBANK: JX964848 GENBANK: JX964849 GENBANK: JX964850
MBio 4 (1) e00572-e00512 [2013-01-22; online 2013-01-22]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
DNA-binding specificities of human transcription factors.
Jolma A, Yan J, Whitington T, ..., Kivioja T, Taipale J
pii: S0092-8674(12)01496-1
Cell 152 (1-2) 327-339 [2013-01-17; online 2013-01-22]
Karolinska High Throughput Center (KHTC)
PubMed DOI Crossref
A genome-wide association study identifies genomic regions for virulence in the non-model organism Heterobasidion annosum s.s.
Dalman K, Himmelstrand K, Olson Å, ..., Brandström-Durling M, Stenlid J
pii: PONE-D-12-26429 pmc: PMC3547014
PLoS ONE 8 (1) e53525 [2013-01-16; online 2013-01-16]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
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.
Nettleton JA, Hivert MF, Lemaitre RN, ..., Meigs JB, Franks PW
pii: kws297 pmc: PMC3707424
Am. J. Epidemiol. 177 (2) 103-115 [2013-01-15; online 2012-12-21]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.
Teschendorff AE, Marabita F, Lechner M, ..., Gomez-Cabrero D, Beck S
pii: bts680 pmc: PMC3546795
Bioinformatics 29 (2) 189-196 [2013-01-15; online 2012-11-24]
Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells.
Paredes JA, Zhou X, Höglund S, Karlsson A
pii: PONE-D-12-23752 pmc: PMC3544874
PLoS ONE 8 (1) e53698 [2013-01-14; online 2013-01-14]
Bioinformatics and Expression Analysis (BEA)
PubMed DOI Crossref
Exome RNA sequencing reveals rare and novel alternative transcripts.
Halvardson J, Zaghlool A, Feuk L
pii: gks816 pmc: PMC3592422
Nucleic Acids Res. 41 (1) e6 [2013-01-07; online 2012-09-04]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.
Liu S, Im H, Bairoch A, ..., Beavis RC, Hancock WS
pmc: PMC4142220 mid: NIHMS431316
J. Proteome Res. 12 (1) 45-57 [2013-01-04; online 2012-12-25]
Cell Profiling
PubMed DOI Crossref
RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.
Danielsson F, Wiking M, Mahdessian D, ..., Uhlén M, Lundberg E
J. Proteome Res. 12 (1) 299-307 [2013-01-04; online 2012-12-12]
Cell Profiling
PubMed DOI Crossref
Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation.
Botling J, Edlund K, Lohr M, ..., Hengstler JG, Micke P
pii: 1078-0432.CCR-12-1139
Clin. Cancer Res. 19 (1) 194-204 [2013-01-01; online 2012-10-04]
Array and Analysis Facility Tissue Profiling
DOI Crossref
The genetic structure of the Lithuanian wolf population
Baltrūnaitė L, Balčiauskas L, Åkesson M
Open Life Sci 8 (5) - [2013-01-01; online 2013-01-01]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Proceedings of the 15th International Congress on Circumpolar Health
International Journal of Circumpolar Health 72 (1) 22447 [2013-01-00; online 2013-08-05]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Large-scale association analysis identifies new risk loci for coronary artery disease.
CARDIoGRAMplusC4D Consortium N, Deloukas P, Kanoni S, ..., Schunkert H, Samani NJ
pii: ng.2480 pmc: PMC3679547 mid: NIHMS468575
Nat. Genet. 45 (1) 25-33 [2013-01-00; online 2012-12-04]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
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.
Cahill N, Bergh AC, Kanduri M, ..., Rosén A, Rosenquist R
pii: leu2012245
Leukemia 27 (1) 150-158 [2013-01-00; online 2012-08-28]
Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime.
Forsberg LA, Absher D, Dumanski JP
pii: jmedgenet-2012-101322 pmc: PMC3534255
J. Med. Genet. 50 (1) 1-10 [2013-01-00; online 2012-11-23]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1.
Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B
pii: genomeA00213-12 pmc: PMC3587937
Genome Announc 1 (1) - [2013-01-00; online 2013-02-21]
NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
PubMed DOI Crossref
Genome-wide profiling of target genes for the systemic lupus erythematosus-associated transcription factors IRF5 and STAT4.
Wang C, Sandling JK, Hagberg N, ..., Eloranta ML, Syvänen AC
pii: annrheumdis-2012-201364
Ann. Rheum. Dis. 72 (1) 96-103 [2013-01-00; online 2012-06-26]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
DOI Crossref
Nanoscale elucidation of Na,K-ATPase isoforms in dendritic spines
Liebmann T, Blom H, Aperia A, Brismar H
Optical Nanoscopy Opt Nanoscopy 2 (1) 6 [2013-00-00; online 2013-00-00]
Advanced Light Microscopy (ALM) [Technology development]
DOI Crossref
The A-CD analogue of 16β,17α-estriol is a potent and highly selective estrogen receptor β agonist
Sauvée C, Schäfer A, Sundén H, ..., Burstein ES, Olsson R
Med. Chem. Commun. 4 (11) 1439 [2013-00-00; online 2013-00-00]
Chemical Biology Consortium Sweden (CBCS) [Collaborative]
SciLifeLab Data Centre
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