{"entity": "researcher", "timestamp": "2026-07-15T07:51:44.262Z", "family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "affiliations": ["Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240"}}, "publications": [{"entity": "publication", "iuid": "a13b9b2a120741f2af40dbd525b2c748", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a13b9b2a120741f2af40dbd525b2c748.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a13b9b2a120741f2af40dbd525b2c748"}}, "title": "Exploration of immune phenotypes in self-sampling citizens", "authors": [{"family": "Dahl", "given": "Leo", "initials": "L", "orcid": "0000-0003-1492-3052", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4df506f315c4289935b935a503efd56.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications.scilifelab.se/researcher/50dffce4f4444dd8b5ff8f9294146a0b.json"}}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Albrecht", "given": "Vincent", "initials": "V", "orcid": "0009-0003-1985-7733", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d422e623e9e449f98853e6830cdd401.json"}}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S", "orcid": "0000-0002-4600-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/310af30b841741a790046af03a3cee6d.json"}}, {"family": "Merid", "given": "Simon Kebede", "initials": "SK", "orcid": "0000-0001-5974-7676", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7a04c6538814b089994c7a822ecf07f.json"}}, {"family": "Mezger", "given": "Anja", "initials": "A", "orcid": "0000-0002-7337-9547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebf61fe41e6f43e4aec2be101de688d4.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Naluai", "given": "\u00c5sa Torinsson", "initials": "\u00c5T"}, {"family": "Beck", "given": "Olof", "initials": "O"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}, {"family": "Bauer", "given": "Stefan", "initials": "S"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M", "orcid": "0000-0002-2357-1020", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b50df8c8ecc45b89574dc76e244b07e.json"}}, {"family": "Roxhed", "given": "Niclas", "initials": "N", "orcid": "0000-0002-7147-6730", "researcher": {"href": "https://publications.scilifelab.se/researcher/3739210caaf14a28898849f20bf6ece5.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal-article", "published": "2026-02-00", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "29", "issue": "2", "pages": "114611", "issn-l": "2589-0042"}, "abstract": "Blood proteins have provided essential insights into how humans responded to the recent pandemic. To expand our understanding beyond patients seeking medical care, we conducted a citizen-centric survey with 2,000 random residents (age: 18-69 years) from Sweden's two largest cities in 2021. With self-sampled dried blood spots (DBS) and health information from 437 (22%) volunteers, we performed multi-analyte COVID-19 serology, measured autoantibodies (AAbs) against 22 interferons, and quantified 502 circulating low-abundant immune-related blood proteins. Antibody assays confirmed self-reported infections (26%) and vaccinations (40%), showed timing-dependent discrepancies in the immune response, and revealed anti-type I interferon AAbs co-occurring frequently alongside natural infections. Proteomics data added plausible mechanistic insights into cell-mediated processes: data-driven analyses revealed 24% of participants presented deviating immune phenotypes linked to infections, immunity, respiratory effects, and age. Multi-molecular DBS analysis of random layperson samples captured the broader spectrum of immune system states, adding relevant insights for clinical and public health investigations.", "doi": "10.1016/j.isci.2025.114611", "pmid": "41630906", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12860695"}, {"db": "pii", "key": "S2589-0042(25)02872-X"}], "notes": [], "created": "2026-02-26T13:37:49.302Z", "modified": "2026-03-24T09:13:34.204Z"}, {"entity": "publication", "iuid": "2327daa01a69409ebeaa040fe7f5fbd3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2327daa01a69409ebeaa040fe7f5fbd3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2327daa01a69409ebeaa040fe7f5fbd3"}}, "title": "Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.", "authors": [{"family": "Garcia", "given": "Maxime", "initials": "M", "orcid": "0000-0003-2827-9261", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cf9b1b223f04296adcb6bd091c548de.json"}}, {"family": "Juhos", "given": "Szilveszter", "initials": "S"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "D\u00edaz De St\u00e5hl", "given": "Teresita", "initials": "T"}, {"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1dc80e61f574293a190f2f3ef464988.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}], "type": "journal article", "published": "2020-01-29", "journal": {"volume": "9", "issn": "2046-1402", "issue": null, "pages": "63", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.", "doi": "10.12688/f1000research.16665.2", "pmid": "32269765", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Long-term Support WABI": "Technology development", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Clinical Genomics Stockholm": "Collaborative", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7111497"}], "notes": [], "created": "2020-04-23T08:58:58.026Z", "modified": "2024-01-16T13:48:43.022Z"}, {"entity": "publication", "iuid": "9797ffcb4104436abf36713e3e05d177", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9797ffcb4104436abf36713e3e05d177.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9797ffcb4104436abf36713e3e05d177"}}, "title": "High throughput barcoding method for genome-scale phasing.", "authors": [{"family": "Redin", "given": "David", "initials": "D"}, {"family": "Frick", "given": "Tobias", "initials": "T"}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2019-12-02", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "18116", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The future of human genomics is one that seeks to resolve the entirety of genetic variation through sequencing. The prospect of utilizing genomics for medical purposes require cost-efficient and accurate base calling, long-range haplotyping capability, and reliable calling of structural variants. Short-read sequencing has lead the development towards such a future but has struggled to meet the latter two of these needs. To address this limitation, we developed a technology that preserves the molecular origin of short sequencing reads, with an insignificant increase to sequencing costs. We demonstrate a novel library preparation method for high throughput barcoding of short reads where millions of random barcodes can be used to reconstruct megabase-scale phase blocks.", "doi": "10.1038/s41598-019-54446-x", "pmid": "31792271", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-54446-x"}, {"db": "pmc", "key": "PMC6889410"}], "notes": [], "created": "2020-01-08T16:49:20.740Z", "modified": "2021-07-07T15:18:57.764Z"}, {"entity": "publication", "iuid": "b1f4d18f745842fda29e557e90de70ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1f4d18f745842fda29e557e90de70ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1f4d18f745842fda29e557e90de70ed"}}, "title": "Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.", "authors": [{"family": "Tiukova", "given": "Ievgeniia A", "initials": "IA", "orcid": "0000-0002-0408-3515", "researcher": {"href": "https://publications.scilifelab.se/researcher/e007c24aef2344d582f2e3d318b3f7cd.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Hoeppner", "given": "Marc P", "initials": "MP"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "S\u00f6derberg", "given": "Jonas", "initials": "J"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}], "type": "journal article", "published": "2019-05-01", "journal": {"volume": "14", "issn": "1932-6203", "issue": "5", "pages": "e0215077", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.", "doi": "10.1371/journal.pone.0215077", "pmid": "31042716", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-32895"}, {"db": "pmc", "key": "PMC6493715"}], "notes": [], "created": "2019-11-24T12:41:36.969Z", "modified": "2021-07-07T15:19:08.434Z"}, {"entity": "publication", "iuid": "f754205bb071486683b1bde1528c6303", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f754205bb071486683b1bde1528c6303.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f754205bb071486683b1bde1528c6303"}}, "title": "Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Pettersson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3120-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfdfac2208ce4d1a877fa4957e2f4ea4.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F", "orcid": "0000-0002-0243-0018", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e630602a0a449e899701c781ee59fb6.json"}}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Syk Lundberg", "given": "Elisabeth", "initials": "E"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1a6b6936aa442384c5aef0eff0715a.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "15", "issn": "1553-7404", "issue": "2", "pages": "e1007858", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Complex chromosomal rearrangements (CCRs) are rearrangements involving more than two chromosomes or more than two breakpoints. Whole genome sequencing (WGS) allows for outstanding high resolution characterization on the nucleotide level in unique sequences of such rearrangements, but problems remain for mapping breakpoints in repetitive regions of the genome, which are known to be prone to rearrangements. Hence, multiple complementary WGS experiments are sometimes needed to solve the structures of CCRs. We have studied three individuals with CCRs: Case 1 and Case 2 presented with de novo karyotypically balanced, complex interchromosomal rearrangements (46,XX,t(2;8;15)(q35;q24.1;q22) and 46,XY,t(1;10;5)(q32;p12;q31)), and Case 3 presented with a de novo, extremely complex intrachromosomal rearrangement on chromosome 1. Molecular cytogenetic investigation revealed cryptic deletions in the breakpoints of chromosome 2 and 8 in Case 1, and on chromosome 10 in Case 2, explaining their clinical symptoms. In Case 3, 26 breakpoints were identified using WGS, disrupting five known disease genes. All rearrangements were subsequently analyzed using optical maps, linked-read WGS, and short-read WGS. In conclusion, we present a case series of three unique de novo CCRs where we by combining the results from the different technologies fully solved the structure of each rearrangement. The power in combining short-read WGS with long-molecule sequencing or optical mapping in these unique de novo CCRs in a clinical setting is demonstrated.", "doi": "10.1371/journal.pgen.1007858", "pmid": "30735495", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-18-00854"}, {"db": "pmc", "key": "PMC6368290"}], "notes": [], "created": "2019-11-25T10:49:59.013Z", "modified": "2024-01-16T13:48:44.771Z"}, {"entity": "publication", "iuid": "51df1c5fe3f94631a980b3a69ab8490c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51df1c5fe3f94631a980b3a69ab8490c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51df1c5fe3f94631a980b3a69ab8490c"}}, "title": "Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization.", "authors": [{"family": "Nazaryan-Petersen", "given": "Lusine", "initials": "L"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Pettersson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3120-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfdfac2208ce4d1a877fa4957e2f4ea4.json"}}, {"family": "Lundin", "given": "Johanna", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "Lieden", "given": "Agne", "initials": "A"}, {"family": "Lovmar", "given": "Lovisa", "initials": "L"}, {"family": "Ottosson", "given": "Jesper", "initials": "J"}, {"family": "Gacic", "given": "Jelena", "initials": "J", "orcid": "0000-0002-1431-7792", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2a1747f125144b48815d5793ac1bc13.json"}}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O", "orcid": "0000-0002-4547-001X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce0614bdc717455b9af64a05ab4aa4aa.json"}}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Hjortsh\u00f8j", "given": "Tina Duelund", "initials": "TD"}, {"family": "Jespersgaard", "given": "Cathrine", "initials": "C"}, {"family": "Houssari", "given": "Rayan", "initials": "R"}, {"family": "Pignata", "given": "Laura", "initials": "L"}, {"family": "Bak", "given": "Mads", "initials": "M"}, {"family": "Tommerup", "given": "Niels", "initials": "N", "orcid": "0000-0003-2304-0112", "researcher": {"href": "https://publications.scilifelab.se/researcher/d163b474ab954465b310cc47ac7403eb.json"}}, {"family": "Lundberg", "given": "Elisabeth Syk", "initials": "ES", "orcid": "0000-0001-5692-725X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f23c7a2e475443ef9fdbbd7b46c9991e.json"}}, {"family": "T\u00fcmer", "given": "Zeynep", "initials": "Z"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2018-11-00", "journal": {"volume": "14", "issn": "1553-7404", "issue": "11", "pages": "e1007780", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Clustered copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) are often reported as germline chromothripsis. However, such cases might need further investigations by massive parallel whole genome sequencing (WGS) in order to accurately define the underlying complex rearrangement, predict the occurrence mechanisms and identify additional complexities. Here, we utilized WGS to delineate the rearrangement structure of 21 clustered CNV carriers first investigated by CMA and identified a total of 83 breakpoint junctions (BPJs). The rearrangements were further sub-classified depending on the patterns observed: I) Cases with only deletions (n = 8) often had additional structural rearrangements, such as insertions and inversions typical to chromothripsis; II) cases with only duplications (n = 7) or III) combinations of deletions and duplications (n = 6) demonstrated mostly interspersed duplications and BPJs enriched with microhomology. In two cases the rearrangement mutational signatures indicated both a breakage-fusion-bridge cycle process and haltered formation of a ring chromosome. Finally, we observed two cases with Alu- and LINE-mediated rearrangements as well as two unrelated individuals with seemingly identical clustered CNVs on 2p25.3, possibly a rare European founder rearrangement. In conclusion, through detailed characterization of the derivative chromosomes we show that multiple mechanisms are likely involved in the formation of clustered CNVs and add further evidence for chromoanagenesis mechanisms in both \"simple\" and highly complex chromosomal rearrangements. Finally, WGS characterization adds positional information, important for a correct clinical interpretation and deciphering mechanisms involved in the formation of these rearrangements.", "doi": "10.1371/journal.pgen.1007780", "pmid": "30419018", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-18-01290"}, {"db": "pmc", "key": "PMC6258378"}], "notes": [], "created": "2019-01-04T14:04:10.399Z", "modified": "2021-07-07T15:19:21.415Z"}, {"entity": "publication", "iuid": "68c53403732e496f9fd2f1e5affc34d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68c53403732e496f9fd2f1e5affc34d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68c53403732e496f9fd2f1e5affc34d3"}}, "title": "Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.", "authors": [{"family": "Hu", "given": "Yue O O", "initials": "YOO", "orcid": "0000-0002-2025-2198", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8675dd0fbc44f892614c848dbade8f.json"}}, {"family": "Ndegwa", "given": "Nelson", "initials": "N", "orcid": "0000-0002-5853-879X", "researcher": {"href": "https://publications.scilifelab.se/researcher/69494d497aca4285a950e335c2978135.json"}}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Johansson", "given": "Sebastian", "initials": "S"}, {"family": "Logue", "given": "J\u00fcrg Brendan", "initials": "JB"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Fagerberg", "given": "Jens", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2018-08-09", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "11907", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.", "doi": "10.1038/s41598-018-29920-7", "pmid": "30093614", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-29920-7"}, {"db": "pmc", "key": "PMC6085348"}], "notes": [], "created": "2018-10-31T19:44:54.553Z", "modified": "2024-01-16T13:48:45.757Z"}, {"entity": "publication", "iuid": "4bce9e4e56a24b87b1fc941557a2ade8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4bce9e4e56a24b87b1fc941557a2ade8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4bce9e4e56a24b87b1fc941557a2ade8"}}, "title": "Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.", "authors": [{"family": "Redin", "given": "David", "initials": "D"}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "He", "given": "Mengxiao", "initials": "M"}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2017-07-27", "journal": {"volume": "45", "issn": "1362-4962", "issue": "13", "pages": "e125", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Data produced with short-read sequencing technologies result in ambiguous haplotyping and a limited capacity to investigate the full repertoire of biologically relevant forms of genetic variation. The notion of haplotype-resolved sequencing data has recently gained traction to reduce this unwanted ambiguity and enable exploration of other forms of genetic variation; beyond studies of just nucleotide polymorphisms, such as compound heterozygosity and structural variations. Here we describe Droplet Barcode Sequencing, a novel approach for creating linked-read sequencing libraries by uniquely barcoding the information within single DNA molecules in emulsion droplets, without the aid of specialty reagents or microfluidic devices. Barcode generation and template amplification is performed simultaneously in a single enzymatic reaction, greatly simplifying the workflow and minimizing assay costs compared to alternative approaches. The method has been applied to phase multiple loci targeting all exons of the highly variable Human Leukocyte Antigen A (HLA-A) gene, with DNA from eight individuals present in the same assay. Barcode-based clustering of sequencing reads confirmed analysis of over 2000 independently assayed template molecules, with an average of 753 reads in support of called polymorphisms. Our results show unequivocal characterization of all alleles present, validated by correspondence against confirmed HLA database entries and haplotyping results from previous studies.", "doi": "10.1093/nar/gkx436", "pmid": "28525570", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3835310"}, {"db": "pmc", "key": "PMC5569991"}], "notes": [], "created": "2017-11-03T16:11:37.322Z", "modified": "2024-01-16T13:48:47.712Z"}, {"entity": "publication", "iuid": "3932c9f238004aaa8daf5320158c70ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3932c9f238004aaa8daf5320158c70ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3932c9f238004aaa8daf5320158c70ff"}}, "title": "Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.", "authors": [{"family": "Engstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Wojdacz", "given": "Tomasz K", "initials": "TK"}, {"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Prezza", "given": "Nicola", "initials": "N"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Vahter", "given": "Marie", "initials": "M"}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "91", "issn": "1432-0738", "issue": "5", "pages": "2067-2078", "title": "Arch. Toxicol.", "issn-l": "0340-5761"}, "abstract": "Arsenic, a carcinogen with immunotoxic effects, is a common contaminant of drinking water and certain food worldwide. We hypothesized that chronic arsenic exposure alters gene expression, potentially by altering DNA methylation of genes encoding central components of the immune system. We therefore analyzed the transcriptomes (by RNA sequencing) and methylomes (by target-enrichment next-generation sequencing) of primary CD4-positive T cells from matched groups of four women each in the Argentinean Andes, with fivefold differences in urinary arsenic concentrations (median concentrations of urinary arsenic in the lower- and high-arsenic groups: 65 and 276 \u03bcg/l, respectively). Arsenic exposure was associated with genome-wide alterations of gene expression; principal component analysis indicated that the exposure explained 53% of the variance in gene expression among the top variable genes and 19% of 28,351 genes were differentially expressed (false discovery rate <0.05) between the exposure groups. Key genes regulating the immune system, such as tumor necrosis factor alpha and interferon gamma, as well as genes related to the NF-kappa-beta complex, were significantly downregulated in the high-arsenic group. Arsenic exposure was associated with genome-wide DNA methylation; the high-arsenic group had 3% points higher genome-wide full methylation (>80% methylation) than the lower-arsenic group. Differentially methylated regions that were hyper-methylated in the high-arsenic group showed enrichment for immune-related gene ontologies that constitute the basic functions of CD4-positive T cells, such as isotype switching and lymphocyte activation and differentiation. In conclusion, chronic arsenic exposure from drinking water was related to changes in the transcriptome and methylome of CD4-positive T cells, both genome wide and in specific genes, supporting the hypothesis that arsenic causes immunotoxicity by interfering with gene expression and regulation.", "doi": "10.1007/s00204-016-1879-4", "pmid": "27838757", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s00204-016-1879-4"}, {"db": "pmc", "key": "PMC5399044"}], "notes": [], "created": "2017-05-03T12:59:46.128Z", "modified": "2024-01-16T13:48:48.019Z"}, {"entity": "publication", "iuid": "7de7ae9e75fe4fa281ab300f10a19c69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7de7ae9e75fe4fa281ab300f10a19c69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7de7ae9e75fe4fa281ab300f10a19c69"}}, "title": "Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation.", "authors": [{"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Gustavsson", "given": "Peter", "initials": "P"}, {"family": "F\u00f6rster", "given": "Alisa", "initials": "A"}, {"family": "Hofmeister", "given": "Wolfgang", "initials": "W"}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Lupski", "given": "James R", "initials": "JR"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Lundberg", "given": "Elisabeth Syk", "initials": "ES"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "38", "issn": "1098-1004", "issue": "2", "pages": "180-192", "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n = 4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by error-prone replication-based repair mechanisms. Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.", "doi": "10.1002/humu.23146", "pmid": "27862604", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5225243"}, {"db": "mid", "key": "NIHMS830031"}], "notes": [], "created": "2017-05-03T12:59:45.241Z", "modified": "2024-01-16T13:48:48.524Z"}, {"entity": "publication", "iuid": "8a8e6eb7f7f94c1fb129b51ef32d3405", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a8e6eb7f7f94c1fb129b51ef32d3405.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a8e6eb7f7f94c1fb129b51ef32d3405"}}, "title": "Cluster Flow: A user-friendly bioinformatics workflow tool.", "authors": [{"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Krueger", "given": "Felix", "initials": "F"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Andrews", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2016-12-06", "journal": {"volume": "5", "issn": "2046-1402", "issue": null, "pages": "2824", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at http://clusterflow.io.", "doi": "10.12688/f1000research.10335.2", "pmid": "28299179", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5310375"}], "notes": [], "created": "2020-06-30T12:52:40.081Z", "modified": "2021-07-07T15:22:42.766Z"}, {"entity": "publication", "iuid": "b7cde7b362a84da3b4a7bd88f1306b69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7cde7b362a84da3b4a7bd88f1306b69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7cde7b362a84da3b4a7bd88f1306b69"}}, "title": "MultiQC: summarize analysis results for multiple tools and samples in a single report.", "authors": [{"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "Magnusson", "given": "M\u00e5ns", "initials": "M"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}], "type": "journal article", "published": "2016-10-01", "journal": {"volume": "32", "issn": "1367-4811", "issue": "19", "pages": "3047-3048", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis.\n\nWe present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization.\n\nMultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports are available at http://multiqc.info\n\nphil.ewels@scilifelab.se.", "doi": "10.1093/bioinformatics/btw354", "pmid": "27312411", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Stockholm (Genomics Applications)": "Technology development", "NGI Stockholm (Genomics Production)": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "btw354"}, {"db": "pmc", "key": "PMC5039924"}], "notes": [], "created": "2017-05-03T13:00:06.264Z", "modified": "2024-01-16T13:48:49.233Z"}, {"entity": "publication", "iuid": "7d3a9a83444049e8b4d26652d57f1ad6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d3a9a83444049e8b4d26652d57f1ad6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d3a9a83444049e8b4d26652d57f1ad6"}}, "title": "Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.", "authors": [{"family": "Ivanov", "given": "Maxim", "initials": "M"}, {"family": "Kals", "given": "Mart", "initials": "M"}, {"family": "Lauschke", "given": "Volker", "initials": "V"}, {"family": "Barragan", "given": "Isabel", "initials": "I"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Ingelman-Sundberg", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2016-08-19", "journal": {"volume": "44", "issn": "1362-4962", "issue": "14", "pages": "6756-6769", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross-comparisons revealed that protocols based on Tet1-assisted bisulfite conversion provided more precise hmC values than TrueMethyl-based methods. A total of 109 454 CpG sites were analyzed by TAB-Methyl-SEQ for mC and hmC in 188 genes from 20 different adult human livers. We describe three types of variability of hepatic hmC profiles: (i) sample-specific variability at 40.8% of CpG sites analyzed, where the local hmC values correlate to the global hmC content of livers (measured by LC-MS), (ii) gene-specific variability, where hmC levels in the coding regions positively correlate to expression of the respective gene and (iii) site-specific variability, where prominent hmC peaks span only 1 to 3 neighboring CpG sites. Our data suggest that both the gene- and site-specific components of hmC variability might contribute to the epigenetic control of hepatic genes. The protocol described here should be useful for targeted DNA analysis in a variety of applications.", "doi": "10.1093/nar/gkw316", "pmid": "27131363", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Clinical Proteomics Mass spectrometry": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gkw316"}, {"db": "pmc", "key": "PMC5001587"}], "notes": [], "created": "2017-05-03T13:00:08.926Z", "modified": "2024-01-16T13:48:49.630Z"}, {"entity": "publication", "iuid": "047ee868b5db45eca47e6761a67fbe44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/047ee868b5db45eca47e6761a67fbe44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/047ee868b5db45eca47e6761a67fbe44"}}, "title": "Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2.", "authors": [{"family": "Prezza", "given": "Nicola", "initials": "N"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Policriti", "given": "Alberto", "initials": "A"}], "type": "journal article", "published": "2016-03-02", "journal": {"volume": "17 Suppl 4", "issn": "1471-2105", "issue": null, "pages": "69", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "Bisulfite treatment of DNA followed by sequencing (BS-seq) has become a standard technique in epigenetic studies, providing researchers with tools for generating single-base resolution maps of whole methylomes. Aligning bisulfite-treated reads, however, is a computationally difficult task: bisulfite treatment decreases the (lexical) complexity of low-methylated genomic regions, and C-to-T mismatches may reflect cytosine unmethylation rather than SNPs or sequencing errors. Further challenges arise both during and after the alignment phase: data structures used by the aligner should be fast and should fit into main memory, and the methylation-caller output should be somehow compressed, due to its significant size.\n\nAs far as data structures employed to align bisulfite-treated reads are concerned, solutions proposed in the literature can be roughly grouped into two main categories: those storing pointers at each text position (e.g. hash tables, suffix trees/arrays), and those using the information-theoretic minimum number of bits (e.g. FM indexes and compressed suffix arrays). The former are fast and memory consuming. The latter are much slower and light. In this paper, we try to close this gap proposing a data structure for aligning bisulfite-treated reads which is at the same time fast, light, and very accurate. We reach this objective by combining a recent theoretical result on succinct hashing with a bisulfite-aware hash function. Furthermore, the new versions of the tools implementing our ideas|the aligner ERNE-BS5 2 and the caller ERNE-METH 2|have been extended with increased downstream compatibility (EPP/Bismark cov output formats), output compression, and support for target enrichment protocols.\n\nExperimental results on public and simulated WGBS libraries show that our algorithmic solution is a competitive tradeoff between hash-based and BWT-based indexes, being as fast and accurate as the former, and as memory-efficient as the latter.\n\nThe new functionalities of our bisulfite aligner and caller make it a fast and memory efficient tool, useful to analyze big datasets with little computational resources, to easily process target enrichment data, and produce statistics such as protocol efficiency and coverage as a function of the distance from target regions.", "doi": "10.1186/s12859-016-0910-3", "pmid": "26961371", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-016-0910-3"}, {"db": "pmc", "key": "PMC4896272"}], "notes": [], "created": "2017-05-03T13:01:06.997Z", "modified": "2021-07-07T15:22:42.670Z"}, {"entity": "publication", "iuid": "dc2cd11e7ff44704ad1f5e7c52f309bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc2cd11e7ff44704ad1f5e7c52f309bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc2cd11e7ff44704ad1f5e7c52f309bc"}}, "title": "T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis.", "authors": [{"family": "Grunewald", "given": "Johan", "initials": "J"}, {"family": "Kaiser", "given": "Ylva", "initials": "Y"}, {"family": "Ostadkarampour", "given": "Mahyar", "initials": "M"}, {"family": "Rivera", "given": "Natalia V", "initials": "NV"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Sylwan", "given": "Lina", "initials": "L"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Sandalova", "given": "Tatiana", "initials": "T"}, {"family": "Ahlgren", "given": "Kerstin M", "initials": "KM"}, {"family": "Wahlstr\u00f6m", "given": "Jan", "initials": "J"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Ronninger", "given": "Marcus", "initials": "M"}, {"family": "Eklund", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2016-03-00", "journal": {"volume": "47", "issn": "1399-3003", "issue": "3", "pages": "898-909", "title": "Eur. Respir. J.", "issn-l": "0903-1936"}, "abstract": "In pulmonary sarcoidosis, CD4(+) T-cells expressing T-cell receptor V\u03b12.3 accumulate in the lungs of HLA-DRB1*03(+) patients. To investigate T-cell receptor-HLA-DRB1*03 interactions underlying recognition of hitherto unknown antigens, we performed detailed analyses of T-cell receptor expression on bronchoalveolar lavage fluid CD4(+) T-cells from sarcoidosis patients.Pulmonary sarcoidosis patients (n=43) underwent bronchoscopy with bronchoalveolar lavage. T-cell receptor \u03b1 and \u03b2 chains of CD4(+) T-cells were analysed by flow cytometry, DNA-sequenced, and three-dimensional molecular models of T-cell receptor-HLA-DRB1*03 complexes generated.Simultaneous expression of V\u03b12.3 with the V\u03b222 chain was identified in the lungs of all HLA-DRB1*03(+) patients. Accumulated V\u03b12.3/V\u03b222-expressing T-cells were highly clonal, with identical or near-identical V\u03b12.3 chain sequences and inter-patient similarities in V\u03b222 chain amino acid distribution. Molecular modelling revealed specific T-cell receptor-HLA-DRB1*03-peptide interactions, with a previously identified, sarcoidosis-associated vimentin peptide, (Vim)429-443 DSLPLVDTHSKRTLL, matching both the HLA peptide-binding cleft and distinct T-cell receptor features perfectly.We demonstrate, for the first time, the accumulation of large clonal populations of specific V\u03b12.3/V\u03b222 T-cell receptor-expressing CD4(+) T-cells in the lungs of HLA-DRB1*03(+) sarcoidosis patients. Several distinct contact points between V\u03b12.3/V\u03b222 receptors and HLA-DRB1*03 molecules suggest presentation of prototypic vimentin-derived peptides.", "doi": "10.1183/13993003.01209-2015", "pmid": "26585430", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "13993003.01209-2015"}], "notes": [], "created": "2017-05-02T12:57:09.283Z", "modified": "2024-01-16T13:48:50.378Z"}, {"entity": "publication", "iuid": "42f4c093ad4944ef8a0a2edfeea4ff25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42f4c093ad4944ef8a0a2edfeea4ff25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42f4c093ad4944ef8a0a2edfeea4ff25"}}, "title": "De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.", "authors": [{"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Tiukova", "given": "Ievgeniia", "initials": "I"}, {"family": "Holmberg", "given": "Kicki", "initials": "K"}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}], "type": "journal article", "published": "2015-11-26", "journal": {"volume": "4", "issn": "2047-217X", "issue": null, "pages": "56", "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": "It remains a challenge to perform de novo assembly using next-generation sequencing (NGS). Despite the availability of multiple sequencing technologies and tools (e.g., assemblers) it is still difficult to assemble new genomes at chromosome resolution (i.e., one sequence per chromosome). Obtaining high quality draft assemblies is extremely important in the case of yeast genomes to better characterise major events in their evolutionary history. The aim of this work is two-fold: on the one hand we want to show how combining different and somewhat complementary technologies is key to improving assembly quality and correctness, and on the other hand we present a de novo assembly pipeline we believe to be beneficial to core facility bioinformaticians. To demonstrate both the effectiveness of combining technologies and the simplicity of the pipeline, here we present the results obtained using the Dekkera bruxellensis genome.\n\nIn this work we used short-read Illumina data and long-read PacBio data combined with the extreme long-range information from OpGen optical maps in the task of de novo genome assembly and finishing. Moreover, we developed NouGAT, a semi-automated pipeline for read-preprocessing, de novo assembly and assembly evaluation, which was instrumental for this work.\n\nWe obtained a high quality draft assembly of a yeast genome, resolved on a chromosomal level. Furthermore, this assembly was corrected for mis-assembly errors as demonstrated by resolving a large collapsed repeat and by receiving higher scores by assembly evaluation tools. With the inclusion of PacBio data we were able to fill about 5 % of the optical mapped genome not covered by the Illumina data.", "doi": "10.1186/s13742-015-0094-1", "pmid": "26617983", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "94"}, {"db": "pmc", "key": "PMC4661999"}], "notes": [], "created": "2017-05-02T12:58:21.226Z", "modified": "2021-07-07T15:22:42.719Z"}, {"entity": "publication", "iuid": "3b4640678c814b81b4501deaea6a6ee1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b4640678c814b81b4501deaea6a6ee1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b4640678c814b81b4501deaea6a6ee1"}}, "title": "Endonuclease specificity and sequence dependence of type IIS restriction enzymes.", "authors": [{"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Terje-Hegge", "given": "Finn", "initials": "F"}, {"family": "Foam", "given": "Napoleon", "initials": "N"}, {"family": "Pettersson", "given": "Erik", "initials": "E"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Lexow", "given": "Preben", "initials": "P"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2015-01-28", "journal": {"volume": "10", "issn": "1932-6203", "issue": "1", "pages": "e0117059", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Restriction enzymes that recognize specific sequences but cleave unknown sequence outside the recognition site are extensively utilized tools in molecular biology. Despite this, systematic functional categorization of cleavage performance has largely been lacking. We established a simple and automatable model system to assay cleavage distance variation (termed slippage) and the sequence dependence thereof. We coupled this to massively parallel sequencing in order to provide sensitive and accurate measurement. With this system 14 enzymes were assayed (AcuI, BbvI, BpmI, BpuEI, BseRI, BsgI, Eco57I, Eco57MI, EcoP15I, FauI, FokI, GsuI, MmeI and SmuI). We report significant variation of slippage ranging from 1-54%, variations in sequence context dependence, as well as variation between isoschizomers. We believe this largely overlooked property of enzymes with shifted cleavage would benefit from further large scale classification and engineering efforts seeking to improve performance. The gained insights of in-vitro performance may also aid the in-vivo understanding of these enzymes.", "doi": "10.1371/journal.pone.0117059", "pmid": "25629514", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-15706"}, {"db": "pmc", "key": "PMC4309577"}, {"db": "SRA", "key": "SRS627913"}], "notes": [], "created": "2017-05-02T12:57:53.663Z", "modified": "2023-06-19T07:51:37.768Z"}, {"entity": "publication", "iuid": "f644bbecaad54a70b4af3aa0563de6a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f644bbecaad54a70b4af3aa0563de6a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f644bbecaad54a70b4af3aa0563de6a4"}}, "title": "The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.", "authors": [{"family": "Wiegand", "given": "Stephan", "initials": "S"}, {"family": "Meier", "given": "Doreen", "initials": "D"}, {"family": "Seehafer", "given": "Carsten", "initials": "C"}, {"family": "Malicki", "given": "Marek", "initials": "M"}, {"family": "Hofmann", "given": "Patrick", "initials": "P"}, {"family": "Schmith", "given": "Anika", "initials": "A"}, {"family": "Winckler", "given": "Thomas", "initials": "T"}, {"family": "F\u00f6ldesi", "given": "Balint", "initials": "B"}, {"family": "Boesler", "given": "Benjamin", "initials": "B"}, {"family": "Nellen", "given": "Wolfgang", "initials": "W"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Avesson", "given": "Lotta", "initials": "L"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}, {"family": "Hammann", "given": "Christian", "initials": "C"}], "type": "journal article", "published": "2014-03-00", "journal": {"volume": "42", "issn": "1362-4962", "issue": "5", "pages": "3330-3345", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the function of centromeres, rendering tight retrotransposition control critical to maintaining chromosome integrity. We report that in deletion strains of the RNA-dependent RNA polymerase RrpC, full-length and shorter DIRS-1 messenger RNAs are strongly enriched. Shorter versions of a hitherto unknown long non-coding RNA in DIRS-1 antisense orientation are also enriched in rrpC- strains. Concurrent with the accumulation of long transcripts, the vast majority of small (21 mer) DIRS-1 RNAs vanish in rrpC- strains. RNASeq reveals an asymmetric distribution of the DIRS-1 small RNAs, both along DIRS-1 and with respect to sense and antisense orientation. We show that RrpC is required for post-transcriptional DIRS-1 silencing and also for spreading of RNA silencing signals. Finally, DIRS-1 mis-regulation in the absence of RrpC leads to retrotransposon mobilization. In summary, our data reveal RrpC as a key player in the silencing of centromeric retrotransposon DIRS-1. RrpC acts at the post-transcriptional level and is involved in spreading of RNA silencing signals, both in the 5' and 3' directions.", "doi": "10.1093/nar/gkt1337", "pmid": "24369430", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "gkt1337"}, {"db": "pmc", "key": "PMC3950715"}], "notes": [], "created": "2017-05-04T14:58:50.055Z", "modified": "2021-07-07T15:22:42.817Z"}, {"entity": "publication", "iuid": "df27a432e7124f1da1ed145232f0c0fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df27a432e7124f1da1ed145232f0c0fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df27a432e7124f1da1ed145232f0c0fe"}}, "title": "Assessment of whole genome amplification for sequence capture and massively parallel sequencing.", "authors": [{"family": "Hasmats", "given": "Johanna", "initials": "J"}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}, {"family": "Orear", "given": "Cedric", "initials": "C"}, {"family": "Validire", "given": "Pierre", "initials": "P"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2014-01-07", "journal": {"volume": "9", "issn": "1932-6203", "issue": "1", "pages": "e84785", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Exome sequence capture and massively parallel sequencing can be combined to achieve inexpensive and rapid global analyses of the functional sections of the genome. The difficulties of working with relatively small quantities of genetic material, as may be necessary when sharing tumor biopsies between collaborators for instance, can be overcome using whole genome amplification. However, the potential drawbacks of using a whole genome amplification technology based on random primers in combination with sequence capture followed by massively parallel sequencing have not yet been examined in detail, especially in the context of mutation discovery in tumor material. In this work, we compare mutations detected in sequence data for unamplified DNA, whole genome amplified DNA, and RNA originating from the same tumor tissue samples from 16 patients diagnosed with non-small cell lung cancer. The results obtained provide a comprehensive overview of the merits of these techniques for mutation analysis. We evaluated the identified genetic variants, and found that most (74%) of them were observed in both the amplified and the unamplified sequence data. Eighty-nine percent of the variations found by WGA were shared with unamplified DNA. We demonstrate a strategy for avoiding allelic bias by including RNA-sequencing information.", "doi": "10.1371/journal.pone.0084785", "pmid": "24409309", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-22492"}, {"db": "pmc", "key": "PMC3883664"}], "notes": [], "created": "2017-05-04T14:58:54.190Z", "modified": "2021-07-08T13:26:08.375Z"}, {"entity": "publication", "iuid": "c522f5cf12954e2ca97ffac12e5e0bfb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c522f5cf12954e2ca97ffac12e5e0bfb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c522f5cf12954e2ca97ffac12e5e0bfb"}}, "title": "Chemical fragmentation for massively parallel sequencing library preparation.", "authors": [{"family": "Gyarmati", "given": "P", "initials": "P"}, {"family": "Song", "given": "Y", "initials": "Y"}, {"family": "H\u00e4llman", "given": "J", "initials": "J"}, {"family": "K\u00e4ller", "given": "M", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}], "type": "journal article", "published": "2013-10-10", "journal": {"volume": "168", "issn": "1873-4863", "issue": "1", "pages": "95-100", "title": "J. Biotechnol.", "issn-l": "0168-1656"}, "abstract": "Fragmentation is essential in most library preparation protocols for use with massively parallel sequencing systems. Complexes that generate hydroxyl radicals, such as iron-EDTA, can be used to introduce random DNA cleavage. Here we describe a chemical fragmentation method that can be incorporated into library preparation protocols for next-generation sequencing workflows. This protocol has been validated by whole genome, amplicon and exome sequencing. Chemical fragmentation is a cost-effective alternative to current fragmentation methods that has no observable sequence bias and requires no instrumentation.", "doi": "10.1016/j.jbiotec.2013.08.020", "pmid": "23994687", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0168-1656(13)00365-9"}], "notes": [], "created": "2017-05-04T14:57:59.697Z", "modified": "2021-07-07T15:22:42.796Z"}, {"entity": "publication", "iuid": "c403f99f84324b52bc5e13ce42920772", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c403f99f84324b52bc5e13ce42920772.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c403f99f84324b52bc5e13ce42920772"}}, "title": "The Norway spruce genome sequence and conifer genome evolution.", "authors": [{"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Wetterbom", "given": "Anna", "initials": "A"}, {"family": "Zuccolo", "given": "Andrea", "initials": "A"}, {"family": "Lin", "given": "Yao-Cheng", "initials": "YC"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Vicedomini", "given": "Riccardo", "initials": "R"}, {"family": "Sahlin", "given": "Kristoffer", "initials": "K"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "Gramzow", "given": "Lydia", "initials": "L"}, {"family": "Holmberg", "given": "Kristina", "initials": "K"}, {"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "Keech", "given": "Olivier", "initials": "O"}, {"family": "Klasson", "given": "Lisa", "initials": "L"}, {"family": "Koriabine", "given": "Maxim", "initials": "M"}, {"family": "Kucukoglu", "given": "Melis", "initials": "M"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Luthman", "given": "Johannes", "initials": "J"}, {"family": "Lysholm", "given": "Fredrik", "initials": "F"}, {"family": "Niittyl\u00e4", "given": "Totte", "initials": "T"}, {"family": "Olson", "given": "Ake", "initials": "A"}, {"family": "Rilakovic", "given": "Nemanja", "initials": "N"}, {"family": "Ritland", "given": "Carol", "initials": "C"}, {"family": "Rossell\u00f3", "given": "Josep A", "initials": "JA"}, {"family": "Sena", "given": "Juliana", "initials": "J"}, {"family": "Svensson", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Talavera-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Thei\u00dfen", "given": "G\u00fcnter", "initials": "G"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}, {"family": "Vanneste", "given": "Kevin", "initials": "K"}, {"family": "Wu", "given": "Zhi-Qiang", "initials": "ZQ"}, {"family": "Zhang", "given": "Bo", "initials": "B"}, {"family": "Zerbe", "given": "Philipp", "initials": "P"}, {"family": "Arvestad", "given": "Lars", "initials": "L"}, {"family": "Bhalerao", "given": "Rishikesh", "initials": "R"}, {"family": "Bohlmann", "given": "Joerg", "initials": "J"}, {"family": "Bousquet", "given": "Jean", "initials": "J"}, {"family": "Garcia Gil", "given": "Rosario", "initials": "R"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "de Jong", "given": "Pieter", "initials": "P"}, {"family": "MacKay", "given": "John", "initials": "J"}, {"family": "Morgante", "given": "Michele", "initials": "M"}, {"family": "Ritland", "given": "Kermit", "initials": "K"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Thompson", "given": "Stacey Lee", "initials": "SL"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2013-05-30", "journal": {"volume": "497", "issn": "1476-4687", "issue": "7451", "pages": "579-584", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.", "doi": "10.1038/nature12211", "pmid": "23698360", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support for Computational Resources": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "nature12211"}], "notes": [], "created": "2017-05-04T14:56:13.625Z", "modified": "2024-01-16T13:48:50.828Z"}, {"entity": "publication", "iuid": "1ffdcc71b4b048d4b6e82279e3a06bca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ffdcc71b4b048d4b6e82279e3a06bca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ffdcc71b4b048d4b6e82279e3a06bca"}}, "title": "Identification and verification of microRNAs by high-throughput sequencing.", "authors": [{"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "Avesson", "given": "Lotta", "initials": "L"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2013-03-16", "journal": {"volume": "983", "issn": "1940-6029", "issue": null, "pages": "125-138", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "High-throughput sequencing methods have become invaluable for detection and analysis of small RNAs. The results are millions of sequences that need to be carefully analyzed by computational methods and preferentially verified by different experimental techniques. Here we describe how to use high-throughput sequencing followed by bioinformatics and northern blot to identify one particular class of small RNA, microRNAs.", "doi": "10.1007/978-1-62703-302-2_7", "pmid": "23494305", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:04.217Z", "modified": "2021-07-07T15:22:42.686Z"}, {"entity": "publication", "iuid": "bb9b79fb1a9f423892352a8eb8c5a56d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb9b79fb1a9f423892352a8eb8c5a56d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb9b79fb1a9f423892352a8eb8c5a56d"}}, "title": "Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.", "authors": [{"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Lexow", "given": "Preben", "initials": "P"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2013-03-09", "journal": {"volume": "3", "issn": "2045-2322", "issue": null, "pages": "1186", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Here we demonstrate the use of short-read massive sequencing systems to in effect achieve longer read lengths through hierarchical molecular tagging. We show how indexed and PCR-amplified targeted libraries are degraded, sub-sampled and arrested at timed intervals to achieve pools of differing average length, each of which is indexed with a new tag. By this process, indices of sample origin, molecular origin, and degree of degradation is incorporated in order to achieve a nested hierarchical structure, later to be utilized in the data processing to order the reads over a longer distance than the sequencing system originally allows. With this protocol we show how continuous regions beyond 3000 bp can be decoded by an Illumina sequencing system, and we illustrate the potential applications by calling variants of the lambda genome, analysing TP53 in cancer cell lines, and targeting a variable canine mitochondrial region.", "doi": "10.1038/srep01186", "pmid": "23470464", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep01186"}, {"db": "pmc", "key": "PMC3592332"}], "notes": [], "created": "2017-05-04T14:58:18.306Z", "modified": "2021-07-08T13:26:08.313Z"}, {"entity": "publication", "iuid": "4ac7c51a01b2483582546addacfcc239", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ac7c51a01b2483582546addacfcc239.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ac7c51a01b2483582546addacfcc239"}}, "title": "Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.", "authors": [{"family": "Solnestam", "given": "Beata Werne", "initials": "BW"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Akan", "given": "Pelin", "initials": "P"}], "type": "comparative study", "published": "2012-10-30", "journal": {"volume": "13", "issn": "1471-2164", "issue": null, "pages": "574", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The majority of published gene-expression studies have used RNA isolated from whole cells, overlooking the potential impact of including nuclear transcriptome in the analyses. In this study, mRNA fractions from the cytoplasm and from whole cells (total RNA) were prepared from three human cell lines and sequenced using massive parallel sequencing.\n\nFor all three cell lines, of about 15000 detected genes approximately 400 to 1400 genes were detected in different amounts in the cytoplasmic and total RNA fractions. Transcripts detected at higher levels in the total RNA fraction had longer coding sequences and higher number of miRNA target sites. Transcripts detected at higher levels in the cytoplasmic fraction were shorter or contained shorter untranslated regions. Nuclear retention of transcripts and mRNA degradation via miRNA pathway might contribute to this differential detection of genes. The consequence of the differential detection was further investigated by comparison to proteomics data. Interestingly, the expression profiles of cytoplasmic and total RNA correlated equally well with protein abundance levels indicating regulation at a higher level.\n\nWe conclude that expression levels derived from the total RNA fraction be regarded as an appropriate estimate of the amount of mRNAs present in a given cell population, independent of the coding sequence length or UTRs.", "doi": "10.1186/1471-2164-13-574", "pmid": "23110385", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "1471-2164-13-574"}, {"db": "pmc", "key": "PMC3495644"}], "notes": [], "created": "2017-05-04T14:55:09.570Z", "modified": "2021-07-08T13:26:08.160Z"}, {"entity": "publication", "iuid": "08724dafbd20444493259361ecf49fb8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08724dafbd20444493259361ecf49fb8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08724dafbd20444493259361ecf49fb8"}}, "title": "Classification of DNA sequences using Bloom filters.", "authors": [{"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Allander", "given": "Tobias", "initials": "T"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Arvestad", "given": "Lars", "initials": "L"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2010-07-01", "journal": {"volume": "26", "issn": "1367-4811", "issue": "13", "pages": "1595-1600", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "New generation sequencing technologies producing increasingly complex datasets demand new efficient and specialized sequence analysis algorithms. Often, it is only the 'novel' sequences in a complex dataset that are of interest and the superfluous sequences need to be removed.\n\nA novel algorithm, fast and accurate classification of sequences (FACSs), is introduced that can accurately and rapidly classify sequences as belonging or not belonging to a reference sequence. FACS was first optimized and validated using a synthetic metagenome dataset. An experimental metagenome dataset was then used to show that FACS achieves comparable accuracy as BLAT and SSAHA2 but is at least 21 times faster in classifying sequences.\n\nSource code for FACS, Bloom filters and MetaSim dataset used is available at http://facs.biotech.kth.se. The Bloom::Faster 1.6 Perl module can be downloaded from CPAN at http://search.cpan.org/ approximately palvaro/Bloom-Faster-1.6/\n\nhenrik.stranneheim@biotech.kth.se; joakiml@biotech.kth.se\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btq230", "pmid": "20472541", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "btq230"}, {"db": "pmc", "key": "PMC2887045"}], "notes": [], "created": "2017-05-04T14:57:09.345Z", "modified": "2021-07-08T13:26:08.074Z"}]}