{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T20:04:25Z","timestamp":1762459465020,"version":"3.37.3"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2017,4,10]],"date-time":"2017-04-10T00:00:00Z","timestamp":1491782400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,3]]},"DOI":"10.1093\/nar\/gkx258","type":"journal-article","created":{"date-parts":[[2017,4,5]],"date-time":"2017-04-05T09:44:52Z","timestamp":1491385492000},"page":"W445-W452","source":"Crossref","is-referenced-by-count":12,"title":["Omicseq: a web-based search engine for exploring omics datasets"],"prefix":"10.1093","volume":"45","author":[{"given":"Xiaobo","family":"Sun","sequence":"first","affiliation":[]},{"given":"William S.","family":"Pittard","sequence":"additional","affiliation":[]},{"given":"Tianlei","family":"Xu","sequence":"additional","affiliation":[]},{"given":"Li","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Michael E.","family":"Zwick","sequence":"additional","affiliation":[]},{"given":"Xiaoqian","family":"Jiang","sequence":"additional","affiliation":[]},{"given":"Fusheng","family":"Wang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1583-146X","authenticated-orcid":false,"given":"Zhaohui S.","family":"Qin","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2017,4,10]]},"reference":[{"key":"key\n\t\t\t\t20180201083703_B1","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","article-title":"Genome-wide mapping of in vivo protein-DNA interactions","volume":"316","author":"Johnson","year":"2007","journal-title":"Science"},{"key":"key\n\t\t\t\t20180201083703_B2","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"key\n\t\t\t\t20180201083703_B3","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/nmeth1068","article-title":"Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing","volume":"4","author":"Robertson","year":"2007","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20180201083703_B4","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20180201083703_B5","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2013update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180201083703_B6","doi-asserted-by":"crossref","first-page":"D54","DOI":"10.1093\/nar\/gkr854","article-title":"The sequence read archive: explosive growth of sequencing data","volume":"40","author":"Kodama","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180201083703_B7","doi-asserted-by":"crossref","first-page":"D747","DOI":"10.1093\/nar\/gkl995","article-title":"ArrayExpress\u2014a public database of microarray experiments and gene expression profiles","volume":"35","author":"Parkinson","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180201083703_B8","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1,092 human genomes","volume":"491","author":"Consortium","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180201083703_B9","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature07385","article-title":"Comprehensive genomic characterization defines human glioblastoma genes and core pathways","volume":"455","author":"Network","year":"2008","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180201083703_B10","doi-asserted-by":"crossref","first-page":"bar026","DOI":"10.1093\/database\/bar026","article-title":"International Cancer Genome Consortium Data Portal\u2014a one-stop shop for cancer genomics data","volume":"2011","author":"Zhang","year":"2011","journal-title":"Database"},{"key":"key\n\t\t\t\t20180201083703_B11","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"Consortium","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180201083703_B12","doi-asserted-by":"crossref","first-page":"1775","DOI":"10.1126\/science.1196914","article-title":"Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project","volume":"330","author":"Gerstein","year":"2010","journal-title":"Science"},{"key":"key\n\t\t\t\t20180201083703_B13","doi-asserted-by":"crossref","first-page":"1787","DOI":"10.1126\/science.1198374","article-title":"Identification of functional elements and regulatory circuits by Drosophila modENCODE","volume":"330","author":"mod","year":"2010","journal-title":"Science"},{"key":"key\n\t\t\t\t20180201083703_B14","doi-asserted-by":"crossref","first-page":"317","DOI":"10.2217\/epi.12.18","article-title":"The NIH Roadmap Epigenomics Program data resource","volume":"4","author":"Chadwick","year":"2012","journal-title":"Epigenomics"},{"key":"key\n\t\t\t\t20180201083703_B15","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","article-title":"Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes","volume":"15","author":"Siepel","year":"2005","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20180201083703_B16","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60,706 humans","volume":"536","author":"Lek","year":"2016","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180201083703_B17","doi-asserted-by":"crossref","first-page":"W122","DOI":"10.1093\/nar\/gkw299","article-title":"GeNemo: a search engine for web-based functional genomic data","volume":"44","author":"Zhang","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180201083703_B18","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/S0169-7552(98)00110-X","article-title":"The anatomy of a large-scale hypertextual Web search engine","volume":"30","author":"Brin","year":"1998","journal-title":"Comput. Networks ISDN Syst."},{"key":"key\n\t\t\t\t20180201083703_B19","doi-asserted-by":"crossref","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180201083703_B20","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20180201083703_B21","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/nmeth.2956","article-title":"TCGA-assembler: open-source software for retrieving and processing TCGA data","volume":"11","author":"Zhu","year":"2014","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20180201083703_B22","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics (Oxford, England)"},{"key":"key\n\t\t\t\t20180201083703_B23","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180201083703_B24","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s13059-016-0881-8","article-title":"A survey of best practices for RNA-seq data analysis","volume":"17","author":"Conesa","year":"2016","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20180201083703_B25","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180201083703_B26","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1093\/bioinformatics\/btu049","article-title":"Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays","volume":"30","author":"Aryee","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180201083703_B27","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1126\/science.1162228","article-title":"Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters","volume":"322","author":"Core","year":"2008","journal-title":"Science"},{"key":"key\n\t\t\t\t20180201083703_B28","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/nrc1299","article-title":"A census of human cancer genes","volume":"4","author":"Futreal","year":"2004","journal-title":"Nat. Rev. Cancer"},{"key":"key\n\t\t\t\t20180201083703_B29","doi-asserted-by":"crossref","first-page":"D805","DOI":"10.1093\/nar\/gku1075","article-title":"COSMIC: exploring the world's knowledge of somatic mutations in human cancer","volume":"43","author":"Forbes","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180201083703_B30","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180201083703_B31","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nature12531","article-title":"Transcriptome and genome sequencing uncovers functional variation in humans","volume":"501","author":"Lappalainen","year":"2013","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180201083703_B32","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1038\/ng.f.217","article-title":"A wiki for the life sciences where authorship matters","volume":"40","author":"Hoffmann","year":"2008","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20180201083703_B33","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/nbt1010-1045","article-title":"The NIH Roadmap Epigenomics Mapping Consortium","volume":"28","author":"Bernstein","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t20180201083703_B34","doi-asserted-by":"crossref","first-page":"127rv123","DOI":"10.1126\/scitranslmed.3003180","article-title":"Beyond PSA: the next generation of prostate cancer biomarkers","volume":"4","author":"Prensner","year":"2012","journal-title":"Sci. Transl. Med."},{"year":"2015","author":"Lucila","article-title":"bioCADDIE white paper \u2013 Data Discovery Index","key":"key\n\t\t\t\t20180201083703_B35"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/45\/W1\/W445\/23740891\/gkx258.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T10:40:55Z","timestamp":1522665655000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/45\/W1\/W445\/3574062"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,4,10]]},"references-count":35,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2017,4,10]]},"published-print":{"date-parts":[[2017,7,3]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkx258","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"type":"print","value":"0305-1048"},{"type":"electronic","value":"1362-4962"}],"subject":[],"published-other":{"date-parts":[[2017,7,3]]},"published":{"date-parts":[[2017,4,10]]}}}