{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T15:40:15Z","timestamp":1772120415920,"version":"3.50.1"},"reference-count":90,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2015,8,6]],"date-time":"2015-08-06T00:00:00Z","timestamp":1438819200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004393","type":"journal-article","created":{"date-parts":[[2015,8,6]],"date-time":"2015-08-06T18:06:34Z","timestamp":1438884394000},"page":"e1004393","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":88,"title":["Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud"],"prefix":"10.1371","volume":"11","author":[{"given":"Malachi","family":"Griffith","sequence":"first","affiliation":[]},{"given":"Jason R.","family":"Walker","sequence":"additional","affiliation":[]},{"given":"Nicholas C.","family":"Spies","sequence":"additional","affiliation":[]},{"given":"Benjamin J.","family":"Ainscough","sequence":"additional","affiliation":[]},{"given":"Obi L.","family":"Griffith","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2015,8,6]]},"reference":[{"issue":"9","key":"ref1","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/nrg2630","article-title":"Genetics of human gene expression: mapping DNA variants that influence gene expression","volume":"10","author":"VG Cheung","year":"2009","journal-title":"Nature reviews Genetics"},{"issue":"9","key":"ref2","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1038\/nbt.2957","article-title":"A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium","volume":"32","year":"2014","journal-title":"Nature biotechnology"},{"issue":"10","key":"ref3","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1038\/nmeth.1503","article-title":"Alternative expression analysis by RNA sequencing","volume":"7","author":"M Griffith","year":"2010","journal-title":"Nature methods"},{"issue":"9","key":"ref4","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1038\/nbt.2972","article-title":"Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study","volume":"32","author":"S Li","year":"2014","journal-title":"Nature biotechnology"},{"issue":"5881","key":"ref5","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1126\/science.1158441","article-title":"The transcriptional landscape of the yeast genome defined by RNA sequencing","volume":"320","author":"U Nagalakshmi","year":"2008","journal-title":"Science"},{"issue":"1","key":"ref6","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Z Wang","year":"2009","journal-title":"Nature reviews Genetics"},{"issue":"30","key":"ref7","doi-asserted-by":"crossref","first-page":"12353","DOI":"10.1073\/pnas.0904720106","article-title":"Chimeric transcript discovery by paired-end transcriptome sequencing","volume":"106","author":"CA Maher","year":"2009","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"5","key":"ref8","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"C Trapnell","year":"2010","journal-title":"Nature biotechnology"},{"issue":"11","key":"ref9","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1038\/nmeth.1517","article-title":"De novo assembly and analysis of RNA-seq data","volume":"7","author":"G Robertson","year":"2010","journal-title":"Nature methods"},{"issue":"7","key":"ref10","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"MG Grabherr","year":"2011","journal-title":"Nature biotechnology"},{"issue":"12","key":"ref11","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1186\/s13059-014-0553-5","article-title":"Evaluation of de novo transcriptome assemblies from RNA-Seq data","volume":"15","author":"B Li","year":"2014","journal-title":"Genome biology"},{"issue":"12","key":"ref12","doi-asserted-by":"crossref","first-page":"R175","DOI":"10.1186\/gb-2008-9-12-r175","article-title":"Annotating genomes with massive-scale RNA sequencing","volume":"9","author":"F Denoeud","year":"2008","journal-title":"Genome biology"},{"issue":"6","key":"ref13","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/nmeth.1613","article-title":"Computational methods for transcriptome annotation and quantification using RNA-seq","volume":"8","author":"M Garber","year":"2011","journal-title":"Nature methods"},{"issue":"1","key":"ref14","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nbt.2450","article-title":"Differential analysis of gene regulation at transcript resolution with RNA-seq","volume":"31","author":"C Trapnell","year":"2013","journal-title":"Nature biotechnology"},{"issue":"3","key":"ref15","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"C Trapnell","year":"2012","journal-title":"Nature protocols"},{"issue":"12","key":"ref16","doi-asserted-by":"crossref","first-page":"2213","DOI":"10.1101\/gr.124321.111","article-title":"Differential expression in RNA-seq: a matter of depth","volume":"21","author":"S Tarazona","year":"2011","journal-title":"Genome research"},{"issue":"12","key":"ref17","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1186\/gb-2010-11-12-220","article-title":"From RNA-seq reads to differential expression results","volume":"11","author":"A Oshlack","year":"2010","journal-title":"Genome biology"},{"issue":"8","key":"ref18","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/nrg2815","article-title":"Genome-wide allele-specific analysis: insights into regulatory variation","volume":"11","author":"T Pastinen","year":"2010","journal-title":"Nature reviews Genetics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1038\/msb.2011.54","article-title":"AlleleSeq: analysis of allele-specific expression and binding in a network framework","volume":"7","author":"J Rozowsky","year":"2011","journal-title":"Molecular systems biology"},{"issue":"1","key":"ref20","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1101\/gr.124107.111","article-title":"Accurate identification of A-to-I RNA editing in human by transcriptome sequencing","volume":"22","author":"JH Bahn","year":"2012","journal-title":"Genome research"},{"issue":"3","key":"ref21","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1038\/nbt.2122","article-title":"Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome","volume":"30","author":"Z Peng","year":"2012","journal-title":"Nature biotechnology"},{"issue":"9","key":"ref22","doi-asserted-by":"crossref","first-page":"1626","DOI":"10.1101\/gr.134957.111","article-title":"RNA editing in the human ENCODE RNA-seq data","volume":"22","author":"E Park","year":"2012","journal-title":"Genome research"},{"issue":"Pt 9","key":"ref23","doi-asserted-by":"crossref","first-page":"1853","DOI":"10.1099\/vir.0.043182-0","article-title":"Application of next-generation sequencing technologies in virology","volume":"93","author":"AD Radford","year":"2012","journal-title":"The Journal of general virology"},{"issue":"1","key":"ref24","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1111\/1469-0691.12056","article-title":"Next-generation sequencing technology in clinical virology","volume":"19","author":"MR Capobianchi","year":"2013","journal-title":"Clinical microbiology and infection: the official publication of the European Society of Clinical Microbiology and Infectious Diseases"},{"issue":"16","key":"ref25","doi-asserted-by":"crossref","first-page":"8916","DOI":"10.1128\/JVI.00340-13","article-title":"Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq","volume":"87","author":"JD Khoury","year":"2013","journal-title":"Journal of virology"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"340620","DOI":"10.1155\/2013\/340620","article-title":"State-of-the-art fusion-finder algorithms sensitivity and specificity","volume":"2013","author":"M Carrara","year":"2013","journal-title":"BioMed research international"},{"issue":"Suppl 7","key":"ref27","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-14-S7-S2","article-title":"State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?","volume":"14","author":"M Carrara","year":"2013","journal-title":"BMC bioinformatics"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1186\/1471-2164-15-824","article-title":"Open-access synthetic spike-in mRNA-seq data for cancer gene fusions","volume":"15","author":"WD Tembe","year":"2014","journal-title":"BMC genomics"},{"issue":"24","key":"ref29","doi-asserted-by":"crossref","first-page":"3556","DOI":"10.1093\/bioinformatics\/btu662","article-title":"Chimera: a Bioconductor package for secondary analysis of fusion products","volume":"30","author":"M Beccuti","year":"2014","journal-title":"Bioinformatics"},{"key":"ref30","article-title":"The landscape and therapeutic relevance of cancer-associated transcript fusions","author":"K Yoshihara","year":"2014","journal-title":"Oncogene"},{"issue":"3","key":"ref31","doi-asserted-by":"crossref","first-page":"e58815","DOI":"10.1371\/journal.pone.0058815","article-title":"Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data","volume":"8","author":"EM Quinn","year":"2013","journal-title":"PloS one"},{"issue":"4","key":"ref32","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/j.ajhg.2013.08.008","article-title":"Reliable identification of genomic variants from RNA-seq data","volume":"93","author":"R Piskol","year":"2013","journal-title":"American journal of human genetics"},{"issue":"3","key":"ref33","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1586\/erm.12.10","article-title":"Exome versus transcriptome sequencing in identifying coding region variants","volume":"12","author":"CS Ku","year":"2012","journal-title":"Expert review of molecular diagnostics"},{"issue":"7234","key":"ref34","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/nature07638","article-title":"Transcriptome sequencing to detect gene fusions in cancer","volume":"458","author":"CA Maher","year":"2009","journal-title":"Nature"},{"issue":"6099","key":"ref35","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1126\/science.1220834","article-title":"Transforming fusions of FGFR and TACC genes in human glioblastoma","volume":"337","author":"D Singh","year":"2012","journal-title":"Science"},{"issue":"6174","key":"ref36","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1126\/science.1249484","article-title":"Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma","volume":"343","author":"JN Honeyman","year":"2014","journal-title":"Science"},{"issue":"7199","key":"ref37","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1038\/nature07002","article-title":"Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution","volume":"453","author":"BT Wilhelm","year":"2008","journal-title":"Nature"},{"issue":"5891","key":"ref38","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1126\/science.1160342","article-title":"A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome","volume":"321","author":"M Sultan","year":"2008","journal-title":"Science"},{"issue":"3","key":"ref39","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.tig.2015.01.001","article-title":"Alternative mRNA transcription, processing, and translation: insights from RNA sequencing","volume":"31","author":"E de Klerk","year":"2015","journal-title":"Trends in genetics: TIG"},{"issue":"1","key":"ref40","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nbt.2024","article-title":"Targeted RNA sequencing reveals the deep complexity of the human transcriptome","volume":"30","author":"TR Mercer","year":"2012","journal-title":"Nature biotechnology"},{"issue":"4","key":"ref41","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1093\/gbe\/evs020","article-title":"Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome","volume":"4","author":"RS Young","year":"2012","journal-title":"Genome biology and evolution"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/1471-2105-15-224","article-title":"MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing","volume":"15","author":"KR Kalari","year":"2014","journal-title":"BMC bioinformatics"},{"issue":"9","key":"ref43","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1038\/nbt.3017","article-title":"Bringing RNA-seq closer to the clinic","volume":"32","author":"K Van Keuren-Jensen","year":"2014","journal-title":"Nature biotechnology"},{"issue":"2","key":"ref44","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nrg2934","article-title":"RNA sequencing: advances, challenges and opportunities","volume":"12","author":"F Ozsolak","year":"2011","journal-title":"Nature reviews Genetics"},{"issue":"17","key":"ref45","doi-asserted-by":"crossref","first-page":"5157","DOI":"10.1093\/nar\/gkg702","article-title":"Simultaneous gene expression analysis of steady-state and actively translated mRNA populations from osteosarcoma MG-63 cells in response to IL-1alpha via an open expression analysis platform","volume":"31","author":"J Ju","year":"2003","journal-title":"Nucleic acids research"},{"issue":"9","key":"ref46","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1186\/gb-2003-4-9-117","article-title":"Comparing protein abundance and mRNA expression levels on a genomic scale","volume":"4","author":"D Greenbaum","year":"2003","journal-title":"Genome biology"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1186\/1471-2164-10-365","article-title":"Correlations between RNA and protein expression profiles in 23 human cell lines","volume":"10","author":"M Gry","year":"2009","journal-title":"BMC genomics"},{"issue":"1","key":"ref48","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.yexcr.2014.01.008","article-title":"Library preparation methods for next-generation sequencing: tone down the bias","volume":"322","author":"EL van Dijk","year":"2014","journal-title":"Experimental cell research"},{"issue":"7","key":"ref49","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/nmeth.2483","article-title":"Comparative analysis of RNA sequencing methods for degraded or low-input samples","volume":"10","author":"X Adiconis","year":"2013","journal-title":"Nature methods"},{"key":"ref50","first-page":"1","article-title":"Current protocols in molecular biology","author":"EA Bogdanov","year":"2010"},{"issue":"6","key":"ref51","doi-asserted-by":"crossref","first-page":"373","DOI":"10.2144\/000113937","article-title":"cDNA normalization by hydroxyapatite chromatography to enrich transcriptome diversity in RNA-seq applications","volume":"53","author":"VA Vandernoot","year":"2012","journal-title":"BioTechniques"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1186\/1471-2164-15-401","article-title":"Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage","volume":"15","author":"SK Archer","year":"2014","journal-title":"BMC genomics"},{"issue":"7","key":"ref53","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1038\/nbt.1910","article-title":"Sequencing technology does not eliminate biological variability","volume":"29","author":"KD Hansen","year":"2011","journal-title":"Nature biotechnology"},{"issue":"8","key":"ref54","doi-asserted-by":"crossref","first-page":"2444","DOI":"10.1073\/pnas.85.8.2444","article-title":"Improved tools for biological sequence comparison","volume":"85","author":"WR Pearson","year":"1988","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"6","key":"ref55","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","article-title":"The Sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants","volume":"38","author":"PJ Cock","year":"2010","journal-title":"Nucleic acids research"},{"issue":"16","key":"ref56","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/1471-2105-15-182","article-title":"Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads","volume":"15","author":"H Jiang","year":"2014","journal-title":"BMC bioinformatics"},{"issue":"15","key":"ref58","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"12","key":"ref59","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1038\/nmeth.2722","article-title":"Systematic evaluation of spliced alignment programs for RNA-seq data","volume":"10","author":"PG Engstrom","year":"2013","journal-title":"Nature methods"},{"issue":"10","key":"ref60","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nrg3068","article-title":"Next-generation transcriptome assembly","volume":"12","author":"JA Martin","year":"2011","journal-title":"Nature reviews Genetics"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1186\/1471-2164-14-465","article-title":"Assessing De Novo transcriptome assembly metrics for consistency and utility","volume":"14","author":"ST O'Neil","year":"2013","journal-title":"BMC genomics"},{"issue":"2","key":"ref62","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"H Thorvaldsdottir","year":"2013","journal-title":"Briefings in bioinformatics"},{"issue":"Web Server issue","key":"ref63","doi-asserted-by":"crossref","first-page":"W615","DOI":"10.1093\/nar\/gks427","article-title":"Savant Genome Browser 2: visualization and analysis for population-scale genomics","volume":"40","author":"M Fiume","year":"2012","journal-title":"Nucleic acids research"},{"issue":"20","key":"ref64","doi-asserted-by":"crossref","first-page":"2730","DOI":"10.1093\/bioinformatics\/btp472","article-title":"The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets","volume":"25","author":"JW Nicol","year":"2009","journal-title":"Bioinformatics"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"2400","DOI":"10.1093\/bioinformatics\/btv034","article-title":"Quantitative visualization of alternative exon expression from RNA-seq data","volume":"31","author":"Y Katz","year":"2015","journal-title":"Bioinformatics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/1471-2105-14-91","article-title":"A comparison of methods for differential expression analysis of RNA-seq data","volume":"14","author":"C Soneson","year":"2013","journal-title":"BMC bioinformatics"},{"issue":"9","key":"ref67","doi-asserted-by":"crossref","first-page":"R95","DOI":"10.1186\/gb-2013-14-9-r95","article-title":"Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data","volume":"14","author":"F Rapaport","year":"2013","journal-title":"Genome biology"},{"issue":"1","key":"ref68","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1093\/bib\/bbt086","article-title":"Comparison of software packages for detecting differential expression in RNA-seq studies","volume":"16","author":"F Seyednasrollah","year":"2015","journal-title":"Briefings in bioinformatics"},{"issue":"8","key":"ref69","doi-asserted-by":"crossref","first-page":"e103207","DOI":"10.1371\/journal.pone.0103207","article-title":"A comparative study of techniques for differential expression analysis on RNA-Seq data","volume":"9","author":"ZH Zhang","year":"2014","journal-title":"PloS one"},{"issue":"2","key":"ref70","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/nmeth.3252","article-title":"Orchestrating high-throughput genomic analysis with Bioconductor","volume":"12","author":"W Huber","year":"2015","journal-title":"Nature methods"},{"issue":"15","key":"ref71","doi-asserted-by":"crossref","first-page":"2479","DOI":"10.1093\/bioinformatics\/bth261","article-title":"Data mining in bioinformatics using Weka","volume":"20","author":"E Frank","year":"2004","journal-title":"Bioinformatics"},{"issue":"5","key":"ref72","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1093\/bioinformatics\/btl671","article-title":"BioWeka\u2014extending the Weka framework for bioinformatics","volume":"23","author":"JE Gewehr","year":"2007","journal-title":"Bioinformatics"},{"issue":"12","key":"ref73","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1093\/bioinformatics\/btu090","article-title":"SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing","volume":"30","author":"X Wang","year":"2014","journal-title":"Bioinformatics"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1186\/1471-2105-10-161","article-title":"GAGE: generally applicable gene set enrichment for pathway analysis","volume":"10","author":"W Luo","year":"2009","journal-title":"BMC bioinformatics"},{"issue":"14","key":"ref75","doi-asserted-by":"crossref","first-page":"1830","DOI":"10.1093\/bioinformatics\/btt285","article-title":"Pathview: an R\/Bioconductor package for pathway-based data integration and visualization","volume":"29","author":"W Luo","year":"2013","journal-title":"Bioinformatics"},{"issue":"2","key":"ref76","doi-asserted-by":"crossref","first-page":"R14","DOI":"10.1186\/gb-2010-11-2-r14","article-title":"Gene ontology analysis for RNA-seq: accounting for selection bias","volume":"11","author":"MD Young","year":"2010","journal-title":"Genome biology"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"6347","DOI":"10.1038\/srep06347","article-title":"GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data","volume":"4","author":"Q Xiong","year":"2014","journal-title":"Scientific reports"},{"issue":"11","key":"ref78","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"P Shannon","year":"2003","journal-title":"Genome research"},{"issue":"11","key":"ref79","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1038\/nmeth.2212","article-title":"A travel guide to Cytoscape plugins","volume":"9","author":"R Saito","year":"2012","journal-title":"Nature methods"},{"issue":"4","key":"ref80","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1038\/leu.2014.303","article-title":"U2AF1 mutations alter sequence specificity of pre-mRNA binding and splicing","volume":"29","author":"T Okeyo-Owuor","year":"2015","journal-title":"Leukemia"},{"issue":"10B","key":"ref81","doi-asserted-by":"crossref","first-page":"2121","DOI":"10.1101\/gr.2596504","article-title":"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)","volume":"14","author":"DS Gerhard","year":"2004","journal-title":"Genome research"},{"issue":"12","key":"ref82","doi-asserted-by":"crossref","first-page":"2324","DOI":"10.1101\/gr.095976.109","article-title":"The completion of the Mammalian Gene Collection (MGC)","volume":"19","author":"MGCP Team","year":"2009","journal-title":"Genome research"},{"issue":"11","key":"ref83","first-page":"3 1","article-title":"RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis","volume":"83","author":"AG Williams","year":"2014","journal-title":"Current protocols in human genetics \/ editorial board"},{"issue":"9","key":"ref84","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"C Trapnell","year":"2009","journal-title":"Bioinformatics"},{"issue":"12","key":"ref85","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1038\/ng.259","article-title":"Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing","volume":"40","author":"Q Pan","year":"2008","journal-title":"Nature genetics"},{"issue":"7221","key":"ref86","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"ET Wang","year":"2008","journal-title":"Nature"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1186\/1471-2164-15-419","article-title":"Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling","volume":"15","author":"W Zhao","year":"2014","journal-title":"BMC genomics"},{"issue":"4","key":"ref88","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1101\/gr.7179508","article-title":"Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells","volume":"18","author":"RD Morin","year":"2008","journal-title":"Genome research"},{"issue":"10","key":"ref89","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1101\/pdb.prot071431","article-title":"Preparation of small RNA libraries for high-throughput sequencing","volume":"2012","author":"C Malone","year":"2012","journal-title":"Cold Spring Harbor protocols"},{"issue":"10","key":"ref90","doi-asserted-by":"crossref","first-page":"e1002216","DOI":"10.1371\/journal.pcbi.1002216","article-title":"BioStar: an online question & answer resource for the bioinformatics community","volume":"7","author":"LD Parnell","year":"2011","journal-title":"PLoS computational biology"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004393","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T06:44:36Z","timestamp":1589006676000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004393"}},"subtitle":[],"editor":[{"given":"Francis","family":"Ouellette","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2015,8,6]]},"references-count":90,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2015,8,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004393","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,8,6]]}}}