{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:10:56Z","timestamp":1772172656645,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007469","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,11,6]],"date-time":"2019-11-06T00:00:00Z","timestamp":1572998400000}}],"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2019,10,25]],"date-time":"2019-10-25T00:00:00Z","timestamp":1571961600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AA026428"],"award-info":[{"award-number":["AA026428"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007469","type":"journal-article","created":{"date-parts":[[2019,10,25]],"date-time":"2019-10-25T14:55:27Z","timestamp":1572015327000},"page":"e1007469","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Uncovering and characterizing splice variants associated with survival in lung cancer patients"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1394-1999","authenticated-orcid":true,"given":"Sean","family":"West","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sushil","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Surinder K.","family":"Batra","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hesham","family":"Ali","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0630-0843","authenticated-orcid":true,"given":"Dario","family":"Ghersi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2019,10,25]]},"reference":[{"key":"pcbi.1007469.ref001","article-title":"Cancer genome landscapes","author":"B Vogelstein","year":"2013","journal-title":"Science"},{"issue":"1","key":"pcbi.1007469.ref002","first-page":"7","article-title":"Cancer statistics, 2017","volume":"67","author":"RL Siegel","year":"2017","journal-title":"CA: a cancer journal for clinicians"},{"key":"pcbi.1007469.ref003","article-title":"Molecular targeted therapy: Treating cancer with specificity","author":"YT Lee","year":"2018","journal-title":"European journal of pharmacology"},{"key":"pcbi.1007469.ref004","doi-asserted-by":"crossref","DOI":"10.1155\/2012\/269570","article-title":"Splicing programs and cancer","volume":"2012","author":"S Germann","year":"2012","journal-title":"Journal of Nucleic Acids"},{"key":"pcbi.1007469.ref005","article-title":"Hallmarks of alternative splicing in cancer","author":"S Oltean","year":"2014","journal-title":"Oncogene"},{"key":"pcbi.1007469.ref006","article-title":"Therapeutic targeting of splicing in cancer","author":"SCW Lee","year":"2016","journal-title":"Nature Medicine"},{"key":"pcbi.1007469.ref007","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.7563.1","article-title":"Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences","volume":"4","author":"C Soneson","year":"2015","journal-title":"F1000Research"},{"issue":"5","key":"pcbi.1007469.ref008","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms","volume":"28","author":"C Trapnell","year":"2010","journal-title":"Nature biotechnology"},{"key":"pcbi.1007469.ref009","article-title":"Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer","author":"E Sebesty\u00e9n","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"pcbi.1007469.ref010","article-title":"ISOexpresso: A web-based platform for isoform-level expression analysis in human cancer","author":"IS Yang","year":"2016","journal-title":"BMC Genomics"},{"issue":"9","key":"pcbi.1007469.ref011","doi-asserted-by":"crossref","first-page":"2215","DOI":"10.1016\/j.celrep.2017.08.012","article-title":"The Functional Impact of Alternative Splicing in Cancer","volume":"20","author":"H Climente-Gonz\u00e1lez","year":"2017","journal-title":"Cell Reports"},{"key":"pcbi.1007469.ref012","doi-asserted-by":"crossref","first-page":"11548","DOI":"10.1038\/ncomms11548","article-title":"SURVIV for survival analysis of mRNA isoform variation","volume":"7","author":"S Shen","year":"2016","journal-title":"Nature communications"},{"issue":"1","key":"pcbi.1007469.ref013","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":"A Conesa","year":"2016","journal-title":"Genome biology"},{"issue":"10","key":"pcbi.1007469.ref014","doi-asserted-by":"crossref","first-page":"e0140072","DOI":"10.1371\/journal.pone.0140072","article-title":"Robust selection algorithm (RSA) for multi-omic biomarker discovery; integration with functional network analysis to identify miRNA regulated pathways in multiple cancers","volume":"10","author":"V Sehgal","year":"2015","journal-title":"PloS one"},{"key":"pcbi.1007469.ref015","doi-asserted-by":"crossref","first-page":"73","DOI":"10.2307\/2532740","article-title":"Maximally selected rank statistics","author":"B Lausen","year":"1992","journal-title":"Biometrics"},{"issue":"W1","key":"pcbi.1007469.ref016","first-page":"W38","article-title":"HMMER web server: 2015 update","volume":"43","author":"RD Finn","year":"2015","journal-title":"Nucleic acids research"},{"issue":"D1","key":"pcbi.1007469.ref017","first-page":"D230","article-title":"Pfam: the protein families database","volume":"42","author":"RD Finn","year":"2013","journal-title":"Nucleic acids research"},{"issue":"1","key":"pcbi.1007469.ref018","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1186\/s12859-019-2960-9","article-title":"FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis","volume":"20","author":"ML Hale","year":"2019","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"pcbi.1007469.ref019","doi-asserted-by":"crossref","first-page":"1973","DOI":"10.1074\/jbc.M609066200","article-title":"Role of RAD51C and XRCC3 in genetic recombination and DNA repair","volume":"282","author":"Y Liu","year":"2007","journal-title":"Journal of Biological Chemistry"},{"issue":"3","key":"pcbi.1007469.ref020","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1158\/0008-5472.CAN-08-3057","article-title":"Loss of Rad51c leads to embryonic lethality and modulation of Trp53-dependent tumorigenesis in mice","volume":"69","author":"SG Kuznetsov","year":"2009","journal-title":"Cancer research"},{"issue":"3","key":"pcbi.1007469.ref021","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1128\/MCB.00489-17","article-title":"RAD51C\/XRCC3 facilitates mitochondrial DNA replication and maintains integrity of the mitochondrial genome","volume":"38","author":"A Mishra","year":"2018","journal-title":"Molecular and cellular biology"},{"issue":"1","key":"pcbi.1007469.ref022","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/s10689-015-9838-4","article-title":"Screening of HELQ in breast and ovarian cancer families","volume":"15","author":"LM Pelttari","year":"2016","journal-title":"Familial cancer"},{"key":"pcbi.1007469.ref023","doi-asserted-by":"crossref","first-page":"2338","DOI":"10.1038\/ncomms3338","article-title":"Human DNA helicase HELQ participates in DNA interstrand crosslink tolerance with ATR and RAD51 paralogs","volume":"4","author":"K ichi Takata","year":"2013","journal-title":"Nature communications"},{"issue":"2","key":"pcbi.1007469.ref024","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.molcel.2005.03.015","article-title":"The UBA2 domain functions as an intrinsic stabilization signal that protects Rad23 from proteasomal degradation","volume":"18","author":"S Heessen","year":"2005","journal-title":"Molecular cell"},{"issue":"5","key":"pcbi.1007469.ref025","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1002\/ijc.28226","article-title":"Roles of Chk1 in cell biology and cancer therapy","volume":"134","author":"Y Zhang","year":"2014","journal-title":"International journal of cancer"},{"issue":"1","key":"pcbi.1007469.ref026","doi-asserted-by":"crossref","first-page":"22","DOI":"10.4161\/trns.1.1.12201","article-title":"The Rad23 ubiquitin receptor, the proteasome and functional specificity in transcriptional control","volume":"1","author":"SL Wade","year":"2010","journal-title":"Transcription"},{"issue":"5","key":"pcbi.1007469.ref027","doi-asserted-by":"crossref","first-page":"936","DOI":"10.3390\/ijms18050936","article-title":"Pan-cancer mutational and transcriptional analysis of the integrator complex","volume":"18","author":"A Federico","year":"2017","journal-title":"International journal of molecular sciences"},{"issue":"5","key":"pcbi.1007469.ref028","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.tibs.2015.03.005","article-title":"Integrator: surprisingly diverse functions in gene expression","volume":"40","author":"D Baillat","year":"2015","journal-title":"Trends in biochemical sciences"},{"issue":"16","key":"pcbi.1007469.ref029","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":"pcbi.1007469.ref030","unstructured":"Patro R, Duggal G, Kingsford C. Salmon: accurate, versatile and ultrafast quantification from RNA-seq data using lightweight-alignment. Biorxiv. 2015; p. 021592."},{"issue":"4","key":"pcbi.1007469.ref031","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1186\/s12859-017-1526-y","article-title":"Comprehensive evaluation of RNA-seq quantification methods for linearity","volume":"18","author":"H Jin","year":"2017","journal-title":"BMC bioinformatics"},{"issue":"1","key":"pcbi.1007469.ref032","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1186\/s12864-017-4002-1","article-title":"Evaluation and comparison of computational tools for RNA-seq isoform quantification","volume":"18","author":"C Zhang","year":"2017","journal-title":"BMC genomics"},{"issue":"D1","key":"pcbi.1007469.ref033","doi-asserted-by":"crossref","first-page":"D379","DOI":"10.1093\/nar\/gkw1102","article-title":"The BioGRID interaction database: 2017 update","volume":"45","author":"A Chatr-Aryamontri","year":"2017","journal-title":"Nucleic acids research"},{"issue":"D1","key":"pcbi.1007469.ref034","first-page":"D379","article-title":"3did: a catalog of domain-based interactions of known three-dimensional structure","volume":"42","author":"R Mosca","year":"2013","journal-title":"Nucleic acids research"},{"issue":"suppl_1","key":"pcbi.1007469.ref035","first-page":"D950","article-title":"COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer","volume":"39","author":"SA Forbes","year":"2010","journal-title":"Nucleic acids research"},{"issue":"1","key":"pcbi.1007469.ref036","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/s13059-016-1029-6","article-title":"MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data","volume":"17","author":"Y Fan","year":"2016","journal-title":"Genome biology"},{"issue":"3","key":"pcbi.1007469.ref037","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nbt.2514","article-title":"Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples","volume":"31","author":"K Cibulskis","year":"2013","journal-title":"Nature biotechnology"},{"issue":"3","key":"pcbi.1007469.ref038","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1093\/bioinformatics\/btr665","article-title":"SomaticSniper: identification of somatic point mutations in whole genome sequencing data","volume":"28","author":"DE Larson","year":"2011","journal-title":"Bioinformatics"},{"key":"pcbi.1007469.ref039","article-title":"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing","author":"DC Koboldt","year":"2012","journal-title":"Genome research"},{"issue":"1","key":"pcbi.1007469.ref040","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s13073-018-0539-0","article-title":"MutationalPatterns: comprehensive genome-wide analysis of mutational processes","volume":"10","author":"F Blokzijl","year":"2018","journal-title":"Genome medicine"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007469","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,11,6]],"date-time":"2019-11-06T00:00:00Z","timestamp":1572998400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007469","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,2]],"date-time":"2022-10-02T13:19:00Z","timestamp":1664716740000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007469"}},"subtitle":[],"editor":[{"given":"Rachel","family":"Karchin","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,10,25]]},"references-count":40,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2019,10,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007469","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/623876","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,10,25]]}}}