{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T03:02:21Z","timestamp":1761102141482},"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2015,1,8]],"date-time":"2015-01-08T00:00:00Z","timestamp":1420675200000},"content-version":"unspecified","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.1004027","type":"journal-article","created":{"date-parts":[[2015,1,8]],"date-time":"2015-01-08T19:08:09Z","timestamp":1420744089000},"page":"e1004027","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":20,"title":["Identification of Constrained Cancer Driver Genes Based on Mutation Timing"],"prefix":"10.1371","volume":"11","author":[{"given":"Thomas","family":"Sakoparnig","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Fried","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,1,8]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: the next generation","volume":"144","author":"D Hanahan","year":"2011","journal-title":"Cell"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1016\/0092-8674(90)90186-I","article-title":"A genetic model for colorectal tumorigenesis","volume":"61","author":"E Fearon","year":"1990","journal-title":"Cell"},{"key":"ref3","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":"R McLendon","year":"2008","journal-title":"Nature"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1038\/nature10166","article-title":"Integrated genomic analyses of ovarian carcinoma","volume":"474","author":"D Bell","year":"2011","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"18545","DOI":"10.1073\/pnas.1010978107","article-title":"Accumulation of driver and passenger mutations during tumor progression","volume":"107","author":"I Bozic","year":"2010","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"20007","DOI":"10.1073\/pnas.0710052104","article-title":"Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma","volume":"104","author":"R Beroukhim","year":"2007","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"6660","DOI":"10.1158\/0008-5472.CAN-09-1133","article-title":"Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations","volume":"69","author":"H Carter","year":"2009","journal-title":"Cancer research"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1093\/bioinformatics\/btq630","article-title":"Identifying cancer driver genes in tumor genome sequencing studies","volume":"27","author":"A Youn","year":"2011","journal-title":"Bioinformatics (Oxford, England)"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/1755-8794-4-34","article-title":"Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors","volume":"4","author":"Ca Miller","year":"2011","journal-title":"BMC medical genomics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1101\/gr.120477.111","article-title":"De novo discovery of mutated driver pathways in cancer","volume":"22","author":"F Vandin","year":"2012","journal-title":"Genome research"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"e1003503","DOI":"10.1371\/journal.pcbi.1003503","article-title":"Modeling mutual exclusivity of cancer mutations","volume":"10","author":"E Szczurek","year":"2014","journal-title":"PLoS computational biology"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1101\/gr.125567.111","article-title":"Mutual exclusivity analysis identifies oncogenic network modules","volume":"22","author":"G Ciriello","year":"2012","journal-title":"Genome research"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"2650","DOI":"10.1038\/srep02650","article-title":"Comprehensive identification of mutational cancer driver genes across 12 tumor types","volume":"3","author":"D Tamborero","year":"2013","journal-title":"Scientific reports"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1038\/nrc3299","article-title":"From cancer genomes to oncogenic drivers, tumour dependencies and therapeutic targets","volume":"12","author":"C Eifert","year":"2012","journal-title":"Nature reviews Cancer"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"893","DOI":"10.3150\/07-BEJ6133","article-title":"Conjunctive Bayesian networks","volume":"13","author":"N Beerenwinkel","year":"2007","journal-title":"Bernoulli"},{"key":"ref16","first-page":"pl1","article-title":"Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal","volume":"6","author":"J Gao","year":"2013","journal-title":"Science signaling"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"R41","DOI":"10.1186\/gb-2011-12-4-r41","article-title":"GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers","volume":"12","author":"CH Mermel","year":"2011","journal-title":"Genome biology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1038\/cdd.2010.153","article-title":"GRAMD4 mimics p53 and mediates the apoptotic function of p73 at mitochondria","volume":"18","author":"K John","year":"2011","journal-title":"Cell death and differentiation"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.ygyno.2004.01.019","article-title":"Ubiquinol cytochrome c reductase (UQCRFS1) gene amplification in primary breast cancer core biopsy samples","volume":"93","author":"Y Ohashi","year":"2004","journal-title":"Gynecologic oncology"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1016\/j.ccr.2011.01.019","article-title":"URI is an oncogene amplified in ovarian cancer cells and is required for their survival","volume":"19","author":"JP Theurillat","year":"2011","journal-title":"Cancer cell"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1002\/gcc.20626","article-title":"The galanin signaling cascade is a candidate pathway regulating oncogenesis in human squamous cell carcinoma","volume":"142","author":"T Sugimoto","year":"2009","journal-title":"Genes, Chromosomes and Cancer"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1690","DOI":"10.1002\/hep.23847","article-title":"Overlapping high-resolution copy number alterations in cancer genomes identified putative cancer genes in hepatocellular carcinoma","volume":"52","author":"CF Chen","year":"2010","journal-title":"Hepatology"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1186\/1471-2407-12-154","article-title":"Carnitine palmitoyltransferase 1A (CPT1A): a transcriptional target of PAX3-FKHR and mediates PAX3-FKHR-dependent motility in alveolar rhabdomyosarcoma cells","volume":"12","author":"L Liu","year":"2012","journal-title":"BMC cancer"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"8407","DOI":"10.1158\/0008-5472.CAN-10-0784","article-title":"Regulation of DNA polymerase POLD4 influences genomic instability in lung cancer","volume":"70","author":"QM Huang","year":"2010","journal-title":"Cancer research"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"3539","DOI":"10.4161\/cc.7.22.7062","article-title":"KDM1A represses transcription of centromeric satellite repeats and maintains the heterochromatic state","volume":"7","author":"D Frescas","year":"2008","journal-title":"Cell Cycle"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1038\/nature11017","article-title":"The landscape of cancer genes and mutational processes in breast cancer","volume":"486","author":"PJ Stephens","year":"2012","journal-title":"Nature"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1038\/nature05933","article-title":"A transforming mutation in the pleckstrin homology domain of AKT1 in cancer","volume":"448","author":"JD Carpten","year":"2007","journal-title":"Nature"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1126\/science.1088759","article-title":"Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2","volume":"302","author":"MC King","year":"2003","journal-title":"Science"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1073\/pnas.1221068110","article-title":"Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation","volume":"110","author":"C Tomasetti","year":"2013","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/35094067","article-title":"APC, signal transduction and genetic instability in colorectal cancer","volume":"1","author":"R Fodde","year":"2001","journal-title":"Nature reviews Cancer"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1097\/PDM.0b013e3181c93fd1","article-title":"NRAS mutations are rare in colorectal cancer","volume":"19","author":"N Irahara","year":"2010","journal-title":"Diagnostic Molecular Pathology"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1056\/NEJMoa1207756","article-title":"Aspirin use, tumor PIK3CA mutation, and colorectal-cancer survival","volume":"367","author":"X Liao","year":"2012","journal-title":"The New England journal of medicine"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/S0025-5564(02)00086-X","article-title":"Estimating an oncogenetic tree when false negatives and positives are present","volume":"176","author":"A Szabo","year":"2002","journal-title":"Mathematical biosciences"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1089\/cmb.1999.6.37","article-title":"Inferring tree models for oncogenesis from comparative genome hybridization data","volume":"6","author":"R Desper","year":"1999","journal-title":"Journal of Computational Biology"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2809","DOI":"10.1093\/bioinformatics\/btp505","article-title":"Quantifying cancer progression with conjunctive Bayesian networks","volume":"25","author":"M Gerstung","year":"2009","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"2318","DOI":"10.1093\/bioinformatics\/bts433","article-title":"Efficient sampling for Bayesian inference of conjunctive Bayesian networks","volume":"28","author":"T Sakoparnig","year":"2012","journal-title":"Bioinformatics"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"e1002337","DOI":"10.1371\/journal.pcbi.1002337","article-title":"A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis","volume":"8","author":"YK Cheng","year":"2012","journal-title":"PLoS computational biology"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1016\/j.cell.2010.11.013","article-title":"An integrated approach to uncover drivers of cancer","volume":"143","author":"UD Akavia","year":"2010","journal-title":"Cell"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1038\/nature11273","article-title":"Chromatin organization is a major influence on regional mutation rates in human cancer cells","volume":"488","author":"B Schuster-B\u00f6ckler","year":"2012","journal-title":"Nature"},{"key":"ref40","unstructured":"R Core Team (2013) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria."}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004027","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T08:18:45Z","timestamp":1589012325000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004027"}},"subtitle":[],"editor":[{"given":"Edwin","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,1,8]]},"references-count":40,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2015,1,8]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004027","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,1,8]]}}}