{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:10:57Z","timestamp":1772172657696,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007451","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,11,21]],"date-time":"2019-11-21T00:00:00Z","timestamp":1574294400000}}],"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2019,11,11]],"date-time":"2019-11-11T00:00:00Z","timestamp":1573430400000},"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.1007451","type":"journal-article","created":{"date-parts":[[2019,11,11]],"date-time":"2019-11-11T13:34:57Z","timestamp":1573479297000},"page":"e1007451","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Uncovering the subtype-specific temporal order of cancer pathway dysregulation"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5178-0188","authenticated-orcid":true,"given":"Sahand","family":"Khakabimamaghani","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8436-209X","authenticated-orcid":true,"given":"Dujian","family":"Ding","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5051-1771","authenticated-orcid":true,"given":"Oliver","family":"Snow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Ester","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2019,11,11]]},"reference":[{"key":"pcbi.1007451.ref001","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":"The Cancer Genome Atlas Research Network","year":"2008","journal-title":"Nature"},{"key":"pcbi.1007451.ref002","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bar026","article-title":"International Cancer Genome Consortium Data Portal\u2014a one-stop shop for cancer genomics data","volume":"2011","author":"J Zhang","year":"2011","journal-title":"Database"},{"issue":"6","key":"pcbi.1007451.ref003","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1089\/cmb.2014.0161","article-title":"Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data","volume":"22","author":"BJ Raphael","year":"2015","journal-title":"Journal of Computational Biology"},{"issue":"12","key":"pcbi.1007451.ref004","doi-asserted-by":"crossref","first-page":"i78","DOI":"10.1093\/bioinformatics\/btu284","article-title":"A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data","volume":"30","author":"I Hajirasouliha","year":"2014","journal-title":"Bioinformatics"},{"key":"pcbi.1007451.ref005","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/978-3-319-31957-5_6","volume-title":"Research in Computational Molecular Biology","author":"N Donmez","year":"2016"},{"issue":"1","key":"pcbi.1007451.ref006","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s13059-015-0602-8","article-title":"PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors","volume":"16","author":"AG Deshwar","year":"2015","journal-title":"Genome biology"},{"issue":"12","key":"pcbi.1007451.ref007","doi-asserted-by":"crossref","first-page":"i62","DOI":"10.1093\/bioinformatics\/btv261","article-title":"Reconstruction of clonal trees and tumor composition from multi-sample sequencing data","volume":"31","author":"M El-Kebir","year":"2015","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1007451.ref008","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/s13059-015-0647-8","article-title":"Fast and scalable inference of multi-sample cancer lineages","volume":"16","author":"V Popic","year":"2015","journal-title":"Genome biology"},{"issue":"9","key":"pcbi.1007451.ref009","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1093\/bioinformatics\/btv003","article-title":"Clonality inference in multiple tumor samples using phylogeny","volume":"31","author":"S Malikic","year":"2015","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1007451.ref010","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s13059-016-0929-9","article-title":"OncoNEM: inferring tumor evolution from single-cell sequencing data","volume":"17","author":"EM Ross","year":"2016","journal-title":"Genome Biology"},{"issue":"1","key":"pcbi.1007451.ref011","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1186\/s13059-016-0936-x","article-title":"Tree inference for single-cell data","volume":"17","author":"K Jahn","year":"2016","journal-title":"Genome biology"},{"issue":"1","key":"pcbi.1007451.ref012","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/s13059-017-1311-2","article-title":"SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models","volume":"18","author":"H Zafar","year":"2017","journal-title":"Genome biology"},{"key":"pcbi.1007451.ref013","article-title":"Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data","author":"S Malikic","year":"2017","journal-title":"bioRxiv"},{"key":"pcbi.1007451.ref014","first-page":"376996","article-title":"PhISCS-A Combinatorial Approach for Sub-perfect Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data","author":"S Malikic","year":"2018","journal-title":"bioRxiv"},{"issue":"5","key":"pcbi.1007451.ref015","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":"ER Fearon","year":"1990","journal-title":"Cell"},{"issue":"1","key":"pcbi.1007451.ref016","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"},{"issue":"6","key":"pcbi.1007451.ref017","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1089\/10665270050514936","article-title":"Distance-Based Reconstruction of Tree Models for Oncogenesis","volume":"7","author":"R Desper","year":"2000","journal-title":"Journal of Computational Biology"},{"issue":"6","key":"pcbi.1007451.ref018","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1089\/cmb.2005.12.584","article-title":"Learning Multiple Evolutionary Pathways from Cross-Sectional Data","volume":"12","author":"N Beerenwinkel","year":"2005","journal-title":"Journal of Computational Biology"},{"issue":"9","key":"pcbi.1007451.ref019","doi-asserted-by":"crossref","first-page":"2106","DOI":"10.1093\/bioinformatics\/bti274","article-title":"Mtreemix: a software package for learning and using mixture models of mutagenetic trees","volume":"21","author":"N Beerenwinkel","year":"2005","journal-title":"Bioinformatics"},{"issue":"10","key":"pcbi.1007451.ref020","doi-asserted-by":"crossref","first-page":"2438","DOI":"10.1093\/bioinformatics\/bti312","article-title":"Estimating cancer survival and clinical outcome based on genetic tumor progression scores","volume":"21","author":"J Rahnenf\u00fchrer","year":"2005","journal-title":"Bioinformatics"},{"key":"pcbi.1007451.ref021","first-page":"163","article-title":"A Global Structural EM Algorithm for a Model of Cancer Progression","volume":"24","author":"A Tofigh","year":"2011","journal-title":"Adv Neural Inform Process Syst"},{"issue":"4","key":"pcbi.1007451.ref022","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1089\/cmb.2006.13.853","article-title":"New Probabilistic Network Models and Algorithms for Oncogenesis","volume":"13","author":"M Hjelm","year":"2006","journal-title":"Journal of Computational Biology"},{"issue":"21","key":"pcbi.1007451.ref023","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"},{"issue":"3","key":"pcbi.1007451.ref024","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1093\/biomet\/asp023","article-title":"Markov models for accumulating mutations","volume":"96","author":"N Beerenwinkel","year":"2009","journal-title":"Biometrika"},{"issue":"2","key":"pcbi.1007451.ref025","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1016\/j.jtbi.2006.03.013","article-title":"Evolution on distributive lattices","volume":"242","author":"N Beerenwinkel","year":"2006","journal-title":"Journal of Theoretical Biology"},{"issue":"4","key":"pcbi.1007451.ref026","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"},{"issue":"18","key":"pcbi.1007451.ref027","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"},{"issue":"6","key":"pcbi.1007451.ref028","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0065773","article-title":"Learning Oncogenetic Networks by Reducing to Mixed Integer Linear Programming","volume":"8","author":"H Shahrabi Farahani","year":"2013","journal-title":"PLOS ONE"},{"issue":"9","key":"pcbi.1007451.ref029","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1038\/s41592-018-0108-x","article-title":"Detecting repeated cancer evolution from multi-region tumor sequencing data","volume":"15","author":"G Caravagna","year":"2018","journal-title":"Nature Methods"},{"issue":"6127","key":"pcbi.1007451.ref030","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1126\/science.1235122","article-title":"Cancer Genome Landscapes","volume":"339","author":"B Vogelstein","year":"2013","journal-title":"Science"},{"key":"pcbi.1007451.ref031","unstructured":"Biological Pathways;. https:\/\/www.genome.gov\/27530687\/."},{"issue":"11","key":"pcbi.1007451.ref032","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0027136","article-title":"The Temporal Order of Genetic and Pathway Alterations in Tumorigenesis","volume":"6","author":"M Gerstung","year":"2011","journal-title":"PLOS ONE"},{"issue":"1","key":"pcbi.1007451.ref033","doi-asserted-by":"crossref","first-page":"1","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"},{"issue":"1","key":"pcbi.1007451.ref034","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"M Kanehisa","year":"2000","journal-title":"Nucleic Acids Research"},{"issue":"8","key":"pcbi.1007451.ref035","doi-asserted-by":"crossref","first-page":"2605","DOI":"10.1096\/fj.08-108985","article-title":"Combinatorial patterns of somatic gene mutations in cancer","volume":"22","author":"CH Yeang","year":"2008","journal-title":"The FASEB Journal"},{"issue":"1","key":"pcbi.1007451.ref036","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"},{"issue":"2","key":"pcbi.1007451.ref037","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"},{"issue":"2","key":"pcbi.1007451.ref038","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"},{"issue":"5","key":"pcbi.1007451.ref039","first-page":"1","article-title":"Simultaneous Identification of Multiple Driver Pathways in Cancer","volume":"9","author":"MDM Leiserson","year":"2013","journal-title":"PLOS Computational Biology"},{"issue":"6","key":"pcbi.1007451.ref040","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1089\/cmb.2016.0171","article-title":"pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics","volume":"24","author":"S Cristea","year":"2017","journal-title":"Journal of Computational Biology"},{"issue":"7","key":"pcbi.1007451.ref041","first-page":"968","article-title":"TiMEx: a waiting time model for mutually exclusive cancer alterations","volume":"32","author":"E Szczurek","year":"2015","journal-title":"Bioinformatics"},{"issue":"7216","key":"pcbi.1007451.ref042","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":"Cancer Genome Atlas Research Network","year":"2008","journal-title":"Nature"},{"issue":"7407","key":"pcbi.1007451.ref043","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1038\/nature11252","article-title":"Comprehensive molecular characterization of human colon and rectal cancer","volume":"487","author":"Cancer Genome Atlas Network","year":"2012","journal-title":"Nature"},{"key":"pcbi.1007451.ref044","unstructured":"National Cancer Institute. NCI Dictionary of Cancer Terms;. https:\/\/www.cancer.gov\/publications\/dictionaries\/cancer-terms\/def\/cancer-subtype."},{"issue":"7","key":"pcbi.1007451.ref045","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1056\/NEJMoa1412098","article-title":"Effect of Mutation Order on Myeloproliferative Neoplasms","volume":"372","author":"CA Ortmann","year":"2015","journal-title":"New England Journal of Medicine"},{"issue":"11","key":"pcbi.1007451.ref046","doi-asserted-by":"crossref","first-page":"e438","DOI":"10.3324\/haematol.2015.129510","article-title":"DNMT3A mutations occur early or late in patients with myeloproliferative neoplasms and mutation order influences phenotype","volume":"100","author":"J Nangalia","year":"2015","journal-title":"Haematologica"},{"key":"pcbi.1007451.ref047","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1007\/978-3-319-05269-4_20","volume-title":"Research in Computational Molecular Biology","author":"BJ Raphael","year":"2014"},{"key":"pcbi.1007451.ref048","doi-asserted-by":"crossref","unstructured":"Agarwal A, Charikar M, Makarychev K, Makarychev Y. (log n) Approximation Algorithms for Min UnCut, Min 2CNF Deletion, and Directed Cut Problems. In: Proceedings of the Thirty-seventh Annual ACM Symposium on Theory of Computing. STOC\u201905. New York, NY, USA: ACM; 2005. p. 573\u2013581. Available from: http:\/\/doi.acm.org\/10.1145\/1060590.1060675.","DOI":"10.1145\/1060590.1060675"},{"issue":"4","key":"pcbi.1007451.ref049","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1038\/nmeth.2883","article-title":"PyClone: statistical inference of clonal population structure in cancer","volume":"11","author":"A Roth","year":"2014","journal-title":"Nat Methods"},{"key":"pcbi.1007451.ref050","unstructured":"Bravo HC, Theussl S. Rcplex: R Interface to CPLEX; 2016. Available from: https:\/\/CRAN.R-project.org\/package=Rcplex."},{"key":"pcbi.1007451.ref051","unstructured":"IBM. CPLEX Optimizer;. https:\/\/www.ibm.com\/analytics\/cplex-optimizer."},{"issue":"2","key":"pcbi.1007451.ref052","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.cell.2013.09.034","article-title":"The somatic genomic landscape of glioblastoma","volume":"155","author":"CW Brennan","year":"2013","journal-title":"Cell"},{"issue":"5","key":"pcbi.1007451.ref053","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1093\/neuonc\/nox183","article-title":"Glioma CpG island methylator phenotype (G-CIMP): biological and clinical implications","volume":"20","author":"TM Malta","year":"2017","journal-title":"Neuro-oncology"},{"issue":"1","key":"pcbi.1007451.ref054","doi-asserted-by":"crossref","first-page":"84","DOI":"10.3748\/wjg.v21.i1.84","article-title":"P53 mutations in colorectal cancer-molecular pathogenesis and pharmacological reactivation","volume":"21","author":"XL Li","year":"2015","journal-title":"World journal of gastroenterology: WJG"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007451","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,11,21]],"date-time":"2019-11-21T00:00:00Z","timestamp":1574294400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007451","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,11,21]],"date-time":"2019-11-21T14:52:58Z","timestamp":1574347978000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007451"}},"subtitle":[],"editor":[{"given":"Rachel","family":"Karchin","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,11,11]]},"references-count":54,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2019,11,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007451","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/625442","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,11,11]]}}}