{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:07:40Z","timestamp":1772172460650,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007246","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,8,14]],"date-time":"2019-08-14T00:00:00Z","timestamp":1565740800000}}],"reference-count":79,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2019,8,2]],"date-time":"2019-08-02T00:00:00Z","timestamp":1564704000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008433","name":"Consejer\u00eda de Educaci\u00f3n, Juventud y Deporte, Comunidad de Madrid","doi-asserted-by":"publisher","award":["PEJD-2016-BMD-2116"],"award-info":[{"award-number":["PEJD-2016-BMD-2116"]}],"id":[{"id":"10.13039\/501100008433","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010198","name":"Ministerio de Econom\u00eda, Industria y Competitividad, Gobierno de Espa\u00f1a","doi-asserted-by":"publisher","award":["BFU2015-67302-R"],"award-info":[{"award-number":["BFU2015-67302-R"]}],"id":[{"id":"10.13039\/501100010198","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.1007246","type":"journal-article","created":{"date-parts":[[2019,8,2]],"date-time":"2019-08-02T13:30:38Z","timestamp":1564752638000},"page":"e1007246","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":37,"title":["Every which way? On predicting tumor evolution using cancer progression models"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6637-9039","authenticated-orcid":true,"given":"Ramon","family":"Diaz-Uriarte","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0043-0882","authenticated-orcid":true,"given":"Claudia","family":"Vasallo","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,8,2]]},"reference":[{"issue":"2","key":"pcbi.1007246.ref001","doi-asserted-by":"crossref","first-page":"a029603","DOI":"10.1101\/cshperspect.a029603","article-title":"Observing Clonal Dynamics across Spatiotemporal Axes: A Prelude to Quantitative Fitness Models for Cancer","volume":"8","author":"AW McPherson","year":"2018","journal-title":"Cold Spring Harb Perspect Med"},{"issue":"8","key":"pcbi.1007246.ref002","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1158\/2159-8290.CD-15-0439","article-title":"Evolutionary Determinants of Cancer","volume":"5","author":"M Greaves","year":"2015","journal-title":"Cancer Discovery"},{"issue":"1","key":"pcbi.1007246.ref003","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.trecan.2015.11.003","article-title":"Cancer Evolution and the Limits of Predictability in Precision Cancer Medicine","volume":"2","author":"KA Lipinski","year":"2016","journal-title":"Trends in Cancer"},{"issue":"6","key":"pcbi.1007246.ref004","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1038\/s41588-018-0128-6","article-title":"Quantification of Subclonal Selection in Cancer from Bulk Sequencing Data","volume":"50","author":"MJ Williams","year":"2018","journal-title":"Nature Genetics"},{"issue":"3","key":"pcbi.1007246.ref005","doi-asserted-by":"crossref","DOI":"10.1038\/s41559-017-0077","article-title":"Predicting Evolution","volume":"1","author":"M L\u00e4ssig","year":"2017","journal-title":"Nature Ecology & Evolution"},{"key":"pcbi.1007246.ref006","unstructured":"Losos JB. Improbable Destinies: Fate, Chance, and the Future of Evolution. S.l.: Riverhead Books; 2018."},{"issue":"1","key":"pcbi.1007246.ref007","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/ng.1034","article-title":"Evolutionary Paths to Antibiotic Resistance under Dynamically Sustained Drug Selection","volume":"44","author":"E Toprak","year":"2012","journal-title":"Nature Genetics"},{"issue":"4","key":"pcbi.1007246.ref008","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/nrg3351","article-title":"Understanding, Predicting and Manipulating the Genotypic Evolution of Antibiotic Resistance","volume":"14","author":"AC Palmer","year":"2013","journal-title":"Nature Reviews Genetics"},{"issue":"21","key":"pcbi.1007246.ref009","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":"11","key":"pcbi.1007246.ref010","doi-asserted-by":"crossref","first-page":"e27136","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":"17","key":"pcbi.1007246.ref011","doi-asserted-by":"crossref","first-page":"i727","DOI":"10.1093\/bioinformatics\/btw459","article-title":"Large-Scale Inference of Conjunctive Bayesian Networks","volume":"32","author":"H Montazeri","year":"2016","journal-title":"Bioinformatics"},{"key":"pcbi.1007246.ref012","doi-asserted-by":"crossref","unstructured":"Szabo A, Boucher KM. Oncogenetic Trees. In: Tan WY, Hanin L, editors. Handbook of Cancer Models with Applications. World Scientific; 2008. p. 1\u201324. Available from: http:\/\/www.worldscibooks.com\/lifesci\/6677.html.","DOI":"10.1142\/9789812779489_0001"},{"issue":"1","key":"pcbi.1007246.ref013","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":"J Comput Biol"},{"issue":"18","key":"pcbi.1007246.ref014","doi-asserted-by":"crossref","first-page":"3016","DOI":"10.1093\/bioinformatics\/btv296","article-title":"CAPRI: Efficient Inference of Cancer Progression Models from Cross-Sectional Data","volume":"31","author":"D Ramazzotti","year":"2015","journal-title":"Bioinformatics"},{"issue":"28","key":"pcbi.1007246.ref015","doi-asserted-by":"crossref","first-page":"E4025","DOI":"10.1073\/pnas.1520213113","article-title":"Algorithmic Methods to Infer the Evolutionary Trajectories in Cancer Progression","volume":"113","author":"G Caravagna","year":"2016","journal-title":"PNAS"},{"issue":"10","key":"pcbi.1007246.ref016","doi-asserted-by":"crossref","first-page":"e108358","DOI":"10.1371\/journal.pone.0108358","article-title":"Inferring Tree Causal Models of Cancer Progression with Probability Raising","volume":"9","author":"L Olde Loohuis","year":"2014","journal-title":"PLOS ONE"},{"issue":"1","key":"pcbi.1007246.ref017","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/sysbio\/syu081","article-title":"Cancer Evolution: Mathematical Models and Computational Inference","volume":"64","author":"N Beerenwinkel","year":"2015","journal-title":"Systematic Biology"},{"issue":"2","key":"pcbi.1007246.ref018","doi-asserted-by":"crossref","first-page":"e1004717","DOI":"10.1371\/journal.pcbi.1004717","article-title":"Computational Cancer Biology: An Evolutionary Perspective","volume":"12","author":"N Beerenwinkel","year":"2016","journal-title":"PLoS Comput Biol"},{"issue":"17","key":"pcbi.1007246.ref019","doi-asserted-by":"crossref","first-page":"2456","DOI":"10.1093\/bioinformatics\/btu319","article-title":"Inferring the Paths of Somatic Evolution in Cancer","volume":"30","author":"N Misra","year":"2014","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"1","key":"pcbi.1007246.ref020","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1073\/pnas.1421839112","article-title":"Only Three Driver Gene Mutations Are Required for the Development of Lung and Colorectal Cancers","volume":"112","author":"C Tomasetti","year":"2015","journal-title":"PNAS"},{"issue":"1","key":"pcbi.1007246.ref021","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1146\/annurev-cancerbio-042016-073434","article-title":"Synthetic Lethality in Cancer Therapeutics","volume":"1","author":"RL Beijersbergen","year":"2017","journal-title":"Annual Review of Cancer Biology"},{"issue":"10","key":"pcbi.1007246.ref022","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/nrg.2017.47","article-title":"Synthetic Lethality and Cancer","volume":"18","author":"NJ O\u2019Neil","year":"2017","journal-title":"Nat Rev Genet"},{"key":"pcbi.1007246.ref023","doi-asserted-by":"crossref","unstructured":"Brouillet S, Annoni H, Ferretti L, Achaz G. MAGELLAN: A Tool to Explore Small Fitness Landscapes. bioRxiv. 2015; p. 031583.","DOI":"10.1101\/031583"},{"key":"pcbi.1007246.ref024","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jtbi.2012.09.028","article-title":"The Peaks and Geometry of Fitness Landscapes","volume":"317","author":"K Crona","year":"2013","journal-title":"Journal of Theoretical Biology"},{"issue":"7","key":"pcbi.1007246.ref025","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nrg3744","article-title":"Empirical Fitness Landscapes and the Predictability of Evolution","volume":"15","author":"JAGM de Visser","year":"2014","journal-title":"Nat Rev Genet"},{"issue":"8","key":"pcbi.1007246.ref026","doi-asserted-by":"crossref","first-page":"e1002134","DOI":"10.1371\/journal.pcbi.1002134","article-title":"Evolutionary Accessibility of Mutational Pathways","volume":"7","author":"J Franke","year":"2011","journal-title":"PLoS Comput Biol"},{"issue":"6264","key":"pcbi.1007246.ref027","doi-asserted-by":"crossref","first-page":"1092","DOI":"10.1126\/science.aac7557","article-title":"Gene Essentiality and Synthetic Lethality in Haploid Human Cells","volume":"350","author":"VA Blomen","year":"2015","journal-title":"Science"},{"issue":"6, Part A","key":"pcbi.1007246.ref028","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/j.ygeno.2014.10.011","article-title":"The Valley-of-Death: Reciprocal Sign Epistasis Constrains Adaptive Trajectories in a Constant, Nutrient Limiting Environment","volume":"104","author":"KE Chiotti","year":"2014","journal-title":"Genomics"},{"issue":"49","key":"pcbi.1007246.ref029","doi-asserted-by":"crossref","first-page":"14085","DOI":"10.1073\/pnas.1612676113","article-title":"On the (Un)Predictability of a Large Intragenic Fitness Landscape","volume":"113","author":"C Bank","year":"2016","journal-title":"PNAS"},{"issue":"2","key":"pcbi.1007246.ref030","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1073\/pnas.1213613110","article-title":"Predictability of Evolution Depends Nonmonotonically on Population Size","volume":"110","author":"IG Szendro","year":"2013","journal-title":"PNAS"},{"issue":"5","key":"pcbi.1007246.ref031","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1093\/bioinformatics\/btx663","article-title":"Cancer Progression Models and Fitness Landscapes: A Many-to-Many Relationship","volume":"34","author":"R Diaz-Uriarte","year":"2018","journal-title":"Bioinformatics"},{"issue":"6","key":"pcbi.1007246.ref032","doi-asserted-by":"crossref","first-page":"e65773","DOI":"10.1371\/journal.pone.0065773","article-title":"Learning Oncogenetic Networks by Reducing to Mixed Integer Linear Programming","volume":"8","author":"HS Farahani","year":"2013","journal-title":"PloS ONE"},{"issue":"18","key":"pcbi.1007246.ref033","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 (Oxford, England)"},{"issue":"1","key":"pcbi.1007246.ref034","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"},{"issue":"41","key":"pcbi.1007246.ref035","doi-asserted-by":"crossref","first-page":"17604","DOI":"10.1073\/pnas.1009117107","article-title":"A Mathematical Framework to Determine the Temporal Sequence of Somatic Genetic Events in Cancer","volume":"107","author":"C Attolini","year":"2010","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"14","key":"pcbi.1007246.ref036","doi-asserted-by":"crossref","first-page":"i389","DOI":"10.1093\/bioinformatics\/btz332","article-title":"Estimating the Predictability of Cancer Evolution","volume":"35","author":"SR Hosseini","year":"2019","journal-title":"Bioinformatics"},{"issue":"2","key":"pcbi.1007246.ref037","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1534\/genetics.114.167668","article-title":"Adaptation in Tunably Rugged Fitness Landscapes: The Rough Mount Fuji Model","volume":"198","author":"J Neidhart","year":"2014","journal-title":"Genetics"},{"issue":"8","key":"pcbi.1007246.ref038","doi-asserted-by":"crossref","first-page":"2910","DOI":"10.1073\/pnas.1213968110","article-title":"Impact of Deleterious Passenger Mutations on Cancer Progression","volume":"110","author":"CD McFarland","year":"2013","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"pcbi.1007246.ref039","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"},{"issue":"12","key":"pcbi.1007246.ref040","doi-asserted-by":"crossref","first-page":"1898","DOI":"10.1093\/bioinformatics\/btx077","article-title":"OncoSimulR: Genetic Simulation with Arbitrary Epistasis and Mutator Genes in Asexual Populations","volume":"33","author":"R Diaz-Uriarte","year":"2017","journal-title":"Bioinformatics"},{"issue":"11","key":"pcbi.1007246.ref041","doi-asserted-by":"crossref","first-page":"e225","DOI":"10.1371\/journal.pcbi.0030225","article-title":"Genetic Progression and the Waiting Time to Cancer","volume":"3","author":"N Beerenwinkel","year":"2007","journal-title":"PLoS computational biology"},{"key":"pcbi.1007246.ref042","doi-asserted-by":"crossref","unstructured":"Wodarz D, Komarova NL. Dynamics of Cancer: Mathematical Foundations of Oncology; 2014.","DOI":"10.1142\/8973"},{"issue":"29","key":"pcbi.1007246.ref043","doi-asserted-by":"crossref","first-page":"10635","DOI":"10.1073\/pnas.0400747101","article-title":"Evolutionary Dynamics of Tumor Suppressor Gene Inactivation","volume":"101","author":"MA Nowak","year":"2004","journal-title":"PNAS"},{"issue":"1544","key":"pcbi.1007246.ref044","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1098\/rstb.2009.0290","article-title":"Beneficial Mutations and the Dynamics of Adaptation in Asexual Populations","volume":"365","author":"PD Sniegowski","year":"2010","journal-title":"Philosophical Transactions of the Royal Society of London B: Biological Sciences"},{"key":"pcbi.1007246.ref045","unstructured":"Crooks GE. On Measures of Entropy and Information; 2017. Available from: http:\/\/threeplusone.com\/on_information.pdf."},{"issue":"1","key":"pcbi.1007246.ref046","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1109\/18.61115","article-title":"Divergence Measures Based on the Shannon Entropy","volume":"37","author":"J Lin","year":"1991","journal-title":"IEEE Transactions on Information theory"},{"issue":"7","key":"pcbi.1007246.ref047","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1080\/0266476042000214501","article-title":"Beta Regression for Modelling Rates and Proportions","volume":"31","author":"S Ferrari","year":"2004","journal-title":"Journal of Applied Statistics"},{"issue":"11","key":"pcbi.1007246.ref048","doi-asserted-by":"crossref","DOI":"10.18637\/jss.v048.i11","article-title":"Extended Beta Regression in R: Shaken, Stirred, Mixed, and Partitioned","volume":"48","author":"B Gr\u00fcn","year":"2012","journal-title":"Journal of Statistical Software"},{"issue":"1","key":"pcbi.1007246.ref049","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1037\/1082-989X.11.1.54","article-title":"A Better Lemon Squeezer? Maximum-Likelihood Regression with Beta-Distributed Dependent Variables","volume":"11","author":"M Smithson","year":"2006","journal-title":"Psychological methods"},{"key":"pcbi.1007246.ref050","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-3242-6","volume-title":"Generalized Linear Models","author":"P McCullagh","year":"1989","edition":"2nd Ed"},{"issue":"2","key":"pcbi.1007246.ref051","doi-asserted-by":"crossref","first-page":"378","DOI":"10.32614\/RJ-2017-066","article-title":"glmmTMB Balances Speed and Flexibility Among Packages for Zero-Inflated Generalized Linear Mixed Modeling","volume":"9","author":"ME Brooks","year":"2017","journal-title":"The R Journal"},{"key":"pcbi.1007246.ref052","volume-title":"An R Companion to Applied Regression","author":"J Fox","year":"2011","edition":"2nd Ed"},{"key":"pcbi.1007246.ref053","unstructured":"R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria; 2018. Available from: https:\/\/www.R-project.org\/."},{"issue":"7418","key":"pcbi.1007246.ref054","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature11412","article-title":"Comprehensive Molecular Portraits of Human Breast Tumours","volume":"490","author":"Cancer Genome Atlas Research Network","year":"2012","journal-title":"Nature"},{"issue":"2","key":"pcbi.1007246.ref055","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/sj.bjc.6601894","article-title":"The COSMIC (Catalogue of Somatic Mutations in Cancer) Database and Website","volume":"91","author":"S Bamford","year":"2004","journal-title":"Br J Cancer"},{"issue":"7216","key":"pcbi.1007246.ref056","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":"5897","key":"pcbi.1007246.ref057","doi-asserted-by":"crossref","first-page":"1801","DOI":"10.1126\/science.1164368","article-title":"Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses","volume":"321","author":"S Jones","year":"2008","journal-title":"Science (New York, NY)"},{"issue":"5897","key":"pcbi.1007246.ref058","doi-asserted-by":"crossref","first-page":"1807","DOI":"10.1126\/science.1164382","article-title":"An Integrated Genomic Analysis of Human Glioblastoma Multiforme","volume":"321","author":"DW Parsons","year":"2008","journal-title":"Science"},{"issue":"5853","key":"pcbi.1007246.ref059","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1126\/science.1145720","article-title":"The Genomic Landscapes of Human Breast and Colorectal Cancers","volume":"318","author":"LD Wood","year":"2007","journal-title":"Science"},{"issue":"2","key":"pcbi.1007246.ref060","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":"7216","key":"pcbi.1007246.ref061","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1038\/nature07423","article-title":"Somatic Mutations Affect Key Pathways in Lung Adenocarcinoma","volume":"455","author":"L Ding","year":"2008","journal-title":"Nature"},{"issue":"7353","key":"pcbi.1007246.ref062","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1038\/nature10166","article-title":"Integrated Genomic Analyses of Ovarian Carcinoma","volume":"474","author":"Cancer Genome Atlas Research Network","year":"2011","journal-title":"Nature"},{"issue":"1","key":"pcbi.1007246.ref063","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1002\/gcc.20224","article-title":"The Interactive Online SKY\/M-FISH & CGH Database and the Entrez Cancer Chromosomes Search Database: Linkage of Chromosomal Aberrations with the Genome Sequence","volume":"44","author":"T Knutsen","year":"2005","journal-title":"Genes, Chromosomes and Cancer"},{"issue":"1","key":"pcbi.1007246.ref064","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/ng.2495","article-title":"Recurrent SETBP1 Mutations in Atypical Chronic Myeloid Leukemia","volume":"45","author":"R Piazza","year":"2013","journal-title":"Nature Genetics"},{"issue":"7407","key":"pcbi.1007246.ref065","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 Research Network","year":"2012","journal-title":"Nature"},{"issue":"3","key":"pcbi.1007246.ref066","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1002\/bimj.200810425","article-title":"Simultaneous Inference in General Parametric Models","volume":"50","author":"T Hothorn","year":"2008","journal-title":"Biom J"},{"issue":"41","key":"pcbi.1007246.ref067","article-title":"Identifying Restrictions in the Order of Accumulation of Mutations during Tumor Progression: Effects of Passengers, Evolutionary Models, and Sampling","volume":"16","author":"R Diaz-Uriarte","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1007246.ref068","article-title":"pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics","author":"S Cristea","year":"2016","journal-title":"Journal of Computational Biology"},{"issue":"00","key":"pcbi.1007246.ref069","first-page":"250","article-title":"Simultaneous Inference of Cancer Pathways and Tumor Progression from CrossSectional Mutation Data","volume":"22","author":"BJ Raphael","year":"2015","journal-title":"Journal of Computational Biology"},{"key":"pcbi.1007246.ref070","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.semcancer.2014.04.002","article-title":"Predictive Genomics: A Cancer Hallmark Network Framework for Predicting Tumor Clinical Phenotypes Using Genome Sequencing Data","volume":"30","author":"E Wang","year":"2015","journal-title":"Seminars in Cancer Biology"},{"issue":"10","key":"pcbi.1007246.ref071","doi-asserted-by":"crossref","first-page":"2298","DOI":"10.1111\/evo.13320","article-title":"What Affects the Predictability of Evolutionary Constraints Using a G-matrix? The Relative Effects of Modular Pleiotropy and Mutational Correlation","volume":"71","author":"J Chebib","year":"2017","journal-title":"Evolution"},{"issue":"45","key":"pcbi.1007246.ref072","doi-asserted-by":"crossref","first-page":"11938","DOI":"10.1073\/pnas.1711927114","article-title":"Molecular Ensembles Make Evolution Unpredictable","volume":"114","author":"ZR Sailer","year":"2017","journal-title":"PNAS"},{"issue":"5","key":"pcbi.1007246.ref073","doi-asserted-by":"crossref","first-page":"e2000644","DOI":"10.1371\/journal.pbio.2000644","article-title":"Phenotypic Heterogeneity Promotes Adaptive Evolution","volume":"15","author":"Z B\u00f3di","year":"2017","journal-title":"PLOS Biology"},{"issue":"1","key":"pcbi.1007246.ref074","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/s41576-018-0069-z","article-title":"The Causes of Evolvability and Their Evolution","volume":"20","author":"JL Payne","year":"2019","journal-title":"Nat Rev Genet"},{"issue":"7","key":"pcbi.1007246.ref075","doi-asserted-by":"crossref","first-page":"180069","DOI":"10.1098\/rsob.180069","article-title":"On the Networked Architecture of Genotype Spaces and Its Critical Effects on Molecular Evolution","volume":"8","author":"J Aguirre","year":"2018","journal-title":"Open Biology"},{"issue":"4","key":"pcbi.1007246.ref076","doi-asserted-by":"crossref","first-page":"e1001296","DOI":"10.1371\/journal.pbio.1001296","article-title":"Nonheritable Cellular Variability Accelerates the Evolutionary Processes of Cancer","volume":"10","author":"SA Frank","year":"2012","journal-title":"PLoS Biol"},{"issue":"11","key":"pcbi.1007246.ref077","doi-asserted-by":"crossref","first-page":"2310","DOI":"10.1111\/j.1420-9101.2011.02373.x","article-title":"Natural Selection. II. Developmental Variability and Evolutionary Rate","volume":"24","author":"SA Frank","year":"2011","journal-title":"Journal of Evolutionary Biology"},{"issue":"1","key":"pcbi.1007246.ref078","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.cell.2011.03.020","article-title":"Genetic Interactions in Cancer Progression and Treatment","volume":"145","author":"A Ashworth","year":"2011","journal-title":"Cell"},{"issue":"9","key":"pcbi.1007246.ref079","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"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007246","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,8,14]],"date-time":"2019-08-14T00:00:00Z","timestamp":1565740800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007246","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T10:15:09Z","timestamp":1589019309000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007246"}},"subtitle":[],"editor":[{"given":"Arne","family":"Traulsen","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,8,2]]},"references-count":79,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2019,8,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007246","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/371039","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,2]]}}}