{"id":"https://openalex.org/W2949890743","doi":"https://doi.org/10.1093/bioinformatics/btx663","title":"Cancer progression models and fitness landscapes: a many-to-many relationship","display_name":"Cancer progression models and fitness landscapes: a many-to-many relationship","publication_year":2017,"publication_date":"2017-10-17","ids":{"openalex":"https://openalex.org/W2949890743","doi":"https://doi.org/10.1093/bioinformatics/btx663","mag":"2949890743"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx663","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx663","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/836/25117623/btx663.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/836/25117623/btx663.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080620893","display_name":"Ram\u00f3n D\u00edaz\u2010Uriarte","orcid":"https://orcid.org/0000-0002-6637-9039"},"institutions":[{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]},{"id":"https://openalex.org/I4210091816","display_name":"Instituto de Investigaciones Biom\u00e9dicas Sols-Morreale","ror":"https://ror.org/00ha1f767","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210091816","https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Ramon Diaz-Uriarte","raw_affiliation_strings":["Department of Biochemistry, Universidad Aut\u00f3noma de Madrid, Instituto de Investigaciones Biom\u00e9dicas \u201cAlberto Sols\u201d (UAM-CSIC), Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Universidad Aut\u00f3noma de Madrid, Instituto de Investigaciones Biom\u00e9dicas \u201cAlberto Sols\u201d (UAM-CSIC), Madrid, Spain","institution_ids":["https://openalex.org/I4210091816","https://openalex.org/I63634437"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5080620893"],"corresponding_institution_ids":["https://openalex.org/I4210091816","https://openalex.org/I63634437"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.2007,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.88707463,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"34","issue":"5","first_page":"836","last_page":"844"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fitness-landscape","display_name":"Fitness landscape","score":0.6283447742462158},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5289981961250305},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38806554675102234},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3584006428718567},{"id":"https://openalex.org/keywords/gerontology","display_name":"Gerontology","score":0.3565453290939331},{"id":"https://openalex.org/keywords/demography","display_name":"Demography","score":0.31986263394355774},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.23045402765274048},{"id":"https://openalex.org/keywords/sociology","display_name":"Sociology","score":0.16729354858398438},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15774962306022644}],"concepts":[{"id":"https://openalex.org/C91852762","wikidata":"https://www.wikidata.org/wiki/Q3307742","display_name":"Fitness landscape","level":3,"score":0.6283447742462158},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5289981961250305},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38806554675102234},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3584006428718567},{"id":"https://openalex.org/C74909509","wikidata":"https://www.wikidata.org/wiki/Q10387","display_name":"Gerontology","level":1,"score":0.3565453290939331},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.31986263394355774},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.23045402765274048},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.16729354858398438},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15774962306022644},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx663","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx663","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/836/25117623/btx663.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:www.tdx.cat:10486/682511","is_oa":false,"landing_page_url":"http://hdl.handle.net/10486/682511","pdf_url":null,"source":{"id":"https://openalex.org/S4306401111","display_name":"Tesis Doctorals en Xarxa (Consorci de Serveis Universitaris de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210090028","host_organization_name":"Consorci de Serveis Universitaris de Catalunya","host_organization_lineage":["https://openalex.org/I4210090028"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:digital.csic.es:10261/188064","is_oa":true,"landing_page_url":"http://hdl.handle.net/10261/188064","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"art\u00edculo"},{"id":"pmh:oai:europepmc.org:4991336","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6031050","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx663","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx663","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/836/25117623/btx663.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6044624198","display_name":null,"funder_award_id":"BFU2015-67302-R","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"}],"funders":[{"id":"https://openalex.org/F4320321595","display_name":"Federaci\u00f3n Espa\u00f1ola de Enfermedades Raras","ror":"https://ror.org/0348bpk17"},{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949890743.pdf","grobid_xml":"https://content.openalex.org/works/W2949890743.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W1528905581","https://openalex.org/W1587094587","https://openalex.org/W1598410563","https://openalex.org/W1662357506","https://openalex.org/W1937970165","https://openalex.org/W1964154017","https://openalex.org/W1970185413","https://openalex.org/W1973563118","https://openalex.org/W1983708207","https://openalex.org/W2001258296","https://openalex.org/W2011759634","https://openalex.org/W2012611161","https://openalex.org/W2013115302","https://openalex.org/W2015631955","https://openalex.org/W2040827479","https://openalex.org/W2041817254","https://openalex.org/W2042536531","https://openalex.org/W2059437408","https://openalex.org/W2069086572","https://openalex.org/W2073294762","https://openalex.org/W2081531630","https://openalex.org/W2101354849","https://openalex.org/W2109860416","https://openalex.org/W2126643167","https://openalex.org/W2136155563","https://openalex.org/W2137549067","https://openalex.org/W2138155367","https://openalex.org/W2148819091","https://openalex.org/W2150073600","https://openalex.org/W2153938747","https://openalex.org/W2156469654","https://openalex.org/W2165327448","https://openalex.org/W2167278498","https://openalex.org/W2171900790","https://openalex.org/W2174686320","https://openalex.org/W2204695746","https://openalex.org/W2209688796","https://openalex.org/W2233432342","https://openalex.org/W2253465175","https://openalex.org/W2259572413","https://openalex.org/W2270380494","https://openalex.org/W2337872996","https://openalex.org/W2402811940","https://openalex.org/W2441755798","https://openalex.org/W2476718998","https://openalex.org/W2526309682","https://openalex.org/W2562809264","https://openalex.org/W2586544027","https://openalex.org/W3098494004","https://openalex.org/W4206439534","https://openalex.org/W4210370111","https://openalex.org/W4238448376","https://openalex.org/W4246887724","https://openalex.org/W4301861531","https://openalex.org/W6682090829","https://openalex.org/W6683238963","https://openalex.org/W6688462648"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"The":[2],"identification":[3],"of":[4,13,15,49,72,118,172,217],"constraints,":[5,42],"due":[6],"to":[7,23,39,66,187,194],"gene":[8],"interactions,":[9],"in":[10,132,152,208],"the":[11,58,85,133,170,188,213],"order":[12],"accumulation":[14],"mutations":[16],"during":[17],"cancer":[18,161],"progression":[19,29],"can":[20,121,205],"allow":[21],"us":[22],"single":[24],"out":[25],"therapeutic":[26],"targets.":[27],"Cancer":[28],"models":[30],"(CPMs)":[31],"use":[32,214],"genotype":[33],"frequency":[34],"data":[35,107,185,230],"from":[36,82,136,181,224],"cross-sectional":[37],"samples":[38],"identify":[40],"these":[41,166,210],"and":[43,84,148,192,215,220],"return":[44],"Directed":[45],"Acyclic":[46],"Graphs":[47],"(DAGs)":[48],"restrictions":[50],"where":[51,88],"arrows":[52],"indicate":[53],"dependencies":[54],"or":[55],"constraints.":[56],"On":[57],"other":[59,183],"hand,":[60],"fitness":[61,86,93,110,149,175],"landscapes,":[62,111],"which":[63,139],"map":[64],"genotypes":[65,119],"fitness,":[67],"contain":[68],"all":[69],"possible":[70],"paths":[71],"tumor":[73],"progression.":[74],"Thus,":[75],"we":[76],"expect":[77],"a":[78],"correspondence":[79],"between":[80],"DAGs":[81,134,195],"CPMs":[83],"landscapes":[87,176],"evolution":[89],"happened.":[90],"But":[91],"many":[92],"landscapes\u2014e.g.":[94],"those":[95],"with":[96,124],"reciprocal":[97,125,202],"sign":[98,126,203],"epistasis\u2014cannot":[99],"be":[100,206],"represented":[101],"by":[102,143],"CPMs.":[103,218],"Results":[104],"Using":[105,159],"simulated":[106],"under":[108],"500":[109],"I":[112,163],"show":[113,164],"that":[114,120,154,165,177,196],"CPMs\u2019":[115],"performance":[116],"(prediction":[117],"exist)":[122],"degrades":[123],"epistasis.":[127],"There":[128],"is":[129,140],"large":[130],"variability":[131],"inferred":[135],"each":[137,182],"landscape,":[138],"also":[141],"affected":[142],"mutation":[144],"rate,":[145],"detection":[146],"regime":[147],"landscape":[150],"features,":[151],"ways":[153],"depend":[155],"on":[156],"CPM":[157],"method.":[158],"three":[160],"datasets,":[162],"problems":[167],"strongly":[168],"affect":[169],"analysis":[171],"empirical":[173],"data:":[174],"are":[178,231],"widely":[179],"different":[180,199],"produce":[184],"similar":[186],"empirically":[189],"observed":[190],"ones":[191],"lead":[193],"infer":[197],"very":[198],"restrictions.":[200],"Because":[201],"epistasis":[204],"common":[207],"cancer,":[209],"results":[211],"question":[212],"interpretation":[216],"Availability":[219],"implementation":[221],"Code":[222],"available":[223,232],"Supplementary":[225,227,229],"Material.":[226],"information":[228],"at":[233],"Bioinformatics":[234],"online.":[235]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
