{"id":"https://openalex.org/W2952030916","doi":"https://doi.org/10.1109/tcbb.2018.2865729","title":"Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach","display_name":"Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach","publication_year":2018,"publication_date":"2018-08-17","ids":{"openalex":"https://openalex.org/W2952030916","doi":"https://doi.org/10.1109/tcbb.2018.2865729","mag":"2952030916"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2018.2865729","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2865729","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038691764","display_name":"Paola Bonizzoni","orcid":"https://orcid.org/0000-0001-7289-4988"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Paola Bonizzoni","raw_affiliation_strings":["Dipartimento di Informatica Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano\u2013Bicocca, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano\u2013Bicocca, Milano, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048411377","display_name":"Simone Ciccolella","orcid":"https://orcid.org/0000-0002-6469-4887"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simone Ciccolella","raw_affiliation_strings":["Dipartimento di Informatica Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano\u2013Bicocca, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano\u2013Bicocca, Milano, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059679442","display_name":"Gianluca Della Vedova","orcid":"https://orcid.org/0000-0001-5584-3089"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gianluca Della Vedova","raw_affiliation_strings":["Dipartimento di Informatica Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano\u2013Bicocca, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano\u2013Bicocca, Milano, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044649325","display_name":"Mauricio Soto","orcid":"https://orcid.org/0000-0001-5977-9467"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mauricio Soto","raw_affiliation_strings":["Dipartimento di Informatica Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano\u2013Bicocca, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano\u2013Bicocca, Milano, Italy","institution_ids":["https://openalex.org/I66752286"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5038691764"],"corresponding_institution_ids":["https://openalex.org/I66752286"],"apc_list":null,"apc_paid":null,"fwci":1.2707,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.77116834,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"16","issue":"5","first_page":"1410","last_page":"1423"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998999834060669,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T11369","display_name":"Genetic factors in colorectal cancer","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6978124380111694},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5601077079772949},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5566740036010742},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4421881139278412},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43400418758392334},{"id":"https://openalex.org/keywords/evolutionary-algorithm","display_name":"Evolutionary algorithm","score":0.43328583240509033},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3543161451816559},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3535193204879761},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27903658151626587},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16823643445968628},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11925968527793884}],"concepts":[{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6978124380111694},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5601077079772949},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5566740036010742},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4421881139278412},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43400418758392334},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.43328583240509033},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3543161451816559},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3535193204879761},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27903658151626587},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16823643445968628},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11925968527793884},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2018.2865729","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2865729","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:boa.unimib.it:10281/214914","is_oa":false,"landing_page_url":"https://ieeexplore.ieee.org/document/8438928","pdf_url":null,"source":{"id":"https://openalex.org/S4306401259","display_name":"BOA (University of Milano-Bicocca)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8411802876","display_name":null,"funder_award_id":"2013-0955","funder_id":"https://openalex.org/F4320321499","funder_display_name":"Fondazione Cariplo"}],"funders":[{"id":"https://openalex.org/F4320321499","display_name":"Fondazione Cariplo","ror":"https://ror.org/01gb56c55"},{"id":"https://openalex.org/F4320332538","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W162544871","https://openalex.org/W190053699","https://openalex.org/W938539187","https://openalex.org/W1534962401","https://openalex.org/W1968657935","https://openalex.org/W1990061958","https://openalex.org/W2002295829","https://openalex.org/W2009720434","https://openalex.org/W2023560061","https://openalex.org/W2027246028","https://openalex.org/W2030646320","https://openalex.org/W2031170804","https://openalex.org/W2041380745","https://openalex.org/W2044433401","https://openalex.org/W2072719910","https://openalex.org/W2074507113","https://openalex.org/W2075503802","https://openalex.org/W2076755063","https://openalex.org/W2111874706","https://openalex.org/W2117797567","https://openalex.org/W2120653759","https://openalex.org/W2122392334","https://openalex.org/W2122451246","https://openalex.org/W2126386241","https://openalex.org/W2134599124","https://openalex.org/W2144847592","https://openalex.org/W2154068087","https://openalex.org/W2157751858","https://openalex.org/W2166815431","https://openalex.org/W2346273585","https://openalex.org/W2482614962","https://openalex.org/W2514535054","https://openalex.org/W2515462796","https://openalex.org/W2762185802","https://openalex.org/W4233815609","https://openalex.org/W4236590756","https://openalex.org/W4241418020","https://openalex.org/W4388212639"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2057191541","https://openalex.org/W2883025420","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2375383082","https://openalex.org/W2604174992","https://openalex.org/W1974895455","https://openalex.org/W3023641210"],"abstract_inverted_index":{"Most":[0],"of":[1,31,60,84,138,147,156,170,188],"the":[2,10,21,29,32,57,63,94,106,112,130,135,145,160,168,189],"evolutionary":[3,22,58,95,118,136,190],"history":[4,59,137,191],"reconstruction":[5,97],"approaches":[6],"are":[7,54,120],"based":[8],"on":[9],"infinite":[11,33],"sites":[12,34],"assumption,":[13],"which":[14],"states":[15],"that":[16,49,75],"mutations":[17,53,80],"appear":[18],"once":[19],"in":[20,56,127,153],"history.":[23],"The":[24,122,196],"Perfect":[25,64,194],"Phylogeny":[26,65,109],"model":[27,66],"is":[28,125,132,198],"result":[30],"assumption":[35],"and":[36,51,81,111,178],"has":[37],"been":[38],"widely":[39],"used":[40],"to":[41,103,133],"infer":[42],"cancer":[43,128,157],"evolution.":[44],"Nonetheless,":[45],"recent":[46],"results":[47],"show":[48],"recurrent":[50],"back":[52],"present":[55],"tumors,":[61],"hence":[62],"might":[67],"be":[68],"too":[69],"restrictive.":[70],"We":[71],"propose":[72],"an":[73,90,164],"approach":[74,183],"allows":[76,101],"losing":[77],"previously":[78],"acquired":[79],"multiple":[82],"acquisitions":[83],"a":[85,139,150,154,185,193],"character.":[86],"Moreover,":[87],"we":[88],"provide":[89],"ILP":[91,182],"formulation":[92,100],"for":[93],"tree":[96],"problem.":[98],"Our":[99],"us":[102],"tackle":[104],"both":[105],"Incomplete":[107],"Directed":[108],"problem":[110,115,124],"Clonal":[113,161],"Reconstruction":[114,162],"when":[116],"general":[117],"models":[119],"considered.":[121],"latter":[123],"fundamental":[126],"genomics,":[129],"goal":[131],"study":[134],"tumor":[140],"considering":[141],"as":[142],"input":[143],"data":[144],"fraction":[146],"cells":[148],"having":[149],"certain":[151],"mutation":[152,172],"set":[155],"samples.":[158],"For":[159],"problem,":[163],"experimental":[165],"analysis":[166],"shows":[167],"advantage":[169],"allowing":[171],"losses.":[173],"Namely,":[174],"by":[175],"analyzing":[176],"real":[177],"simulated":[179],"datasets,":[180],"our":[181],"provides":[184],"better":[186],"interpretation":[187],"than":[192],"Phylogeny.":[195],"software":[197],"at":[199],"https://github.com/AlgoLab/gppf.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":2}],"updated_date":"2026-03-28T08:17:26.163206","created_date":"2019-06-27T00:00:00"}
