{"id":"https://openalex.org/W2887247095","doi":"https://doi.org/10.1093/bioinformatics/bty683","title":"MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP","display_name":"MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP","publication_year":2018,"publication_date":"2018-08-07","ids":{"openalex":"https://openalex.org/W2887247095","doi":"https://doi.org/10.1093/bioinformatics/bty683","mag":"2887247095","pmid":"https://pubmed.ncbi.nlm.nih.gov/30101335"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty683","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty683","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/769/27994754/bty683.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","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/769/27994754/bty683.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020973068","display_name":"Edin Husi\u0107","orcid":"https://orcid.org/0000-0002-6708-5112"},"institutions":[{"id":"https://openalex.org/I909854389","display_name":"London School of Economics and Political Science","ror":"https://ror.org/0090zs177","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I909854389"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Edin Husi\u0107","raw_affiliation_strings":["Department of Mathematics, London School of Economics and Political Science, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, London School of Economics and Political Science, London, UK","institution_ids":["https://openalex.org/I909854389"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100357340","display_name":"Xinyue Li","orcid":"https://orcid.org/0009-0000-9238-0458"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Xinyue Li","raw_affiliation_strings":["Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I32943570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002440751","display_name":"Ademir Hujdurovi\u0107","orcid":"https://orcid.org/0000-0001-8892-9938"},"institutions":[{"id":"https://openalex.org/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Ademir Hujdurovi\u0107","raw_affiliation_strings":["University of Primorska, UP FAMNIT, Koper, Slovenia","University of Primorska, UP IAM, Koper, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Primorska, UP FAMNIT, Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]},{"raw_affiliation_string":"University of Primorska, UP IAM, Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040117147","display_name":"Miika Mehine","orcid":"https://orcid.org/0000-0003-0443-0625"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Miika Mehine","raw_affiliation_strings":["Genome-Scale Biology Research Program, Research Programs Unit, Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Medicum, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome-Scale Biology Research Program, Research Programs Unit, Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Medicum, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061874157","display_name":"Rom\u00e9o Rizzi","orcid":"https://orcid.org/0000-0002-2387-0952"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Romeo Rizzi","raw_affiliation_strings":["Department of Computer Science, University of Verona, Verona, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Verona, Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043558409","display_name":"Veli M\u00e4kinen","orcid":"https://orcid.org/0000-0003-4454-1493"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Veli M\u00e4kinen","raw_affiliation_strings":["Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I32943570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027970574","display_name":"Martin Milani\u010d","orcid":"https://orcid.org/0000-0002-8222-8097"},"institutions":[{"id":"https://openalex.org/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Martin Milani\u010d","raw_affiliation_strings":["University of Primorska, UP FAMNIT, Koper, Slovenia","University of Primorska, UP IAM, Koper, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Primorska, UP FAMNIT, Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]},{"raw_affiliation_string":"University of Primorska, UP IAM, Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063897224","display_name":"Alexandru I. Tomescu","orcid":"https://orcid.org/0000-0002-5747-8350"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Alexandru I Tomescu","raw_affiliation_strings":["Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I32943570"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5027970574","https://openalex.org/A5063897224"],"corresponding_institution_ids":["https://openalex.org/I118905719","https://openalex.org/I133731052","https://openalex.org/I32943570"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7524,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.63770368,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"35","issue":"5","first_page":"769","last_page":"777"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.8708999752998352,"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":0.8708999752998352,"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/T11369","display_name":"Genetic factors in colorectal cancer","score":0.027899999171495438,"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"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.023399999365210533,"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/phylogenetics","display_name":"Phylogenetics","score":0.6813668012619019},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5935232043266296},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5648648738861084},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.5206405520439148},{"id":"https://openalex.org/keywords/most-recent-common-ancestor","display_name":"Most recent common ancestor","score":0.49428319931030273},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46757984161376953},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.4366513788700104},{"id":"https://openalex.org/keywords/descendant","display_name":"Descendant","score":0.4273899495601654},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41952764987945557},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4187275469303131},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32367587089538574},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1618238091468811},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1208951473236084},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09756839275360107}],"concepts":[{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6813668012619019},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5935232043266296},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5648648738861084},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.5206405520439148},{"id":"https://openalex.org/C197583594","wikidata":"https://www.wikidata.org/wiki/Q1052390","display_name":"Most recent common ancestor","level":4,"score":0.49428319931030273},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46757984161376953},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.4366513788700104},{"id":"https://openalex.org/C201811572","wikidata":"https://www.wikidata.org/wiki/Q188518","display_name":"Descendant","level":2,"score":0.4273899495601654},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41952764987945557},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4187275469303131},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32367587089538574},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1618238091468811},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1208951473236084},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09756839275360107},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/bty683","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty683","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/769/27994754/bty683.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":"pmid:30101335","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30101335","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:repozitorij.upr.si:IzpisGradiva.php?id=9788","is_oa":true,"landing_page_url":"https://repozitorij.upr.si/IzpisGradiva.php?id=9788","pdf_url":null,"source":{"id":"https://openalex.org/S4377196486","display_name":"Repository of the University of Primorsk (University of Primorska)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I118905719","host_organization_name":"University of Primorska","host_organization_lineage":["https://openalex.org/I118905719"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics, pp. 1-8, 2018.","raw_type":"info:eu-repo/semantics/other"},{"id":"pmh:oai:eprints.lse.ac.uk:100274","is_oa":true,"landing_page_url":null,"pdf_url":"http://eprints.lse.ac.uk/100274/1/bty683.pdf","source":{"id":"https://openalex.org/S4306401593","display_name":"London School of Economics and Political Science Research Online (London School of Economics and Political Science)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I909854389","host_organization_name":"London School of Economics and Political Science","host_organization_lineage":["https://openalex.org/I909854389"],"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":"Article"},{"id":"pmh:oai:europepmc.org:5389910","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6394401","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":"","raw_type":"Text"},{"id":"pmh:oai:helda.helsinki.fi:10138/303691","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/303691","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6394401","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6394401","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty683","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty683","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/5/769/27994754/bty683.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/G3992360688","display_name":"The infrastructure group at University of Primorska","funder_award_id":"I0-0035","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G4249711515","display_name":"Independence in domination in structured graph classes","funder_award_id":"J1-7051","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G5436026661","display_name":null,"funder_award_id":"274977","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G6699426047","display_name":"Graphs and Odd Automorphisms","funder_award_id":"N1-0038","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G8316966982","display_name":"Grafi, grupe, konfiguracije in geometrije (Slovene)","funder_award_id":"N1-0032","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G8447924143","display_name":"Algebra, discrete mathematics, probability and game theory","funder_award_id":"P1-0285","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G8650182799","display_name":"Oddness degree of transitive permutation groups","funder_award_id":"N1-0062","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G8982709776","display_name":"Traversability in vertex-transitive graphs","funder_award_id":"J1-9110","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"}],"funders":[{"id":"https://openalex.org/F1744609432","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2887247095.pdf","grobid_xml":"https://content.openalex.org/works/W2887247095.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1550376883","https://openalex.org/W1730095690","https://openalex.org/W1968657935","https://openalex.org/W1986888627","https://openalex.org/W1990061958","https://openalex.org/W1994815346","https://openalex.org/W2002295829","https://openalex.org/W2052975116","https://openalex.org/W2065076110","https://openalex.org/W2074507113","https://openalex.org/W2109991075","https://openalex.org/W2111874706","https://openalex.org/W2112997276","https://openalex.org/W2114095872","https://openalex.org/W2122392334","https://openalex.org/W2124810156","https://openalex.org/W2137337001","https://openalex.org/W2144847592","https://openalex.org/W2147849085","https://openalex.org/W2154598603","https://openalex.org/W2155943701","https://openalex.org/W2166815431","https://openalex.org/W2168156874","https://openalex.org/W2192492580","https://openalex.org/W2482614962","https://openalex.org/W2515462796","https://openalex.org/W2585248318","https://openalex.org/W2734435792","https://openalex.org/W2785754681","https://openalex.org/W2888081897","https://openalex.org/W2962973261","https://openalex.org/W3123103866","https://openalex.org/W4230324426"],"related_works":["https://openalex.org/W1925942709","https://openalex.org/W2047683846","https://openalex.org/W2044902158","https://openalex.org/W2082154838","https://openalex.org/W2109912052","https://openalex.org/W1976332671","https://openalex.org/W1711527768","https://openalex.org/W3161742475","https://openalex.org/W2944037351","https://openalex.org/W890790393"],"abstract_inverted_index":{"MOTIVATION:":[0],"Discovering":[1],"the":[2,19,22,58,61,74,81,108,123,137],"evolution":[3],"of":[4,21,60,83,110,113,155],"a":[5,14,35,67,85,102,133],"tumor":[6,54,62,75,124],"may":[7],"help":[8],"identify":[9],"driver":[10],"mutations":[11],"and":[12,37,98,112],"provide":[13],"more":[15,151],"comprehensive":[16],"view":[17],"on":[18],"history":[20],"tumor.":[23],"Recent":[24],"studies":[25],"have":[26],"tackled":[27],"this":[28,42],"problem":[29,69],"using":[30],"multiple":[31],"samples":[32,49,76],"sequenced":[33],"from":[34],"tumor,":[36],"due":[38],"to":[39,72,121,132,148],"clinical":[40],"implications,":[41],"has":[43],"attracted":[44],"great":[45],"interest.":[46],"However,":[47],"such":[48],"usually":[50],"mix":[51],"several":[52,78],"distinct":[53],"subclones,":[55],"which":[56],"confounds":[57],"discovery":[59],"phylogeny.":[63,88,125],"RESULTS:":[64],"We":[65,89,106],"study":[66],"natural":[68],"formulation":[70,95],"requiring":[71],"decompose":[73],"into":[77,101],"subclones":[79],"with":[80],"objective":[82],"forming":[84],"minimum":[86],"perfect":[87],"propose":[90],"an":[91],"Integer":[92],"Linear":[93],"Programming":[94],"for":[96],"it,":[97],"implement":[99],"it":[100],"method":[103],"called":[104],"MIPUP.":[105],"tested":[107],"ability":[109],"MIPUP":[111,129,160],"four":[114,142],"popular":[115],"tools":[116],"LICHeE,":[117],"AncesTree,":[118],"CITUP,":[119],"Treeomics":[120],"reconstruct":[122],"On":[126,141],"simulated":[127],"data,":[128],"shows":[130],"up":[131],"34%":[134],"improvement":[135],"under":[136],"ancestor-descendant":[138],"relations":[139],"metric.":[140],"real":[143],"datasets,":[144],"MIPUP's":[145],"reconstructions":[146],"proved":[147],"be":[149],"generally":[150],"faithful":[152],"than":[153],"those":[154],"LICHeE.":[156],"AVAILABILITY":[157],"AND":[158],"IMPLEMENTATION:":[159],"is":[161],"available":[162,173],"at":[163,174],"https://github.com/zhero9/MIPUP":[164],"as":[165],"open":[166],"source.":[167],"SUPPLEMENTARY":[168],"INFORMATION:":[169],"Supplementary":[170],"data":[171],"are":[172],"Bioinformatics":[175],"online.":[176]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
