{"id":"https://openalex.org/W2614716373","doi":"https://doi.org/10.1186/s13015-017-0103-2","title":"Complexity and algorithms for copy-number evolution problems","display_name":"Complexity and algorithms for copy-number evolution problems","publication_year":2017,"publication_date":"2017-05-16","ids":{"openalex":"https://openalex.org/W2614716373","doi":"https://doi.org/10.1186/s13015-017-0103-2","mag":"2614716373","pmid":"https://pubmed.ncbi.nlm.nih.gov/28515774"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-017-0103-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0103-2","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0103-2","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0103-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089040838","display_name":"Mohammed El-Kebir","orcid":"https://orcid.org/0000-0002-1468-2407"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]},{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohammed El-Kebir","raw_affiliation_strings":["Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI 02912 USA","Department of Computer Science, Princeton University, Princeton, NJ 08540 USA","Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI 02912 USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Department of Computer Science, Princeton University, Princeton, NJ 08540 USA","institution_ids":["https://openalex.org/I20089843"]},{"raw_affiliation_string":"Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025899028","display_name":"Benjamin J. Raphael","orcid":"https://orcid.org/0000-0003-1274-048X"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]},{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benjamin J. Raphael","raw_affiliation_strings":["Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI 02912 USA","Department of Computer Science, Princeton University, Princeton, NJ 08540 USA","Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI 02912 USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Department of Computer Science, Princeton University, Princeton, NJ 08540 USA","institution_ids":["https://openalex.org/I20089843"]},{"raw_affiliation_string":"Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038806020","display_name":"Ron Shamir","orcid":"https://orcid.org/0000-0003-1889-9870"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Ron Shamir","raw_affiliation_strings":["School of Computer Science, Tel Aviv University, Tel Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046958549","display_name":"Roded Sharan","orcid":"https://orcid.org/0000-0001-8363-4882"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Roded Sharan","raw_affiliation_strings":["School of Computer Science, Tel Aviv University, Tel Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015317678","display_name":"Simone Zaccaria","orcid":"https://orcid.org/0000-0002-5265-7392"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]},{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]},{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]},{"id":"https://openalex.org/I4210140564","display_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Milano Bicocca","ror":"https://ror.org/03xejxm22","country_code":"IT","type":"facility","lineage":["https://openalex.org/I160013858","https://openalex.org/I4210140564"]},{"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","US"],"is_corresponding":false,"raw_author_name":"Simone Zaccaria","raw_affiliation_strings":["Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI 02912 USA","Department of Computer Science, Princeton University, Princeton, NJ 08540 USA","Dipartimento di Informatica Sistemistica e Comunicazione (DISCo), Univ. degli Studi di Milano-Bicocca, Milan, Italy","Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI 02912 USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Department of Computer Science, Princeton University, Princeton, NJ 08540 USA","institution_ids":["https://openalex.org/I20089843"]},{"raw_affiliation_string":"Dipartimento di Informatica Sistemistica e Comunicazione (DISCo), Univ. degli Studi di Milano-Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I189158943","https://openalex.org/I4210140564","https://openalex.org/I66752286"]},{"raw_affiliation_string":"Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082025487","display_name":"Meirav Zehavi","orcid":"https://orcid.org/0000-0002-3636-5322"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Meirav Zehavi","raw_affiliation_strings":["School of Computer Science, Tel Aviv University, Tel Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059177758","display_name":"Ron Zeira","orcid":"https://orcid.org/0000-0003-2477-3078"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Ron Zeira","raw_affiliation_strings":["School of Computer Science, Tel Aviv University, Tel Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5025899028","https://openalex.org/A5038806020"],"corresponding_institution_ids":["https://openalex.org/I16391192","https://openalex.org/I20089843","https://openalex.org/I27804330"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":1.5108,"has_fulltext":true,"cited_by_count":47,"citation_normalized_percentile":{"value":0.80488937,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"12","issue":"1","first_page":"13","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.6381999850273132,"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":0.6381999850273132,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.15379999577999115,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.10050000250339508,"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/computer-science","display_name":"Computer science","score":0.6970253586769104},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5574107766151428}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6970253586769104},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5574107766151428}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13015-017-0103-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0103-2","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0103-2","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:28515774","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28515774","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:f7d810119b154eaeb04d06d395d9dd70","is_oa":true,"landing_page_url":"https://doaj.org/article/f7d810119b154eaeb04d06d395d9dd70","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 12, Iss 1, Pp 1-11 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4284524","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5433102","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:10.1186/s13015-017-0103-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-017-0103-2","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0103-2","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G201924742","display_name":null,"funder_award_id":"317/13","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"},{"id":"https://openalex.org/G2089771574","display_name":null,"funder_award_id":"R01HG005690","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4632009408","display_name":"Computational Approaches for Structural Variation Studies in Genomes","funder_award_id":"5r01hg005690-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4791905715","display_name":null,"funder_award_id":"41/11","funder_id":"https://openalex.org/F4320335016","funder_display_name":"Israeli Centers for Research Excellence"}],"funders":[{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"},{"id":"https://openalex.org/F4320322596","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49"},{"id":"https://openalex.org/F4320323278","display_name":"Council for Higher Education","ror":"https://ror.org/036mqp197"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334164","display_name":"Simons Institute for the Theory of Computing, University of California Berkeley","ror":null},{"id":"https://openalex.org/F4320335016","display_name":"Israeli Centers for Research Excellence","ror":"https://ror.org/03w2v9593"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2614716373.pdf","grobid_xml":"https://content.openalex.org/works/W2614716373.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1965001144","https://openalex.org/W1967304777","https://openalex.org/W2002295829","https://openalex.org/W2010873488","https://openalex.org/W2060425093","https://openalex.org/W2069399470","https://openalex.org/W2083213362","https://openalex.org/W2088735033","https://openalex.org/W2108643617","https://openalex.org/W2114095872","https://openalex.org/W2122392334","https://openalex.org/W2144847592","https://openalex.org/W2156411023","https://openalex.org/W2235662455","https://openalex.org/W2502685008","https://openalex.org/W2543676470","https://openalex.org/W2749989373","https://openalex.org/W4233815609"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W4391913857"],"abstract_inverted_index":{"Cancer":[0],"is":[1,26,164,178,197],"an":[2,185,201],"evolutionary":[3],"process":[4],"characterized":[5],"by":[6,75,90,143,154],"the":[7,32,50,70,91,119,129,144,159,167,181,191,215],"accumulation":[8],"of":[9,15,24,34,36,41,43,72,94,121,161,219],"somatic":[10],"mutations":[11,25],"in":[12,59,63,180],"a":[13,19,47,73,114,135,172],"population":[14],"cells":[16],"that":[17,117,158,177,206],"form":[18],"tumor.":[20],"One":[21],"frequent":[22],"type":[23],"copy":[27],"number":[28,33,40,93],"aberrations,":[29],"which":[30],"alter":[31],"copies":[35,42],"genomic":[37],"regions.":[38],"The":[39],"each":[44],"position":[45],"along":[46],"chromosome":[48],"constitutes":[49],"chromosome\u2019s":[51],"copy-number":[52],"profile.":[53],"Understanding":[54],"how":[55],"such":[56,157],"profiles":[57,147,156],"evolve":[58],"cancer":[60],"can":[61],"assist":[62],"both":[64],"diagnosis":[65],"and":[66,78,80,148,184,199,217],"prognosis.":[67],"We":[68,213],"model":[69],"evolution":[71],"tumor":[74],"segmental":[76],"deletions":[77],"amplifications,":[79],"gauge":[81],"distance":[82],"from":[83],"profile":[84,116,182],"$$\\mathbf":[85,88,99,102],"{a}$$":[86,100],"to":[87,97,112,123,208],"{b}$$":[89,103],"minimum":[92],"events":[95],"needed":[96],"transform":[98],"into":[101],".":[104],"Given":[105,126],"two":[106],"profiles,":[107,128],"our":[108,220],"first":[109],"problem":[110,169,193,210],"aims":[111],"find":[113],"parental":[115],"minimizes":[118],"sum":[120,160],"distances":[122,163],"its":[124],"children.":[125],"k":[127,139,145],"second,":[130],"more":[131],"general":[132],"problem,":[133],"seeks":[134],"phylogenetic":[136],"tree,":[137],"whose":[138,149],"leaves":[140],"are":[141,152],"labeled":[142,153],"given":[146],"internal":[150],"vertices":[151],"ancestral":[155],"edge":[162],"minimum.":[165],"For":[166,190],"former":[168],"we":[170,194],"give":[171,200],"pseudo-polynomial":[173],"dynamic":[174],"programming":[175],"algorithm":[176],"linear":[179,187,203],"length,":[183],"integer":[186,202],"program":[188,204],"formulation.":[189],"latter":[192],"show":[195],"it":[196],"NP-hard":[198],"formulation":[205],"scales":[207],"practical":[209],"instance":[211],"sizes.":[212],"assess":[214],"efficiency":[216],"quality":[218],"algorithms":[221],"on":[222],"simulated":[223],"instances.":[224],"https://github.com/raphael-group/CNT-ILP":[225]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}