{"id":"https://openalex.org/W4411337161","doi":"https://doi.org/10.1109/tcbbio.2025.3580476","title":"Perfect phylogenies via the Minimum Uncovering Branching Problem: Efficiently Solvable Cases","display_name":"Perfect phylogenies via the Minimum Uncovering Branching Problem: Efficiently Solvable Cases","publication_year":2025,"publication_date":"2025-06-16","ids":{"openalex":"https://openalex.org/W4411337161","doi":"https://doi.org/10.1109/tcbbio.2025.3580476","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811250"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3580476","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3580476","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2506.18578","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023358971","display_name":"Narmina Baghirova","orcid":"https://orcid.org/0000-0002-4702-673X"},"institutions":[{"id":"https://openalex.org/I154338468","display_name":"University of Fribourg","ror":"https://ror.org/022fs9h90","country_code":"CH","type":"education","lineage":["https://openalex.org/I154338468"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Narmina Baghirova","raw_affiliation_strings":["Department of Decision Support and Operations Research, University of Fribourg, Fribourg, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-4702-673X","affiliations":[{"raw_affiliation_string":"Department of Decision Support and Operations Research, University of Fribourg, Fribourg, Switzerland","institution_ids":["https://openalex.org/I154338468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022905636","display_name":"Esther Galby","orcid":"https://orcid.org/0009-0004-5398-2770"},"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"]},{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["SE","SI"],"is_corresponding":false,"raw_author_name":"Esther Galby","raw_affiliation_strings":["Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg, Sweden","FAMNIT and IAM, University of Primorska, Koper, Slovenia"],"raw_orcid":"https://orcid.org/0009-0004-5398-2770","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg, Sweden","institution_ids":["https://openalex.org/I66862912"]},{"raw_affiliation_string":"FAMNIT and IAM, University of Primorska, Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]}]},{"author_position":"last","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"]},{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]},{"id":"https://openalex.org/I881427289","display_name":"University of Gothenburg","ror":"https://ror.org/01tm6cn81","country_code":"SE","type":"education","lineage":["https://openalex.org/I881427289"]}],"countries":["SE","SI"],"is_corresponding":false,"raw_author_name":"Martin Milani\u010d","raw_affiliation_strings":["FAMNIT and IAM, University of Primorska, Koper, Slovenia","Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-8222-8097","affiliations":[{"raw_affiliation_string":"FAMNIT and IAM, University of Primorska, Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden","institution_ids":["https://openalex.org/I66862912","https://openalex.org/I881427289"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5023358971"],"corresponding_institution_ids":["https://openalex.org/I154338468"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12064086,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"5","first_page":"2043","last_page":"2056"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9204999804496765,"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"}},"topics":[{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9204999804496765,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.91839998960495,"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/T12162","display_name":"Cellular Automata and Applications","score":0.911899983882904,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/branching","display_name":"Branching (polymer chemistry)","score":0.6765292882919312},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.44379886984825134},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.42865025997161865},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.4067862629890442},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3809550404548645},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3752015233039856},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3368121087551117},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33367452025413513},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1175186038017273}],"concepts":[{"id":"https://openalex.org/C206175624","wikidata":"https://www.wikidata.org/wiki/Q595731","display_name":"Branching (polymer chemistry)","level":2,"score":0.6765292882919312},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.44379886984825134},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.42865025997161865},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.4067862629890442},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3809550404548645},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3752015233039856},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3368121087551117},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33367452025413513},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1175186038017273},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbbio.2025.3580476","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3580476","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811250","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811250","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:arXiv.org:2506.18578","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2506.18578","pdf_url":"https://arxiv.org/pdf/2506.18578","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"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":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:freidok.uni-freiburg.de:280937","is_oa":false,"landing_page_url":"https://freidok.uni-freiburg.de/data/280937","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics. - 22, 5 (2025) , 2043-2056, ISSN: 2998-4165","raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2506.18578","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2506.18578","pdf_url":"https://arxiv.org/pdf/2506.18578","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"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":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"display_name":"Climate action","id":"https://metadata.un.org/sdg/13","score":0.47999998927116394}],"awards":[{"id":"https://openalex.org/G3992360688","display_name":null,"funder_award_id":"I0-0035","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"}],"funders":[{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1967304777","https://openalex.org/W1994815346","https://openalex.org/W2012329067","https://openalex.org/W2057052228","https://openalex.org/W2074507113","https://openalex.org/W2112997276","https://openalex.org/W2169586176","https://openalex.org/W2192492580","https://openalex.org/W2406547600","https://openalex.org/W2887247095","https://openalex.org/W2914414140","https://openalex.org/W2962973261","https://openalex.org/W3174949429","https://openalex.org/W4234024706","https://openalex.org/W4254807835","https://openalex.org/W4386749297","https://openalex.org/W4390098007","https://openalex.org/W4404948693"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2462424100","https://openalex.org/W2014836299","https://openalex.org/W2034871982","https://openalex.org/W2148974013","https://openalex.org/W2130873474","https://openalex.org/W2034850439","https://openalex.org/W1974919125","https://openalex.org/W2022364537","https://openalex.org/W2141653867"],"abstract_inverted_index":{"In":[0,161],"this":[1,162,166,180],"paper,":[2,163],"we":[3,164],"present":[4],"new":[5,213],"efficiently":[6],"solvable":[7,174],"cases":[8],"of":[9,38,60,77,79,101,122,137,149,187],"the":[10,42,58,67,73,80,84,90,95,102,119,131,154,171,184,192],"Minimum":[11],"Uncovering":[12],"Branching":[13],"problem,":[14],"an":[15,126],"optimization":[16],"problem":[17,34,74,96,132,172,193],"with":[18,109],"applications":[19],"in":[20,31,66,75,107,175,198,205],"cancer":[21],"genomics":[22],"introduced":[23],"by":[24,83,168,182],"Hujdurovi\u0107,":[25],"Husi\u0107,":[26],"Milani\u010d,":[27],"Rizzi,":[28],"and":[29,41,93,114,125,140,190,201,218],"Tomescu":[30],"2018.":[32],"The":[33],"involves":[35],"a":[36,123,142,212],"family":[37],"finite":[39],"sets,":[40],"goal":[43],"is":[44,133,173],"to":[45,50,111,194],"map":[46],"each":[47],"non-maximal":[48],"set":[49,53,86],"exactly":[51],"one":[52],"that":[54,130,141,170],"contains":[55],"it,":[56],"minimizing":[57],"sum":[59],"uncovered":[61],"elements":[62],"across":[63],"all":[64],"sets":[65,92],"family.":[68],"Hujdurovi\u0107":[69],"et":[70],"al.":[71],"formulated":[72],"terms":[76],"branchings":[78],"digraph":[81],"formed":[82],"proper":[85],"inclusion":[87],"relation":[88],"on":[89,99],"input":[91],"studied":[94],"complexity":[97,156],"based":[98],"properties":[100,186],"corresponding":[103],"partially":[104,206],"ordered":[105,207],"set,":[106],"particular,":[108],"respect":[110],"its":[112],"height":[113,139],"width,":[115,151],"defined":[116],"respectively":[117],"as":[118],"maximum":[120,196,202],"cardinality":[121],"chain":[124],"antichain.":[127],"They":[128],"showed":[129],"APX-complete":[134],"for":[135,147,157,222],"instances":[136,148,159],"bounded":[138,150],"constant-factor":[143],"approximation":[144],"algorithm":[145],"exists":[146],"but":[152],"left":[153],"exact":[155],"bounded-width":[158],"open.":[160],"answer":[165],"question":[167],"proving":[169],"polynomial":[176],"time.":[177],"We":[178,209],"derive":[179],"result":[181],"examining":[183],"structural":[185],"optimal":[188],"solutions":[189],"reducing":[191],"computing":[195],"matchings":[197],"bipartite":[199],"graphs":[200],"weight":[203],"antichains":[204],"sets.":[208],"also":[210],"introduce":[211],"polynomially":[214],"computable":[215],"lower":[216],"bound":[217],"identify":[219],"another":[220],"condition":[221],"polynomial-time":[223],"solvability.":[224]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
