{"id":"https://openalex.org/W2974251191","doi":"https://doi.org/10.1109/tcbb.2019.2942015","title":"Reconciliation Reconsidered: In Search of a Most Representative Reconciliation in the Duplication-Transfer-Loss Model","display_name":"Reconciliation Reconsidered: In Search of a Most Representative Reconciliation in the Duplication-Transfer-Loss Model","publication_year":2019,"publication_date":"2019-09-17","ids":{"openalex":"https://openalex.org/W2974251191","doi":"https://doi.org/10.1109/tcbb.2019.2942015","mag":"2974251191","pmid":"https://pubmed.ncbi.nlm.nih.gov/31722482"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2942015","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2942015","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","pubmed"],"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/A5077256004","display_name":"Melissa Grueter","orcid":null},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Melissa Grueter","raw_affiliation_strings":["Harvey Mudd College, Claremont, CA, USA"],"affiliations":[{"raw_affiliation_string":"Harvey Mudd College, Claremont, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044184195","display_name":"Kalani Duran","orcid":"https://orcid.org/0000-0001-8348-6330"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kalani Duran","raw_affiliation_strings":["Harvey Mudd College, Claremont, CA, USA"],"affiliations":[{"raw_affiliation_string":"Harvey Mudd College, Claremont, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016952484","display_name":"Ramya Ramalingam","orcid":null},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ramya Ramalingam","raw_affiliation_strings":["Harvey Mudd College, Claremont, CA, USA"],"affiliations":[{"raw_affiliation_string":"Harvey Mudd College, Claremont, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081839833","display_name":"Ran Libeskind-Hadas","orcid":"https://orcid.org/0000-0001-9120-1948"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ran Libeskind-Hadas","raw_affiliation_strings":["Harvey Mudd College, Claremont, CA, USA"],"affiliations":[{"raw_affiliation_string":"Harvey Mudd College, Claremont, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5077256004"],"corresponding_institution_ids":["https://openalex.org/I133543626"],"apc_list":null,"apc_paid":null,"fwci":0.5114,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.64584881,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"18","issue":"6","first_page":"2136","last_page":"2143"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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/T14049","display_name":"Plant and Fungal Species Descriptions","score":0.9933000206947327,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9914000034332275,"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/maximum-parsimony","display_name":"Maximum parsimony","score":0.8657928705215454},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7656984329223633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5216506123542786},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.5178273320198059},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.4689447581768036},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4136221706867218},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3891173303127289},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36418581008911133},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17696377635002136},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09914961457252502},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.07527610659599304}],"concepts":[{"id":"https://openalex.org/C22799545","wikidata":"https://www.wikidata.org/wiki/Q1805805","display_name":"Maximum parsimony","level":5,"score":0.8657928705215454},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7656984329223633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5216506123542786},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.5178273320198059},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4689447581768036},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4136221706867218},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3891173303127289},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36418581008911133},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17696377635002136},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09914961457252502},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.07527610659599304},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"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":"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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2019.2942015","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2942015","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":"pmid:31722482","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31722482","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/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6418997412","display_name":null,"funder_award_id":"IIS-1419739","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W157609093","https://openalex.org/W1980217038","https://openalex.org/W2026560157","https://openalex.org/W2027455555","https://openalex.org/W2096789062","https://openalex.org/W2100091570","https://openalex.org/W2110014387","https://openalex.org/W2112755610","https://openalex.org/W2117000771","https://openalex.org/W2132318428","https://openalex.org/W2134771735","https://openalex.org/W2144345157","https://openalex.org/W2147428165","https://openalex.org/W2148231054","https://openalex.org/W2326872503","https://openalex.org/W2529177684","https://openalex.org/W2608631538","https://openalex.org/W2795914492","https://openalex.org/W2809600310","https://openalex.org/W6606317737"],"related_works":["https://openalex.org/W2520823390","https://openalex.org/W4300265711","https://openalex.org/W2963820820","https://openalex.org/W2174809885","https://openalex.org/W2963207658","https://openalex.org/W2883025420","https://openalex.org/W2057191541","https://openalex.org/W2949296710","https://openalex.org/W1992658754","https://openalex.org/W2111939425"],"abstract_inverted_index":{"Maximum":[0],"parsimony":[1,45,50,78],"reconciliation":[2,33,51,79,110],"is":[3,34],"a":[4,43,76,108],"fundamental":[5,103],"technique":[6],"for":[7,55],"studying":[8],"the":[9,38,56,59,68,71,102,113],"evolutionary":[10],"histories":[11],"of":[12,14,61,70,105,116],"pairs":[13],"entities":[15],"such":[16,62],"as":[17],"genes":[18],"and":[19,22,24,26,89],"species,":[20],"parasites":[21],"hosts,":[23],"species":[25],"their":[27],"biogeographical":[28],"habitats.":[29],"In":[30],"these":[31],"contexts,":[32],"generally":[35],"performed":[36],"using":[37],"duplication-transfer-loss":[39],"(DTL)":[40],"model":[41],"in":[42],"maximum":[44,49,77],"framework.":[46],"While":[47],"efficient":[48],"algorithms":[52],"are":[53,86],"known":[54],"DTL":[57],"model,":[58],"number":[60],"reconciliations":[63],"can":[64,111],"grow":[65],"exponentially":[66],"with":[67],"sizes":[69],"two":[72],"phylogenetic":[73],"trees.":[74],"Choosing":[75],"arbitrarily":[80],"may":[81,90],"lead":[82],"to":[83],"conclusions":[84],"that":[85],"not":[87],"supported,":[88],"even":[91],"be":[92],"contradicted,":[93],"by":[94],"other":[95],"equally":[96],"optimal":[97,117],"reconciliations.":[98,118],"This":[99],"paper":[100],"addresses":[101],"problem":[104],"how":[106],"well":[107],"single":[109],"represent":[112],"entire":[114],"space":[115]},"counts_by_year":[{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}