{"id":"https://openalex.org/W2747222535","doi":"https://doi.org/10.1145/3088512","title":"Reconciliation With Nonbinary Gene Trees Revisited","display_name":"Reconciliation With Nonbinary Gene Trees Revisited","publication_year":2017,"publication_date":"2017-08-17","ids":{"openalex":"https://openalex.org/W2747222535","doi":"https://doi.org/10.1145/3088512","mag":"2747222535"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1145/3088512","pdf_url":null,"source":{"id":"https://openalex.org/S118992489","display_name":"Journal of the ACM","issn_l":"0004-5411","issn":["0004-5411","1557-735X"],"is_oa":false,"is_in_doaj":false,"is_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-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/A5103176848","display_name":"Y. Zheng","orcid":"https://orcid.org/0000-0002-4617-3252"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"funder","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Yu Zheng","raw_affiliation_strings":["National University of Singapore, Singapore"],"affiliations":[{"raw_affiliation_string":"National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012300835","display_name":"Louxin Zhang","orcid":"https://orcid.org/0000-0003-0260-824X"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"funder","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Louxin Zhang","raw_affiliation_strings":["National University of Singapore, Singapore"],"affiliations":[{"raw_affiliation_string":"National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.203,"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":3,"citation_normalized_percentile":{"value":0.335743,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":75,"max":77},"biblio":{"volume":"64","issue":"4","first_page":"1","last_page":"28"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9999,"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":0.9999,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9954,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.9928,"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/tree","display_name":"Tree (set theory)","score":0.6591196},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.5583025},{"id":"https://openalex.org/keywords/tree-rearrangement","display_name":"Tree rearrangement","score":0.5169396},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.4826563}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7066643},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6591196},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.624423},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6125729},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.5583025},{"id":"https://openalex.org/C53208351","wikidata":"https://www.wikidata.org/wiki/Q7837630","display_name":"Tree rearrangement","level":4,"score":0.5169396},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5166481},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5003865},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.4826563},{"id":"https://openalex.org/C100560664","wikidata":"https://www.wikidata.org/wiki/Q3608019","display_name":"K-ary tree","level":4,"score":0.46628854},{"id":"https://openalex.org/C84927040","wikidata":"https://www.wikidata.org/wiki/Q6057306","display_name":"Interval tree","level":4,"score":0.42879507},{"id":"https://openalex.org/C197855036","wikidata":"https://www.wikidata.org/wiki/Q380172","display_name":"Binary tree","level":2,"score":0.41098252},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36253273},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.358193},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.352493},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32270876},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31585342},{"id":"https://openalex.org/C163797641","wikidata":"https://www.wikidata.org/wiki/Q2067937","display_name":"Tree structure","level":3,"score":0.30683023},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.27195352},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.24070555},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22642866},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.120058656}],"mesh":[],"locations_count":1,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1145/3088512","pdf_url":null,"source":{"id":"https://openalex.org/S118992489","display_name":"Journal of the ACM","issn_l":"0004-5411","issn":["0004-5411","1557-735X"],"is_oa":false,"is_in_doaj":false,"is_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":null,"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":44,"referenced_works":["https://openalex.org/W1533994827","https://openalex.org/W1576387209","https://openalex.org/W1931647778","https://openalex.org/W1972157500","https://openalex.org/W1972390207","https://openalex.org/W1978858440","https://openalex.org/W1990453950","https://openalex.org/W1991217882","https://openalex.org/W1992140809","https://openalex.org/W1995040285","https://openalex.org/W2017051353","https://openalex.org/W2027533695","https://openalex.org/W2039334367","https://openalex.org/W2042696830","https://openalex.org/W2044630770","https://openalex.org/W2046946959","https://openalex.org/W2054624670","https://openalex.org/W2061646232","https://openalex.org/W2065375138","https://openalex.org/W2067547496","https://openalex.org/W2090493969","https://openalex.org/W2091918228","https://openalex.org/W2096789062","https://openalex.org/W2099321785","https://openalex.org/W2100668314","https://openalex.org/W2110014387","https://openalex.org/W2113923028","https://openalex.org/W2120864016","https://openalex.org/W2123169853","https://openalex.org/W2124908487","https://openalex.org/W2132318428","https://openalex.org/W2135281627","https://openalex.org/W2144345157","https://openalex.org/W2145608399","https://openalex.org/W2157616815","https://openalex.org/W2159266221","https://openalex.org/W2159447863","https://openalex.org/W2161444534","https://openalex.org/W2166106146","https://openalex.org/W22269019","https://openalex.org/W2330868067","https://openalex.org/W4285719527","https://openalex.org/W598887167","https://openalex.org/W93958072"],"related_works":["https://openalex.org/W4244673516","https://openalex.org/W3169685561","https://openalex.org/W3022865202","https://openalex.org/W2501849745","https://openalex.org/W2382364329","https://openalex.org/W2117536196","https://openalex.org/W2107381954","https://openalex.org/W2074513192","https://openalex.org/W2022598760","https://openalex.org/W1510719821"],"abstract_inverted_index":{"By":[0],"reconciling":[1],"the":[2,10,72,89,134,145],"phylogenetic":[3],"tree":[4,63,69,142],"of":[5,91,106,113,128],"a":[6,66,94,103],"gene":[7,40,62],"family":[8],"with":[9,23,65],"corresponding":[11],"species":[12,68],"tree,":[13],"it":[14],"is":[15,98],"possible":[16],"to":[17,28,58],"infer":[18],"lineage-specific":[19],"duplications":[20],"and":[21,26,31,80,110,137],"losses":[22],"high":[24],"confidence":[25],"hence":[27],"annotate":[29],"orthologs":[30],"paralogs.":[32],"The":[33,96],"currently":[34],"available":[35],"reconciliation":[36,143],"methods":[37,140],"for":[38,45,119,133,141],"nonbinary":[39],"trees":[41],"are":[42],"computationally":[43],"expensive":[44],"genome-scale":[46],"applications.":[47],"We":[48],"present":[49],"four":[50],"O":[51],"(|":[52],"G":[53,64],"|+|":[54],"S":[55,70],"|)":[56],"algorithms":[57],"reconcile":[59],"an":[60,126],"arbitrary":[61],"binary":[67],"in":[71,93,125,131,144],"duplication,":[73],"loss,":[74],"duploss":[75],"(also":[76],"known":[77],"as":[78],"mutation),":[79],"deep":[81],"coalescence":[82],"cost":[83,147],"models,":[84],"where":[85],"|\u00b7":[86],"|":[87],"denotes":[88],"number":[90],"nodes":[92],"tree.":[95],"improvement":[97],"achieved":[99],"through":[100],"two":[101],"innovations:":[102],"linear-time":[104],"computation":[105],"compressed":[107],"child-image":[108,120],"subtrees":[109],"efficient":[111],"reconstruction":[112],"irreducible":[114],"duplication":[115],"histories.":[116],"Our":[117],"technique":[118],"subtree":[121],"compression":[122],"also":[123],"results":[124],"order":[127],"magnitude":[129],"speedup":[130],"runtime":[132],"dynamic":[135],"programming":[136],"Wagner":[138],"parsimony--based":[139],"affine":[146],"model.":[148]},"abstract_inverted_index_v3":null,"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2747222535","counts_by_year":[{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2025-03-19T18:44:07.433402","created_date":"2017-08-31"}