{"id":"https://openalex.org/W2748479319","doi":"https://doi.org/10.1145/3107411.3108220","title":"An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution","display_name":"An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2748479319","doi":"https://doi.org/10.1145/3107411.3108220","mag":"2748479319"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3108220","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108220","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"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/A5100440229","display_name":"Lei Li","orcid":"https://orcid.org/0000-0001-5478-5681"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lei Li","raw_affiliation_strings":["University of Connecticut, Storrs, CT, USA"],"affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024793976","display_name":"Mukul S. Bansal","orcid":"https://orcid.org/0000-0003-0039-2596"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mukul S. Bansal","raw_affiliation_strings":["University of Connecticut, Storrs, CT, USA"],"affiliations":[{"raw_affiliation_string":"University of Connecticut, Storrs, CT, USA","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100440229"],"corresponding_institution_ids":["https://openalex.org/I140172145"],"apc_list":null,"apc_paid":null,"fwci":0.1063,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.48372522,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"611","last_page":"611"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9918000102043152,"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":0.9918000102043152,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9103000164031982,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.689332127571106},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6633476614952087},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6320486068725586},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.6062464714050293},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5698328018188477},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49940991401672363},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.46611979603767395},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.45327627658843994},{"id":"https://openalex.org/keywords/gene-family","display_name":"Gene family","score":0.4388046860694885},{"id":"https://openalex.org/keywords/molecular-evolution","display_name":"Molecular evolution","score":0.4289083778858185},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42672401666641235},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36955857276916504},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3509182333946228},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2832930088043213},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24326321482658386},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20869013667106628},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16627150774002075}],"concepts":[{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.689332127571106},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6633476614952087},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6320486068725586},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.6062464714050293},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5698328018188477},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49940991401672363},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.46611979603767395},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.45327627658843994},{"id":"https://openalex.org/C5911399","wikidata":"https://www.wikidata.org/wiki/Q2278983","display_name":"Gene family","level":4,"score":0.4388046860694885},{"id":"https://openalex.org/C166393388","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Molecular evolution","level":4,"score":0.4289083778858185},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42672401666641235},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36955857276916504},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3509182333946228},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2832930088043213},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24326321482658386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20869013667106628},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16627150774002075},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3108220","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108220","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.5699999928474426,"display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G4634191259","display_name":null,"funder_award_id":"1553421","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1914610732","https://openalex.org/W4402529160","https://openalex.org/W3126460685","https://openalex.org/W3025364102","https://openalex.org/W2999254484","https://openalex.org/W2002623332","https://openalex.org/W1970221653","https://openalex.org/W2810780526","https://openalex.org/W4236246458","https://openalex.org/W3040603050"],"abstract_inverted_index":{"The":[0,161],"majority":[1],"of":[2,7,24,55,75,105,121,129,177,224,242,277,287],"genes":[3,50,88,90,292],"in":[4,290,296],"eukaryotes":[5],"consist":[6],"multiple":[8],"protein":[9,25],"domains":[10,85],"that":[11,59,84,124,184,200,264],"can":[12],"be":[13],"independently":[14],"lost":[15],"or":[16,31],"gained":[17],"during":[18],"evolution.":[19,134],"This":[20],"gain":[21],"and":[22,36,57,65,89,108,110,132,152,170,180,229,237,280,283,293],"loss":[23],"domains,":[26,106],"through":[27],"domain":[28,122,181,227,288],"duplications,":[29],"transfers,":[30],"losses,":[32],"has":[33,270],"important":[34],"evolutionary":[35,60,252],"functional":[37],"consequences":[38],"for":[39,45,112,158,213],"genes.":[40,76],"Yet,":[41],"most":[42],"computational":[43,98,196,246],"methods":[44],"studying":[46],"gene":[47,145,150,178,231,294],"evolution":[48,56,104,123,147,183],"view":[49,176],"as":[51,63],"the":[52,103,127,138,193,201,214,240,250,266,275,285],"basic":[53],"unit":[54],"assume":[58],"processes":[61],"such":[62],"duplications":[64],"losses":[66],"act":[67],"on":[68,73,274,284],"entire":[69],"genes,":[70,107],"rather":[71],"than":[72],"parts":[74],"Specifically,":[77,189],"even":[78],"though":[79],"it":[80],"is":[81,185,205],"well":[82],"understood":[83],"evolve":[86],"inside":[87,91],"species,":[92,236,298],"there":[93],"do":[94],"not":[95],"exist":[96],"any":[97],"frameworks":[99],"to":[100,187,220,300],"simultaneously":[101],"model":[102,120,136,163,269],"species":[109,153],"account":[111],"their":[113],"inter-dependency.":[114],"Here,":[115],"we":[116,190],"develop":[117],"a":[118,172,221,271],"three-tree":[119,195,268],"explicitly":[125,156],"captures":[126],"interdependence":[128],"domain-,":[130],"gene-,":[131],"species-level":[133],"Our":[135,260],"extends":[137],"classical":[139],"phylogenetic":[140],"reconciliation":[141],"framework,":[142,197],"which":[143],"infers":[144],"family":[146,179,182],"by":[148,155,248],"comparing":[149,249],"trees":[151,228,232],"tree,":[154],"accounting":[157],"domain-level":[159,165,279],"events.":[160],"new":[162,194,245,267],"decouples":[164],"events":[166,169],"from":[167,233],"gene-level":[168,281],"provides":[171],"much":[173],"more":[174],"fine-grained":[175],"easy":[186],"interpret.":[188],"(i)":[191],"introduce":[192],"(ii)":[198],"prove":[199],"associated":[202],"optimization":[203],"problem":[204],"NP-hard,":[206],"(iii)":[207],"devise":[208],"an":[209],"efficient":[210],"heuristic":[211],"solution":[212],"problem,":[215],"(iv)":[216],"apply":[217],"our":[218,244],"algorithm":[219],"large":[222],"dataset":[223],"about":[225],"4000":[226],"7000":[230],"12":[234],"fly":[235],"(v)":[238],"demonstrate":[239],"impact":[241,273],"using":[243,257,265],"framework":[247],"inferred":[251],"histories":[253],"against":[254],"those":[255],"obtained":[256],"existing":[258,301],"approaches.":[259,302],"experimental":[261],"results":[262],"show":[263],"significant":[272],"inference":[276,286],"both":[278],"events,":[282],"content":[289,295],"ancestral":[291,297],"compared":[299]},"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}