{"id":"https://openalex.org/W3187893169","doi":"https://doi.org/10.3390/a14080231","title":"Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages","display_name":"Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages","publication_year":2021,"publication_date":"2021-08-05","ids":{"openalex":"https://openalex.org/W3187893169","doi":"https://doi.org/10.3390/a14080231","mag":"3187893169"},"language":"en","primary_location":{"id":"doi:10.3390/a14080231","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a14080231","pdf_url":"https://www.mdpi.com/1999-4893/14/8/231/pdf?version=1628221957","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"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","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1999-4893/14/8/231/pdf?version=1628221957","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075916330","display_name":"Samson Weiner","orcid":"https://orcid.org/0009-0001-3701-9907"},"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":"Samson Weiner","raw_affiliation_strings":["Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, 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":true,"raw_author_name":"Mukul S. Bansal","raw_affiliation_strings":["Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA","Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5024793976"],"corresponding_institution_ids":["https://openalex.org/I140172145"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.3218,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.55807164,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"14","issue":"8","first_page":"231","last_page":"231"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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":0.9987999796867371,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9139000177383423,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.761658787727356},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.6266219019889832},{"id":"https://openalex.org/keywords/transfer","display_name":"Transfer (computing)","score":0.5720189809799194},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49365076422691345},{"id":"https://openalex.org/keywords/horizontal-gene-transfer","display_name":"Horizontal gene transfer","score":0.473514586687088},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.4638407826423645},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4550006687641144},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.34690573811531067},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.32692983746528625},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2620030641555786},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2139723002910614},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.20383238792419434},{"id":"https://openalex.org/keywords/astrophysics","display_name":"Astrophysics","score":0.0653698742389679}],"concepts":[{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.761658787727356},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.6266219019889832},{"id":"https://openalex.org/C2776175482","wikidata":"https://www.wikidata.org/wiki/Q1195816","display_name":"Transfer (computing)","level":2,"score":0.5720189809799194},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49365076422691345},{"id":"https://openalex.org/C92938381","wikidata":"https://www.wikidata.org/wiki/Q83185","display_name":"Horizontal gene transfer","level":4,"score":0.473514586687088},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.4638407826423645},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4550006687641144},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.34690573811531067},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32692983746528625},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2620030641555786},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2139723002910614},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.20383238792419434},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0653698742389679},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/a14080231","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a14080231","pdf_url":"https://www.mdpi.com/1999-4893/14/8/231/pdf?version=1628221957","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"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","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:0e325cba459d447cbe26b0b968dd9bae","is_oa":true,"landing_page_url":"https://doaj.org/article/0e325cba459d447cbe26b0b968dd9bae","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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, Vol 14, Iss 8, p 231 (2021)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1999-4893/14/8/231/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/a14080231","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Algorithms; Volume 14; Issue 8; Pages: 231","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/a14080231","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a14080231","pdf_url":"https://www.mdpi.com/1999-4893/14/8/231/pdf?version=1628221957","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"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","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6012743651","display_name":null,"funder_award_id":"1615573","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8819509965","display_name":null,"funder_award_id":"1616514","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":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3187893169.pdf","grobid_xml":"https://content.openalex.org/works/W3187893169.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W157609093","https://openalex.org/W1490843365","https://openalex.org/W1608963388","https://openalex.org/W1970909551","https://openalex.org/W1986968252","https://openalex.org/W2076385002","https://openalex.org/W2096789062","https://openalex.org/W2110014387","https://openalex.org/W2112755610","https://openalex.org/W2117000771","https://openalex.org/W2121562498","https://openalex.org/W2132318428","https://openalex.org/W2132553324","https://openalex.org/W2135894797","https://openalex.org/W2138113680","https://openalex.org/W2138882560","https://openalex.org/W2143162227","https://openalex.org/W2144345157","https://openalex.org/W2144454528","https://openalex.org/W2147428165","https://openalex.org/W2148231054","https://openalex.org/W2149582283","https://openalex.org/W2149681675","https://openalex.org/W2159545652","https://openalex.org/W2287141830","https://openalex.org/W2620962860","https://openalex.org/W2754614350","https://openalex.org/W2799551362","https://openalex.org/W2972421638","https://openalex.org/W2977811825","https://openalex.org/W2991771055","https://openalex.org/W3099842447","https://openalex.org/W3103391276"],"related_works":["https://openalex.org/W4388014327","https://openalex.org/W2115382138","https://openalex.org/W2264917134","https://openalex.org/W1883409887","https://openalex.org/W2367076742","https://openalex.org/W2022927779","https://openalex.org/W2086569686","https://openalex.org/W3012252241","https://openalex.org/W147961746","https://openalex.org/W4394142679"],"abstract_inverted_index":{"Duplication-Transfer-Loss":[0],"(DTL)":[1],"reconciliation":[2,32,90,108,190,195,224,237],"is":[3,71],"a":[4,122,206],"widely":[5],"used":[6],"computational":[7],"technique":[8],"for":[9,20,35,55,74,111,126,168,199,244,265,297],"understanding":[10],"gene":[11,17,48],"family":[12],"evolution":[13,46],"and":[14,28,58,76,131,201,274,289],"inferring":[15,75,280],"horizontal":[16,78,99],"transfer":[18,79,100,112,127,151],"(transfer":[19],"short)":[21],"in":[22,83,88,205],"microbes.":[23],"However,":[24],"most":[25],"existing":[26,213],"models":[27,105],"implementations":[29],"of":[30,38,47,61,106,141,166,174,263,271,279],"DTL":[31,107,175,189,236,272],"cannot":[33,132],"account":[34,110],"the":[36,45,56,84,89,135,138,164,172,193,221,234,254,261,269,277,290],"effect":[37],"unsampled":[39,63,102,114,129,143,169,200,266,283],"or":[40,144],"extinct":[41,145,202],"species":[42,64,85,139,203],"lineages":[43,86,115,130,170,204,267,284],"on":[44,137,171,268],"families,":[49],"likely":[50,93],"affecting":[51],"their":[52],"accuracy.":[53],"Accounting":[54],"presence":[57],"possible":[59],"impact":[60,165,262],"any":[62,159],"lineages,":[65],"including":[66],"those":[67],"that":[68,109,197,217],"are":[69,92],"extinct,":[70],"especially":[72],"important":[73],"studying":[77],"since":[80],"many":[81],"genes":[82],"represented":[87],"analysis":[91],"to":[94,162,212,259],"have":[95,116],"been":[96,118],"acquired":[97],"through":[98],"from":[101,113,128,282],"lineages.":[103],"While":[104],"already":[117],"proposed,":[119],"they":[120],"use":[121],"relatively":[123],"simple":[124],"framework":[125],"explicitly":[133],"infer":[134],"location":[136],"tree":[140],"each":[142],"lineage":[146],"associated":[147],"with":[148],"an":[149,187,241],"identified":[150],"event.":[152],"Furthermore,":[153],"there":[154],"does":[155],"not":[156],"yet":[157],"exist":[158],"systematic":[160,256],"studies":[161],"assess":[163,260],"accounting":[167,264],"accuracy":[173,270],"reconciliation.":[176],"In":[177],"this":[178,298],"work,":[179],"we":[180],"address":[181],"these":[182],"deficiencies":[183],"by":[184],"(i)":[185],"introducing":[186],"extended":[188],"model,":[191,196,238],"called":[192],"DTLx":[194,223,247],"accounts":[198],"new,":[207],"more":[208],"functional":[209],"manner":[210],"compared":[211],"models,":[214],"(ii)":[215],"showing":[216],"optimal":[218,246],"reconciliations":[219,248],"under":[220,233,285],"new":[222,287],"model":[225,288,296],"can":[226],"be":[227],"computed":[228],"just":[229],"as":[230,232],"efficiently":[231],"fastest":[235],"(iii)":[239],"providing":[240],"efficient":[242],"algorithm":[243],"sampling":[245],"uniformly":[249],"at":[250],"random,":[251],"(iv)":[252],"performing":[253],"first":[255],"simulation":[257],"study":[258],"reconciliation,":[273],"(v)":[275],"comparing":[276],"accuracies":[278],"transfers":[281],"our":[286],"only":[291],"other":[292],"previously":[293],"proposed":[294],"parsimony-based":[295],"problem.":[299]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2021-08-16T00:00:00"}