{"id":"https://openalex.org/W2136258184","doi":"https://doi.org/10.1093/gbe/evt132","title":"Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals","display_name":"Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals","publication_year":2013,"publication_date":"2013-09-06","ids":{"openalex":"https://openalex.org/W2136258184","doi":"https://doi.org/10.1093/gbe/evt132","mag":"2136258184","pmid":"https://pubmed.ncbi.nlm.nih.gov/24013106","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3814191"},"language":"en","primary_location":{"id":"doi:10.1093/gbe/evt132","doi":"https://doi.org/10.1093/gbe/evt132","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gbe/evt132","pdf_url":"https://academic.oup.com/gbe/article-pdf/5/10/1800/17917580/evt132.pdf","source":{"id":"https://openalex.org/S10195028","display_name":"Genome Biology and Evolution","issn_l":"1759-6653","issn":["1759-6653"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-d","doyens","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Biology and Evolution","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/gbe/article-pdf/5/10/1800/17917580/evt132.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047780258","display_name":"Daniel A. Dalquen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Daniel A. Dalquen","raw_affiliation_strings":["Computational Biochemistry Research Group, ETH Zurich, Z\u00fcrich, Switzerland","Swiss Institute of Bioinformatics, Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biochemistry Research Group, ETH Zurich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050068380","display_name":"Christophe Dessimoz","orcid":"https://orcid.org/0000-0002-2170-853X","observed_orcids":["https://orcid.org/0000-0002-2170-853X"]},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["CH","GB"],"is_corresponding":true,"raw_author_name":"Christophe Dessimoz","raw_affiliation_strings":["Computational Biochemistry Research Group, ETH Zurich, Z\u00fcrich, Switzerland","European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom","Swiss Institute of Bioinformatics, Z\u00fcrich, Switzerland","University College London, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biochemistry Research Group, ETH Zurich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"University College London, London, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5047780258","https://openalex.org/A5050068380"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I1303153112","https://openalex.org/I35440088","https://openalex.org/I45129253"],"apc_list":{"value":2850,"currency":"USD","value_usd":2850},"apc_paid":{"value":2850,"currency":"USD","value_usd":2850},"fwci":2.7493,"has_fulltext":true,"cited_by_count":94,"citation_normalized_percentile":{"value":0.920451,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":100},"biblio":{"volume":"5","issue":"10","first_page":"1800","last_page":"1806"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9961000084877014,"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":0.9961000084877014,"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":0.0013000000035390258,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.0007999999797903001,"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/orthology-inference","display_name":"orthology inference","score":0.8830000162124634},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"gene duplication","score":0.9129999876022339},{"id":"https://openalex.org/keywords/ortholog-detection","display_name":"ortholog detection","score":0.5220000147819519},{"id":"https://openalex.org/keywords/plants","display_name":"plants","score":0.38100001215934753},{"id":"https://openalex.org/keywords/animals","display_name":"animals","score":0.9769999980926514},{"id":"https://openalex.org/keywords/bacteria","display_name":"bacteria","score":0.4580000042915344},{"id":"https://openalex.org/keywords/archaea","display_name":"archaea","score":0.9079999923706055},{"id":"https://openalex.org/keywords/simulated-data","display_name":"simulated data","score":0.32899999618530273}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8708754181861877},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.7163147330284119},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.711392343044281},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6816580295562744},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5746283531188965},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5651510953903198},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.5309904217720032},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.508997917175293},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4586280882358551},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39832162857055664},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.365189790725708},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.06337931752204895},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/gbe/evt132","doi":"https://doi.org/10.1093/gbe/evt132","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gbe/evt132","pdf_url":"https://academic.oup.com/gbe/article-pdf/5/10/1800/17917580/evt132.pdf","source":{"id":"https://openalex.org/S10195028","display_name":"Genome Biology and Evolution","issn_l":"1759-6653","issn":["1759-6653"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-d","doyens","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Biology and Evolution","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2804584","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3814191","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3814191","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3814191","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Biol Evol","raw_type":"Text"},{"id":"pmid:24013106","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24013106","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,"listed_in":[],"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":"Genome biology and evolution","raw_type":"Letter"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.902.6912","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.902.6912","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://gbe.oxfordjournals.org/content/early/2013/09/06/gbe.evt132.full.pdf","raw_type":"text"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1405553","doi":null,"is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/1405553/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Genome Biology and Evolution , 5 (10) pp. 1800-1806. (2013)","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/gbe/evt132","doi":"https://doi.org/10.1093/gbe/evt132","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gbe/evt132","pdf_url":"https://academic.oup.com/gbe/article-pdf/5/10/1800/17917580/evt132.pdf","source":{"id":"https://openalex.org/S10195028","display_name":"Genome Biology and Evolution","issn_l":"1759-6653","issn":["1759-6653"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-d","doyens","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Biology and Evolution","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G125759156","display_name":"The Million Protein, Thousand Species Tree(s) of Life","funder_award_id":"136461","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2136258184.pdf","grobid_xml":"https://content.openalex.org/works/W2136258184.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1485242531","https://openalex.org/W1971231926","https://openalex.org/W1981791726","https://openalex.org/W1995117714","https://openalex.org/W1997130867","https://openalex.org/W2007447692","https://openalex.org/W2009234149","https://openalex.org/W2019572077","https://openalex.org/W2048448217","https://openalex.org/W2055043387","https://openalex.org/W2062018285","https://openalex.org/W2075171145","https://openalex.org/W2082202339","https://openalex.org/W2100874222","https://openalex.org/W2114250447","https://openalex.org/W2134396951","https://openalex.org/W2140161828","https://openalex.org/W2143157299","https://openalex.org/W2159266221"],"related_works":["https://openalex.org/W2140161828","https://openalex.org/W2105791696","https://openalex.org/W1519797976","https://openalex.org/W2137057090","https://openalex.org/W3033758445","https://openalex.org/W1991842822","https://openalex.org/W1542595575","https://openalex.org/W7008155138","https://openalex.org/W1967909513","https://openalex.org/W4285069269"],"abstract_inverted_index":{"Bidirectional":[0],"best":[1],"hits":[2],"(BBH),":[3],"which":[4,103],"entails":[5],"identifying":[6],"the":[7,30,48,62,93,100,141,144,153,173],"pairs":[8],"of":[9,72,78,105,136,143,152,156,167],"genes":[10],"in":[11,29,54,66,117,159],"two":[12],"different":[13],"genomes":[14],"that":[15,150],"are":[16,80,107,170],"more":[17],"similar":[18],"to":[19,25,40,82],"each":[20],"other":[21,27,31],"than":[22],"either":[23],"is":[24,33],"any":[26],"gene":[28,157],"genome,":[32],"a":[34,75],"simple":[35],"and":[36,52,56,58,119,128,161],"widely":[37],"used":[38],"method":[39],"infer":[41],"orthology.":[42],"A":[43],"recent":[44],"study":[45,95],"has":[46],"analyzed":[47],"link":[49],"between":[50],"BBH":[51,67,79,174],"orthology":[53],"bacteria":[55],"archaea":[57],"concluded":[59],"that,":[60],"given":[61],"very":[63],"high":[64,76,154],"consistency":[65],"they":[68],"observed":[69],"among":[70],"triplets":[71],"neighboring":[73],"genes,":[74],"proportion":[77,104],"likely":[81],"be":[83],"bona":[84],"fide":[85],"orthologs.":[86],"However,":[87],"limited":[88],"by":[89,172],"their":[90],"analysis":[91],"setup,":[92],"previous":[94,145],"could":[96],"not":[97],"easily":[98],"test":[99],"reverse":[101],"question:":[102],"orthologs":[106],"BBH?":[108],"In":[109],"this":[110,115],"follow-up":[111],"study,":[112,146],"we":[113],"consider":[114],"question":[116],"theory":[118],"answer":[120],"it":[121],"based":[122],"on":[123],"conceptual":[124],"arguments,":[125],"simulated":[126],"data,":[127],"real":[129],"biological":[130],"data":[131],"from":[132],"all":[133],"three":[134],"domains":[135],"life.":[137],"Our":[138],"analyses":[139],"corroborate":[140],"findings":[142],"but":[147],"also":[148],"show":[149],"because":[151],"rate":[155],"duplication":[158],"plants":[160],"animals,":[162],"as":[163,165],"much":[164],"60%":[166],"orthologous":[168],"relations":[169],"missed":[171],"criterion.":[175]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":15},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2016-06-24T00:00:00"}