{"id":"https://openalex.org/W3182507784","doi":"https://doi.org/10.1093/bioinformatics/btab328","title":"Gene tree and species tree reconciliation with endosymbiotic gene transfer","display_name":"Gene tree and species tree reconciliation with endosymbiotic gene transfer","publication_year":2021,"publication_date":"2021-05-04","ids":{"openalex":"https://openalex.org/W3182507784","doi":"https://doi.org/10.1093/bioinformatics/btab328","mag":"3182507784","pmid":"https://pubmed.ncbi.nlm.nih.gov/34252921"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab328","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab328","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i120/39620297/btab328.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i120/39620297/btab328.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028363985","display_name":"Yoann Anselmetti","orcid":"https://orcid.org/0000-0002-6689-1163"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yoann Anselmetti","raw_affiliation_strings":["D\u00e9partement d'informatique, Universit\u00e9 de Sherbrooke, 2500, boulevard de l'Universit\u00e9 , Sherbrooke (Qu\u00e9bec) J1K 2R1, Canada"],"affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique, Universit\u00e9 de Sherbrooke, 2500, boulevard de l'Universit\u00e9 , Sherbrooke (Qu\u00e9bec) J1K 2R1, Canada","institution_ids":["https://openalex.org/I135117807"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041470344","display_name":"Nadia El-Mabrouk","orcid":"https://orcid.org/0000-0002-5385-1015"},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Nadia El-Mabrouk","raw_affiliation_strings":["D\u00e9partement d'informatique et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al , CP 6128 succ Centre-Ville, Montr\u00e9al, Qu\u00e9bec H3C 3J7, Canada"],"affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique et de recherche op\u00e9rationnelle, Universit\u00e9 de Montr\u00e9al , CP 6128 succ Centre-Ville, Montr\u00e9al, Qu\u00e9bec H3C 3J7, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016796629","display_name":"Manuel Lafond","orcid":"https://orcid.org/0000-0002-5305-7372"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Manuel Lafond","raw_affiliation_strings":["D\u00e9partement d'informatique, Universit\u00e9 de Sherbrooke, 2500, boulevard de l'Universit\u00e9 , Sherbrooke (Qu\u00e9bec) J1K 2R1, Canada"],"affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique, Universit\u00e9 de Sherbrooke, 2500, boulevard de l'Universit\u00e9 , Sherbrooke (Qu\u00e9bec) J1K 2R1, Canada","institution_ids":["https://openalex.org/I135117807"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004463624","display_name":"A\u00efda Ouangraoua","orcid":"https://orcid.org/0000-0002-2040-4948"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"A\u00efda Ouangraoua","raw_affiliation_strings":["D\u00e9partement d'informatique, Universit\u00e9 de Sherbrooke, 2500, boulevard de l'Universit\u00e9 , Sherbrooke (Qu\u00e9bec) J1K 2R1, Canada"],"affiliations":[{"raw_affiliation_string":"D\u00e9partement d'informatique, Universit\u00e9 de Sherbrooke, 2500, boulevard de l'Universit\u00e9 , Sherbrooke (Qu\u00e9bec) J1K 2R1, Canada","institution_ids":["https://openalex.org/I135117807"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5041470344"],"corresponding_institution_ids":["https://openalex.org/I70931966"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.732,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.69125514,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"37","issue":"Supplement_1","first_page":"i120","last_page":"i132"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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":0.9983999729156494,"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/T11470","display_name":"Legume Nitrogen Fixing Symbiosis","score":0.9922000169754028,"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/T12134","display_name":"Insect symbiosis and bacterial influences","score":0.9330000281333923,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect 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"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.8358398675918579},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7811999320983887},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.7721508741378784},{"id":"https://openalex.org/keywords/horizontal-gene-transfer","display_name":"Horizontal gene transfer","score":0.7664057016372681},{"id":"https://openalex.org/keywords/mitochondrial-dna","display_name":"Mitochondrial DNA","score":0.6774049997329712},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.668317973613739},{"id":"https://openalex.org/keywords/nuclear-gene","display_name":"Nuclear gene","score":0.567331075668335},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.561514675617218},{"id":"https://openalex.org/keywords/genome-evolution","display_name":"Genome evolution","score":0.5487632155418396},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47892674803733826},{"id":"https://openalex.org/keywords/eukaryote","display_name":"Eukaryote","score":0.4262154698371887},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.41602444648742676}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8358398675918579},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7811999320983887},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.7721508741378784},{"id":"https://openalex.org/C92938381","wikidata":"https://www.wikidata.org/wiki/Q83185","display_name":"Horizontal gene transfer","level":4,"score":0.7664057016372681},{"id":"https://openalex.org/C24586158","wikidata":"https://www.wikidata.org/wiki/Q27075","display_name":"Mitochondrial DNA","level":3,"score":0.6774049997329712},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.668317973613739},{"id":"https://openalex.org/C20750100","wikidata":"https://www.wikidata.org/wiki/Q7068120","display_name":"Nuclear gene","level":4,"score":0.567331075668335},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.561514675617218},{"id":"https://openalex.org/C174600577","wikidata":"https://www.wikidata.org/wiki/Q5533491","display_name":"Genome evolution","level":4,"score":0.5487632155418396},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47892674803733826},{"id":"https://openalex.org/C2779413310","wikidata":"https://www.wikidata.org/wiki/Q19088","display_name":"Eukaryote","level":4,"score":0.4262154698371887},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.41602444648742676}],"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":"D010802","descriptor_name":"Phylogeny","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013559","descriptor_name":"Symbiosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013559","descriptor_name":"Symbiosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013559","descriptor_name":"Symbiosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab328","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab328","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i120/39620297/btab328.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34252921","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34252921","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8312264","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8312264","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,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab328","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab328","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i120/39620297/btab328.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.5600000023841858,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3182507784.pdf","grobid_xml":"https://content.openalex.org/works/W3182507784.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W64395886","https://openalex.org/W1501400124","https://openalex.org/W1966369330","https://openalex.org/W1973395046","https://openalex.org/W1978858440","https://openalex.org/W1992957467","https://openalex.org/W2010175959","https://openalex.org/W2061646232","https://openalex.org/W2118207809","https://openalex.org/W2124105487","https://openalex.org/W2131944877","https://openalex.org/W2132318428","https://openalex.org/W2132553324","https://openalex.org/W2132926880","https://openalex.org/W2134824589","https://openalex.org/W2135281627","https://openalex.org/W2135611147","https://openalex.org/W2136252135","https://openalex.org/W2141052558","https://openalex.org/W2144345157","https://openalex.org/W2150917623","https://openalex.org/W2157321139","https://openalex.org/W2157360426","https://openalex.org/W2162282699","https://openalex.org/W2163892779","https://openalex.org/W2169940135","https://openalex.org/W2767078779","https://openalex.org/W2787651215","https://openalex.org/W2883395410","https://openalex.org/W2937178077","https://openalex.org/W2949124547","https://openalex.org/W2976303698","https://openalex.org/W3012517325","https://openalex.org/W3090324809","https://openalex.org/W4231886136","https://openalex.org/W6783900302"],"related_works":["https://openalex.org/W2167535206","https://openalex.org/W2184775635","https://openalex.org/W1661979114","https://openalex.org/W2790719714","https://openalex.org/W2018383140","https://openalex.org/W2032602742","https://openalex.org/W2022927779","https://openalex.org/W2156424038","https://openalex.org/W2071352397","https://openalex.org/W2152876917"],"abstract_inverted_index":{"EndoRex":[0],"implementation":[1],"and":[2],"supporting":[3],"data":[4],"are":[5],"available":[6],"on":[7],"the":[8],"GitHub":[9],"repository":[10],"via":[11],"https://github.com/AEVO-lab/EndoRex.":[12]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}