{"id":"https://openalex.org/W4304479873","doi":"https://doi.org/10.1093/bioinformatics/btac669","title":"Tree2GD: a phylogenomic method to detect large-scale gene duplication events","display_name":"Tree2GD: a phylogenomic method to detect large-scale gene duplication events","publication_year":2022,"publication_date":"2022-10-11","ids":{"openalex":"https://openalex.org/W4304479873","doi":"https://doi.org/10.1093/bioinformatics/btac669","pmid":"https://pubmed.ncbi.nlm.nih.gov/36218394"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac669","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac669","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/23/5317/47466059/btac669.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/23/5317/47466059/btac669.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078555345","display_name":"Duoyuan Chen","orcid":"https://orcid.org/0000-0001-8621-340X"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Duoyuan Chen","raw_affiliation_strings":["State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University , Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012638162","display_name":"Taikui Zhang","orcid":"https://orcid.org/0000-0002-0309-161X"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]},{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Taikui Zhang","raw_affiliation_strings":["Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, PA 16802, USA","State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University , Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, PA 16802, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064015375","display_name":"Yamao Chen","orcid":"https://orcid.org/0000-0002-9472-4936"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yamao Chen","raw_affiliation_strings":["State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University , Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029214336","display_name":"Hong M\u0101","orcid":"https://orcid.org/0000-0001-8717-4422"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hong Ma","raw_affiliation_strings":["Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, PA 16802, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, The Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park, PA 16802, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012916132","display_name":"Ji Qi","orcid":"https://orcid.org/0000-0001-7135-0524"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ji Qi","raw_affiliation_strings":["State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University , Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5012916132"],"corresponding_institution_ids":["https://openalex.org/I24943067"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":5.2636,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.95170739,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"38","issue":"23","first_page":"5317","last_page":"5321"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9983999729156494,"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"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9983999729156494,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9975000023841858,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9919000267982483,"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/gene-duplication","display_name":"Gene duplication","score":0.8656036853790283},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.6557781100273132},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5942150950431824},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5204146504402161},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47075846791267395},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4329102635383606},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.35796570777893066},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.11789268255233765},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.08137086033821106}],"concepts":[{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.8656036853790283},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.6557781100273132},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5942150950431824},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5204146504402161},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47075846791267395},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4329102635383606},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.35796570777893066},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.11789268255233765},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.08137086033821106}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":true},{"descriptor_ui":"D020440","descriptor_name":"Gene Duplication","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},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac669","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac669","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/23/5317/47466059/btac669.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36218394","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36218394","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac669","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac669","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/23/5317/47466059/btac669.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6399999856948853,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G2082826544","display_name":null,"funder_award_id":"Postdoctoral","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6462806282","display_name":null,"funder_award_id":"2019M661344","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G7001516894","display_name":null,"funder_award_id":"2019M6","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G7752873037","display_name":null,"funder_award_id":"2019M66","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G8721107296","display_name":null,"funder_award_id":"32070247","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"},{"id":"https://openalex.org/F4320321851","display_name":"Fudan University","ror":"https://ror.org/013q1eq08"},{"id":"https://openalex.org/F4320326863","display_name":"State Key Laboratory of Genetic Engineering","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4304479873.pdf","grobid_xml":"https://content.openalex.org/works/W4304479873.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W1900937478","https://openalex.org/W2001374342","https://openalex.org/W2003062832","https://openalex.org/W2045204781","https://openalex.org/W2057652201","https://openalex.org/W2058378183","https://openalex.org/W2061918046","https://openalex.org/W2064912476","https://openalex.org/W2080177252","https://openalex.org/W2096620535","https://openalex.org/W2119311177","https://openalex.org/W2125346198","https://openalex.org/W2132926880","https://openalex.org/W2144345157","https://openalex.org/W2159664363","https://openalex.org/W2164094120","https://openalex.org/W2187590948","https://openalex.org/W2278476911","https://openalex.org/W2325985707","https://openalex.org/W2403944210","https://openalex.org/W2444314350","https://openalex.org/W2513727910","https://openalex.org/W2517856198","https://openalex.org/W2529838505","https://openalex.org/W2595990302","https://openalex.org/W2612079819","https://openalex.org/W2614081736","https://openalex.org/W2616265326","https://openalex.org/W2728605235","https://openalex.org/W2756236522","https://openalex.org/W2781873368","https://openalex.org/W2788647397","https://openalex.org/W2791076745","https://openalex.org/W2794774827","https://openalex.org/W2795734346","https://openalex.org/W2800883607","https://openalex.org/W2802960899","https://openalex.org/W2891365708","https://openalex.org/W2900629010","https://openalex.org/W2910743782","https://openalex.org/W2939460054","https://openalex.org/W2949203785","https://openalex.org/W2951208971","https://openalex.org/W2951464304","https://openalex.org/W2952085735","https://openalex.org/W2953169567","https://openalex.org/W2955134475","https://openalex.org/W2980360366","https://openalex.org/W2981543307","https://openalex.org/W2988260981","https://openalex.org/W3005235420","https://openalex.org/W3006424385","https://openalex.org/W3025356271","https://openalex.org/W3026288815","https://openalex.org/W3041243944","https://openalex.org/W3089959412","https://openalex.org/W3131992635","https://openalex.org/W4210353260","https://openalex.org/W4229487902","https://openalex.org/W4233651241","https://openalex.org/W6730257837","https://openalex.org/W6754720370","https://openalex.org/W6770544248"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W4388014327","https://openalex.org/W2115382138","https://openalex.org/W2304205445","https://openalex.org/W2050456981","https://openalex.org/W1912284124","https://openalex.org/W2039614575","https://openalex.org/W3025364102","https://openalex.org/W3127109662","https://openalex.org/W2034625591"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
