{"id":"https://openalex.org/W2047909238","doi":"https://doi.org/10.1093/nar/gks490","title":"KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa","display_name":"KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa","publication_year":2012,"publication_date":"2012-06-06","ids":{"openalex":"https://openalex.org/W2047909238","doi":"https://doi.org/10.1093/nar/gks490","mag":"2047909238","pmid":"https://pubmed.ncbi.nlm.nih.gov/22675073"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gks490","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks490","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gks490","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063430399","display_name":"Francisco Pereira Lobo","orcid":"https://orcid.org/0000-0002-9671-9313"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]},{"id":"https://openalex.org/I199691007","display_name":"Brazilian Agricultural Research Corporation","ror":"https://ror.org/0482b5b22","country_code":"BR","type":"government","lineage":["https://openalex.org/I199691007"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Francisco P. Lobo","raw_affiliation_strings":["Laborat\u00f3rio Multiusu\u00e1rio de Bioinform\u00e1tica, Embrapa Inform\u00e1tica Agropecu\u00e1ria, Campinas, S\u00e3o Paulo 13083 886, Brazil. franciscolobo@gmail.com","Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio Multiusu\u00e1rio de Bioinform\u00e1tica, Embrapa Inform\u00e1tica Agropecu\u00e1ria, Campinas, S\u00e3o Paulo 13083 886, Brazil. franciscolobo@gmail.com","institution_ids":["https://openalex.org/I199691007"]},{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003395641","display_name":"Ma\u00edra R. Rodrigues","orcid":"https://orcid.org/0000-0003-3193-9558"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Ma\u00edra R. Rodrigues","raw_affiliation_strings":["Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"affiliations":[{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009096424","display_name":"Gisele Rodrigues","orcid":"https://orcid.org/0000-0002-8526-2258"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Gisele O. L. Rodrigues","raw_affiliation_strings":["Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"affiliations":[{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013186255","display_name":"Heron Oliveira Hil\u00e1rio","orcid":"https://orcid.org/0000-0002-2548-1053"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Heron O. Hil\u00e1rio","raw_affiliation_strings":["Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"affiliations":[{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086872890","display_name":"Raoni A. Souza","orcid":null},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Raoni A. Souza","raw_affiliation_strings":["Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"affiliations":[{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069682981","display_name":"Andreas Tauch","orcid":null},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Andreas Tauch","raw_affiliation_strings":["Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"affiliations":[{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101908133","display_name":"Anderson Miyoshi","orcid":"https://orcid.org/0000-0002-0480-8993"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Anderson Miyoshi","raw_affiliation_strings":["Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"affiliations":[{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103365723","display_name":"Glaura C. Franco","orcid":"https://orcid.org/0000-0002-7994-8448"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Glaura C. Franco","raw_affiliation_strings":["Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"affiliations":[{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090969979","display_name":"Vasco Azevedo","orcid":"https://orcid.org/0000-0002-4775-2280"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Vasco Azevedo","raw_affiliation_strings":["Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"affiliations":[{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060357821","display_name":"Gl\u00f3ria Regina Franco","orcid":"https://orcid.org/0000-0001-5245-2365"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Gl\u00f3ria R. Franco","raw_affiliation_strings":["Universidade Federal de Minas Gerais, Belo Horizonte, Brazil"],"affiliations":[{"raw_affiliation_string":"Universidade Federal de Minas Gerais, Belo Horizonte, Brazil","institution_ids":["https://openalex.org/I110200422"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5063430399"],"corresponding_institution_ids":["https://openalex.org/I110200422","https://openalex.org/I199691007"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.4034,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.62036434,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"40","issue":"W1","first_page":"W491","last_page":"W497"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9955999851226807,"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":0.9847999811172485,"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/biology","display_name":"Biology","score":0.9674022793769836},{"id":"https://openalex.org/keywords/monophyly","display_name":"Monophyly","score":0.8884400129318237},{"id":"https://openalex.org/keywords/taxon","display_name":"Taxon","score":0.6056755781173706},{"id":"https://openalex.org/keywords/homologous-chromosome","display_name":"Homologous chromosome","score":0.5499899387359619},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.47134634852409363},{"id":"https://openalex.org/keywords/zoology","display_name":"Zoology","score":0.3811754882335663},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.31892457604408264},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31393569707870483},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2609952688217163},{"id":"https://openalex.org/keywords/paleontology","display_name":"Paleontology","score":0.1794469654560089},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.11086398363113403}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9674022793769836},{"id":"https://openalex.org/C12326286","wikidata":"https://www.wikidata.org/wiki/Q210958","display_name":"Monophyly","level":5,"score":0.8884400129318237},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.6056755781173706},{"id":"https://openalex.org/C64894306","wikidata":"https://www.wikidata.org/wiki/Q849622","display_name":"Homologous chromosome","level":3,"score":0.5499899387359619},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.47134634852409363},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","level":1,"score":0.3811754882335663},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.31892457604408264},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31393569707870483},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2609952688217163},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.1794469654560089},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.11086398363113403}],"mesh":[{"descriptor_ui":"D002952","descriptor_name":"Citric Acid Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002952","descriptor_name":"Citric Acid Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002952","descriptor_name":"Citric Acid Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004755","descriptor_name":"Enterobacteriaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006019","descriptor_name":"Glycolysis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006019","descriptor_name":"Glycolysis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006019","descriptor_name":"Glycolysis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056546","descriptor_name":"Lactobacillales","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D056546","descriptor_name":"Lactobacillales","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D056546","descriptor_name":"Lactobacillales","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D056546","descriptor_name":"Lactobacillales","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D056546","descriptor_name":"Lactobacillales","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D056546","descriptor_name":"Lactobacillales","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D056546","descriptor_name":"Lactobacillales","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056546","descriptor_name":"Lactobacillales","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056546","descriptor_name":"Lactobacillales","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gks490","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks490","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:22675073","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22675073","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:2409785","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3394310","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,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:nar:40/W1/W491","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/40/W1/W491","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pub.librecat.org:2523617","is_oa":false,"landing_page_url":"https://pub.uni-bielefeld.de/record/2523617","pdf_url":null,"source":{"id":"https://openalex.org/S4306401671","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Lobo FP, Rodrigues MR, Rodrigues GOL, et al. KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa. &lt;em&gt;Nucleic Acids Research&lt;/em&gt;. 2012;40(W1):W491-W497.","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/nar/gks490","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks490","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W617584505","https://openalex.org/W621074288","https://openalex.org/W1532211152","https://openalex.org/W2025086931","https://openalex.org/W2029918421","https://openalex.org/W2034864998","https://openalex.org/W2041303239","https://openalex.org/W2054822023","https://openalex.org/W2068379791","https://openalex.org/W2073354998","https://openalex.org/W2092748220","https://openalex.org/W2104199520","https://openalex.org/W2108539496","https://openalex.org/W2123060905","https://openalex.org/W2128301757","https://openalex.org/W2129563923","https://openalex.org/W2130189525","https://openalex.org/W2130410032","https://openalex.org/W2133465414","https://openalex.org/W2133500149","https://openalex.org/W2138956739","https://openalex.org/W2142302575","https://openalex.org/W2156661861","https://openalex.org/W2156966633","https://openalex.org/W2157501583","https://openalex.org/W2166359595","https://openalex.org/W2170530228"],"related_works":["https://openalex.org/W4200199661","https://openalex.org/W2503477847","https://openalex.org/W4280583302","https://openalex.org/W2105404896","https://openalex.org/W2947651821","https://openalex.org/W1923231248","https://openalex.org/W2383763250","https://openalex.org/W248275141","https://openalex.org/W1530905560","https://openalex.org/W2518331723"],"abstract_inverted_index":{"The":[0,90],"enrichment":[1,29],"analysis":[2,30],"is":[3,37,199],"a":[4,38,63,100],"standard":[5],"procedure":[6],"to":[7,46,66,75,106,152],"interpret":[8],"'omics'":[9],"experiments":[10],"that":[11,182],"generate":[12],"large":[13],"gene":[14],"lists":[15],"as":[16,19,161],"outputs,":[17],"such":[18,160],"transcriptomics":[20],"and":[21,109,142,175],"protemics.":[22],"However,":[23],"despite":[24],"the":[25,114,162,190],"huge":[26],"success":[27],"of":[28,34,41,43,50,70,80,117,126,165,170,192],"in":[31,73,83,94,99,130,157,173,179,189],"these":[32,158],"classes":[33],"experiments,":[35],"there":[36],"surprising":[39],"lack":[40],"application":[42],"this":[44],"methodology":[45],"survey":[47],"other":[48],"categories":[49],"large-scale":[51],"biological":[52,111],"data":[53],"available.":[54],"Here,":[55],"we":[56],"report":[57],"Kegg":[58],"Orthology":[59],"enrichMent-Online":[60],"DetectiOn":[61],"(KOMODO),":[62],"web":[64],"tool":[65],"systematically":[67],"investigate":[68,110],"groups":[69,79],"monophyletic":[71],"genomes":[72],"order":[74],"detect":[76,185],"significantly":[77,148],"enriched":[78],"homologous":[81],"genes":[82],"one":[84],"taxon":[85],"when":[86],"compared":[87],"with":[88],"another.":[89],"results":[91],"are":[92],"displayed":[93],"their":[95,136],"proper":[96],"biochemical":[97],"roles":[98],"visual,":[101],"explorative":[102],"way,":[103],"allowing":[104],"users":[105],"easily":[107],"formulate":[108],"hypotheses":[112],"regarding":[113,135],"taxonomical":[115],"distribution":[116],"genomic":[118,194],"elements.":[119],"We":[120],"validated":[121],"KOMODO":[122,183,198],"by":[123],"analyzing":[124],"portions":[125],"central":[127],"carbon":[128,137],"metabolism":[129,138],"two":[131],"taxa":[132],"extensively":[133],"studied":[134],"profile":[139],"(Enterobacteriaceae":[140],"family":[141],"Lactobacillales":[143,174],"order).":[144],"Most":[145],"enzymatic":[146],"activities":[147],"biased":[149],"were":[150],"related":[151],"known":[153,168],"key":[154],"metabolic":[155],"traits":[156],"taxa,":[159],"distinct":[163],"fates":[164],"pyruvate":[166],"(the":[167],"tendency":[169],"lactate":[171],"production":[172],"its":[176],"complete":[177],"oxidation":[178],"Enterobacteriaceae),":[180],"demonstrating":[181],"could":[184],"biologically":[186],"meaningful":[187],"differences":[188],"frequencies":[191],"shared":[193],"elements":[195],"among":[196],"taxa.":[197],"freely":[200],"available":[201],"at":[202],"http://komodotool.org.":[203]},"counts_by_year":[{"year":2015,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
