{"id":"https://openalex.org/W4249769906","doi":"https://doi.org/10.1109/csb.2004.1332525","title":"A graph analysis method to detect metabolic sub-networks based on phylogenetic profile","display_name":"A graph analysis method to detect metabolic sub-networks based on phylogenetic profile","publication_year":2004,"publication_date":"2004-11-08","ids":{"openalex":"https://openalex.org/W4249769906","doi":"https://doi.org/10.1109/csb.2004.1332525"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2004.1332525","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332525","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067878040","display_name":"S. Miyake","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"S. Miyake","raw_affiliation_strings":["Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Toyonaka, Osaka, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Toyonaka, Osaka, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043707615","display_name":"Y. Takenaka","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Y. Takenaka","raw_affiliation_strings":["Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Toyonaka, Osaka, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Toyonaka, Osaka, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029041468","display_name":"H. Matsuda","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"Osaka University","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"H. Matsuda","raw_affiliation_strings":["Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Toyonaka, Osaka, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Toyonaka, Osaka, Japan","institution_ids":["https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5067878040"],"corresponding_institution_ids":["https://openalex.org/I98285908"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.50341686,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"603","last_page":"604"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9990000128746033,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9990000128746033,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9988999962806702,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9894000291824341,"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/kegg","display_name":"KEGG","score":0.772734522819519},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7695108652114868},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5878035426139832},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5761759281158447},{"id":"https://openalex.org/keywords/archaea","display_name":"Archaea","score":0.5689594149589539},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.506895124912262},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5057768821716309},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4363168776035309},{"id":"https://openalex.org/keywords/graph-theory","display_name":"Graph theory","score":0.4294433891773224},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3567271828651428},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32521575689315796},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3081914782524109},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17275258898735046},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1521989107131958},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14288926124572754},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.08410969376564026}],"concepts":[{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.772734522819519},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7695108652114868},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5878035426139832},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5761759281158447},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.5689594149589539},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.506895124912262},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5057768821716309},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4363168776035309},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.4294433891773224},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3567271828651428},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32521575689315796},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3081914782524109},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17275258898735046},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1521989107131958},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14288926124572754},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.08410969376564026},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/csb.2004.1332525","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332525","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W2018045523","https://openalex.org/W2140000393","https://openalex.org/W4252706339"],"related_works":["https://openalex.org/W1964572291","https://openalex.org/W4387948744","https://openalex.org/W1987520879","https://openalex.org/W184793361","https://openalex.org/W2352732738","https://openalex.org/W1607298653","https://openalex.org/W2123060905","https://openalex.org/W4240162843","https://openalex.org/W2559588208","https://openalex.org/W2977457557"],"abstract_inverted_index":{"To":[0],"elucidate":[1],"fundamental":[2],"constituting":[3],"principle":[4],"of":[5,11,21,38,52,56,71,82],"functional":[6],"modules":[7],"or":[8],"building":[9],"blocks":[10],"metabolic":[12,39,80,109],"networks,":[13],"computational":[14],"methods":[15],"to":[16,33,63,78,107],"analyze":[17],"the":[18,50,53,69,72,79,93,103,108],"network":[19],"structure":[20],"metabolism":[22],"are":[23],"getting":[24],"much":[25],"attention.":[26],"We":[27,45,58],"propose":[28],"a":[29],"graph":[30],"search":[31],"method":[32],"extract":[34],"highly":[35,99],"conserved":[36,100],"sub-networks":[37,101],"networks":[40,81],"based":[41],"on":[42],"phylogenetic":[43,54],"profile.":[44],"formulated":[46,60],"reaction-conservation":[47],"score":[48,62],"for":[49],"measure":[51],"conservation":[55],"reactions.":[57],"also":[59],"compound-conservation":[61],"eliminate":[64],"biologically-meaningless":[65],"compounds":[66],"and":[67,90,124],"reduce":[68],"size":[70],"networks.":[73],"By":[74],"applying":[75],"our":[76],"approach":[77],"19":[83],"representative":[84],"organisms":[85],"selected":[86],"from":[87],"bacteria,":[88],"archaea,":[89],"eukaryotes":[91],"in":[92,111,119],"KEGG":[94],"database,":[95],"we":[96,113],"detected":[97],"some":[98],"among":[102],"organisms.":[104],"Comparing":[105],"them":[106],"maps":[110],"KEGG,":[112],"found":[114],"they":[115],"were":[116],"mainly":[117],"included":[118],"energy":[120],"metabolism,":[121,123],"sugar":[122],"amino":[125],"acid":[126],"metabolism.":[127]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
