{"id":"https://openalex.org/W2056584222","doi":"https://doi.org/10.1073/pnas.0509737102","title":"Mapping of orthologous genes in the context of biological pathways: An application of integer programming","display_name":"Mapping of orthologous genes in the context of biological pathways: An application of integer programming","publication_year":2005,"publication_date":"2005-12-22","ids":{"openalex":"https://openalex.org/W2056584222","doi":"https://doi.org/10.1073/pnas.0509737102","mag":"2056584222","pmid":"https://pubmed.ncbi.nlm.nih.gov/16373500"},"language":"en","primary_location":{"id":"doi:10.1073/pnas.0509737102","is_oa":false,"landing_page_url":"https://doi.org/10.1073/pnas.0509737102","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://doi.org/10.1073/pnas.0509737102","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110127468","display_name":"Fenglou Mao","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fenglou Mao","raw_affiliation_strings":["Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062568388","display_name":"Zhengchang Su","orcid":"https://orcid.org/0000-0003-4636-3440"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]},{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhengchang Su","raw_affiliation_strings":["Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026918414","display_name":"Victor Olman","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Victor Olman","raw_affiliation_strings":["Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053687986","display_name":"Phuongan Dam","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Phuongan Dam","raw_affiliation_strings":["Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100662209","display_name":"Zhi\u2010Jie Liu","orcid":"https://orcid.org/0000-0001-7279-2893"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]},{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhijie Liu","raw_affiliation_strings":["Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I165733156"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020171946","display_name":"Ying Xu","orcid":"https://orcid.org/0000-0002-7856-3343"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ying Xu","raw_affiliation_strings":["Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Laboratory, Biochemistry and Molecular Biology Department, University of Georgia, A110 Life Science Building, 120 Green Street, Athens, GA 30602; and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I165733156"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5110127468"],"corresponding_institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I165733156"],"apc_list":null,"apc_paid":null,"fwci":1.9691,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.85316031,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"103","issue":"1","first_page":"129","last_page":"134"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.994700014591217,"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/genome","display_name":"Genome","score":0.6134968400001526},{"id":"https://openalex.org/keywords/regulon","display_name":"Regulon","score":0.5950881838798523},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5497737526893616},{"id":"https://openalex.org/keywords/operon","display_name":"Operon","score":0.538129985332489},{"id":"https://openalex.org/keywords/orthologous-gene","display_name":"Orthologous Gene","score":0.5164706707000732},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4792490005493164},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.4638388752937317},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.45753318071365356},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4372154176235199},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.42876821756362915},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.426636278629303},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4149840474128723},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.40633276104927063},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3879287540912628},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35914134979248047},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1934681534767151},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.19023990631103516},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19002553820610046},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.10944029688835144},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.08747687935829163}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6134968400001526},{"id":"https://openalex.org/C62361671","wikidata":"https://www.wikidata.org/wiki/Q1754612","display_name":"Regulon","level":4,"score":0.5950881838798523},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5497737526893616},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.538129985332489},{"id":"https://openalex.org/C2909108991","wikidata":"https://www.wikidata.org/wiki/Q414601","display_name":"Orthologous Gene","level":4,"score":0.5164706707000732},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4792490005493164},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.4638388752937317},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.45753318071365356},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4372154176235199},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.42876821756362915},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.426636278629303},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4149840474128723},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.40633276104927063},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3879287540912628},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35914134979248047},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1934681534767151},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.19023990631103516},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19002553820610046},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.10944029688835144},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.08747687935829163},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040481","descriptor_name":"Genome Components","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040481","descriptor_name":"Genome Components","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040481","descriptor_name":"Genome Components","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1073/pnas.0509737102","is_oa":false,"landing_page_url":"https://doi.org/10.1073/pnas.0509737102","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},{"id":"pmid:16373500","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16373500","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":"Proceedings of the National Academy of Sciences of the United States of America","raw_type":null},{"id":"pmh:oai:europepmc.org:279560","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1325003","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1325003","is_oa":true,"landing_page_url":"http://doi.org/10.1073/pnas.0509737102","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc Natl Acad Sci U S A","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:1325003","is_oa":true,"landing_page_url":"http://doi.org/10.1073/pnas.0509737102","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc Natl Acad Sci U S A","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1494526651","https://openalex.org/W1512810258","https://openalex.org/W1515662611","https://openalex.org/W1533263158","https://openalex.org/W1562819315","https://openalex.org/W1574470162","https://openalex.org/W1608344100","https://openalex.org/W1610001324","https://openalex.org/W1679505054","https://openalex.org/W1808859530","https://openalex.org/W1863042168","https://openalex.org/W1890088071","https://openalex.org/W1938034723","https://openalex.org/W1986105390","https://openalex.org/W1989511261","https://openalex.org/W1990453950","https://openalex.org/W1995117714","https://openalex.org/W2003482560","https://openalex.org/W2007321101","https://openalex.org/W2010980078","https://openalex.org/W2015106370","https://openalex.org/W2032619610","https://openalex.org/W2034718856","https://openalex.org/W2053096433","https://openalex.org/W2073850887","https://openalex.org/W2077278144","https://openalex.org/W2079585735","https://openalex.org/W2084902262","https://openalex.org/W2090063098","https://openalex.org/W2090672353","https://openalex.org/W2096731969","https://openalex.org/W2097307883","https://openalex.org/W2102199998","https://openalex.org/W2107424557","https://openalex.org/W2116356176","https://openalex.org/W2121891431","https://openalex.org/W2125678029","https://openalex.org/W2145393087","https://openalex.org/W2153010156","https://openalex.org/W2154044807","https://openalex.org/W2158714788","https://openalex.org/W2160453515","https://openalex.org/W2164366364","https://openalex.org/W2165177592","https://openalex.org/W2167788763","https://openalex.org/W2480349439","https://openalex.org/W3149686652","https://openalex.org/W4248559339","https://openalex.org/W6600018615","https://openalex.org/W6602945306","https://openalex.org/W6611473997"],"related_works":["https://openalex.org/W61127607","https://openalex.org/W1984136937","https://openalex.org/W4281651837","https://openalex.org/W2132790938","https://openalex.org/W2171972144","https://openalex.org/W1796329565","https://openalex.org/W1976388816","https://openalex.org/W2004986663","https://openalex.org/W1544013284","https://openalex.org/W2038893582"],"abstract_inverted_index":{"Mapping":[0],"biological":[1,15],"pathways":[2],"across":[3,56,105],"microbial":[4,57,85],"genomes":[5,106],"is":[6,82],"a":[7,84,92,122,148,158],"highly":[8],"important":[9],"technique":[10],"in":[11,127],"functional":[12],"studies":[13],"of":[14,45,79,160],"systems.":[16],"Existing":[17],"methods":[18,180],"mainly":[19],"rely":[20],"on":[21,157],"sequence-based":[22],"orthologous":[23],"gene":[24],"mapping,":[25],"which":[26],"often":[27],"leads":[28],"to":[29,102,107],"suboptimal":[30],"mapping":[31,55],"results":[32],"because":[33],"sequence-similarity":[34,183],"information":[35,41,70,170,184],"alone":[36],"does":[37],"not":[38],"contain":[39],"sufficient":[40],"for":[42,53,137],"accurate":[43],"identification":[44],"orthology":[46],"relationship.":[47],"Here":[48],"we":[49],"present":[50],"an":[51,134],"algorithm":[52,60,136,146],"pathway":[54,86],"genomes.":[58],"The":[59],"takes":[61],"into":[62,91,121],"account":[63],"both":[64],"sequence":[65,110],"similarity":[66,111],"and":[67,74,143],"genomic":[68,168],"structure":[69,169],"such":[71],"as":[72,147,171],"operons":[73,94],"regulons.":[75,96],"One":[76],"basic":[77],"premise":[78],"our":[80],"approach":[81],"that":[83,115,166,181],"could":[87,173],"generally":[88],"be":[89,119],"decomposed":[90],"few":[93,123],"or":[95],"We":[97,131,153,164],"formulated":[98],"the":[99,113,116,128,145,176],"pathway-mapping":[100,177],"problem":[101,142],"map":[103],"genes":[104,118],"maximize":[108],"their":[109],"under":[112],"constraint":[114],"mapped":[117],"grouped":[120],"operons,":[124],"preferably":[125],"coregulated":[126],"target":[129],"genome.":[130],"have":[132,154],"developed":[133],"integer-programming":[135],"solving":[138],"this":[139],"constrained":[140],"optimization":[141],"implemented":[144],"computer":[149],"software":[150],"program,":[151],"p-map.":[152],"tested":[155],"p-map":[156],"number":[159],"known":[161],"homologous":[162],"pathways.":[163],"conclude":[165],"using":[167],"constraints":[172],"greatly":[174],"improve":[175],"accuracy":[178],"over":[179],"use":[182],"alone.":[185]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}