{"id":"https://openalex.org/W1490264010","doi":"https://doi.org/10.1109/csb.2003.1227429","title":"Computational inference of regulatory pathways in microbes","display_name":"Computational inference of regulatory pathways in microbes","publication_year":2004,"publication_date":"2004-03-30","ids":{"openalex":"https://openalex.org/W1490264010","doi":"https://doi.org/10.1109/csb.2003.1227429","mag":"1490264010"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2003.1227429","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227429","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","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/A5062568388","display_name":"Zhengchang Su","orcid":"https://orcid.org/0000-0003-4636-3440"},"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Z. Su","raw_affiliation_strings":["Divisions of Life Sciences and Computer Sciences & Mathematics, Oak Ridge National Laboratory, Protein Informatics Group"],"affiliations":[{"raw_affiliation_string":"Divisions of Life Sciences and Computer Sciences & Mathematics, Oak Ridge National Laboratory, Protein Informatics Group","institution_ids":["https://openalex.org/I1289243028"]}]},{"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. Dam","raw_affiliation_strings":["Divisions of Life Sciences and Computer Sciences & Mathematics, Oak Ridge National Laboratory, Protein Informatics Group"],"affiliations":[{"raw_affiliation_string":"Divisions of Life Sciences and Computer Sciences & Mathematics, Oak Ridge National Laboratory, Protein Informatics Group","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004740576","display_name":"X. Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"X. Chen","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California Riverside, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California Riverside, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"V. Olman","raw_affiliation_strings":["Divisions of Life Sciences and Computer Sciences & Mathematics, Oak Ridge National Laboratory, Protein Informatics Group"],"affiliations":[{"raw_affiliation_string":"Divisions of Life Sciences and Computer Sciences & Mathematics, Oak Ridge National Laboratory, Protein Informatics Group","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101911266","display_name":"Tao Jiang","orcid":"https://orcid.org/0000-0003-3833-4498"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Jiang","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California Riverside, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California Riverside, USA","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013071861","display_name":"Brian Palenik","orcid":"https://orcid.org/0000-0002-3717-9046"},"institutions":[{"id":"https://openalex.org/I150209017","display_name":"Scripps Institution of Oceanography","ror":"https://ror.org/04v7hvq31","country_code":"US","type":"facility","lineage":["https://openalex.org/I150209017","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. Palenik","raw_affiliation_strings":["Scripps Institute of Oceanography, University of California, San Diego, USA"],"affiliations":[{"raw_affiliation_string":"Scripps Institute of Oceanography, University of California, San Diego, USA","institution_ids":["https://openalex.org/I150209017","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088506150","display_name":"Yan\u2010Peng Xu","orcid":"https://orcid.org/0000-0001-8764-4412"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Y. Xu","raw_affiliation_strings":["Divisions of Life Sciences and Computer Sciences & Mathematics, Oak Ridge National Laboratory, Protein Informatics Group"],"affiliations":[{"raw_affiliation_string":"Divisions of Life Sciences and Computer Sciences & Mathematics, Oak Ridge National Laboratory, Protein Informatics Group","institution_ids":["https://openalex.org/I1289243028"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5062568388"],"corresponding_institution_ids":["https://openalex.org/I1289243028"],"apc_list":null,"apc_paid":null,"fwci":0.4678,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.59064129,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"631","last_page":"631"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9954000115394592,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9937999844551086,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/inference","display_name":"Inference","score":0.776063084602356},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6236112713813782},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5778364539146423},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5693621635437012},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.5277743339538574},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.4228174090385437},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3665691614151001},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32147830724716187},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31852513551712036},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17475539445877075}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.776063084602356},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6236112713813782},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5778364539146423},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5693621635437012},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.5277743339538574},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.4228174090385437},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3665691614151001},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32147830724716187},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31852513551712036},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17475539445877075},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/csb.2003.1227429","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227429","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2055243143","https://openalex.org/W2086525401","https://openalex.org/W2006735166","https://openalex.org/W2079327011","https://openalex.org/W2053325634","https://openalex.org/W3178279768","https://openalex.org/W193851735","https://openalex.org/W2773861473","https://openalex.org/W1971903861","https://openalex.org/W3033622206"],"abstract_inverted_index":{"We":[0],"present":[1,145],"a":[2,13,58,146],"computational":[3,128],"protocol":[4,31,129],"for":[5,42,70],"inference":[6,66],"of":[7,21,33,39,61,67,86,88,106,121,133,148,152,161],"regulatory":[8],"and":[9,26,80,101,104,155],"signaling":[10],"pathways":[11,41,69,137],"in":[12,97,138,159],"microbial":[14,43],"cell,":[15],"through":[16],"mining":[17],"\"high-throughput\"":[18],"biological":[19],"data":[20,113],"various":[22],"types,":[23],"literature":[24],"search,":[25],"computer-assisted":[27],"human":[28],"inference.":[29],"This":[30],"consists":[32],"four":[34],"key":[35],"components:":[36],"(a)":[37],"construction":[38,132],"template":[40,77],"genomes":[44],"related":[45],"to":[46,92,130],"the":[47,71,76,89,98,107,119,131,134,149,162],"target":[48,68,72,81,90],"genome,":[49,73],"which":[50],"have":[51,125],"either":[52],"been":[53],"thoroughly":[54],"studied":[55],"or":[56,114],"had":[57],"significant":[59],"amount":[60],"relevant":[62],"experimental":[63,112],"data,":[64],"(b)":[65],"by":[74],"combining":[75],"pathway":[78,99,108,154],"models":[79,109],"genome-specific":[82],"information,":[83],"(c)":[84],"assignment":[85],"genes":[87],"genome":[91],"each":[93],"individual":[94],"functional":[95],"roles":[96],"model,":[100],"(d)":[102],"validation":[103],"refinement":[105],"using":[110],"pathway-specific":[111],"other":[115],"information.":[116],"To":[117],"demonstrate":[118],"effectiveness":[120],"this":[122,127,142,153],"procedure,":[123],"we":[124,144],"applied":[126],"phosphorus":[135],"assimilation":[136],"synechococcus":[139],"WH8102.":[140],"In":[141],"paper,":[143],"model":[147],"core":[150],"component":[151],"provide":[156],"our":[157],"justification":[158],"support":[160],"predicted":[163],"model.":[164]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
