{"id":"https://openalex.org/W2135816732","doi":"https://doi.org/10.1093/bioinformatics/btp283","title":"Optimizing static thermodynamic models of transcriptional regulation","display_name":"Optimizing static thermodynamic models of transcriptional regulation","publication_year":2009,"publication_date":"2009-04-27","ids":{"openalex":"https://openalex.org/W2135816732","doi":"https://doi.org/10.1093/bioinformatics/btp283","mag":"2135816732","pmid":"https://pubmed.ncbi.nlm.nih.gov/19398449"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp283","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp283","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/13/1640/16887918/btp283.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/13/1640/16887918/btp283.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107979977","display_name":"Denis C. Bauer","orcid":"https://orcid.org/0000-0001-8033-9810"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Denis C. Bauer","raw_affiliation_strings":["Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld. 4072, Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld. 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017222669","display_name":"Timothy L. Bailey","orcid":"https://orcid.org/0000-0002-7018-9342"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Timothy L. Bailey","raw_affiliation_strings":["Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld. 4072, Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld. 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5107979977"],"corresponding_institution_ids":["https://openalex.org/I165143802"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.674,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.70109391,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"25","issue":"13","first_page":"1640","last_page":"1646"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.991599977016449,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.991599977016449,"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":0.9757999777793884,"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/computer-science","display_name":"Computer science","score":0.5547771453857422}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5547771453857422}],"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":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btp283","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp283","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/13/1640/16887918/btp283.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19398449","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19398449","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},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.567.8542","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.567.8542","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2009/04/27/bioinformatics.btp283.full.pdf","raw_type":"text"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:180591","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2732318","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2732318","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp283","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp283","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/13/1640/16887918/btp283.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7040031003","display_name":null,"funder_award_id":"RO-1 RR021692-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135816732.pdf","grobid_xml":"https://content.openalex.org/works/W2135816732.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W64811297","https://openalex.org/W1497256448","https://openalex.org/W1970486372","https://openalex.org/W1975420528","https://openalex.org/W1979591743","https://openalex.org/W1980253661","https://openalex.org/W2013989044","https://openalex.org/W2028582548","https://openalex.org/W2041966847","https://openalex.org/W2075861065","https://openalex.org/W2114061545","https://openalex.org/W2114787995"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"In":[0,83],"this":[1],"study,":[2],"we":[3,85],"evaluate":[4,28],"the":[5,19,55,67,91],"'optimization":[6],"landscape'":[7],"of":[8,11,15,21,24,34,40],"a":[9,22,44,49,72,98,109],"class":[10],"static,":[12],"quantitative":[13],"models":[14],"regulation":[16],"and":[17,48],"explore":[18],"efficiency":[20],"range":[23],"optimization":[25,30,56],"methods.":[26,69,82],"We":[27,52],"eight":[29],"methods:":[31],"two":[32],"variants":[33,39],"simulated":[35],"annealing":[36],"(SA),":[37],"four":[38],"gradient":[41],"descent":[42],"(GD),":[43],"hybrid":[45],"SA/GD":[46],"algorithm":[47],"genetic":[50],"algorithm.":[51],"show":[53],"that":[54],"landscape":[57],"has":[58],"numerous":[59],"local":[60],"optima,":[61],"resulting":[62],"in":[63,104],"poor":[64],"performance":[65],"for":[66],"GD":[68],"SA":[70,107],"with":[71,108],"simple":[73,110],"geometric":[74],"cooling":[75,95,111],"schedule":[76],"performs":[77],"best":[78],"among":[79],"all":[80],"tested":[81],"particular,":[84],"see":[86],"no":[87],"advantage":[88],"to":[89],"using":[90,106],"more":[92],"sophisticated":[93],"'LAM'":[94],"schedule.":[96,112],"Overall,":[97],"good":[99],"approximate":[100],"solution":[101],"is":[102],"achievable":[103],"minutes":[105]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}