{"id":"https://openalex.org/W2166990188","doi":"https://doi.org/10.1186/1752-0509-4-142","title":"Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects","display_name":"Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects","publication_year":2010,"publication_date":"2010-10-24","ids":{"openalex":"https://openalex.org/W2166990188","doi":"https://doi.org/10.1186/1752-0509-4-142","mag":"2166990188","pmid":"https://pubmed.ncbi.nlm.nih.gov/20969803"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-4-142","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-142","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-142","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-142","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081010556","display_name":"Jacqueline M. Dresch","orcid":"https://orcid.org/0000-0001-7626-4959"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacqueline M Dresch","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA","Department of Mathematics, Michigan State University, East Lansing, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Mathematics, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050915170","display_name":"Xiaozhou Liu","orcid":"https://orcid.org/0000-0003-1923-3026"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaozhou Liu","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077344420","display_name":"David N. Arnosti","orcid":"https://orcid.org/0000-0003-0983-6982"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David N Arnosti","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033580922","display_name":"Ahmet Ay","orcid":"https://orcid.org/0000-0002-0726-5461"},"institutions":[{"id":"https://openalex.org/I39660569","display_name":"Colgate University","ror":"https://ror.org/05d23ve83","country_code":"US","type":"education","lineage":["https://openalex.org/I39660569"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ahmet Ay","raw_affiliation_strings":["Department of Biology, Colgate University, Hamilton, NY, USA","Department of Mathematics, Colgate University, Hamilton, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Colgate University, Hamilton, NY, USA","institution_ids":["https://openalex.org/I39660569"]},{"raw_affiliation_string":"Department of Mathematics, Colgate University, Hamilton, NY, USA","institution_ids":["https://openalex.org/I39660569"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5033580922"],"corresponding_institution_ids":["https://openalex.org/I39660569"],"apc_list":null,"apc_paid":null,"fwci":2.858,"has_fulltext":true,"cited_by_count":52,"citation_normalized_percentile":{"value":0.91121495,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"4","issue":"1","first_page":"142","last_page":"142"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.8461999893188477,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.8461999893188477,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0917000025510788,"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":0.014499999582767487,"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/cooperativity","display_name":"Cooperativity","score":0.8665429353713989},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.6509482264518738},{"id":"https://openalex.org/keywords/repressor","display_name":"Repressor","score":0.5972062349319458},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.5207388401031494},{"id":"https://openalex.org/keywords/activator","display_name":"Activator (genetics)","score":0.49480074644088745},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.48702698945999146},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.45179250836372375},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4501386880874634},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44105294346809387},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.4262765944004059},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.4168154299259186},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.39246076345443726},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3196718096733093},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2593153715133667},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2441369891166687}],"concepts":[{"id":"https://openalex.org/C166014724","wikidata":"https://www.wikidata.org/wiki/Q337217","display_name":"Cooperativity","level":2,"score":0.8665429353713989},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.6509482264518738},{"id":"https://openalex.org/C158448853","wikidata":"https://www.wikidata.org/wiki/Q425218","display_name":"Repressor","level":4,"score":0.5972062349319458},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5207388401031494},{"id":"https://openalex.org/C88045685","wikidata":"https://www.wikidata.org/wiki/Q174576","display_name":"Activator (genetics)","level":3,"score":0.49480074644088745},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.48702698945999146},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.45179250836372375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4501386880874634},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44105294346809387},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.4262765944004059},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.4168154299259186},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.39246076345443726},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3196718096733093},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2593153715133667},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2441369891166687},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/1752-0509-4-142","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-142","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-142","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:20969803","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20969803","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:commons.clarku.edu:faculty_biology-1130","is_oa":true,"landing_page_url":"https://commons.clarku.edu/faculty_biology/130","pdf_url":null,"source":{"id":"https://openalex.org/S4377196688","display_name":"Clark Digital Commons (Clark University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I130785548","host_organization_name":"Clark University","host_organization_lineage":["https://openalex.org/I130785548"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Biology","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:fe767d27f7e247d9adf26fa8f055cd04","is_oa":false,"landing_page_url":"https://doaj.org/article/fe767d27f7e247d9adf26fa8f055cd04","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"BMC Systems Biology, Vol 4, Iss 1, p 142 (2010)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt0qs4659j","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/0qs4659j","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, vol 4, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2987881","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2987881","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"},{"id":"pmh:qt0qs4659j","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/0qs4659j","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Dresch, Jacqueline M; Liu, Xiaozhou; Arnosti, David N; & Ay, Ahmet. (2010). Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects. BMC Systems Biology, 4(1), 142. doi: http://dx.doi.org/10.1186/1752-0509-4-142. Retrieved from: http://www.escholarship.org/uc/item/0qs4659j","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-4-142","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-142","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-142","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4351271309","display_name":null,"funder_award_id":"GM56976","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320320298","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33"},{"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/W2166990188.pdf","grobid_xml":"https://content.openalex.org/works/W2166990188.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1619644015","https://openalex.org/W1623155147","https://openalex.org/W1976760416","https://openalex.org/W1977055260","https://openalex.org/W1980253661","https://openalex.org/W1981184720","https://openalex.org/W1986683530","https://openalex.org/W1991138583","https://openalex.org/W2017615592","https://openalex.org/W2022851401","https://openalex.org/W2027946350","https://openalex.org/W2041966847","https://openalex.org/W2043564369","https://openalex.org/W2044278781","https://openalex.org/W2048013262","https://openalex.org/W2051603199","https://openalex.org/W2060833676","https://openalex.org/W2075861065","https://openalex.org/W2086412406","https://openalex.org/W2086453622","https://openalex.org/W2089520569","https://openalex.org/W2090943376","https://openalex.org/W2095809934","https://openalex.org/W2103838923","https://openalex.org/W2137300432","https://openalex.org/W2138766682","https://openalex.org/W2151868609","https://openalex.org/W2152803686","https://openalex.org/W2154615478","https://openalex.org/W2161304688","https://openalex.org/W2167193572","https://openalex.org/W2286663840","https://openalex.org/W4241793634","https://openalex.org/W4254733679"],"related_works":["https://openalex.org/W1893155809","https://openalex.org/W2082929826","https://openalex.org/W1967829049","https://openalex.org/W3100859731","https://openalex.org/W2157865104","https://openalex.org/W2166977752","https://openalex.org/W2140908476","https://openalex.org/W87952807","https://openalex.org/W3208125806","https://openalex.org/W4253640260"],"abstract_inverted_index":{"BACKGROUND:":[0],"Quantitative":[1],"models":[2,133],"of":[3,25,50,68,78,88,138,177,230,258,272,280],"gene":[4,98],"expression":[5],"generate":[6],"parameter":[7,47,101,116,209,274,281],"values":[8,102,147,155,275],"that":[9,143,187,189,205,211,223],"can":[10,283],"shed":[11],"light":[12],"on":[13,85,164,197],"biological":[14,70,172,259,297],"features":[15],"such":[16,31],"as":[17,218,237,239],"transcription":[18],"factor":[19],"activity,":[20],"cooperativity,":[21],"and":[22,125,161,174,256],"local":[23,124],"effects":[24,173],"repressors.":[26],"An":[27],"important":[28],"element":[29],"in":[30,46,118,144,266,296],"investigations":[32],"is":[33],"sensitivity":[34,52,63,117,127,137,250],"analysis,":[35],"which":[36,91],"determines":[37],"how":[38,290],"strongly":[39],"a":[40,76,182],"model's":[41],"output":[42],"reacts":[43],"to":[44,59,96,115,129,134,192,252,268,288],"variations":[45],"values.":[48],"Parameters":[49],"low":[51],"may":[53,64,74,234],"not":[54,213,235],"be":[55,75,236,294],"accurately":[56],"estimated,":[57],"leading":[58],"unwarranted":[60],"conclusions.":[61],"Low":[62],"reflect":[65],"the":[66,69,79,86,136,175,178,194,215,219,227,247,270,285],"nature":[67],"data,":[71],"or":[72],"it":[73],"result":[77],"model":[80,254],"structure.":[81],"Here,":[82],"we":[83,185],"focus":[84],"analysis":[87,251],"thermodynamic":[89,277],"models,":[90],"have":[92,103],"been":[93,104,113],"used":[94,261],"extensively":[95],"analyze":[97],"transcription.":[99],"Extracted":[100],"interpreted":[105,295],"biologically,":[106],"but":[107],"until":[108],"now":[109],"little":[110],"attention":[111],"has":[112],"given":[114],"this":[119],"context.":[120],"RESULTS:":[121],"We":[122,141,203],"apply":[123],"global":[126],"analyses":[128],"two":[130,228],"recent":[131],"transcriptional":[132,231,264],"determine":[135,269,289],"individual":[139],"parameters.":[140],"show":[142,204],"one":[145],"case,":[146,184],"for":[148,156,249,262,276],"repressor":[149],"efficiencies":[150],"are":[151,159,200,207],"very":[152],"sensitive,":[153],"while":[154],"protein":[157],"cooperativities":[158],"not,":[160],"provide":[162,284],"insights":[163],"why":[165],"these":[166],"differential":[167],"sensitivities":[168,282],"stem":[169],"from":[170],"both":[171],"structure":[176],"applied":[179],"models.":[180,278],"In":[181],"second":[183],"demonstrate":[186],"parameters":[188],"were":[190],"thought":[191],"prove":[193],"system's":[195],"dependence":[196],"activator-activator":[198],"cooperativity":[199],"relatively":[201],"insensitive.":[202],"there":[206],"numerous":[208],"sets":[210],"do":[212],"satisfy":[214],"relationships":[216],"proferred":[217],"optimal":[220],"solutions,":[221],"indicating":[222],"structural":[224],"differences":[225],"between":[226],"types":[229],"enhancers":[232],"analyzed":[233],"simple":[238],"altered":[240],"activator":[241],"cooperativity.":[242],"CONCLUSIONS:":[243],"Our":[244],"results":[245,292],"emphasize":[246],"need":[248],"examine":[253],"construction":[255],"forms":[257],"data":[260],"modeling":[263,291],"processes,":[265],"order":[267],"significance":[271],"estimated":[273],"Knowledge":[279],"necessary":[286],"context":[287],"should":[293],"systems.":[298]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":9}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}