{"id":"https://openalex.org/W1427970225","doi":"https://doi.org/10.3233/isb-150465","title":"A simple model for Lutz and Bujard\u2019s controllable promoters and its application for analyzing a simple genetic oscillator","display_name":"A simple model for Lutz and Bujard\u2019s controllable promoters and its application for analyzing a simple genetic oscillator","publication_year":2015,"publication_date":"2015-07-03","ids":{"openalex":"https://openalex.org/W1427970225","doi":"https://doi.org/10.3233/isb-150465","mag":"1427970225","pmid":"https://pubmed.ncbi.nlm.nih.gov/25720352"},"language":"en","primary_location":{"id":"doi:10.3233/isb-150465","is_oa":true,"landing_page_url":"https://doi.org/10.3233/isb-150465","pdf_url":"https://content.iospress.com:443/download/in-silico-biology/isb465?id=in-silico-biology%2Fisb465","source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"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":"In Silico Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://content.iospress.com:443/download/in-silico-biology/isb465?id=in-silico-biology%2Fisb465","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057609825","display_name":"CG Zamora-Chimal","orcid":null},"institutions":[{"id":"https://openalex.org/I4210138439","display_name":"Centro de Investigaci\u00f3n en Materiales Avanzados","ror":"https://ror.org/03h954e30","country_code":"MX","type":"facility","lineage":["https://openalex.org/I4210138439"]},{"id":"https://openalex.org/I59361560","display_name":"Instituto Polit\u00e9cnico Nacional","ror":"https://ror.org/059sp8j34","country_code":"MX","type":"education","lineage":["https://openalex.org/I59361560"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"CG Zamora-Chimal","raw_affiliation_strings":["Centro de Investigaci\u00f3n y de Estudios Avanzados del IPN, Unidad Monterrey, Parque de Investigaci\u00f3n e Innovaci\u00f3n Tecnol\u00f3gica, Apodaca NL, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro de Investigaci\u00f3n y de Estudios Avanzados del IPN, Unidad Monterrey, Parque de Investigaci\u00f3n e Innovaci\u00f3n Tecnol\u00f3gica, Apodaca NL, M\u00e9xico","institution_ids":["https://openalex.org/I59361560","https://openalex.org/I4210138439"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109841714","display_name":"E. S. Zeron","orcid":null},"institutions":[{"id":"https://openalex.org/I59361560","display_name":"Instituto Polit\u00e9cnico Nacional","ror":"https://ror.org/059sp8j34","country_code":"MX","type":"education","lineage":["https://openalex.org/I59361560"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"ES Zeron","raw_affiliation_strings":["Centro de Investigaci\u00f3n y de Estudios Avanzados del IPN, Departamento de Matem\u00e1ticas, Av. Instituto Polit\u00e9cnico Nacional M\u00e9xico DF, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro de Investigaci\u00f3n y de Estudios Avanzados del IPN, Departamento de Matem\u00e1ticas, Av. Instituto Polit\u00e9cnico Nacional M\u00e9xico DF, M\u00e9xico","institution_ids":["https://openalex.org/I59361560"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5109841714"],"corresponding_institution_ids":["https://openalex.org/I59361560"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.016287,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"12","issue":"1-2","first_page":"69","last_page":"82"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9943000078201294,"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":0.9864000082015991,"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/cooperativity","display_name":"Cooperativity","score":0.7202051281929016},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.5809938907623291},{"id":"https://openalex.org/keywords/lac-repressor","display_name":"Lac repressor","score":0.5414488315582275},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.48175692558288574},{"id":"https://openalex.org/keywords/repressor","display_name":"Repressor","score":0.47602468729019165},{"id":"https://openalex.org/keywords/psychological-repression","display_name":"Psychological repression","score":0.46921172738075256},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.38751015067100525},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3286043405532837},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2600992023944855},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2520500421524048},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.16917520761489868}],"concepts":[{"id":"https://openalex.org/C166014724","wikidata":"https://www.wikidata.org/wiki/Q337217","display_name":"Cooperativity","level":2,"score":0.7202051281929016},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.5809938907623291},{"id":"https://openalex.org/C113629113","wikidata":"https://www.wikidata.org/wiki/Q4345509","display_name":"Lac repressor","level":5,"score":0.5414488315582275},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.48175692558288574},{"id":"https://openalex.org/C158448853","wikidata":"https://www.wikidata.org/wiki/Q425218","display_name":"Repressor","level":4,"score":0.47602468729019165},{"id":"https://openalex.org/C186310378","wikidata":"https://www.wikidata.org/wiki/Q941796","display_name":"Psychological repression","level":4,"score":0.46921172738075256},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.38751015067100525},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3286043405532837},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2600992023944855},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2520500421524048},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.16917520761489868},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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":"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":"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":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.3233/isb-150465","is_oa":true,"landing_page_url":"https://doi.org/10.3233/isb-150465","pdf_url":"https://content.iospress.com:443/download/in-silico-biology/isb465?id=in-silico-biology%2Fisb465","source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"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":"In Silico Biology","raw_type":"journal-article"},{"id":"pmid:25720352","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25720352","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":"In silico biology","raw_type":null},{"id":"pmh:oai:europepmc.org:3887862","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4923745","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3233/isb-150465","is_oa":true,"landing_page_url":"https://doi.org/10.3233/isb-150465","pdf_url":"https://content.iospress.com:443/download/in-silico-biology/isb465?id=in-silico-biology%2Fisb465","source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"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":"In Silico Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.6000000238418579}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1427970225.pdf","grobid_xml":"https://content.openalex.org/works/W1427970225.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W456191","https://openalex.org/W1714548","https://openalex.org/W208046272","https://openalex.org/W1498806721","https://openalex.org/W1523595721","https://openalex.org/W1591758727","https://openalex.org/W1603900493","https://openalex.org/W1607751721","https://openalex.org/W1645305843","https://openalex.org/W1974021446","https://openalex.org/W1980879384","https://openalex.org/W1982334966","https://openalex.org/W1985039493","https://openalex.org/W1995514232","https://openalex.org/W2002902680","https://openalex.org/W2003409413","https://openalex.org/W2005535920","https://openalex.org/W2007085003","https://openalex.org/W2021539568","https://openalex.org/W2022064097","https://openalex.org/W2037531165","https://openalex.org/W2039571025","https://openalex.org/W2050482128","https://openalex.org/W2063670296","https://openalex.org/W2122291638","https://openalex.org/W2132828256","https://openalex.org/W2135054636","https://openalex.org/W2146784596","https://openalex.org/W2148641266","https://openalex.org/W2155418451","https://openalex.org/W2160785313","https://openalex.org/W2279626446","https://openalex.org/W4250181240"],"related_works":["https://openalex.org/W2114561860","https://openalex.org/W2071142615","https://openalex.org/W2009504506","https://openalex.org/W2171546080","https://openalex.org/W1531492600","https://openalex.org/W1995183151","https://openalex.org/W1984874903","https://openalex.org/W2121322585","https://openalex.org/W456191","https://openalex.org/W1975202485"],"abstract_inverted_index":{"We":[0,45,162],"develop":[1],"an":[2],"exact":[3],"and":[4,10,59,68,186],"flexible":[5],"mathematical":[6],"model":[7,37,48,166],"for":[8,22,167],"Lutz":[9,58],"Bujard's":[11],"controllable":[12],"promoters.":[13],"It":[14],"can":[15,103,154],"be":[16,104,107,155,158],"used":[17],"as":[18,72,160],"a":[19,173],"building":[20],"block":[21],"modeling":[23],"genetic":[24,175],"systems":[25],"based":[26],"on":[27],"them.":[28],"Special":[29],"attention":[30],"is":[31],"paid":[32],"to":[33,106,147,157,171],"deduce":[34],"all":[35],"the":[36,51,62,66,73,82,97,140,151,165,168],"parameters":[38],"from":[39],"reported":[40],"(in":[41],"vitro)":[42],"experimental":[43],"data.":[44],"validate":[46],"our":[47],"by":[49,57,65,81,116,123,179],"comparing":[50],"regulatory":[52],"ranges":[53,63],"measured":[54,84],"in":[55,127],"vivo":[56],"Bujard":[60],"against":[61],"predicted":[64],"model,":[67],"which":[69],"are":[70,114],"calculated":[71],"reporter":[74],"activity":[75,83],"obtained":[76],"under":[77,85],"inducing":[78],"conditions":[79],"divided":[80],"maximal":[86],"repression.":[87],"In":[88],"particular,":[89],"we":[90,136],"verify":[91],"Bond":[92],"et":[93,181],"al.":[94,182],"assertion":[95],"that":[96,139,142],"cooperativity":[98],"between":[99],"two":[100,143],"lac":[101,125],"operators":[102,149],"assumed":[105,156],"negligible":[108,159],"when":[109],"their":[110],"central":[111],"base":[112],"pairs":[113],"separated":[115],"22":[117],"or":[118],"32":[119],"bp":[120],"[Gene":[121],"repression":[122],"minimal":[124],"loops":[126],"vivo,":[128],"Nucleic":[129],"Acids":[130],"Res,":[131],"38":[132],"(2010)":[133],"8072-8082].":[134],"Moreover,":[135],"also":[137],"find":[138],"probability":[141],"repressors":[144],"LacI":[145],"bind":[146],"these":[148],"at":[150],"same":[152],"time":[153],"well.":[161],"finally":[163],"use":[164],"promoter":[169],"P(LlacO-1)":[170],"analyze":[172],"synthetic":[174,188],"oscillator":[176],"recently":[177],"build":[178],"Stricker":[180],"[A":[183],"fast,":[184],"robust":[185],"tunable":[187],"gene":[189],"oscillator,":[190],"Nature,":[191],"456":[192],"(2008)":[193],"516-519].":[194]},"counts_by_year":[],"updated_date":"2026-06-18T08:10:14.011955","created_date":"2025-10-10T00:00:00"}
