{"id":"https://openalex.org/W3144664798","doi":null,"title":"RULE-BASED MODELING OF TRANSCRIPTIONAL ATTENUATION AT THE TRYPTOPHAN OPERON","display_name":"RULE-BASED MODELING OF TRANSCRIPTIONAL ATTENUATION AT THE TRYPTOPHAN OPERON","publication_year":2014,"publication_date":"2014-01-31","ids":{"openalex":"https://openalex.org/W3144664798","mag":"3144664798"},"language":"en","primary_location":{"id":"pmh:oai:CiteSeerX.psu:10.1.1.416.2052","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.416.2052","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.informs-sim.org/wsc09papers/088.pdf","raw_type":"text"},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"M. D. Rossetti","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2279609970","display_name":"Universit\u00e9 de Lille","ror":"https://ror.org/02kzqn938","country_code":"FR","type":"education","lineage":["https://openalex.org/I2279609970"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"M. D. Rossetti","raw_affiliation_strings":["University of Lille, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Lille, France","institution_ids":["https://openalex.org/I2279609970"]}]},{"author_position":"middle","author":{"id":null,"display_name":"R. R. Hill","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2279609970","display_name":"Universit\u00e9 de Lille","ror":"https://ror.org/02kzqn938","country_code":"FR","type":"education","lineage":["https://openalex.org/I2279609970"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"R. R. Hill","raw_affiliation_strings":["University of Lille, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Lille, France","institution_ids":["https://openalex.org/I2279609970"]}]},{"author_position":"middle","author":{"id":null,"display_name":"B. Johansson","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"B. Johansson","raw_affiliation_strings":["BioComputing group, LIFL & IRI (CNRS UMR 8022 & USR 3078), Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioComputing group, LIFL & IRI (CNRS UMR 8022 & USR 3078), Italy","institution_ids":["https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":null,"display_name":"A. Dunkin","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Dunkin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"R. G. Ingalls","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. G. Ingalls","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084003101","display_name":"C\u00e9line Kuttler","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"C\u00e9line Kuttler","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090587385","display_name":"C\u00e9dric Lhoussaine","orcid":"https://orcid.org/0000-0002-3970-3761","observed_orcids":["https://orcid.org/0000-0002-3970-3761"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"C\u00e9dric Lhoussaine","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5067270597","display_name":"Mirabelle Nebut","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mirabelle Nebut","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2203,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.51354029,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9678000211715698,"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":0.9678000211715698,"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":0.01269999984651804,"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":0.006500000134110451,"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/transcriptional-attenuation","display_name":"transcriptional attenuation","score":0.9909999966621399},{"id":"https://openalex.org/keywords/tryptophan-operon","display_name":"tryptophan operon","score":0.9980000257492065},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.8889999985694885},{"id":"https://openalex.org/keywords/rna-mediated-gene-regulation","display_name":"RNA-mediated gene regulation","score":0.8849999904632568},{"id":"https://openalex.org/keywords/stochastic-modeling","display_name":"stochastic modeling","score":0.4819999933242798},{"id":"https://openalex.org/keywords/rule-based-modeling","display_name":"rule-based models","score":0.7509999871253967},{"id":"https://openalex.org/keywords/chemical-reaction-networks","display_name":"chemical reaction networks","score":0.5920000076293945},{"id":"https://openalex.org/keywords/pi-calculus","display_name":"\u03c0-calculus","score":0.6690000295639038},{"id":"https://openalex.org/keywords/master-equation","display_name":"master equation","score":0.4169999957084656}],"concepts":[{"id":"https://openalex.org/C96601446","wikidata":"https://www.wikidata.org/wiki/Q287043","display_name":"trp operon","level":5,"score":0.8911283612251282},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.7903538942337036},{"id":"https://openalex.org/C184652730","wikidata":"https://www.wikidata.org/wiki/Q2357982","display_name":"Attenuation","level":2,"score":0.601256787776947},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5508284568786621},{"id":"https://openalex.org/C2776706248","wikidata":"https://www.wikidata.org/wiki/Q181003","display_name":"Tryptophan","level":3,"score":0.4869176149368286},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.379438579082489},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.34909963607788086},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27324342727661133},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2331215739250183},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.143854022026062},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.07520681619644165},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.059482425451278687},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.05088752508163452}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:CiteSeerX.psu:10.1.1.416.2052","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.416.2052","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.informs-sim.org/wsc09papers/088.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W323766208","https://openalex.org/W599362336","https://openalex.org/W1495757226","https://openalex.org/W1501525671","https://openalex.org/W1505169662","https://openalex.org/W1535522418","https://openalex.org/W1541434994","https://openalex.org/W1583295953","https://openalex.org/W1587551937","https://openalex.org/W1604669046","https://openalex.org/W1806423210","https://openalex.org/W1849859304","https://openalex.org/W1946177469","https://openalex.org/W1974251842","https://openalex.org/W1983350265","https://openalex.org/W1986649132","https://openalex.org/W1999460219","https://openalex.org/W2007742983","https://openalex.org/W2015557667","https://openalex.org/W2023537137","https://openalex.org/W2025479764","https://openalex.org/W2042321087","https://openalex.org/W2056474690","https://openalex.org/W2064974862","https://openalex.org/W2065219357","https://openalex.org/W2067599724","https://openalex.org/W2069941324","https://openalex.org/W2090900888","https://openalex.org/W2095935008","https://openalex.org/W2108654339","https://openalex.org/W2112642778","https://openalex.org/W2130321031","https://openalex.org/W2131367352","https://openalex.org/W2133158038","https://openalex.org/W2136626795","https://openalex.org/W2139504329","https://openalex.org/W2144063122","https://openalex.org/W2151157246","https://openalex.org/W2151251638","https://openalex.org/W2156569015","https://openalex.org/W2165714871","https://openalex.org/W2169193349","https://openalex.org/W2175715045","https://openalex.org/W2340390498","https://openalex.org/W2500362014","https://openalex.org/W3022982124","https://openalex.org/W4206370914"],"related_works":["https://openalex.org/W7096790848","https://openalex.org/W2102016003","https://openalex.org/W649181662","https://openalex.org/W2000522152","https://openalex.org/W1813061629","https://openalex.org/W6891642658","https://openalex.org/W7095303982","https://openalex.org/W2911346384","https://openalex.org/W2136340808","https://openalex.org/W2095253740"],"abstract_inverted_index":{"Transcriptional":[0],"attenuation":[1],"at":[2],"E.coli\u2019s":[3],"tryptophan":[4],"operon":[5],"is":[6,51,63],"a":[7,19],"prime":[8],"example":[9],"of":[10,23,27,35,73,82,103],"RNA-mediated":[11],"gene":[12],"regulation.":[13],"In":[14],"this":[15],"paper,":[16],"we":[17,91],"present":[18],"discrete":[20],"stochastic":[21],"model":[22,37,78,106],"the":[24,101,118],"fine-grained":[25],"control":[26,102],"attenuation,":[28],"based":[29,116],"on":[30,117],"chemical":[31,74],"reactions.":[32,75],"Stochastic":[33],"simulation":[34],"our":[36,77],"confirms":[38],"results":[39],"that":[40,69],"were":[41],"previously":[42],"obtained":[43],"by":[44],"master":[45,56],"or":[46],"differential":[47],"equations.":[48],"Our":[49,105],"approach":[50],"easier":[52],"to":[53,66,98,124],"understand":[54],"than":[55,87],"equations,":[57],"although":[58],"mathematically":[59],"well":[60],"founded.":[61],"It":[62],"compact":[64],"due":[65],"rule":[67],"schemas":[68],"define":[70],"finite":[71],"sets":[72],"Moreover,":[76],"makes":[79],"intense":[80],"use":[81],"reaction":[83],"rules":[84,95],"with":[85],"more":[86],"two":[88],"reactants.":[89],"As":[90],"show,":[92],"such":[93],"n-ary":[94],"are":[96,122],"essential":[97],"concisely":[99],"capture":[100],"attenuation.":[104],"could":[107],"not":[108],"adequately":[109],"be":[110],"represented":[111],"in":[112],"object-centered":[113],"modeling":[114],"languages":[115],"pi-calculus,":[119],"because":[120],"these":[121],"limited":[123],"binary":[125],"interactions.":[126],"1":[127]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2021-04-13T00:00:00"}
