{"id":"https://openalex.org/W1877452576","doi":"https://doi.org/10.23919/ecc.2013.6669756","title":"Stochastic simulation of enzymatic reactions under transcriptional feedback regulation","display_name":"Stochastic simulation of enzymatic reactions under transcriptional feedback regulation","publication_year":2013,"publication_date":"2013-07-01","ids":{"openalex":"https://openalex.org/W1877452576","doi":"https://doi.org/10.23919/ecc.2013.6669756","mag":"1877452576"},"language":"en","primary_location":{"id":"doi:10.23919/ecc.2013.6669756","is_oa":false,"landing_page_url":"https://doi.org/10.23919/ecc.2013.6669756","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 European Control Conference (ECC)","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/A5049621342","display_name":"Jean\u2010Baptiste Lugagne","orcid":"https://orcid.org/0000-0002-8374-6590"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en informatique et en automatique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Jean-Baptiste Lugagne","raw_affiliation_strings":["INRIA Paris-Rocquencourt, France","INRIA, Paris-Rocquencourt, Le Chesnay, France"],"affiliations":[{"raw_affiliation_string":"INRIA Paris-Rocquencourt, France","institution_ids":["https://openalex.org/I1326498283"]},{"raw_affiliation_string":"INRIA, Paris-Rocquencourt, Le Chesnay, France","institution_ids":["https://openalex.org/I1326498283"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016017194","display_name":"Diego A. Oyarz\u00fan","orcid":"https://orcid.org/0000-0002-0381-5278"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Diego A. Oyarzun","raw_affiliation_strings":["Department of Bioengineering, Imperial College London, UK","Dept. of Bioeng., Imperial Coll. London, London, , UK"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Imperial College London, UK","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Dept. of Bioeng., Imperial Coll. London, London, , UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086007559","display_name":"Guy\u2010Bart Stan","orcid":"https://orcid.org/0000-0002-5560-902X"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Guy-Bart V. Stan","raw_affiliation_strings":["Department of Bioengineering, Imperial College London, UK","Dept. of Bioeng., Imperial Coll. London, London, , UK"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Imperial College London, UK","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Dept. of Bioeng., Imperial Coll. London, London, , UK","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5049621342"],"corresponding_institution_ids":["https://openalex.org/I1326498283"],"apc_list":null,"apc_paid":null,"fwci":0.1497,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.55276253,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"3646","last_page":"3651"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9980999827384949,"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":0.9926999807357788,"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/computer-science","display_name":"Computer science","score":0.5394287109375},{"id":"https://openalex.org/keywords/stochastic-process","display_name":"Stochastic process","score":0.5284250378608704},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.5106320977210999},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"Stochastic simulation","score":0.4804506003856659},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.44950640201568604},{"id":"https://openalex.org/keywords/markov-process","display_name":"Markov process","score":0.44899338483810425},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4113960564136505},{"id":"https://openalex.org/keywords/control-theory","display_name":"Control theory (sociology)","score":0.3849722146987915},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23446622490882874},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10997647047042847},{"id":"https://openalex.org/keywords/control","display_name":"Control (management)","score":0.10821318626403809},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.08965197205543518}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5394287109375},{"id":"https://openalex.org/C8272713","wikidata":"https://www.wikidata.org/wiki/Q176737","display_name":"Stochastic process","level":2,"score":0.5284250378608704},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.5106320977210999},{"id":"https://openalex.org/C25915931","wikidata":"https://www.wikidata.org/wiki/Q4180825","display_name":"Stochastic simulation","level":2,"score":0.4804506003856659},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.44950640201568604},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.44899338483810425},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4113960564136505},{"id":"https://openalex.org/C47446073","wikidata":"https://www.wikidata.org/wiki/Q5165890","display_name":"Control theory (sociology)","level":3,"score":0.3849722146987915},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23446622490882874},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10997647047042847},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.10821318626403809},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.08965197205543518},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.23919/ecc.2013.6669756","is_oa":false,"landing_page_url":"https://doi.org/10.23919/ecc.2013.6669756","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 European Control Conference (ECC)","raw_type":"proceedings-article"},{"id":"pmh:oai:HAL:hal-00935727v1","is_oa":false,"landing_page_url":"https://inria.hal.science/hal-00935727","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"European Control Conference (ECC), Jul 2013, Zurich, Switzerland. pp.3646-3651","raw_type":"Conference papers"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7200000286102295,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1509581155","https://openalex.org/W1966507944","https://openalex.org/W1988791304","https://openalex.org/W2009026991","https://openalex.org/W2009163705","https://openalex.org/W2016337236","https://openalex.org/W2032619610","https://openalex.org/W2053240640","https://openalex.org/W2073265884","https://openalex.org/W2073554905","https://openalex.org/W2107342968","https://openalex.org/W2122121413","https://openalex.org/W2127535453","https://openalex.org/W2155418451","https://openalex.org/W2164200677","https://openalex.org/W2167900930","https://openalex.org/W2168221215","https://openalex.org/W2171280873"],"related_works":["https://openalex.org/W2379651310","https://openalex.org/W2113019827","https://openalex.org/W1541249122","https://openalex.org/W2413828414","https://openalex.org/W2367222340","https://openalex.org/W1567439243","https://openalex.org/W1993731165","https://openalex.org/W2016787741","https://openalex.org/W2095860056","https://openalex.org/W2034420270"],"abstract_inverted_index":{"The":[0,161],"interaction":[1],"between":[2],"gene":[3,28],"expression":[4,29],"and":[5,58,139],"metabolism":[6],"is":[7,30,62],"a":[8,59,80,120,143],"form":[9],"of":[10,37,43,94,113,133,136,153,158,173,179,189,200],"feedback":[11,39,105],"control":[12],"that":[13,68,109,193],"allows":[14],"cells":[15],"to":[16,23,45,63,90,99,142,156,167],"up-":[17],"or":[18,198],"downregulate":[19],"specific":[20],"reactions":[21],"according":[22],"the":[24,35,41,46,85,95,111,116,130,134,137,151,154,170,174,184,187,190,196],"environmental":[25],"conditions.":[26],"Although":[27],"an":[31,100],"inherently":[32],"stochastic":[33,65],"process,":[34],"effect":[36],"genetic":[38,104,201],"on":[40,84],"propagation":[42],"noise":[44,202],"metabolic":[47],"layer":[48],"remains":[49],"largely":[50],"unexplored.":[51],"These":[52],"systems":[53],"operate":[54],"in":[55,74,110,146,203],"two":[56],"timescales,":[57],"major":[60],"challenge":[61],"devise":[64],"simulation":[66,81,132],"techniques":[67],"can":[69,128,164,194],"cope":[70],"with":[71],"this":[72,125],"stiffness":[73],"reasonable":[75],"computational":[76,147],"time.":[77],"We":[78,107,149],"propose":[79],"technique,":[82],"based":[83],"slow-scale":[86],"Stochastic":[87],"Simulation":[88],"Algorithm,":[89],"rapidly":[91],"compute":[92,169],"realizations":[93],"Markov":[96],"process":[97],"associated":[98],"enzymatic":[101,159,204],"reaction":[102],"under":[103],"regulation.":[106],"show":[108],"case":[112],"constant":[114],"substrate,":[115,140],"enzyme-substrate":[117],"complexes":[118],"have":[119],"binomial":[121],"stationary":[122,171],"distribution.":[123],"With":[124],"result":[126],"we":[127],"avoid":[129],"explicit":[131],"binding/dissociation":[135],"enzyme":[138],"leading":[141],"significant":[144],"improvement":[145],"speed.":[148],"discuss":[150],"extension":[152],"algorithm":[155],"networks":[157],"reactions.":[160,205],"proposed":[162],"method":[163],"be":[165],"used":[166],"systematically":[168],"distributions":[172],"species":[175],"for":[176,186],"different":[177],"combinations":[178],"model":[180],"parameters,":[181],"thus":[182],"opening":[183],"way":[185],"identification":[188],"cellular":[191],"processes":[192],"modulate":[195],"amplification":[197],"attenuation":[199]},"counts_by_year":[{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
