{"id":"https://openalex.org/W2158462678","doi":"https://doi.org/10.5075/epfl-thesis-5088","title":"Propagation Models for Biochemical Reaction Networks","display_name":"Propagation Models for Biochemical Reaction Networks","publication_year":2011,"publication_date":"2011-01-01","ids":{"openalex":"https://openalex.org/W2158462678","doi":"https://doi.org/10.5075/epfl-thesis-5088","mag":"2158462678"},"language":"en","primary_location":{"id":"pmh:oai:infoscience.tind.io:165774","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/165774","pdf_url":"http://infoscience.epfl.ch/record/165774","source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"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":"http://infoscience.epfl.ch/record/165774","raw_type":"Text"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://infoscience.epfl.ch/record/165774","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031958902","display_name":"Maria-Emanuela-Canini Mateescu","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Mateescu, Maria-Emanuela-Canini","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5031958902"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"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":0.9998999834060669,"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":0.9973999857902527,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9842000007629395,"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/ordinary-differential-equation","display_name":"Ordinary differential equation","score":0.6522171497344971},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.5794517397880554},{"id":"https://openalex.org/keywords/ode","display_name":"Ode","score":0.5675488114356995},{"id":"https://openalex.org/keywords/continuous-time-markov-chain","display_name":"Continuous-time Markov chain","score":0.5626972913742065},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.5597584843635559},{"id":"https://openalex.org/keywords/master-equation","display_name":"Master equation","score":0.5438719987869263},{"id":"https://openalex.org/keywords/differential-equation","display_name":"Differential equation","score":0.5152247548103333},{"id":"https://openalex.org/keywords/markov-process","display_name":"Markov process","score":0.4569987654685974},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.4431424140930176},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.39085882902145386},{"id":"https://openalex.org/keywords/markov-model","display_name":"Markov model","score":0.34578973054885864},{"id":"https://openalex.org/keywords/balance-equation","display_name":"Balance equation","score":0.30861419439315796},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.26363715529441833},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13080361485481262}],"concepts":[{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.6522171497344971},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5794517397880554},{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.5675488114356995},{"id":"https://openalex.org/C147080032","wikidata":"https://www.wikidata.org/wiki/Q176720","display_name":"Continuous-time Markov chain","level":5,"score":0.5626972913742065},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.5597584843635559},{"id":"https://openalex.org/C128805008","wikidata":"https://www.wikidata.org/wiki/Q722878","display_name":"Master equation","level":3,"score":0.5438719987869263},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.5152247548103333},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.4569987654685974},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.4431424140930176},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.39085882902145386},{"id":"https://openalex.org/C163836022","wikidata":"https://www.wikidata.org/wiki/Q6771326","display_name":"Markov model","level":3,"score":0.34578973054885864},{"id":"https://openalex.org/C158917313","wikidata":"https://www.wikidata.org/wiki/Q4849964","display_name":"Balance equation","level":4,"score":0.30861419439315796},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.26363715529441833},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13080361485481262},{"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/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:infoscience.tind.io:165774","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/165774","pdf_url":"http://infoscience.epfl.ch/record/165774","source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"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":"http://infoscience.epfl.ch/record/165774","raw_type":"Text"},{"id":"doi:10.5075/epfl-thesis-5088","is_oa":true,"landing_page_url":"https://doi.org/10.5075/epfl-thesis-5088","pdf_url":null,"source":{"id":"https://openalex.org/S4306400488","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"thesis"},{"id":"mag:2158462678","is_oa":false,"landing_page_url":"https://infoscience.epfl.ch/record/165774","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:infoscience.tind.io:165774","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/165774","pdf_url":"http://infoscience.epfl.ch/record/165774","source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"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":"http://infoscience.epfl.ch/record/165774","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.4000000059604645,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2158462678.pdf","grobid_xml":"https://content.openalex.org/works/W2158462678.grobid-xml"},"referenced_works_count":105,"referenced_works":["https://openalex.org/W11463020","https://openalex.org/W176066871","https://openalex.org/W280723784","https://openalex.org/W1266757872","https://openalex.org/W1502788968","https://openalex.org/W1509923322","https://openalex.org/W1513249631","https://openalex.org/W1513764144","https://openalex.org/W1514324734","https://openalex.org/W1519577127","https://openalex.org/W1525935082","https://openalex.org/W1534618379","https://openalex.org/W1535517661","https://openalex.org/W1568755071","https://openalex.org/W1575619134","https://openalex.org/W1583191255","https://openalex.org/W1591559721","https://openalex.org/W1592379908","https://openalex.org/W1623281517","https://openalex.org/W1725290782","https://openalex.org/W1806344101","https://openalex.org/W1946177469","https://openalex.org/W1961672089","https://openalex.org/W1966963894","https://openalex.org/W1974855260","https://openalex.org/W1976443948","https://openalex.org/W1978319180","https://openalex.org/W1978329448","https://openalex.org/W1983350265","https://openalex.org/W1984121732","https://openalex.org/W1986669897","https://openalex.org/W1988791304","https://openalex.org/W1991263093","https://openalex.org/W1996377517","https://openalex.org/W1999836359","https://openalex.org/W2002083262","https://openalex.org/W2002184237","https://openalex.org/W2003058193","https://openalex.org/W2008206597","https://openalex.org/W2010309395","https://openalex.org/W2011432832","https://openalex.org/W2011951852","https://openalex.org/W2012482128","https://openalex.org/W2014550367","https://openalex.org/W2018435536","https://openalex.org/W2019768978","https://openalex.org/W2028916057","https://openalex.org/W2031470941","https://openalex.org/W2040258732","https://openalex.org/W2043785977","https://openalex.org/W2043896870","https://openalex.org/W2044784465","https://openalex.org/W2045762009","https://openalex.org/W2057602562","https://openalex.org/W2059053384","https://openalex.org/W2062856462","https://openalex.org/W2065219357","https://openalex.org/W2065952296","https://openalex.org/W2066210260","https://openalex.org/W2066440682","https://openalex.org/W2066594542","https://openalex.org/W2067136705","https://openalex.org/W2067398978","https://openalex.org/W2067463757","https://openalex.org/W2069596643","https://openalex.org/W2074401358","https://openalex.org/W2084924279","https://openalex.org/W2085061065","https://openalex.org/W2090311494","https://openalex.org/W2096610849","https://openalex.org/W2102653059","https://openalex.org/W2102787760","https://openalex.org/W2106565812","https://openalex.org/W2108208689","https://openalex.org/W2108210068","https://openalex.org/W2114738666","https://openalex.org/W2121523192","https://openalex.org/W2121777611","https://openalex.org/W2122510266","https://openalex.org/W2130727150","https://openalex.org/W2134759932","https://openalex.org/W2137088684","https://openalex.org/W2139324000","https://openalex.org/W2141803002","https://openalex.org/W2149827235","https://openalex.org/W2152221608","https://openalex.org/W2155007800","https://openalex.org/W2155418451","https://openalex.org/W2157239333","https://openalex.org/W2164096878","https://openalex.org/W2167246417","https://openalex.org/W2169677553","https://openalex.org/W2171280873","https://openalex.org/W2171720907","https://openalex.org/W2172755394","https://openalex.org/W2183172051","https://openalex.org/W2268548990","https://openalex.org/W2492760372","https://openalex.org/W2585424667","https://openalex.org/W2622039200","https://openalex.org/W2751862591","https://openalex.org/W2912904668","https://openalex.org/W2952167521","https://openalex.org/W2964749875","https://openalex.org/W3026026050"],"related_works":["https://openalex.org/W2066594542","https://openalex.org/W2149827235","https://openalex.org/W1862398452","https://openalex.org/W1516256348","https://openalex.org/W2239197073","https://openalex.org/W2480793383","https://openalex.org/W2889466991","https://openalex.org/W2585429805","https://openalex.org/W3212811990","https://openalex.org/W3100321310","https://openalex.org/W3205880914","https://openalex.org/W2226209033","https://openalex.org/W1956206657","https://openalex.org/W3206786992","https://openalex.org/W3135032925","https://openalex.org/W3102716280","https://openalex.org/W34472511","https://openalex.org/W2999850070","https://openalex.org/W2977480662","https://openalex.org/W9075488"],"abstract_inverted_index":{"In":[0,206,299],"this":[1,162,241],"thesis":[2],"we":[3,155,282,292,306,354,436],"investigate":[4],"different":[5],"ways":[6],"of":[7,11,22,31,43,49,68,74,79,133,137,147,161,236,247,295,303,316,324,371,385,395,427,433],"approximating":[8],"the":[9,12,27,40,47,72,77,80,119,130,143,158,207,210,217,234,237,245,248,271,275,300,313,325,357,360,365,372,379,386,393,396,402,424,428,438,449,454],"solution":[10,67],"chemical":[13,238,249],"master":[14,239,250],"equation":[15,114,243,251],"(CME).":[16],"The":[17,65],"CME":[18,70],"is":[19,62,71,212,221,244,256,331],"a":[20,50,55,69,85,151,177,186,190,200,224,229,259,409,416],"system":[21,326,373,387],"differential":[23,113,230,242],"equations":[24],"that":[25,53,99,154,281,311,442],"models":[26,149,310,441],"stochastic":[28,308,314,397,410],"transient":[29,66],"behaviour":[30,315],"biochemical":[32,126,317],"reaction":[33,127,318],"networks.":[34],"It":[35],"does":[36,341],"so":[37],"by":[38,96,228,288,320],"describing":[39],"time":[41,87],"evolution":[42],"probability":[44,204,254],"distribution":[45],"over":[46,76],"states":[48,78],"Markov":[51,82,104],"chain":[52,83],"represents":[54],"biological":[56],"network,":[57],"and":[58,90,110,176,274,286,400,415],"thus":[59,287],"its":[60],"stochasticity":[61,340],"only":[63,445],"implicit.":[64],"vector":[73],"probabilities":[75,446],"corresponding":[81,439],"at":[84],"certain":[86],"point":[88],"t,":[89],"it":[91,220],"has":[92,168],"traditionally":[93],"been":[94],"obtained":[95],"applying":[97],"methods":[98,268,297],"are":[100,129,140],"general":[101,111,145],"to":[102,198,359],"continuous-time":[103,218],"chains:":[105],"uniformization,":[106],"Krylov":[107],"subspace":[108],"methods,":[109],"ordinary":[112],"(ODE)":[115],"solvers":[116],"such":[117,269,350],"as":[118,270],"fourth":[120,276],"order":[121,197,277],"Runge-Kutta":[122,278],"method.":[123],"Even":[124],"though":[125],"networks":[128,319],"main":[131],"application":[132],"our":[134,138,304],"work,":[135],"some":[136,322,369,383],"results":[139],"presented":[141],"in":[142,157,174,180,196,216,223,233],"more":[144],"framework":[146],"propagation":[148,165,171,183,211,264,290,440],"(PM),":[150],"computational":[152],"formalism":[153],"introduce":[156,355],"first":[159,366],"part":[160,302,411,418],"thesis.":[163],"Each":[164],"model":[166,199],"N":[167,202],"two":[169],"associated":[170],"processes,":[172],"one":[173,179,367,381],"discrete-time":[175,208],"second":[178,301,380],"continuous-time.":[181],"These":[182],"processes":[184,265],"propagate":[185,443],"generic":[187],"mass":[188,255],"through":[189,258],"discrete":[191,260],"state":[192,261],"space.":[193,262],"For":[194,431],"example,":[195],"CME,":[201],"propagates":[203],"mass.":[205],"case":[209,219,235],"done":[213,222,332],"step-wise,":[214],"while":[215,422],"continuous":[225,451],"flow":[226],"defined":[227],"equation.":[231],"Again,":[232],"equation,":[240],"equivalent":[246],"itself":[252],"where":[253],"propagated":[257],"Discrete-time":[263],"can":[266],"encode":[267],"uniformization":[272],"method":[273,280],"integration":[279],"have":[283],"mentioned":[284],"above,":[285],"optimizing":[289],"algorithms":[291,435],"optimize":[293],"both":[294],"these":[296,434],"simultaneously.":[298],"thesis,":[305],"define":[307],"hybrid":[309,351],"approximate":[312],"treating":[321],"variables":[323,370,384],"deterministically.":[327],"This":[328],"deterministic":[329,417,429,455],"approximation":[330],"for":[333,338,453],"species":[334],"with":[335,374,388],"large":[336],"populations,":[337],"which":[339,353],"not":[342,444],"play":[343],"an":[344],"important":[345],"role.":[346],"We":[347],"propose":[348],"three":[349],"models,":[352],"from":[356],"coarsest":[358],"most":[361],"refined":[362],"one:":[363],"(i)":[364],"replaces":[368,382],"their":[375,389],"overall":[376],"expectations,":[377],"(ii)":[378],"expectations":[390],"conditioned":[391],"on":[392],"values":[394],"variables,":[398],"(iii)":[399],"finally,":[401],"third":[403],"one,":[404],"splits":[405],"each":[406,432],"variable":[407],"into":[408],"(for":[412,419],"low":[413],"valuations)":[414],"high":[420],"valuations),":[421],"tracking":[423],"conditional":[425],"expectation":[426],"part.":[430],"give":[437],"but":[447],"also":[448],"respective":[450],"approximations":[452],"variables.":[456]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2025-10-10T00:00:00"}
