{"id":"https://openalex.org/W2151362395","doi":"https://doi.org/10.1093/bioinformatics/btg409","title":"Hybrid simulation of cellular behavior","display_name":"Hybrid simulation of cellular behavior","publication_year":2004,"publication_date":"2004-02-11","ids":{"openalex":"https://openalex.org/W2151362395","doi":"https://doi.org/10.1093/bioinformatics/btg409","mag":"2151362395","pmid":"https://pubmed.ncbi.nlm.nih.gov/14960457"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg409","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg409","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/316/48905193/bioinformatics_20_3_316.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/316/48905193/bioinformatics_20_3_316.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043639364","display_name":"Thomas R. Kiehl","orcid":"https://orcid.org/0000-0002-1559-6391"},"institutions":[{"id":"https://openalex.org/I4210134512","display_name":"GE Global Research (United States)","ror":"https://ror.org/03e06qt98","country_code":"US","type":"company","lineage":["https://openalex.org/I4210134512"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Thomas R. Kiehl","raw_affiliation_strings":["Bioinformatics Laboratory, GE Global Research, 1 Research Circle, Schenectady, NY 12309, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Laboratory, GE Global Research, 1 Research Circle, Schenectady, NY 12309, USA","institution_ids":["https://openalex.org/I4210134512"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009233020","display_name":"R. M. Mattheyses","orcid":null},"institutions":[{"id":"https://openalex.org/I4210134512","display_name":"GE Global Research (United States)","ror":"https://ror.org/03e06qt98","country_code":"US","type":"company","lineage":["https://openalex.org/I4210134512"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert M. Mattheyses","raw_affiliation_strings":["Bioinformatics Laboratory , GE Global Research , 1 Research Circle , Schenectady NY 12309 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Laboratory , GE Global Research , 1 Research Circle , Schenectady NY 12309 , USA","institution_ids":["https://openalex.org/I4210134512"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063870525","display_name":"Melvin K. Simmons","orcid":null},"institutions":[{"id":"https://openalex.org/I4210134512","display_name":"GE Global Research (United States)","ror":"https://ror.org/03e06qt98","country_code":"US","type":"company","lineage":["https://openalex.org/I4210134512"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melvin K. Simmons","raw_affiliation_strings":["Bioinformatics Laboratory , GE Global Research , 1 Research Circle , Schenectady NY 12309 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Laboratory , GE Global Research , 1 Research Circle , Schenectady NY 12309 , USA","institution_ids":["https://openalex.org/I4210134512"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5043639364"],"corresponding_institution_ids":["https://openalex.org/I4210134512"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.5503,"has_fulltext":true,"cited_by_count":125,"citation_normalized_percentile":{"value":0.95569136,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"20","issue":"3","first_page":"316","last_page":"322"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9948999881744385,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9878000020980835,"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/computer-science","display_name":"Computer science","score":0.6984184384346008},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"Stochastic simulation","score":0.6748547554016113},{"id":"https://openalex.org/keywords/synchronizing","display_name":"Synchronizing","score":0.6370129585266113},{"id":"https://openalex.org/keywords/hybrid-system","display_name":"Hybrid system","score":0.52232426404953},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.5124338269233704},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.4648856818675995},{"id":"https://openalex.org/keywords/discrete-event-simulation","display_name":"Discrete event simulation","score":0.46055543422698975},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.361754834651947},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.20960882306098938},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.15869289636611938},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13165012001991272}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6984184384346008},{"id":"https://openalex.org/C25915931","wikidata":"https://www.wikidata.org/wiki/Q4180825","display_name":"Stochastic simulation","level":2,"score":0.6748547554016113},{"id":"https://openalex.org/C162932704","wikidata":"https://www.wikidata.org/wiki/Q1058791","display_name":"Synchronizing","level":3,"score":0.6370129585266113},{"id":"https://openalex.org/C50897621","wikidata":"https://www.wikidata.org/wiki/Q2665508","display_name":"Hybrid system","level":2,"score":0.52232426404953},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.5124338269233704},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.4648856818675995},{"id":"https://openalex.org/C147203929","wikidata":"https://www.wikidata.org/wiki/Q574814","display_name":"Discrete event simulation","level":2,"score":0.46055543422698975},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.361754834651947},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.20960882306098938},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.15869289636611938},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13165012001991272},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010582","descriptor_name":"Bacteriophage lambda","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D010582","descriptor_name":"Bacteriophage lambda","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D010582","descriptor_name":"Bacteriophage lambda","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013598","descriptor_name":"Systems Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013598","descriptor_name":"Systems Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013598","descriptor_name":"Systems Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btg409","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg409","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/316/48905193/bioinformatics_20_3_316.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:14960457","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14960457","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg409","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg409","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/3/316/48905193/bioinformatics_20_3_316.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5400000214576721,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2151362395.pdf","grobid_xml":"https://content.openalex.org/works/W2151362395.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1582298918","https://openalex.org/W1593308984","https://openalex.org/W1660272337","https://openalex.org/W1835045972","https://openalex.org/W1946177469","https://openalex.org/W1978319180","https://openalex.org/W1997212828","https://openalex.org/W2023574837","https://openalex.org/W2040890820","https://openalex.org/W2046451925","https://openalex.org/W2084924279","https://openalex.org/W2085338988","https://openalex.org/W2087234479","https://openalex.org/W2096337402","https://openalex.org/W2099798492","https://openalex.org/W2102787760","https://openalex.org/W2121905803","https://openalex.org/W2123280311","https://openalex.org/W2131067724","https://openalex.org/W2143784594","https://openalex.org/W2155418451","https://openalex.org/W2159482845","https://openalex.org/W3008437073"],"related_works":["https://openalex.org/W2111968378","https://openalex.org/W2074923295","https://openalex.org/W4238469347","https://openalex.org/W2061161876","https://openalex.org/W4248101254","https://openalex.org/W2573980643","https://openalex.org/W2251558844","https://openalex.org/W4230201446","https://openalex.org/W2799822012","https://openalex.org/W1972113763"],"abstract_inverted_index":{"MOTIVATION:":[0],"To":[1],"be":[2,13],"valuable":[3],"to":[4,15,54,61,71,106],"biological":[5,63],"or":[6],"biomedical":[7],"research,":[8],"in":[9,75,87,118,126,166],"silico":[10],"methods":[11],"must":[12],"scaled":[14],"complex":[16,44],"pathways":[17],"and":[18,122,136,161],"large":[19,43,107],"numbers":[20],"of":[21,47,100,109,145,163],"interacting":[22],"molecular":[23,48],"species.":[24],"The":[25],"correct":[26],"method":[27,156],"for":[28,42,115,157],"performing":[29],"such":[30,127],"simulations,":[31],"discrete":[32],"event":[33],"simulation":[34,90,121,134,152],"by":[35,50,91,140],"Monte":[36],"Carlo":[37],"generation,":[38],"is":[39,59],"computationally":[40],"costly":[41],"systems.":[45],"Approximation":[46],"behavior":[49,57,99,144,165],"continuous":[51,89],"models":[52],"fails":[53],"capture":[55],"stochastic":[56,98,164],"that":[58],"essential":[60],"many":[62],"phenomena.":[64],"RESULTS:":[65],"We":[66,111,129],"present":[67,112],"a":[68,88,119,154],"novel":[69],"approach":[70,95],"building":[72],"hybrid":[73,120,133],"simulations":[74],"which":[76],"some":[77],"processes":[78,84],"are":[79,85],"simulated":[80],"discretely,":[81],"while":[82],"other":[83],"handled":[86],"differential":[92],"equations.":[93],"This":[94],"preserves":[96],"the":[97,124,132,142,146,159],"cellular":[101],"pathways,":[102],"yet":[103],"enables":[104],"scaling":[105],"populations":[108],"molecules.":[110],"an":[113],"algorithm":[114,135],"synchronizing":[116],"data":[117],"discuss":[123],"trade-offs":[125],"simulation.":[128],"have":[130,137],"implemented":[131],"validated":[138],"it":[139],"simulating":[141],"statistical":[143],"well-known":[147],"lambda":[148],"phage":[149],"switch.":[150],"Hybrid":[151],"provides":[153],"new":[155],"exploring":[158],"sources":[160],"nature":[162],"cells.":[167]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":4}],"updated_date":"2026-06-17T06:14:20.161405","created_date":"2025-10-10T00:00:00"}
