{"id":"https://openalex.org/W1996756820","doi":"https://doi.org/10.1145/2644817","title":"Stochastic Model Checking of Genetic Circuits","display_name":"Stochastic Model Checking of Genetic Circuits","publication_year":2014,"publication_date":"2014-12-30","ids":{"openalex":"https://openalex.org/W1996756820","doi":"https://doi.org/10.1145/2644817","mag":"1996756820"},"language":"en","primary_location":{"id":"doi:10.1145/2644817","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2644817","pdf_url":null,"source":{"id":"https://openalex.org/S96198239","display_name":"ACM Journal on Emerging Technologies in Computing Systems","issn_l":"1550-4832","issn":["1550-4832","1550-4840"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Journal on Emerging Technologies in Computing Systems","raw_type":"journal-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/A5047908665","display_name":"Curtis Madsen","orcid":"https://orcid.org/0000-0002-0254-0364"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Curtis Madsen","raw_affiliation_strings":["Newcastle University, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Newcastle University, United Kingdom","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009667070","display_name":"Zhen Zhang","orcid":"https://orcid.org/0000-0001-6710-9826"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhen Zhang","raw_affiliation_strings":["University of Utah, Salt Lake City, UT","University of Utah; Salt Lake City; UT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Utah, Salt Lake City, UT","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"University of Utah; Salt Lake City; UT","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082955901","display_name":"Nicholas Roehner","orcid":"https://orcid.org/0000-0003-4957-1552"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Roehner","raw_affiliation_strings":["University of Utah, Salt Lake City, UT","University of Utah; Salt Lake City; UT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Utah, Salt Lake City, UT","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"University of Utah; Salt Lake City; UT","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103171582","display_name":"Chris Winstead","orcid":"https://orcid.org/0000-0001-5238-5852"},"institutions":[{"id":"https://openalex.org/I121980950","display_name":"Utah State University","ror":"https://ror.org/00h6set76","country_code":"US","type":"education","lineage":["https://openalex.org/I121980950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Winstead","raw_affiliation_strings":["Utah State University, Logon, UT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Utah State University, Logon, UT","institution_ids":["https://openalex.org/I121980950"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111386695","display_name":"Chris J. Myers","orcid":null},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Myers","raw_affiliation_strings":["University of Utah, Salt Lake City, UT","University of Utah; Salt Lake City; UT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Utah, Salt Lake City, UT","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"University of Utah; Salt Lake City; UT","institution_ids":["https://openalex.org/I223532165"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.427,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.62859521,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"11","issue":"3","first_page":"1","last_page":"21"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9611999988555908,"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":0.9577999711036682,"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":0.6808747053146362},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.6287955045700073},{"id":"https://openalex.org/keywords/electronic-circuit","display_name":"Electronic circuit","score":0.6146847009658813},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.5015075206756592},{"id":"https://openalex.org/keywords/state-space","display_name":"State space","score":0.4916260838508606},{"id":"https://openalex.org/keywords/model-checking","display_name":"Model checking","score":0.4354928433895111},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.421619713306427},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.4115142822265625},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32891857624053955},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1728740632534027},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.16162559390068054},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.15943452715873718},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10817736387252808},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.09794315695762634}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6808747053146362},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.6287955045700073},{"id":"https://openalex.org/C134146338","wikidata":"https://www.wikidata.org/wiki/Q1815901","display_name":"Electronic circuit","level":2,"score":0.6146847009658813},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.5015075206756592},{"id":"https://openalex.org/C72434380","wikidata":"https://www.wikidata.org/wiki/Q230930","display_name":"State space","level":2,"score":0.4916260838508606},{"id":"https://openalex.org/C110251889","wikidata":"https://www.wikidata.org/wiki/Q1569697","display_name":"Model checking","level":2,"score":0.4354928433895111},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.421619713306427},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.4115142822265625},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32891857624053955},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1728740632534027},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.16162559390068054},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.15943452715873718},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10817736387252808},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.09794315695762634},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/2644817","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2644817","pdf_url":null,"source":{"id":"https://openalex.org/S96198239","display_name":"ACM Journal on Emerging Technologies in Computing Systems","issn_l":"1550-4832","issn":["1550-4832","1550-4840"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Journal on Emerging Technologies in Computing Systems","raw_type":"journal-article"},{"id":"pmh:oai:digitalcommons.usu.edu:ece_facpub-1138","is_oa":false,"landing_page_url":"https://digitalcommons.usu.edu/ece_facpub/136","pdf_url":null,"source":{"id":"https://openalex.org/S4377196327","display_name":"Digital Commons - USU (Utah State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121980950","host_organization_name":"Utah State University","host_organization_lineage":["https://openalex.org/I121980950"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Electrical and Computer Engineering Faculty Publications","raw_type":"text"},{"id":"pmh:oai:digitalcommons.usu.edu:ece_facpub-1204","is_oa":false,"landing_page_url":"https://digitalcommons.usu.edu/cgi/viewcontent.cgi?article=1204&context=ece_facpub","pdf_url":null,"source":{"id":"https://openalex.org/S4377196327","display_name":"Digital Commons - USU (Utah State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121980950","host_organization_name":"Utah State University","host_organization_lineage":["https://openalex.org/I121980950"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Electrical and Computer Engineering Faculty Publications","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","score":0.49000000953674316,"display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W11463020","https://openalex.org/W35463602","https://openalex.org/W165850321","https://openalex.org/W1514324734","https://openalex.org/W1516256348","https://openalex.org/W1534797499","https://openalex.org/W1535517661","https://openalex.org/W1573985420","https://openalex.org/W1645305843","https://openalex.org/W1842089573","https://openalex.org/W1859458367","https://openalex.org/W1890385119","https://openalex.org/W1968856189","https://openalex.org/W1973890190","https://openalex.org/W1974272479","https://openalex.org/W1987003260","https://openalex.org/W1989284002","https://openalex.org/W1989431662","https://openalex.org/W1997982531","https://openalex.org/W1998422337","https://openalex.org/W2007072455","https://openalex.org/W2011432832","https://openalex.org/W2018075920","https://openalex.org/W2029370898","https://openalex.org/W2034375827","https://openalex.org/W2041226400","https://openalex.org/W2045095831","https://openalex.org/W2047575149","https://openalex.org/W2047882868","https://openalex.org/W2066594542","https://openalex.org/W2077480167","https://openalex.org/W2078734278","https://openalex.org/W2088846696","https://openalex.org/W2091167328","https://openalex.org/W2094216282","https://openalex.org/W2101506009","https://openalex.org/W2109082753","https://openalex.org/W2129064518","https://openalex.org/W2132828256","https://openalex.org/W2134759932","https://openalex.org/W2147306790","https://openalex.org/W2149202606","https://openalex.org/W2153517004","https://openalex.org/W2155418451","https://openalex.org/W2158979830","https://openalex.org/W2172162088","https://openalex.org/W2256672332","https://openalex.org/W2335196113","https://openalex.org/W2528252365","https://openalex.org/W2605543710","https://openalex.org/W2622039200","https://openalex.org/W4243003743","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2394139409","https://openalex.org/W1572578464","https://openalex.org/W1497647456","https://openalex.org/W2362295904","https://openalex.org/W2493800215","https://openalex.org/W2149299285","https://openalex.org/W3158759410","https://openalex.org/W2106934209","https://openalex.org/W4205778860","https://openalex.org/W1974155069"],"abstract_inverted_index":{"Synthetic":[0],"genetic":[1,32,73,132,181,185],"circuits":[2,133],"have":[3],"a":[4,113,124,196],"number":[5,85],"of":[6,41,71,86,131,158,179],"exciting":[7],"potential":[8],"applications":[9],"such":[10],"as":[11,83,199],"cleaning":[12],"up":[13],"toxic":[14],"waste,":[15],"hunting":[16],"and":[17,21,24,30,59,142,183],"killing":[18],"tumor":[19],"cells,":[20],"producing":[22],"drugs":[23],"bio-fuels":[25],"more":[26],"efficiently.":[27],"When":[28],"designing":[29],"analyzing":[31,143],"circuits,":[33,74],"researchers":[34],"are":[35],"often":[36],"interested":[37],"in":[38,123,195],"the":[39,51,63,84,117],"probability":[40],"observing":[42],"certain":[43,120],"behaviors.":[44],"Discerning":[45],"these":[46,102],"probabilities":[47,103],"typically":[48],"involves":[49],"simulating":[50],"circuit":[52],"to":[53,79,96,100,129,149,174],"produce":[54],"some":[55],"time":[56],"series":[57],"data":[58],"computing":[60],"statistics":[61],"over":[62],"resulting":[64],"data.":[65],"However,":[66],"for":[67,115],"very":[68],"rare":[69],"behaviors":[70],"complex":[72],"it":[75],"becomes":[76],"computationally":[77],"intractable":[78],"obtain":[80],"good":[81],"results":[82,189,194],"required":[87],"simulation":[88],"runs":[89],"grows":[90],"exponentially.":[91],"It":[92],"is,":[93],"therefore,":[94],"necessary":[95],"apply":[97],"numerical":[98],"methods":[99],"determine":[101],"directly.":[104],"This":[105],"article":[106],"describes":[107],"how":[108,168],"stochastic":[109,152],"model":[110],"checking":[111],",":[112],"method":[114,170,193],"determining":[116],"likelihood":[118],"that":[119,191],"events":[121],"occur":[122],"system,":[125],"can":[126,171],"by":[127,134],"applied":[128],"models":[130],"translating":[135],"them":[136,144],"into":[137],"continuous-time":[138],"Markov":[139,146],"chains":[140],"(CTMCs)":[141],"using":[145],"chain":[147],"analysis":[148],"check":[150],"continuous":[151],"logic":[153],"(CSL)":[154],"properties.":[155],"The":[156],"utility":[157],"this":[159,169,192],"approach":[160],"is":[161],"demonstrated":[162],"with":[163,201],"several":[164],"case":[165],"studies":[166],"illustrating":[167],"be":[172],"used":[173],"perform":[175],"design":[176],"space":[177],"exploration":[178],"two":[180,184],"oscillators":[182],"state-holding":[186],"elements.":[187],"Our":[188],"show":[190],"substantial":[197],"speedup":[198],"compared":[200],"conventional":[202],"simulation-based":[203],"approaches.":[204]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
