{"id":"https://openalex.org/W2160084035","doi":"https://doi.org/10.1093/bioinformatics/btq389","title":"Bayesian experts in exploring reaction kinetics of transcription circuits","display_name":"Bayesian experts in exploring reaction kinetics of transcription circuits","publication_year":2010,"publication_date":"2010-09-04","ids":{"openalex":"https://openalex.org/W2160084035","doi":"https://doi.org/10.1093/bioinformatics/btq389","mag":"2160084035"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq389","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq389","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/18/i589/48859112/bioinformatics_26_18_i589.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/18/i589/48859112/bioinformatics_26_18_i589.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031629643","display_name":"Ryo Yoshida","orcid":"https://orcid.org/0000-0001-8092-0162"},"institutions":[{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4210134673","display_name":"The Institute of Statistical Mathematics","ror":"https://ror.org/03jcejr58","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210134673","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Ryo Yoshida","raw_affiliation_strings":["The Institute of Statistical Mathematics, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan"],"affiliations":[{"raw_affiliation_string":"The Institute of Statistical Mathematics, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan","institution_ids":["https://openalex.org/I4210134673","https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017765466","display_name":"Masaya Saito","orcid":"https://orcid.org/0000-0002-4840-6515"},"institutions":[{"id":"https://openalex.org/I4210134673","display_name":"The Institute of Statistical Mathematics","ror":"https://ror.org/03jcejr58","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210134673","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masaya M. Saito","raw_affiliation_strings":["The Institute of Statistical Mathematics, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan"],"affiliations":[{"raw_affiliation_string":"The Institute of Statistical Mathematics, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan","institution_ids":["https://openalex.org/I4210134673","https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042802869","display_name":"Hiromichi Nagao","orcid":"https://orcid.org/0000-0003-4314-5093"},"institutions":[{"id":"https://openalex.org/I4210134673","display_name":"The Institute of Statistical Mathematics","ror":"https://ror.org/03jcejr58","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210134673","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiromichi Nagao","raw_affiliation_strings":["The Institute of Statistical Mathematics, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan"],"affiliations":[{"raw_affiliation_string":"The Institute of Statistical Mathematics, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan","institution_ids":["https://openalex.org/I4210134673","https://openalex.org/I4210158934"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062020503","display_name":"Tomoyuki Higuchi","orcid":"https://orcid.org/0000-0003-3021-3173"},"institutions":[{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4210134673","display_name":"The Institute of Statistical Mathematics","ror":"https://ror.org/03jcejr58","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210134673","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tomoyuki Higuchi","raw_affiliation_strings":["The Institute of Statistical Mathematics, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan"],"affiliations":[{"raw_affiliation_string":"The Institute of Statistical Mathematics, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan","institution_ids":["https://openalex.org/I4210134673","https://openalex.org/I4210158934"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5031629643"],"corresponding_institution_ids":["https://openalex.org/I4210134673","https://openalex.org/I4210158934"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4066,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.64099733,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"26","issue":"18","first_page":"i589","last_page":"i595"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9976000189781189,"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":0.9976000189781189,"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/T10848","display_name":"Advanced Multi-Objective Optimization Algorithms","score":0.983299970626831,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9735999703407288,"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/in-silico","display_name":"In silico","score":0.703511655330658},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6692495346069336},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5923764705657959},{"id":"https://openalex.org/keywords/parametric-statistics","display_name":"Parametric statistics","score":0.4924336373806},{"id":"https://openalex.org/keywords/dirichlet-distribution","display_name":"Dirichlet distribution","score":0.43907594680786133},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3456451892852783},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1943594515323639},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19350135326385498},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19229942560195923},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.10266292095184326}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.703511655330658},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6692495346069336},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5923764705657959},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.4924336373806},{"id":"https://openalex.org/C169214877","wikidata":"https://www.wikidata.org/wiki/Q981016","display_name":"Dirichlet distribution","level":3,"score":0.43907594680786133},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3456451892852783},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1943594515323639},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19350135326385498},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19229942560195923},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.10266292095184326},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C182310444","wikidata":"https://www.wikidata.org/wiki/Q1332643","display_name":"Boundary value problem","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btq389","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq389","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/18/i589/48859112/bioinformatics_26_18_i589.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2935439","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2935439","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq389","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq389","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/18/i589/48859112/bioinformatics_26_18_i589.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160084035.pdf","grobid_xml":"https://content.openalex.org/works/W2160084035.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1499965417","https://openalex.org/W1599969036","https://openalex.org/W1970076554","https://openalex.org/W1975954590","https://openalex.org/W1988437463","https://openalex.org/W1989760523","https://openalex.org/W2010104326","https://openalex.org/W2062882942","https://openalex.org/W2091797506","https://openalex.org/W2100169396","https://openalex.org/W2106927126","https://openalex.org/W2120625059","https://openalex.org/W2126802411","https://openalex.org/W2127498532","https://openalex.org/W2141239733","https://openalex.org/W2143883853","https://openalex.org/W2144323650","https://openalex.org/W2150750144","https://openalex.org/W2151098983","https://openalex.org/W2154751475","https://openalex.org/W2156435365","https://openalex.org/W2161080454","https://openalex.org/W2163833586","https://openalex.org/W2167008303","https://openalex.org/W2528271650","https://openalex.org/W6644400803","https://openalex.org/W6678950323","https://openalex.org/W6682728839"],"related_works":["https://openalex.org/W2912862995","https://openalex.org/W3129816939","https://openalex.org/W2985427592","https://openalex.org/W2101501829","https://openalex.org/W2003194288","https://openalex.org/W2400569965","https://openalex.org/W2060263731","https://openalex.org/W391093122","https://openalex.org/W1521239975","https://openalex.org/W4361305867"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Biochemical":[2],"reactions":[3],"in":[4,24,62,90,111,156],"cells":[5],"are":[6,65],"made":[7],"of":[8,11,37,42,93,131,155,163],"several":[9],"types":[10],"biological":[12],"circuits.":[13],"In":[14],"current":[15],"systems":[16],"biology,":[17],"making":[18],"differential":[19],"equation":[20],"(DE)":[21],"models":[22,63,113],"simulatable":[23],"silico":[25,157],"has":[26,51],"been":[27],"an":[28],"appealing,":[29],"general":[30],"approach":[31,82],"to":[32,58,67,83,119,137],"uncover":[33],"a":[34,43,78,94,145],"complex":[35],"world":[36],"biochemical":[38,73],"reaction":[39,108],"dynamics.":[40],"Despite":[41],"need":[44],"for":[45],"simulation-aided":[46],"studies,":[47],"our":[48],"research":[49],"field":[50],"yet":[52],"provided":[53],"no":[54],"clear":[55],"answers:":[56],"how":[57],"specify":[59],"kinetic":[60,117],"values":[61],"that":[64,144,161],"difficult":[66],"measure":[68],"from":[69],"experimental/theoretical":[70],"analyses":[71],"on":[72,107],"kinetics.":[74],"Results:":[75],"We":[76],"present":[77],"novel":[79],"non-parametric":[80],"Bayesian":[81,101,146],"this":[84],"problem.":[85],"The":[86,124],"key":[87],"idea":[88],"lies":[89],"the":[91,120,138,178],"development":[92],"Dirichlet":[95],"process":[96],"(DP)":[97],"prior":[98,126],"distribution,":[99],"called":[100],"experts,":[102],"which":[103],"reflects":[104],"substantive":[105],"knowledge":[106],"mechanisms":[109],"inherent":[110],"given":[112],"and":[114],"experimentally":[115],"observable":[116],"evidences":[118],"subsequent":[121],"parameter":[122,133],"search.":[123],"DP":[125],"identifies":[127],"significant":[128],"local":[129],"regions":[130],"unknown":[132,153],"space":[134],"before":[135],"proceeding":[136],"posterior":[139],"analyses.":[140],"This":[141],"article":[142],"reports":[143],"expert-inducing":[147],"stochastic":[148],"search":[149],"can":[150],"effectively":[151],"explore":[152],"parameters":[154],"transcription":[158],"circuits":[159],"such":[160],"solutions":[162],"DEs":[164],"reproduce":[165],"transcriptomic":[166],"time":[167],"course":[168],"profiles.":[169],"Availability:":[170],"A":[171],"sample":[172],"source":[173],"code":[174],"is":[175],"available":[176],"at":[177],"URL":[179],"http://daweb.ism.ac.jp/\u223cyoshidar/lisdas/":[180],"Contact:":[181],"yoshidar@ism.ac.jp":[182]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2016-06-24T00:00:00"}
