{"id":"https://openalex.org/W1968347726","doi":"https://doi.org/10.1142/s021972000600176x","title":"A NEW REGULATORY INTERACTION SUGGESTED BY SIMULATIONS FOR CIRCADIAN GENETIC CONTROL MECHANISM IN MAMMALS","display_name":"A NEW REGULATORY INTERACTION SUGGESTED BY SIMULATIONS FOR CIRCADIAN GENETIC CONTROL MECHANISM IN MAMMALS","publication_year":2006,"publication_date":"2006-02-01","ids":{"openalex":"https://openalex.org/W1968347726","doi":"https://doi.org/10.1142/s021972000600176x","mag":"1968347726","pmid":"https://pubmed.ncbi.nlm.nih.gov/16568547"},"language":"en","primary_location":{"id":"doi:10.1142/s021972000600176x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972000600176x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5113762836","display_name":"Hiroshi Matsuno","orcid":null},"institutions":[{"id":"https://openalex.org/I173915773","display_name":"Yamaguchi University","ror":"https://ror.org/03cxys317","country_code":"JP","type":"education","lineage":["https://openalex.org/I173915773"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"HIROSHI MATSUNO","raw_affiliation_strings":["Faculty of Science, Yamaguchi University, 1677-1, Yoshida, Yamaguchi 753-8512, Japan"],"affiliations":[{"raw_affiliation_string":"Faculty of Science, Yamaguchi University, 1677-1, Yoshida, Yamaguchi 753-8512, Japan","institution_ids":["https://openalex.org/I173915773"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111770825","display_name":"Shin\u2010Ichi T. Inouye","orcid":null},"institutions":[{"id":"https://openalex.org/I173915773","display_name":"Yamaguchi University","ror":"https://ror.org/03cxys317","country_code":"JP","type":"education","lineage":["https://openalex.org/I173915773"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"SHIN-ICHI T. INOUYE","raw_affiliation_strings":["Faculty of Science, Yamaguchi University, 1677-1, Yoshida, Yamaguchi 753-8512, Japan"],"affiliations":[{"raw_affiliation_string":"Faculty of Science, Yamaguchi University, 1677-1, Yoshida, Yamaguchi 753-8512, Japan","institution_ids":["https://openalex.org/I173915773"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011204238","display_name":"YASUKI OKITSU","orcid":null},"institutions":[{"id":"https://openalex.org/I173915773","display_name":"Yamaguchi University","ror":"https://ror.org/03cxys317","country_code":"JP","type":"education","lineage":["https://openalex.org/I173915773"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"YASUKI OKITSU","raw_affiliation_strings":["Faculty of Science, Yamaguchi University, 1677-1, Yoshida, Yamaguchi 753-8512, Japan"],"affiliations":[{"raw_affiliation_string":"Faculty of Science, Yamaguchi University, 1677-1, Yoshida, Yamaguchi 753-8512, Japan","institution_ids":["https://openalex.org/I173915773"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112550493","display_name":"Yasushi Fujii","orcid":null},"institutions":[{"id":"https://openalex.org/I173915773","display_name":"Yamaguchi University","ror":"https://ror.org/03cxys317","country_code":"JP","type":"education","lineage":["https://openalex.org/I173915773"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"YASUSHI FUJII","raw_affiliation_strings":["Faculty of Science, Yamaguchi University, 1677-1, Yoshida, Yamaguchi 753-8512, Japan"],"affiliations":[{"raw_affiliation_string":"Faculty of Science, Yamaguchi University, 1677-1, Yoshida, Yamaguchi 753-8512, Japan","institution_ids":["https://openalex.org/I173915773"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088167618","display_name":"Satoru Miyano","orcid":"https://orcid.org/0000-0002-1753-6616"},"institutions":[{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"SATORU MIYANO","raw_affiliation_strings":["Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minatoku, Tokyo 108-8639, Japan","Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan"],"affiliations":[{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minatoku, Tokyo 108-8639, Japan","institution_ids":["https://openalex.org/I161296585"]},{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan","institution_ids":["https://openalex.org/I161296585"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5113762836"],"corresponding_institution_ids":["https://openalex.org/I173915773"],"apc_list":null,"apc_paid":null,"fwci":1.68127855,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.78603528,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"04","issue":"01","first_page":"139","last_page":"153"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.992900013923645,"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":0.992900013923645,"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/T10342","display_name":"Circadian rhythm and melatonin","score":0.9785000085830688,"subfield":{"id":"https://openalex.org/subfields/2807","display_name":"Endocrine and Autonomic Systems"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11268","display_name":"Light effects on plants","score":0.9559000134468079,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/petri-net","display_name":"Petri net","score":0.7593319416046143},{"id":"https://openalex.org/keywords/circadian-clock","display_name":"Circadian clock","score":0.6442803740501404},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.6154018640518188},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5498587489128113},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5289133787155151},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5255172252655029},{"id":"https://openalex.org/keywords/circadian-rhythm","display_name":"Circadian rhythm","score":0.4186321496963501},{"id":"https://openalex.org/keywords/control","display_name":"Control (management)","score":0.4120393395423889},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.35277098417282104},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34584149718284607},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.28150689601898193},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2541279196739197},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.18548855185508728}],"concepts":[{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.7593319416046143},{"id":"https://openalex.org/C38606739","wikidata":"https://www.wikidata.org/wiki/Q5121352","display_name":"Circadian clock","level":3,"score":0.6442803740501404},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.6154018640518188},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5498587489128113},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5289133787155151},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5255172252655029},{"id":"https://openalex.org/C121446783","wikidata":"https://www.wikidata.org/wiki/Q208353","display_name":"Circadian rhythm","level":2,"score":0.4186321496963501},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.4120393395423889},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35277098417282104},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34584149718284607},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.28150689601898193},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2541279196739197},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.18548855185508728},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002940","descriptor_name":"Circadian Rhythm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002940","descriptor_name":"Circadian Rhythm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002940","descriptor_name":"Circadian Rhythm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s021972000600176x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972000600176x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:16568547","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16568547","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1482095202","https://openalex.org/W1489737525","https://openalex.org/W1548263401","https://openalex.org/W1974736479","https://openalex.org/W1975954590","https://openalex.org/W2003302378","https://openalex.org/W2026903455","https://openalex.org/W2047279254","https://openalex.org/W2064693528","https://openalex.org/W2088842371","https://openalex.org/W2104290916","https://openalex.org/W2112215450","https://openalex.org/W2118967648","https://openalex.org/W2137252071","https://openalex.org/W2159280477","https://openalex.org/W2162505680","https://openalex.org/W2168271199","https://openalex.org/W2170078281","https://openalex.org/W2412839122","https://openalex.org/W2507091891","https://openalex.org/W2517690003","https://openalex.org/W4249538237"],"related_works":["https://openalex.org/W1551257573","https://openalex.org/W4230983483","https://openalex.org/W1980200158","https://openalex.org/W2154794415","https://openalex.org/W2132799268","https://openalex.org/W1538101305","https://openalex.org/W2140682486","https://openalex.org/W4285097245","https://openalex.org/W2090209293","https://openalex.org/W3136837454"],"abstract_inverted_index":{"Knowledge":[0],"of":[1,20,26,66,69,102,106,119,132,139,151,165],"molecular":[2],"biological":[3,29,43,90,173],"systems":[4],"is":[5,12],"increasing":[6],"at":[7],"an":[8,36],"amazing":[9],"pace.":[10],"It":[11],"becoming":[13],"harder":[14],"to":[15,34,40,57,172],"intuitively":[16],"evaluate":[17],"the":[18,24,27,42,88,103,113,120,133,144,163,166],"significance":[19],"each":[21],"interaction":[22],"between":[23],"molecules":[25],"complex":[28],"systems.":[30,174],"Hence,":[31],"we":[32,48,98],"need":[33],"develop":[35],"efficient":[37],"computational":[38,84],"method":[39],"explore":[41],"mechanisms.":[44],"In":[45],"this":[46],"study,":[47],"employed":[49],"a":[50,83,129,140],"hybrid":[51,167],"functional":[52,168],"Petri":[53,169],"net":[54,170],"in":[55,79,148],"order":[56],"analyze":[58],"mammalian":[59],"circadian":[60,121],"genetic":[61,122],"control":[62,123],"mechanisms,":[63,124],"which":[64],"consists":[65],"feedback":[67],"loops":[68],"clock":[70,107,158],"genes":[71],"and":[72,92,110,154],"generates":[73],"endogenous":[74],"near":[75],"24":[76],"h":[77],"rhythms":[78],"mammals.":[80],"We":[81,135],"constructed":[82],"model":[85,115,146],"based":[86],"on":[87],"available":[89],"data,":[91],"by":[93],"using":[94],"Genomic":[95],"Object":[96],"Net,":[97],"performed":[99],"computer":[100],"simulations":[101],"time":[104,152],"courses":[105,153],"gene":[108],"transcription":[109],"translation.":[111],"Although":[112],"original":[114,145],"successfully":[116],"reproduced":[117],"most":[118],"two":[125],"discrepancies":[126],"remained":[127],"despite":[128],"wide":[130],"selection":[131],"parameters.":[134],"found":[136],"that":[137],"addition":[138],"hypothetical":[141],"path":[142],"into":[143],"result":[147],"successful":[149],"simulation":[150],"phase":[155],"relationships":[156],"among":[157],"genes.":[159],"This":[160],"also":[161],"demonstrates":[162],"usefulness":[164],"approach":[171]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
