{"id":"https://openalex.org/W2101462174","doi":"https://doi.org/10.1142/s0219720005001144","title":"DIZZY: STOCHASTIC SIMULATION OF LARGE-SCALE GENETIC REGULATORY NETWORKS (SUPPLEMENTARY MATERIAL)","display_name":"DIZZY: STOCHASTIC SIMULATION OF LARGE-SCALE GENETIC REGULATORY NETWORKS (SUPPLEMENTARY MATERIAL)","publication_year":2005,"publication_date":"2005-04-01","ids":{"openalex":"https://openalex.org/W2101462174","doi":"https://doi.org/10.1142/s0219720005001144","mag":"2101462174","pmid":"https://pubmed.ncbi.nlm.nih.gov/15852514"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720005001144","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720005001144","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/A5091354698","display_name":"Stephen A. Ramsey","orcid":"https://orcid.org/0000-0002-2168-5403"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"STEPHEN RAMSEY","raw_affiliation_strings":["Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, United States"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, United States","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039478108","display_name":"David Orrell","orcid":"https://orcid.org/0000-0002-1281-025X"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"DAVID ORRELL","raw_affiliation_strings":["Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, United States"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, United States","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047714102","display_name":"Hamid Bolouri","orcid":"https://orcid.org/0000-0001-8068-426X"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"HAMID BOLOURI","raw_affiliation_strings":["Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, United States"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, United States","institution_ids":["https://openalex.org/I3148997608"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5091354698"],"corresponding_institution_ids":["https://openalex.org/I3148997608"],"apc_list":null,"apc_paid":null,"fwci":0.7384,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.68844629,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"03","issue":"02","first_page":"437","last_page":"454"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9926000237464905,"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":0.9764999747276306,"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/scale","display_name":"Scale (ratio)","score":0.5858702659606934},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4531852900981903},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42055079340934753},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32030409574508667},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.15841922163963318},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.07875657081604004}],"concepts":[{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5858702659606934},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4531852900981903},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42055079340934753},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32030409574508667},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.15841922163963318},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.07875657081604004}],"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":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"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":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720005001144","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720005001144","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:15852514","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15852514","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W74322794","https://openalex.org/W1644882639","https://openalex.org/W1966105707","https://openalex.org/W1973890190","https://openalex.org/W1974272479","https://openalex.org/W1975954590","https://openalex.org/W1987129107","https://openalex.org/W1988891505","https://openalex.org/W1992242854","https://openalex.org/W2003621030","https://openalex.org/W2007006124","https://openalex.org/W2027528771","https://openalex.org/W2042321087","https://openalex.org/W2046451925","https://openalex.org/W2072670807","https://openalex.org/W2074401358","https://openalex.org/W2078119846","https://openalex.org/W2078734278","https://openalex.org/W2084924279","https://openalex.org/W2104855667","https://openalex.org/W2110796675","https://openalex.org/W2111167674","https://openalex.org/W2113950027","https://openalex.org/W2121777611","https://openalex.org/W2131429754","https://openalex.org/W2143938206","https://openalex.org/W2150908245","https://openalex.org/W2151362395","https://openalex.org/W2151947274","https://openalex.org/W2159675211","https://openalex.org/W2164055371","https://openalex.org/W2170120409","https://openalex.org/W2170788736","https://openalex.org/W2518419123","https://openalex.org/W3145128584","https://openalex.org/W4372046852","https://openalex.org/W4403300129"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W2046158694","https://openalex.org/W1993764875","https://openalex.org/W1641042124","https://openalex.org/W2013243191","https://openalex.org/W2147794249"],"abstract_inverted_index":null,"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":6}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
