{"id":"https://openalex.org/W2582500913","doi":null,"title":"Mathematical modeling approaches for dynamical analysis of protein regulatory networks with applications to the budding yeast cell cycle and the circadian rhythm in cyanobacteria","display_name":"Mathematical modeling approaches for dynamical analysis of protein regulatory networks with applications to the budding yeast cell cycle and the circadian rhythm in cyanobacteria","publication_year":2011,"publication_date":"2011-10-24","ids":{"openalex":"https://openalex.org/W2582500913","mag":"2582500913"},"language":"en","primary_location":{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/29492","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/29492","pdf_url":"http://hdl.handle.net/10919/29492","source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/10919/29492","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013407366","display_name":"Teeraphan Laomettachit","orcid":"https://orcid.org/0000-0003-3194-1391","observed_orcids":["https://orcid.org/0000-0003-3194-1391"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Teeraphan Laomettachit","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-3194-1391","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5013407366"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994999766349792,"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":0.9994999766349792,"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":9.999999747378752e-05,"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":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-regulatory-networks","display_name":"protein regulatory networks","score":0.9300000071525574},{"id":"https://openalex.org/keywords/rule-based-modeling","display_name":"rule-based models","score":0.8130000233650208},{"id":"https://openalex.org/keywords/rate-law","display_name":"rate law","score":0.8809999823570251},{"id":"https://openalex.org/keywords/circadian-rhythm","display_name":"circadian rhythm","score":0.878000020980835},{"id":"https://openalex.org/keywords/cyanobacteria","display_name":"cyanobacteria","score":0.9990000128746033},{"id":"https://openalex.org/keywords/dynamic-analysis","display_name":"dynamic analysis","score":0.6439999938011169},{"id":"https://openalex.org/keywords/model-validation","display_name":"model validation","score":0.4729999899864197}],"concepts":[{"id":"https://openalex.org/C2992884146","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Budding yeast","level":4,"score":0.8236709237098694},{"id":"https://openalex.org/C121446783","wikidata":"https://www.wikidata.org/wiki/Q208353","display_name":"Circadian rhythm","level":2,"score":0.7238628268241882},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5249716639518738},{"id":"https://openalex.org/C2779222958","wikidata":"https://www.wikidata.org/wiki/Q45422","display_name":"Yeast","level":2,"score":0.5014758110046387},{"id":"https://openalex.org/C135343436","wikidata":"https://www.wikidata.org/wiki/Q170406","display_name":"Rhythm","level":2,"score":0.48226767778396606},{"id":"https://openalex.org/C2779669040","wikidata":"https://www.wikidata.org/wiki/Q93315","display_name":"Cyanobacteria","level":3,"score":0.4435192346572876},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4128875136375427},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39626437425613403},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.33640238642692566},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.31464195251464844},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.31328248977661133},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16632002592086792},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.11277011036872864},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.06301009654998779},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/29492","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/29492","pdf_url":"http://hdl.handle.net/10919/29492","source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},{"id":"mag:2582500913","doi":null,"is_oa":false,"landing_page_url":"https://vtechworks.lib.vt.edu/handle/10919/29492","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/29492","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/29492","pdf_url":"http://hdl.handle.net/10919/29492","source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dissertation"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2582500913.pdf","grobid_xml":"https://content.openalex.org/works/W2582500913.grobid-xml"},"referenced_works_count":75,"referenced_works":["https://openalex.org/W55455380","https://openalex.org/W1486453207","https://openalex.org/W1522185757","https://openalex.org/W1573602524","https://openalex.org/W1588726268","https://openalex.org/W1590458072","https://openalex.org/W1607824205","https://openalex.org/W1645305843","https://openalex.org/W1884388113","https://openalex.org/W1963684521","https://openalex.org/W1964446365","https://openalex.org/W1966967749","https://openalex.org/W1975586684","https://openalex.org/W1979385177","https://openalex.org/W1982588549","https://openalex.org/W1987311230","https://openalex.org/W1992810416","https://openalex.org/W1992927069","https://openalex.org/W1993390469","https://openalex.org/W1996984709","https://openalex.org/W1999269191","https://openalex.org/W2010900077","https://openalex.org/W2013947447","https://openalex.org/W2014918426","https://openalex.org/W2020411151","https://openalex.org/W2024195317","https://openalex.org/W2026237039","https://openalex.org/W2029217862","https://openalex.org/W2029361184","https://openalex.org/W2031369606","https://openalex.org/W2035571475","https://openalex.org/W2037992356","https://openalex.org/W2038763999","https://openalex.org/W2042321087","https://openalex.org/W2043911313","https://openalex.org/W2046451925","https://openalex.org/W2046855815","https://openalex.org/W2047697718","https://openalex.org/W2053961182","https://openalex.org/W2054585632","https://openalex.org/W2058221907","https://openalex.org/W2062029454","https://openalex.org/W2064397441","https://openalex.org/W2065257772","https://openalex.org/W2067077009","https://openalex.org/W2067109731","https://openalex.org/W2069941324","https://openalex.org/W2073390681","https://openalex.org/W2075415801","https://openalex.org/W2077326330","https://openalex.org/W2082071299","https://openalex.org/W2082904244","https://openalex.org/W2082979850","https://openalex.org/W2091719092","https://openalex.org/W2098515048","https://openalex.org/W2098579568","https://openalex.org/W2099693848","https://openalex.org/W2103238897","https://openalex.org/W2109110326","https://openalex.org/W2122087821","https://openalex.org/W2133401281","https://openalex.org/W2134759932","https://openalex.org/W2137244330","https://openalex.org/W2142622103","https://openalex.org/W2144063122","https://openalex.org/W2150750144","https://openalex.org/W2150767223","https://openalex.org/W2152868594","https://openalex.org/W2153100796","https://openalex.org/W2155418451","https://openalex.org/W2157989234","https://openalex.org/W2160594729","https://openalex.org/W2163493106","https://openalex.org/W2166132142","https://openalex.org/W2167154952"],"related_works":["https://openalex.org/W2163300538","https://openalex.org/W2902378012","https://openalex.org/W67015093","https://openalex.org/W2739726893","https://openalex.org/W7095992246","https://openalex.org/W4402303063","https://openalex.org/W7033598062","https://openalex.org/W1664082905","https://openalex.org/W2594785334","https://openalex.org/W7100405638"],"abstract_inverted_index":{"Mathematical":[0],"modeling":[1,109,183,222,253],"has":[2],"become":[3],"increasingly":[4],"popular":[5],"as":[6,133,184],"a":[7,28,85,91,95,107,142,185,198,217,243],"tool":[8],"to":[9,57,68,140,168,187,206,234,257],"study":[10],"regulatory":[11,34,63,144,245],"interactions":[12,76],"within":[13],"gene-protein":[14],"networks.":[15],"From":[16],"the":[17,24,32,50,59,69,102,115,152,169,176,195,204,214,249,258],"modeler's":[18],"perspective,":[19],"two":[20],"challenges":[21],"arise":[22],"in":[23,114,213,263],"process":[25],"of":[26,42,47,72,89,120,155,158,200,242,251,260],"building":[27],"mathematical":[29,87,190,218],"model.":[30],"First,":[31],"same":[33],"network":[35,92],"can":[36,93,137],"be":[37,94,138],"translated":[38],"into":[39,117],"different":[40,45,126,156,239],"types":[41,157],"models":[43],"at":[44],"levels":[46],"detail,":[48],"and":[49,75,83,97,160,228],"modeler":[51,196],"must":[52],"choose":[53],"an":[54],"appropriate":[55],"level":[56],"describe":[58],"network.":[60,145,215],"Second,":[61],"realistic":[62,86],"networks":[64,116],"are":[65,123],"complicated":[66],"due":[67],"large":[70],"number":[71],"biochemical":[73],"species":[74],"that":[77,111,136,148,202],"govern":[78],"any":[79],"physiological":[80],"process.":[81],"Constructing":[82],"validating":[84],"model":[88,219],"such":[90],"difficult":[96],"lengthy":[98],"task.":[99],"To":[100,174],"confront":[101,175],"first":[103],"challenge,":[104,178],"we":[105,161],"develop":[106],"new":[108],"approach":[110,150],"classifies":[112],"components":[113],"three":[118,130],"classes":[119,131],"variables,":[121],"which":[122],"described":[124],"by":[125,165,254],"rate":[127],"laws.":[128],"These":[129],"serve":[132],"\"building":[134],"blocks\"":[135],"connected":[139],"build":[141,188],"complex":[143,189],"We":[146,247],"show":[147],"our":[149],"combines":[151],"best":[153],"features":[154],"models,":[159],"demonstrate":[162,248],"its":[163],"utility":[164],"applying":[166,255],"it":[167,256],"budding":[170],"yeast":[171],"cell":[172],"cycle.":[173],"second":[177],"modelers":[179,233],"have":[180],"developed":[181],"rule-based":[182,221,252],"framework":[186],"models.":[191],"In":[192],"this":[193],"approach,":[194],"describes":[197],"set":[199],"rules":[201],"instructs":[203],"computer":[205],"automatically":[207],"generate":[208],"all":[209],"possible":[210],"chemical":[211],"reactions":[212],"Building":[216],"using":[220],"is":[223],"not":[224],"only":[225],"less":[226],"time-consuming":[227],"error-prone,":[229],"but":[230],"also":[231],"allows":[232],"account":[235],"comprehensively":[236],"for":[237],"many":[238],"mechanistic":[240],"details":[241],"molecular":[244],"system.":[246],"potential":[250],"generation":[259],"circadian":[261],"rhythms":[262],"cyanobacteria.":[264]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-09-01T08:31:24.195828","created_date":"2017-02-03T00:00:00"}