{"id":"https://openalex.org/W2243469245","doi":"https://doi.org/10.5220/0004739601170122","title":"Towards a Large Integrated Model of Signal Transduction and Gene Regulation Events in Mammalian Cells","display_name":"Towards a Large Integrated Model of Signal Transduction and Gene Regulation Events in Mammalian Cells","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2243469245","doi":"https://doi.org/10.5220/0004739601170122","mag":"2243469245"},"language":"en","primary_location":{"id":"doi:10.5220/0004739601170122","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0004739601170122","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.5220/0004739601170122","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054647246","display_name":"Liam G. Fearnley","orcid":"https://orcid.org/0000-0003-2198-5411"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Liam G. Fearnley","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023552489","display_name":"Mark A. Ragan","orcid":"https://orcid.org/0000-0003-1672-7020"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mark A. Ragan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5061172047","display_name":"Lars K. Nielsen","orcid":"https://orcid.org/0000-0001-8191-3511"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lars K. Nielsen","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5054647246"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13120348,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"117","last_page":"122"},"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":0.9991999864578247,"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":0.9973000288009644,"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/encode","display_name":"ENCODE","score":0.6262759566307068},{"id":"https://openalex.org/keywords/transduction","display_name":"Transduction (biophysics)","score":0.6152483820915222},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5872299075126648},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5834474563598633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5593655109405518},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.5401701927185059},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.4851027727127075},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.48324570059776306},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.440887451171875},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4368186593055725},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4299851357936859},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4181376099586487},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35523998737335205},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.17658230662345886},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1640585958957672}],"concepts":[{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.6262759566307068},{"id":"https://openalex.org/C15152581","wikidata":"https://www.wikidata.org/wiki/Q7833966","display_name":"Transduction (biophysics)","level":2,"score":0.6152483820915222},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5872299075126648},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5834474563598633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5593655109405518},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.5401701927185059},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4851027727127075},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.48324570059776306},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.440887451171875},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4368186593055725},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4299851357936859},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4181376099586487},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35523998737335205},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.17658230662345886},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1640585958957672},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5220/0004739601170122","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0004739601170122","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.5220/0004739601170122","is_oa":true,"landing_page_url":"https://doi.org/10.5220/0004739601170122","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1821858011","https://openalex.org/W1980396134","https://openalex.org/W1982705558","https://openalex.org/W1983196674","https://openalex.org/W2055003617","https://openalex.org/W2058221907","https://openalex.org/W2081781433","https://openalex.org/W2092755129","https://openalex.org/W2096595244","https://openalex.org/W2110841384","https://openalex.org/W2119596771","https://openalex.org/W2126787953","https://openalex.org/W2135118930","https://openalex.org/W2145899141","https://openalex.org/W2158217645","https://openalex.org/W2317767119"],"related_works":["https://openalex.org/W2949927938","https://openalex.org/W2029387041","https://openalex.org/W2135896045","https://openalex.org/W2010571965","https://openalex.org/W1973268559","https://openalex.org/W2884256268","https://openalex.org/W2002709996","https://openalex.org/W2131025197","https://openalex.org/W3128451840","https://openalex.org/W4387092964"],"abstract_inverted_index":{"Recent":[0],"work":[1],"has":[2],"generated":[3],"whole-cell":[4],"and":[5,23,34,36,41,69,107,124,152,163],"whole-process":[6],"models":[7,66],"capable":[8,51],"of":[9,29,39,52,56,112,129,140,160,178],"predicting":[10,53],"phenotype":[11],"in":[12,20,73,126,188],"simple":[13],"organisms.":[14],"The":[15],"approaches":[16],"used":[17],"are":[18,154],"hindered":[19],"higher":[21],"organisms":[22],"more-complex":[24],"cells":[25],"by":[26,137],"a":[27,47,60],"lack":[28,139],"kinetic":[30,130],"parameters":[31],"for":[32],"reactions":[33],"events,":[35],"the":[37,54,70,110,113,127,138,158,176,184],"difficulty":[38],"measuring":[40],"estimating":[42],"these.":[43],"Here,":[44],"we":[45,164],"outline":[46],"large,":[48],"two-process":[49],"model":[50,173],"effects":[55],"gene":[57,74,143],"expression":[58,75,144],"on":[59],"signal":[61,67,115],"transduction":[62,68,116],"network.":[63],"Our":[64],"method":[65,104],"processes":[71],"involved":[72],"as":[76,150,183],"two":[77],"separate":[78],"systems,":[79],"solved":[80],"iteratively.":[81],"We":[82,99],"show":[83],"that":[84,102,166],"this":[85,168],"approach":[86,121],"is":[87,105,133],"sufficient":[88],"to":[89,109,157],"capture":[90],"functionally":[91],"significant":[92],"behaviour":[93],"resulting":[94],"from":[95],"common":[96],"network":[97],"motifs.":[98],"further":[100],"demonstrate":[101],"our":[103,171],"scalable":[106],"efficient":[108],"size":[111],"largest":[114],"databases":[117],"currently":[118],"available.":[119],"This":[120],"enables":[122],"analysis":[123],"prediction":[125],"absence":[128],"data,":[131],"but":[132],"itself":[134],"held":[135],"back":[136],"detailed":[141],"large-scale":[142],"models.":[145],"However,":[146],"research":[147],"consortia":[148],"such":[149,182],"ENCODE":[151],"FANTOM":[153],"rapidly":[155],"adding":[156],"knowledge":[159],"transcriptional":[161],"regulation,":[162],"anticipate":[165],"incorporating":[167],"data":[169],"into":[170],"regulatory":[172],"could":[174],"allow":[175],"modelling":[177],"complex":[179],"cellular":[180,189],"phenomena":[181],"structured":[185],"progression":[186],"seen":[187],"differentiation.":[190]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}