{"id":"https://openalex.org/W2095034361","doi":"https://doi.org/10.1109/gensips.2010.5719671","title":"Dynamic and static analysis of transcriptional regulatory networks in a hierarchical context","display_name":"Dynamic and static analysis of transcriptional regulatory networks in a hierarchical context","publication_year":2010,"publication_date":"2010-11-01","ids":{"openalex":"https://openalex.org/W2095034361","doi":"https://doi.org/10.1109/gensips.2010.5719671","mag":"2095034361"},"language":"en","primary_location":{"id":"doi:10.1109/gensips.2010.5719671","is_oa":false,"landing_page_url":"https://doi.org/10.1109/gensips.2010.5719671","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5053178517","display_name":"Nitin Bhardwaj","orcid":"https://orcid.org/0000-0002-5813-7005"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"N Bhardwaj","raw_affiliation_strings":["Program in Computational Biology and Bioinformatics, Yale University, New Heaven, CT, USA","Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA"],"affiliations":[{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Yale University, New Heaven, CT, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042321575","display_name":"Mark Gerstein","orcid":"https://orcid.org/0000-0002-9746-3719"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M Gerstein","raw_affiliation_strings":["Department of Computer Science, Yale University, New Heaven, CT, USA","Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yale University, New Heaven, CT, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5053178517"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12387436,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9936000108718872,"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":0.9936000108718872,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9929999709129333,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.9822999835014343,"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/autocracy","display_name":"Autocracy","score":0.6409734487533569},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.6060062646865845},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5592183470726013},{"id":"https://openalex.org/keywords/parallels","display_name":"Parallels","score":0.5062159895896912},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4568120241165161},{"id":"https://openalex.org/keywords/corporate-governance","display_name":"Corporate governance","score":0.4468749165534973},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4249127209186554},{"id":"https://openalex.org/keywords/intuition","display_name":"Intuition","score":0.41712749004364014},{"id":"https://openalex.org/keywords/hierarchical-organization","display_name":"Hierarchical organization","score":0.4154636263847351},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3867684304714203},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32224535942077637},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26887619495391846},{"id":"https://openalex.org/keywords/democracy","display_name":"Democracy","score":0.20857110619544983},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19541212916374207},{"id":"https://openalex.org/keywords/business","display_name":"Business","score":0.1881769299507141},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1468624770641327},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.14299815893173218},{"id":"https://openalex.org/keywords/economics","display_name":"Economics","score":0.13768339157104492}],"concepts":[{"id":"https://openalex.org/C144661447","wikidata":"https://www.wikidata.org/wiki/Q173424","display_name":"Autocracy","level":4,"score":0.6409734487533569},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.6060062646865845},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5592183470726013},{"id":"https://openalex.org/C2775922551","wikidata":"https://www.wikidata.org/wiki/Q7135033","display_name":"Parallels","level":2,"score":0.5062159895896912},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4568120241165161},{"id":"https://openalex.org/C39389867","wikidata":"https://www.wikidata.org/wiki/Q380767","display_name":"Corporate governance","level":2,"score":0.4468749165534973},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4249127209186554},{"id":"https://openalex.org/C132010649","wikidata":"https://www.wikidata.org/wiki/Q189222","display_name":"Intuition","level":2,"score":0.41712749004364014},{"id":"https://openalex.org/C2780217385","wikidata":"https://www.wikidata.org/wiki/Q2389284","display_name":"Hierarchical organization","level":2,"score":0.4154636263847351},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3867684304714203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32224535942077637},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26887619495391846},{"id":"https://openalex.org/C555826173","wikidata":"https://www.wikidata.org/wiki/Q7174","display_name":"Democracy","level":3,"score":0.20857110619544983},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19541212916374207},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.1881769299507141},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1468624770641327},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.14299815893173218},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.13768339157104492},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/gensips.2010.5719671","is_oa":false,"landing_page_url":"https://doi.org/10.1109/gensips.2010.5719671","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.5699999928474426}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2277794996","https://openalex.org/W2504593154","https://openalex.org/W4244588036","https://openalex.org/W1964879957","https://openalex.org/W4235632730","https://openalex.org/W2005046750","https://openalex.org/W4390115938","https://openalex.org/W2807806191","https://openalex.org/W1534056076","https://openalex.org/W2808752767"],"abstract_inverted_index":{"Gene":[0],"regulatory":[1,42],"networks":[2,43,90,109],"have":[3,200],"been":[4],"shown":[5],"to":[6,142,145,150,223],"share":[7],"some":[8,23],"common":[9],"aspects":[10],"with":[11,160],"commonplace":[12],"social":[13],"governance":[14],"structures":[15],"such":[16],"as":[17],"hierarchies.":[18,167],"Thus,":[19],"we":[20,36,82,103,191],"can":[21],"get":[22],"intuition":[24],"into":[25,31],"their":[26,93],"organization":[27],"by":[28],"arranging":[29],"them":[30],"well-known":[32],"hierarchical":[33,50],"layouts.":[34],"Here":[35],"study":[37,151],"a":[38,49,201],"wide":[39],"range":[40],"of":[41,61,95,158,177,186,226],"(transcriptional,":[44],"modification":[45],"and":[46,66,81,88,97,119,162,209,233],"phosphorylation)":[47],"in":[48,76,106,134,174],"context":[51],"for":[52,85],"five":[53],"evolutionarily":[54],"diverse":[55],"species.":[56],"We":[57,168,217],"specify":[58],"three":[59],"levels":[60,87,199],"regulators":[62,178],"-":[63,68],"top,":[64],"middle":[65,112,139],"bottom":[67],"which":[69],"collectively":[70],"regulate":[71],"the":[72,77,108,111,115,155,166,175,180,224],"non-regulator":[73],"targets":[74],"lying":[75],"lowest":[78],"fourth":[79],"level,":[80],"define":[83],"quantities":[84],"nodes,":[86],"entire":[89],"that":[91,105,120,131,193,196],"measure":[92],"degree":[94],"collaboration":[96],"autocratic":[98],"or":[99,184,188],"democratic":[100],"character.":[101],"Overall":[102],"show":[104],"all":[107],"studied,":[110],"level":[113,176],"has":[114,132],"highest":[116],"collaborative":[117],"propensity":[118],"co-regulatory":[121],"partnerships":[122],"occur":[123],"most":[124,144],"frequently":[125],"amongst":[126],"mid-level":[127],"regulators,":[128],"an":[129],"observation":[130],"parallels":[133],"efficient":[135],"corporate":[136],"settings":[137],"where":[138],"managers":[140],"need":[141],"interact":[143],"ensure":[146],"organizational":[147],"effectiveness.":[148],"Then":[149],"dynamic":[152],"effects,":[153],"superimpose":[154],"phenotypic":[156],"effects":[157],"tampering":[159],"nodes":[161,187],"edges":[163],"directly":[164],"onto":[165],"reconstruct":[169],"modified":[170],"hierarchies":[171],"reflecting":[172],"changes":[173],"within":[179],"hierarchy":[181],"upon":[182],"deletions":[183],"insertions":[185],"edges.":[189],"Overall,":[190],"find":[192],"rewiring":[194],"events":[195],"affect":[197],"upper":[198],"more":[202],"dramatic":[203],"effect":[204],"on":[205],"cell":[206],"proliferation":[207],"rate":[208],"survival":[210],"than":[211],"do":[212],"those":[213],"involving":[214],"lower":[215],"levels.":[216],"also":[218],"investigate":[219],"other":[220],"features":[221],"connected":[222],"importance":[225],"upper-level":[227],"regulators:":[228],"expression":[229,234],"divergence,":[230],"back-up":[231],"copies":[232],"level.":[235]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}