{"id":"https://openalex.org/W136117639","doi":null,"title":"Investigating the evolution of diversity and complexity of Prokaryotic gene regulatory networks using in silico models","display_name":"Investigating the evolution of diversity and complexity of Prokaryotic gene regulatory networks using in silico models","publication_year":2009,"publication_date":"2009-12-15","ids":{"openalex":"https://openalex.org/W136117639","mag":"136117639"},"language":"en","primary_location":{"id":"pmh:oai:etheses.bham.ac.uk:349","doi":null,"is_oa":false,"landing_page_url":"http://etheses.bham.ac.uk/349/1/Jenkins09PhD.pdf","pdf_url":"http://etheses.bham.ac.uk/349/1/Jenkins09PhD.pdf","source":{"id":"https://openalex.org/S4306402357","display_name":"University of Birmingham Institutional Research Archive (University of Birmingham)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I79619799","host_organization_name":"University of Birmingham","host_organization_lineage":["https://openalex.org/I79619799"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/10068/967175","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103563452","display_name":"Dafyd J. Jenkins","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Dafyd J. Jenkins","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5103563452"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"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":0.9175000190734863,"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":0.9175000190734863,"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":0.06849999725818634,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.003000000026077032,"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/gene-regulatory-network-evolution","display_name":"gene regulatory network evolution","score":0.9200000166893005},{"id":"https://openalex.org/keywords/prokaryotes","display_name":"prokaryotes","score":0.9490000009536743},{"id":"https://openalex.org/keywords/global-gene-regulation","display_name":"global gene regulation","score":0.7770000100135803},{"id":"https://openalex.org/keywords/repression","display_name":"repression","score":0.8169999718666077},{"id":"https://openalex.org/keywords/genome-size","display_name":"genome size","score":0.6060000061988831},{"id":"https://openalex.org/keywords/energy-regulation","display_name":"energy regulation","score":0.6039999723434448},{"id":"https://openalex.org/keywords/attractor-states","display_name":"attractor states","score":0.6980000138282776},{"id":"https://openalex.org/keywords/network-complexity","display_name":"network complexity","score":0.5270000100135803},{"id":"https://openalex.org/keywords/environmental-complexity","display_name":"environmental complexity","score":0.7149999737739563},{"id":"https://openalex.org/keywords/adaptive-evolution","display_name":"adaptive evolution","score":0.3720000088214874},{"id":"https://openalex.org/keywords/mrna-stability","display_name":"mRNA stability","score":0.6079999804496765}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7891396284103394},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7350265979766846},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6533843874931335},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5431186556816101},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.538128137588501},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.529503583908081},{"id":"https://openalex.org/C171578705","wikidata":"https://www.wikidata.org/wiki/Q5418700","display_name":"Evolutionary dynamics","level":3,"score":0.4593302607536316},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4235851764678955},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.42295753955841064},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.41375818848609924},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41293007135391235},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:etheses.bham.ac.uk:349","doi":null,"is_oa":false,"landing_page_url":"http://etheses.bham.ac.uk/349/1/Jenkins09PhD.pdf","pdf_url":"http://etheses.bham.ac.uk/349/1/Jenkins09PhD.pdf","source":{"id":"https://openalex.org/S4306402357","display_name":"University of Birmingham Institutional Research Archive (University of Birmingham)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I79619799","host_organization_name":"University of Birmingham","host_organization_lineage":["https://openalex.org/I79619799"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Thesis"},{"id":"pmh:oai:uilis.unsyiah.ac.id:32688","doi":null,"is_oa":false,"landing_page_url":"http://uilis.unsyiah.ac.id/opentheses/items/show/32688","pdf_url":null,"source":{"id":"https://openalex.org/S4377196378","display_name":"UPT. Syiah Kuala University Library (Syiah Kuala University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I187494767","host_organization_name":"Universitas Syiah Kuala","host_organization_lineage":["https://openalex.org/I187494767"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Thesis"},{"id":"pmh:hdl:10068/967175","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10068/967175","pdf_url":null,"source":{"id":"https://openalex.org/S4377196900","display_name":"OpenGrey (Institut de l'Information Scientifique et Technique)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1295345811","host_organization_name":"Institut de l'Information Scientifique et Technique","host_organization_lineage":["https://openalex.org/I1295345811"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"U - Thesis"},{"id":"mag:136117639","doi":null,"is_oa":false,"landing_page_url":"http://etheses.bham.ac.uk/349/","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:hdl:10068/967175","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10068/967175","pdf_url":null,"source":{"id":"https://openalex.org/S4377196900","display_name":"OpenGrey (Institut de l'Information Scientifique et Technique)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1295345811","host_organization_name":"Institut de l'Information Scientifique et Technique","host_organization_lineage":["https://openalex.org/I1295345811"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"U - Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":110,"referenced_works":["https://openalex.org/W58859871","https://openalex.org/W179756065","https://openalex.org/W1497256448","https://openalex.org/W1514601905","https://openalex.org/W1529898704","https://openalex.org/W1557270760","https://openalex.org/W1808967201","https://openalex.org/W1853355017","https://openalex.org/W1936630560","https://openalex.org/W1952540142","https://openalex.org/W1964343149","https://openalex.org/W1966967728","https://openalex.org/W1968331537","https://openalex.org/W1970018776","https://openalex.org/W1971224531","https://openalex.org/W1973081915","https://openalex.org/W1975154158","https://openalex.org/W1978319180","https://openalex.org/W1983153145","https://openalex.org/W1989921625","https://openalex.org/W2005946215","https://openalex.org/W2006662238","https://openalex.org/W2007858891","https://openalex.org/W2008620264","https://openalex.org/W2020369705","https://openalex.org/W2023403198","https://openalex.org/W2025853251","https://openalex.org/W2031822229","https://openalex.org/W2032619610","https://openalex.org/W2035604667","https://openalex.org/W2036349801","https://openalex.org/W2036573675","https://openalex.org/W2038012561","https://openalex.org/W2038763999","https://openalex.org/W2039751039","https://openalex.org/W2042321087","https://openalex.org/W2044775606","https://openalex.org/W2045645277","https://openalex.org/W2049725457","https://openalex.org/W2051116946","https://openalex.org/W2053279361","https://openalex.org/W2053670382","https://openalex.org/W2055043387","https://openalex.org/W2055993805","https://openalex.org/W2056594786","https://openalex.org/W2061834091","https://openalex.org/W2065328929","https://openalex.org/W2070889260","https://openalex.org/W2074937753","https://openalex.org/W2077776831","https://openalex.org/W2078734278","https://openalex.org/W2078969200","https://openalex.org/W2080540350","https://openalex.org/W2088866770","https://openalex.org/W2088919509","https://openalex.org/W2091198609","https://openalex.org/W2101674614","https://openalex.org/W2102216585","https://openalex.org/W2102243804","https://openalex.org/W2103331163","https://openalex.org/W2104266531","https://openalex.org/W2104669330","https://openalex.org/W2107112420","https://openalex.org/W2108020239","https://openalex.org/W2109110326","https://openalex.org/W2109339694","https://openalex.org/W2110065044","https://openalex.org/W2110699703","https://openalex.org/W2110838395","https://openalex.org/W2111167674","https://openalex.org/W2111967267","https://openalex.org/W2112609377","https://openalex.org/W2113721899","https://openalex.org/W2113983551","https://openalex.org/W2116791869","https://openalex.org/W2120289437","https://openalex.org/W2121105996","https://openalex.org/W2126606094","https://openalex.org/W2127057035","https://openalex.org/W2130910556","https://openalex.org/W2131706188","https://openalex.org/W2134440848","https://openalex.org/W2134657106","https://openalex.org/W2136340808","https://openalex.org/W2137088684","https://openalex.org/W2139670593","https://openalex.org/W2140175819","https://openalex.org/W2140347764","https://openalex.org/W2140401788","https://openalex.org/W2142723924","https://openalex.org/W2143947945","https://openalex.org/W2147276070","https://openalex.org/W2151422033","https://openalex.org/W2151907070","https://openalex.org/W2151936673","https://openalex.org/W2152407435","https://openalex.org/W2152607628","https://openalex.org/W2153624566","https://openalex.org/W2154687435","https://openalex.org/W2155123192","https://openalex.org/W2156389165","https://openalex.org/W2156425900","https://openalex.org/W2159993062","https://openalex.org/W2162170584","https://openalex.org/W2162325607","https://openalex.org/W2167746224","https://openalex.org/W2168330282","https://openalex.org/W2171280873","https://openalex.org/W2171501215","https://openalex.org/W2295343779"],"related_works":["https://openalex.org/W2089823102","https://openalex.org/W2078723571","https://openalex.org/W1965189848","https://openalex.org/W4413805314","https://openalex.org/W7099238067","https://openalex.org/W1975154158","https://openalex.org/W2525183674","https://openalex.org/W2134763495","https://openalex.org/W3027504373","https://openalex.org/W1079606341"],"abstract_inverted_index":{"There":[0],"is":[1,48,53,166,199],"much":[2],"debate":[3],"about":[4],"the":[5,26,34,124],"evolutionary":[6,27],"origins":[7,28],"of":[8,29,36,70,110,126,155,161],"diversity":[9],"and":[10,33,100,138,186,193],"many":[11],"complex":[12,30],"gene":[13,41,66,129,144,163,197],"regulatory":[14,42,164],"network":[15,43,89,115,165],"features,":[16,31],"such":[17],"as":[18,202],"global":[19],"regulation.":[20],"Using":[21],"novel":[22],"in":[23,40,56,148,175],"silico":[24],"models":[25],"heterogeneity":[32],"role":[35],"stochastic":[37,127,142],"molecular":[38],"processes":[39],"evolution":[44],"are":[45,106,121,146],"investigated.":[46],"It":[47],"shown":[49],"that:":[50],"i)":[51],"Repression":[52],"essential,":[54],"even":[55],"constant":[57],"environments,":[58],"due":[59],"to":[60,76,91],"energetic":[61],"constraints.":[62],"ii)":[63],"Stochastic":[64],"basal":[65,128,143,156],"expression":[67],"forces":[68],"shrinkage":[69],"genomes,":[71],"whilst":[72],"its":[73],"absence":[74],"leads":[75],"\u2018bloating\u2019.":[77],"iii)":[78],"Models":[79],"evolved":[80,93,111],"towards":[81],"a":[82,86,162],"biological":[83],"goal":[84],"have":[85],"very":[87],"different":[88],"structure":[90],"nonadaptively":[92],"models.":[94],"iv)":[95],"Unstable":[96],"mRNA,":[97],"stable":[98],"protein":[99],"rapid":[101],"but":[102],"robust":[103],"replication":[104],"times":[105],"strongly":[107,200],"selected":[108,201],"properties":[109],"networks.":[112],"v)":[113],"Multiple":[114],"solutions":[116],"within":[117],"identical":[118],"environmental":[119,169,184],"conditions":[120],"observed":[122,147],"with":[123,136,140],"presence":[125],"expression.":[130,157],"vi)":[131],"Two":[132],"attractor":[133],"states,":[134],"one":[135,139],"high,":[137],"low":[141],"expression,":[145],"networks":[149],"which":[150],"can":[151,190],"evolve":[152],"their":[153],"levels":[154],"vii)":[158],"Functional":[159,172],"complexity":[160,173],"dependent":[167],"on":[168],"complexity.":[170],"viii)":[171],"evolves":[174],"hierarchical":[176],"stages,":[177],"requiring":[178],"\u2018core\u2019":[179],"energy":[180,205],"regulation":[181,198,206],"mechanisms":[182],"before":[183],"responses":[185],"adaptations":[187],"for":[188],"growth":[189],"be":[191],"sustained":[192],"fixed.":[194],"ix)":[195],"Global":[196],"an":[203],"efficient":[204],"mechanism":[207]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
