{"id":"https://openalex.org/W1986200293","doi":"https://doi.org/10.1109/cibcb.2012.6217237","title":"Evolution in silico of genes with multiple regulatory modules on the example of the Drosophila segmentation gene hunchback","display_name":"Evolution in silico of genes with multiple regulatory modules on the example of the Drosophila segmentation gene hunchback","publication_year":2012,"publication_date":"2012-05-01","ids":{"openalex":"https://openalex.org/W1986200293","doi":"https://doi.org/10.1109/cibcb.2012.6217237","mag":"1986200293"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2012.6217237","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2012.6217237","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","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/A5002399513","display_name":"Alexander V. Spirov","orcid":"https://orcid.org/0000-0002-0509-6203"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A. V. Spirov","raw_affiliation_strings":["Computer Science and CEWIT, SUNY Stony Brook, Stony Brook, NY, USA","Computer Science and CEWIT, SUNY Stony Brook, New York, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and CEWIT, SUNY Stony Brook, Stony Brook, NY, USA","institution_ids":["https://openalex.org/I59553526"]},{"raw_affiliation_string":"Computer Science and CEWIT, SUNY Stony Brook, New York, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024247574","display_name":"David M. Holloway","orcid":"https://orcid.org/0000-0002-3865-0725"},"institutions":[{"id":"https://openalex.org/I174167972","display_name":"British Columbia Institute of Technology","ror":"https://ror.org/01p65pg69","country_code":"CA","type":"education","lineage":["https://openalex.org/I174167972"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"D. M. Holloway","raw_affiliation_strings":["Mathematics Department, British Columbia Institute of Technology, Burnaby, BC, Canada","Mathematics Dept., British Columbia Institute of Technology, Burnaby, Canada"],"affiliations":[{"raw_affiliation_string":"Mathematics Department, British Columbia Institute of Technology, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I174167972"]},{"raw_affiliation_string":"Mathematics Dept., British Columbia Institute of Technology, Burnaby, Canada","institution_ids":["https://openalex.org/I174167972"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5002399513"],"corresponding_institution_ids":["https://openalex.org/I59553526"],"apc_list":null,"apc_paid":null,"fwci":0.5253,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.6369324,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"5","issue":null,"first_page":"244","last_page":"251"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","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/T10222","display_name":"Genomics and Chromatin Dynamics","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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.9962999820709229,"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/in-silico","display_name":"In silico","score":0.8630220293998718},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6623386740684509},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6405069828033447},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.580047070980072},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5520737171173096},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.44455111026763916},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.44022318720817566},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3898933529853821},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.36941084265708923},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36897796392440796},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22328594326972961},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17206528782844543}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.8630220293998718},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6623386740684509},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6405069828033447},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.580047070980072},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5520737171173096},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.44455111026763916},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.44022318720817566},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3898933529853821},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.36941084265708923},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36897796392440796},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22328594326972961},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17206528782844543}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2012.6217237","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2012.6217237","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W81844578","https://openalex.org/W312600982","https://openalex.org/W1681307731","https://openalex.org/W1911065410","https://openalex.org/W1967141690","https://openalex.org/W1982037385","https://openalex.org/W1984336487","https://openalex.org/W1993852484","https://openalex.org/W2004485739","https://openalex.org/W2010795839","https://openalex.org/W2014366092","https://openalex.org/W2019998456","https://openalex.org/W2025665146","https://openalex.org/W2038591490","https://openalex.org/W2038701440","https://openalex.org/W2041791362","https://openalex.org/W2051561348","https://openalex.org/W2053850816","https://openalex.org/W2056290740","https://openalex.org/W2056680906","https://openalex.org/W2076083354","https://openalex.org/W2077122170","https://openalex.org/W2080444658","https://openalex.org/W2084728047","https://openalex.org/W2087859062","https://openalex.org/W2088252348","https://openalex.org/W2103526067","https://openalex.org/W2111936337","https://openalex.org/W2118581428","https://openalex.org/W2122373933","https://openalex.org/W2133870073","https://openalex.org/W2135061355","https://openalex.org/W2136154640","https://openalex.org/W2141948525","https://openalex.org/W2146759626","https://openalex.org/W2168059187","https://openalex.org/W2171193618","https://openalex.org/W2341283081"],"related_works":["https://openalex.org/W2912862995","https://openalex.org/W3129816939","https://openalex.org/W2985427592","https://openalex.org/W2101501829","https://openalex.org/W2003194288","https://openalex.org/W2400569965","https://openalex.org/W2060263731","https://openalex.org/W391093122","https://openalex.org/W1521239975","https://openalex.org/W4361305867"],"abstract_inverted_index":{"We":[0,42,86],"use":[1,43],"in":[2,18,74,89,123,128,132,135,143,144],"silico":[3,145],"evolution":[4],"to":[5,45,58,64,105,111],"study":[6],"the":[7,23,30,36,40,47,53,83,90,96,140,162],"generation":[8],"of":[9,16,39,49,62,69,82,92,151],"gene":[10,26],"regulatory":[11,27],"structures.":[12],"A":[13],"particular":[14,130],"area":[15],"interest":[17],"evolutionary":[19,146],"development":[20],"(evo-devo)":[21],"is":[22,155],"correspondence":[24,116],"between":[25],"sequences":[28],"on":[29,95],"DNA":[31],"(cis-regulatory":[32],"modules,":[33],"CRMs)":[34],"and":[35],"spatial":[37,65,102],"expression":[38],"genes.":[41],"computation":[44],"investigate":[46],"incorporation":[48],"new":[50],"CRMs":[51,99],"into":[52],"genome.":[54],"Simulations":[55],"allow":[56],"us":[57],"characterize":[59],"different":[60,84],"cases":[61,71,150],"CRM":[63],"pattern":[66,125],"correspondence.":[67],"Many":[68],"these":[70],"are":[72],"seen":[73],"biological":[75,149],"examples;":[76],"our":[77],"simulations":[78],"indicate":[79],"relative":[80],"advantages":[81,160],"scenarios.":[85],"find":[87],"that,":[88],"absence":[91],"specific":[93],"constraints":[94],"CRM-pattern":[97,114],"correspondence,":[98],"controlling":[100],"multiple":[101],"domains":[103,126],"tend":[104],"evolve":[106,117],"very":[107],"quickly.":[108],"Genes":[109],"constrained":[110],"a":[112,129],"one-to-one":[113],"domain":[115],"more":[118],"slowly.":[119],"Of":[120],"these,":[121],"systems":[122],"which":[124],"appear":[127],"order":[131],"evolution,":[133],"as":[134],"insect":[136],"segmentation":[137],"mechanisms,":[138],"take":[139],"longest":[141],"time":[142,163],"searches.":[147],"For":[148],"this":[152],"type,":[153],"it":[154],"likely":[156],"that":[157],"other":[158],"selective":[159],"outweigh":[161],"costs.":[164]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}