{"id":"https://openalex.org/W2086944191","doi":"https://doi.org/10.1142/s0129626414400040","title":"Evolutionary Design of Gene Networks: Forced Evolution by Genomic Parasites","display_name":"Evolutionary Design of Gene Networks: Forced Evolution by Genomic Parasites","publication_year":2014,"publication_date":"2014-06-01","ids":{"openalex":"https://openalex.org/W2086944191","doi":"https://doi.org/10.1142/s0129626414400040","mag":"2086944191","pmid":"https://pubmed.ncbi.nlm.nih.gov/25558118"},"language":"en","primary_location":{"id":"doi:10.1142/s0129626414400040","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0129626414400040","pdf_url":null,"source":{"id":"https://openalex.org/S18360026","display_name":"Parallel Processing Letters","issn_l":"0129-6264","issn":["0129-6264","1793-642X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319815","host_organization_name":"World Scientific","host_organization_lineage":["https://openalex.org/P4310319815"],"host_organization_lineage_names":["World Scientific"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Parallel Processing Letters","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4279919","any_repository_has_fulltext":true},"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/I163234304","display_name":"Institute of Evolutionary Physiology and Biochemistry","ror":"https://ror.org/02vf4sk45","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I163234304","https://openalex.org/I4210115279"]},{"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":["RU","US"],"is_corresponding":true,"raw_author_name":"A. V. Spirov","raw_affiliation_strings":["Computer Science and CEWIT, SUNY Stony Brook, 1500 Stony Brook Road, Stony Brook, NY 11794, USA","The Sechenov Institute of Evolutionary Physiology &amp; Biochemistry, Thorez Pr. 44, St.-Petersburg, 2194223, Russia"],"affiliations":[{"raw_affiliation_string":"Computer Science and CEWIT, SUNY Stony Brook, 1500 Stony Brook Road, Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]},{"raw_affiliation_string":"The Sechenov Institute of Evolutionary Physiology &amp; Biochemistry, Thorez Pr. 44, St.-Petersburg, 2194223, Russia","institution_ids":["https://openalex.org/I163234304"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5097457862","display_name":"E. A. Zagriychuk","orcid":null},"institutions":[{"id":"https://openalex.org/I163234304","display_name":"Institute of Evolutionary Physiology and Biochemistry","ror":"https://ror.org/02vf4sk45","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I163234304","https://openalex.org/I4210115279"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"E. A. Zagriychuk","raw_affiliation_strings":["The Sechenov Institute of Evolutionary Physiology &amp; Biochemistry, Thorez Pr. 44, St.-Petersburg, 2194223, Russia"],"affiliations":[{"raw_affiliation_string":"The Sechenov Institute of Evolutionary Physiology &amp; Biochemistry, Thorez Pr. 44, St.-Petersburg, 2194223, Russia","institution_ids":["https://openalex.org/I163234304"]}]},{"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, 3700 Willingdon Avenue, Burnaby, B.C., Canada, V5G 3H2, Canada"],"affiliations":[{"raw_affiliation_string":"Mathematics Department, British Columbia Institute of Technology, 3700 Willingdon Avenue, Burnaby, B.C., Canada, V5G 3H2, Canada","institution_ids":["https://openalex.org/I174167972"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5002399513"],"corresponding_institution_ids":["https://openalex.org/I163234304","https://openalex.org/I59553526"],"apc_list":null,"apc_paid":null,"fwci":0.6867,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.75330892,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"24","issue":"02","first_page":"1440004","last_page":"1440004"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9959999918937683,"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"}},"topics":[{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9959999918937683,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9850000143051147,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9545000195503235,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5031606554985046},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4525252878665924},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44004693627357483},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39083975553512573},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3686434030532837},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3591367304325104}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5031606554985046},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4525252878665924},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44004693627357483},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39083975553512573},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3686434030532837},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3591367304325104}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1142/s0129626414400040","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0129626414400040","pdf_url":null,"source":{"id":"https://openalex.org/S18360026","display_name":"Parallel Processing Letters","issn_l":"0129-6264","issn":["0129-6264","1793-642X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319815","host_organization_name":"World Scientific","host_organization_lineage":["https://openalex.org/P4310319815"],"host_organization_lineage_names":["World Scientific"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Parallel Processing Letters","raw_type":"journal-article"},{"id":"pmid:25558118","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25558118","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Parallel processing letters","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4279919","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4279919","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Parallel Process Lett","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4279919","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4279919","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Parallel Process Lett","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6200000047683716}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":68,"referenced_works":["https://openalex.org/W130232500","https://openalex.org/W1497734866","https://openalex.org/W1506718397","https://openalex.org/W1513093379","https://openalex.org/W1516096933","https://openalex.org/W1522541248","https://openalex.org/W1533873536","https://openalex.org/W1555689267","https://openalex.org/W1560976090","https://openalex.org/W1572671086","https://openalex.org/W1580772087","https://openalex.org/W1581004196","https://openalex.org/W1582237901","https://openalex.org/W1603509790","https://openalex.org/W1729182382","https://openalex.org/W1919765549","https://openalex.org/W1965368044","https://openalex.org/W1968175031","https://openalex.org/W1969860532","https://openalex.org/W1986200293","https://openalex.org/W1991138583","https://openalex.org/W1992415335","https://openalex.org/W1993414024","https://openalex.org/W1994677936","https://openalex.org/W2004289452","https://openalex.org/W2005272877","https://openalex.org/W2008864177","https://openalex.org/W2009269708","https://openalex.org/W2010586622","https://openalex.org/W2010795839","https://openalex.org/W2032682319","https://openalex.org/W2034536549","https://openalex.org/W2036527184","https://openalex.org/W2038157607","https://openalex.org/W2038378062","https://openalex.org/W2041231245","https://openalex.org/W2047759247","https://openalex.org/W2048013262","https://openalex.org/W2053076760","https://openalex.org/W2055560965","https://openalex.org/W2059289565","https://openalex.org/W2063076326","https://openalex.org/W2080252841","https://openalex.org/W2088252348","https://openalex.org/W2099949533","https://openalex.org/W2101186976","https://openalex.org/W2101443742","https://openalex.org/W2109680439","https://openalex.org/W2110146147","https://openalex.org/W2111857816","https://openalex.org/W2111936337","https://openalex.org/W2117564498","https://openalex.org/W2136154640","https://openalex.org/W2137057693","https://openalex.org/W2137600096","https://openalex.org/W2141948525","https://openalex.org/W2148950943","https://openalex.org/W2149545618","https://openalex.org/W2155802383","https://openalex.org/W2161481249","https://openalex.org/W2165853777","https://openalex.org/W2167889627","https://openalex.org/W2341283081","https://openalex.org/W2422272716","https://openalex.org/W2488906289","https://openalex.org/W2574841843","https://openalex.org/W2984808340","https://openalex.org/W4251302249"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2034625591","https://openalex.org/W2061542922"],"abstract_inverted_index":{"The":[0],"co-evolution":[1],"of":[2,14,18,43,55,59,112,119],"species":[3],"with":[4],"their":[5,116],"genomic":[6],"parasites":[7],"(transposons)":[8],"is":[9],"thought":[10],"to":[11,53,62,65],"be":[12],"one":[13],"the":[15,34,40,66,71,101,110],"primary":[16],"ways":[17],"rewiring":[19],"gene":[20],"regulatory":[21],"networks":[22],"(GRNs).":[23],"We":[24,37,69,105],"develop":[25],"a":[26,79],"framework":[27],"for":[28,49],"conducting":[29],"evolutionary":[30,47],"computations":[31],"(EC)":[32],"using":[33],"transposon":[35],"mechanism.":[36],"find":[38],"that":[39],"selective":[41],"pressure":[42],"transposons":[44],"can":[45,77,91],"speed":[46],"searches":[48],"solutions":[50],"and":[51,115],"lead":[52],"outgrowth":[54],"GRNs":[56,75,86,114],"(through":[57],"co-option":[58],"new":[60],"genes":[61],"acquire":[63],"insensitivity":[64],"attacking":[67],"transposons).":[68],"test":[70],"approach":[72],"by":[73,103],"finding":[74],"which":[76],"solve":[78],"fundamental":[80],"problem":[81],"in":[82,87,109],"developmental":[83],"biology:":[84],"how":[85],"early":[88],"embryo":[89],"development":[90],"robustly":[92],"read":[93],"maternal":[94],"signaling":[95],"gradients,":[96],"despite":[97],"continued":[98],"attacks":[99],"on":[100],"genome":[102],"transposons.":[104],"observed":[106],"co-evolutionary":[107],"oscillations":[108],"abundance":[111],"particular":[113],"transposons,":[117],"reminiscent":[118],"predator-prey":[120],"or":[121],"host-parasite":[122],"dynamics.":[123]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
