{"id":"https://openalex.org/W2094921372","doi":"https://doi.org/10.1186/1471-2105-12-56","title":"Simulated evolution applied to study the genetic code optimality using a model of codon reassignments","display_name":"Simulated evolution applied to study the genetic code optimality using a model of codon reassignments","publication_year":2011,"publication_date":"2011-02-21","ids":{"openalex":"https://openalex.org/W2094921372","doi":"https://doi.org/10.1186/1471-2105-12-56","mag":"2094921372","pmid":"https://pubmed.ncbi.nlm.nih.gov/21338505"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-56","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-56","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-56","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-56","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089427591","display_name":"Jos\u00e9 S\u00e1ntos","orcid":"https://orcid.org/0000-0002-4212-1367"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Jos\u00e9 Santos","raw_affiliation_strings":["Department of Computer Science, University of A Coru\u00f1a, Campus de Elvi\u00f1a s/n, 15071 A Coru\u00f1a, Spain. santos@udc.es","[Department of Computer Science, University of A Coru\u00f1a, Coruna, Spain]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of A Coru\u00f1a, Campus de Elvi\u00f1a s/n, 15071 A Coru\u00f1a, Spain. santos@udc.es","institution_ids":["https://openalex.org/I11019714"]},{"raw_affiliation_string":"[Department of Computer Science, University of A Coru\u00f1a, Coruna, Spain]","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042207033","display_name":"\u00c1ngel Monteagudo","orcid":"https://orcid.org/0000-0001-5185-8902"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"\u00c1ngel Monteagudo","raw_affiliation_strings":["Department of Computer Science, University of A Coru\u00f1a, Campus de Elvi\u00f1a s/n, 15071 A, Coru\u00f1a, Spain","[Department of Computer Science, University of A Coru\u00f1a, Coruna, Spain]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of A Coru\u00f1a, Campus de Elvi\u00f1a s/n, 15071 A, Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]},{"raw_affiliation_string":"[Department of Computer Science, University of A Coru\u00f1a, Coruna, Spain]","institution_ids":["https://openalex.org/I11019714"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5089427591"],"corresponding_institution_ids":["https://openalex.org/I11019714"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.2433,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.55834239,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"12","issue":"1","first_page":"56","last_page":"56"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.989300012588501,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.989300012588501,"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/T12029","display_name":"DNA and Biological Computing","score":0.001500000013038516,"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":0.0010999999940395355,"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/genetic-code","display_name":"Genetic code","score":0.839425802230835},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6483150124549866},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.6230537295341492},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3389095067977905},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22952476143836975},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1285601556301117},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09109795093536377},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.07917791604995728}],"concepts":[{"id":"https://openalex.org/C10853874","wikidata":"https://www.wikidata.org/wiki/Q180618","display_name":"Genetic code","level":3,"score":0.839425802230835},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6483150124549866},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.6230537295341492},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3389095067977905},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22952476143836975},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1285601556301117},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09109795093536377},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.07917791604995728},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-12-56","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-56","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-56","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21338505","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21338505","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:d1720649bb65454fa43ceb78ea82ff94","is_oa":true,"landing_page_url":"https://doaj.org/article/d1720649bb65454fa43ceb78ea82ff94","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 56 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2082616","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3053255","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-56","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-56","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-56","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2094921372.pdf","grobid_xml":"https://content.openalex.org/works/W2094921372.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W14944655","https://openalex.org/W647610110","https://openalex.org/W1487556868","https://openalex.org/W1594976728","https://openalex.org/W1606746638","https://openalex.org/W1969600369","https://openalex.org/W1978595049","https://openalex.org/W1983092742","https://openalex.org/W1992289347","https://openalex.org/W1992513326","https://openalex.org/W1992787480","https://openalex.org/W1995143868","https://openalex.org/W1998894699","https://openalex.org/W2000271800","https://openalex.org/W2018892842","https://openalex.org/W2021649088","https://openalex.org/W2054592804","https://openalex.org/W2062715887","https://openalex.org/W2064068553","https://openalex.org/W2072391778","https://openalex.org/W2080018045","https://openalex.org/W2081704490","https://openalex.org/W2091023609","https://openalex.org/W2098015235","https://openalex.org/W2100681850","https://openalex.org/W2105943646","https://openalex.org/W2116100216","https://openalex.org/W2134398014","https://openalex.org/W2139931049","https://openalex.org/W2140139413","https://openalex.org/W2163198599","https://openalex.org/W2167485371","https://openalex.org/W2294832214","https://openalex.org/W2915198056","https://openalex.org/W3023540311","https://openalex.org/W3157789364","https://openalex.org/W4251933787"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W1521141500","https://openalex.org/W4386881369","https://openalex.org/W1840178582","https://openalex.org/W2028550959","https://openalex.org/W2909998738","https://openalex.org/W3009119289","https://openalex.org/W2803882549"],"abstract_inverted_index":{"BACKGROUND:":[0],"As":[1],"the":[2,24,33,42,57,61,66,77,82,86,110,121,125,132,142,146,149,155,171,179,198,205,210,215,222,235,240,245,253,256,266,278,281,292,298,301,306,309,319,322,328,332,342,346],"canonical":[3,25,67,83,122,180,257,267,282,347],"code":[4,27,69,84,123,157,182,218,224,269,283],"is":[5,183,225,270],"not":[6,336],"universal,":[7],"different":[8],"theories":[9,54],"about":[10],"its":[11,275,339],"origin":[12],"and":[13,76,104,170,204,325],"organization":[14],"have":[15],"appeared.":[16],"The":[17],"optimization":[18],"or":[19],"level":[20,58],"of":[21,23,44,59,131,134,148,192,201,239,255,280,308,321,331,341,345],"adaptation":[22],"genetic":[26,68,95,156,181,217,258,268,311,348],"was":[28,243],"measured":[29],"taking":[30],"into":[31,289],"account":[32,290],"harmful":[34],"consequences":[35],"resulting":[36],"from":[37,166,186,227,272],"point":[38],"mutations":[39],"leading":[40],"to":[41,55,97,108,118,176,251,338],"replacement":[43],"one":[45,195],"amino":[46,159],"acid":[47,160],"for":[48,99],"another.":[49],"There":[50],"are":[51,287,315,335],"two":[52,190,211,293],"basic":[53],"measure":[56],"optimization:":[60],"statistical":[62,150,333],"approach,":[63,79,151,173],"which":[64,80,152,174,213],"compares":[65,81],"with":[70,85,291,318],"many":[71],"randomly":[72],"generated":[73],"alternative":[74,115],"ones,":[75],"engineering":[78,172,323],"best":[87,302],"possible":[88,229,303],"alternative.":[89],"RESULTS:":[90],"Here":[91],"we":[92],"used":[93,189,208],"a":[94,106,138,167,228],"algorithm":[96,247],"search":[98],"better":[100,163],"adapted":[101],"hypothetical":[102,193],"codes":[103,304],"as":[105,295],"method":[107],"guess":[109],"difficulty":[111,250],"in":[112,124,141,209,316],"finding":[113],"such":[114],"codes,":[116],"allowing":[117],"clearly":[119,263],"situate":[120],"fitness":[126],"landscape.":[127],"This":[128],"novel":[129],"proposal":[130],"use":[133,147],"evolutionary":[135,246],"computing":[136],"provides":[137],"new":[139],"perspective":[140],"open":[143],"debate":[144],"between":[145],"postulates":[153,320],"that":[154,178,196,265,300,327],"conserves":[158],"properties":[161],"far":[162,185,226,271],"than":[164],"expected":[165],"random":[168],"code,":[169],"tends":[175],"indicate":[177,326],"still":[184],"optimal.":[187],"We":[188],"models":[191],"codes:":[194],"reflects":[197,214],"known":[199],"examples":[200],"codon":[202,241],"reassignment":[203],"model":[206,238],"most":[207],"approaches":[212],"current":[216],"translation":[219],"table.":[220],"Although":[221],"standard":[223,310],"optimum":[230],"considering":[231],"both":[232],"models,":[233,294],"when":[234,285],"more":[236,249],"realistic":[237],"reassignments":[242],"used,":[244],"had":[248],"overcome":[252],"efficiency":[254,279,344],"code.":[259,312,349],"CONCLUSIONS:":[260],"Simulated":[261],"evolution":[262],"reveals":[264],"optimal":[273],"regarding":[274],"optimization.":[276],"Nevertheless,":[277],"increases":[284],"mistranslations":[286],"taken":[288],"indicated":[296],"by":[297],"fact":[299],"show":[305],"patterns":[307],"Our":[313],"results":[314],"accordance":[317],"approach":[324,334],"main":[329],"arguments":[330],"enough":[337],"assertion":[340],"extreme":[343]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
