{"id":"https://openalex.org/W2070120657","doi":"https://doi.org/10.1080/03081070500502967","title":"CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes","display_name":"CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes","publication_year":2006,"publication_date":"2006-01-31","ids":{"openalex":"https://openalex.org/W2070120657","doi":"https://doi.org/10.1080/03081070500502967","mag":"2070120657"},"language":"en","primary_location":{"id":"doi:10.1080/03081070500502967","is_oa":false,"landing_page_url":"https://doi.org/10.1080/03081070500502967","pdf_url":null,"source":{"id":"https://openalex.org/S145553572","display_name":"International Journal of General Systems","issn_l":"0308-1079","issn":["0308-1079","1026-7492","1563-5104"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547"],"host_organization_lineage_names":["Taylor & Francis"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of General Systems","raw_type":"journal-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/A5038575631","display_name":"Xiu\u2010Feng Wan","orcid":"https://orcid.org/0000-0003-2629-9234"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"X.-F. Wan","raw_affiliation_strings":["University of Missouri, Digital Biology Laboratory, Department of Computer Science , Columbia, MO, 65211, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Digital Biology Laboratory, Department of Computer Science , Columbia, MO, 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011788533","display_name":"Jizhong Zhou","orcid":"https://orcid.org/0000-0003-2014-0564"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Zhou","raw_affiliation_strings":["Oak Ridge National Laboratory, Environmental Sciences Division , Oak Ridge, TN, 37831, USA","Oak Ridge National Laboratory, Environmental Sciences Division, Oak Ridge, TN 37831, USA"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory, Environmental Sciences Division , Oak Ridge, TN, 37831, USA","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Oak Ridge National Laboratory, Environmental Sciences Division, Oak Ridge, TN 37831, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082428303","display_name":"Dong Xu","orcid":"https://orcid.org/0000-0002-4809-0514"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"D. Xu","raw_affiliation_strings":["University of Missouri, Digital Biology Laboratory, Department of Computer Science , Columbia, MO, 65211, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri, Digital Biology Laboratory, Department of Computer Science , Columbia, MO, 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082428303"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":0.2649,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.56726022,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"35","issue":"1","first_page":"109","last_page":"125"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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":1.0,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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/T11482","display_name":"RNA modifications and cancer","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"}}],"keywords":[{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.9118058085441589},{"id":"https://openalex.org/keywords/synonymous-substitution","display_name":"Synonymous substitution","score":0.5146511793136597},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4940353035926819},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4785459637641907},{"id":"https://openalex.org/keywords/gc-content","display_name":"GC-content","score":0.4596005082130432},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4594889283180237},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.42643728852272034},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.42144694924354553},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4171696901321411}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.9118058085441589},{"id":"https://openalex.org/C138025448","wikidata":"https://www.wikidata.org/wiki/Q7662597","display_name":"Synonymous substitution","level":5,"score":0.5146511793136597},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4940353035926819},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4785459637641907},{"id":"https://openalex.org/C42251679","wikidata":"https://www.wikidata.org/wiki/Q933491","display_name":"GC-content","level":4,"score":0.4596005082130432},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4594889283180237},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.42643728852272034},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.42144694924354553},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4171696901321411},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1080/03081070500502967","is_oa":false,"landing_page_url":"https://doi.org/10.1080/03081070500502967","pdf_url":null,"source":{"id":"https://openalex.org/S145553572","display_name":"International Journal of General Systems","issn_l":"0308-1079","issn":["0308-1079","1026-7492","1563-5104"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547"],"host_organization_lineage_names":["Taylor & Francis"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of General Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306250","display_name":"Battelle","ror":"https://ror.org/01h5tnr73"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"},{"id":"https://openalex.org/F4320338287","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W616447529","https://openalex.org/W623131249","https://openalex.org/W1550695177","https://openalex.org/W1603411458","https://openalex.org/W1610001324","https://openalex.org/W1878315031","https://openalex.org/W1974557906","https://openalex.org/W1977790594","https://openalex.org/W1986136768","https://openalex.org/W1990453950","https://openalex.org/W1997031479","https://openalex.org/W2000828331","https://openalex.org/W2002677631","https://openalex.org/W2009170200","https://openalex.org/W2018590530","https://openalex.org/W2019375816","https://openalex.org/W2030205072","https://openalex.org/W2031984001","https://openalex.org/W2033145713","https://openalex.org/W2034140573","https://openalex.org/W2039313637","https://openalex.org/W2040857454","https://openalex.org/W2047521874","https://openalex.org/W2051043527","https://openalex.org/W2058433720","https://openalex.org/W2060020017","https://openalex.org/W2065120930","https://openalex.org/W2068691391","https://openalex.org/W2070163065","https://openalex.org/W2076925679","https://openalex.org/W2093034082","https://openalex.org/W2100002703","https://openalex.org/W2102332636","https://openalex.org/W2113824405","https://openalex.org/W2133636765","https://openalex.org/W2133790733","https://openalex.org/W2138653126","https://openalex.org/W2138721124","https://openalex.org/W2141524685","https://openalex.org/W2151632575","https://openalex.org/W2156536014","https://openalex.org/W2164618276","https://openalex.org/W2165810656","https://openalex.org/W2165810896","https://openalex.org/W4213265720"],"related_works":["https://openalex.org/W2391050383","https://openalex.org/W2092093943","https://openalex.org/W2153784832","https://openalex.org/W2059628904","https://openalex.org/W2113191934","https://openalex.org/W1983257336","https://openalex.org/W2108090983","https://openalex.org/W2992558252","https://openalex.org/W2885909283","https://openalex.org/W2360418514"],"abstract_inverted_index":{"Codon":[0],"usage":[1,14,55,71,88,95,131],"bias":[2,15,56,72,96,147],"reveals":[3],"the":[4,12,67,111,138,157,164,180],"silent":[5],"molecular":[6],"evolution":[7],"pattern.":[8],"Previous":[9],"research":[10],"showed":[11],"codon":[13,33,54,70,87,94,130,139,146],"was":[16,107],"associated":[17,127],"with":[18,124,128,137,168],"many":[19],"biological":[20],"processes,":[21],"such":[22],"as":[23,85],"protein":[24],"expression":[25,192],"level,":[26],"genetic":[27],"coding":[28],"error":[29],"minimization,":[30],"mRNA":[31,185],"stability,":[32],"context,":[34],"tRNA":[35],"richness,":[36],"CpG":[37],"suppression,":[38],"DNA":[39],"methylation,":[40],"and":[41,98,151,161,163,173,184],"tissue":[42],"or":[43],"organ":[44],"specificity.":[45],"In":[46,101,176],"this":[47,102],"paper":[48],"we":[49,77,178],"reviewed":[50],"major":[51],"methods":[52,62],"of":[53,60,69,113,166],"measurement.":[57],"Since":[58],"most":[59],"existing":[61],"are":[63],"only":[64],"suitable":[65],"for":[66,144],"comparison":[68],"within":[73,97],"a":[74,79,117],"single":[75],"genome,":[76],"introduced":[78],"new":[80],"informatics":[81],"index,":[82],"referred":[83],"to":[84,91,109,122],"synonymous":[86,93],"order":[89],"(SCUO),":[90],"measure":[92],"across":[99],"genomes.":[100],"method,":[103],"Shannon":[104],"informational":[105],"theory":[106],"applied":[108],"describe":[110],"SCUO":[112,160,167,183],"each":[114],"gene":[115,169,171],"using":[116,190],"value":[118],"ranging":[119],"from":[120],"0":[121],"1,":[123],"larger":[125],"values":[126],"greater":[129],"bias.":[132],"We":[133,154],"compared":[134],"our":[135],"method":[136,143],"adaptation":[140],"index":[141],"(CAI)":[142],"measuring":[145],"in":[148,187],"Escherichia":[149],"coli":[150],"Sacharomyces":[152],"cerevisiae.":[153],"also":[155],"studied":[156],"correlation":[158,181],"between":[159,182],"CAI,":[162],"relation":[165],"length,":[170],"function,":[172],"GC":[174],"composition.":[175],"addition,":[177],"explored":[179],"abundance":[186],"S.":[188],"cerevisiae":[189],"SAGE":[191],"data.":[193],"The":[194],"software":[195],"package":[196],"codonO":[197],"is":[198],"freely":[199],"available":[200],"at":[201],"http://digbio.missouri.edu/\u223cwanx/cu/codonO/.":[202]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"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"}