{"id":"https://openalex.org/W1963936925","doi":"https://doi.org/10.1186/1471-2105-13-62","title":"CBDB: The codon bias database","display_name":"CBDB: The codon bias database","publication_year":2012,"publication_date":"2012-04-26","ids":{"openalex":"https://openalex.org/W1963936925","doi":"https://doi.org/10.1186/1471-2105-13-62","mag":"1963936925","pmid":"https://pubmed.ncbi.nlm.nih.gov/22536831"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-62","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-62","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-62","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/10.1186/1471-2105-13-62","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060275425","display_name":"Adam Hilterbrand","orcid":null},"institutions":[{"id":"https://openalex.org/I1925986","display_name":"Loyola University Chicago","ror":"https://ror.org/04b6x2g63","country_code":"US","type":"education","lineage":["https://openalex.org/I1925986"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Adam Hilterbrand","raw_affiliation_strings":["Department of Biology, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL 60660, USA","Department of Biology, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL, 60660, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL 60660, USA","institution_ids":[]},{"raw_affiliation_string":"Department of Biology, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL, 60660, USA","institution_ids":["https://openalex.org/I1925986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004877981","display_name":"Joseph W. Saelens","orcid":"https://orcid.org/0000-0002-6263-7950"},"institutions":[{"id":"https://openalex.org/I1925986","display_name":"Loyola University Chicago","ror":"https://ror.org/04b6x2g63","country_code":"US","type":"education","lineage":["https://openalex.org/I1925986"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph Saelens","raw_affiliation_strings":["Bioinformatics Program, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL, 60660, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Program, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL, 60660, USA","institution_ids":["https://openalex.org/I1925986"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033333203","display_name":"Catherine Putonti","orcid":"https://orcid.org/0000-0003-3049-5991"},"institutions":[{"id":"https://openalex.org/I1925986","display_name":"Loyola University Chicago","ror":"https://ror.org/04b6x2g63","country_code":"US","type":"education","lineage":["https://openalex.org/I1925986"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Catherine Putonti","raw_affiliation_strings":["Bioinformatics Program, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL, 60660, USA","Department of Biology, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL, 60660, USA","Department of Computer Science, Loyola University Chicago, 820 N Michigan Avenue, Chicago, IL, 60611, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Program, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL, 60660, USA","institution_ids":["https://openalex.org/I1925986"]},{"raw_affiliation_string":"Department of Biology, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL, 60660, USA","institution_ids":["https://openalex.org/I1925986"]},{"raw_affiliation_string":"Department of Computer Science, Loyola University Chicago, 820 N Michigan Avenue, Chicago, IL, 60611, USA","institution_ids":["https://openalex.org/I1925986"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060275425"],"corresponding_institution_ids":["https://openalex.org/I1925986"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.342,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.78878349,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"13","issue":"1","first_page":"62","last_page":"62"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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":0.998199999332428,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9948999881744385,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.9068818688392639},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.666326105594635},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5805975198745728},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.486247181892395},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4600546061992645},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4543459117412567},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3749929666519165},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.26611918210983276},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.08141884207725525}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.9068818688392639},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.666326105594635},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5805975198745728},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.486247181892395},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4600546061992645},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4543459117412567},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3749929666519165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.26611918210983276},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.08141884207725525}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-13-62","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-62","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-62","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:22536831","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22536831","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:ecommons.luc.edu:bioinformatics_facpub-1002","is_oa":true,"landing_page_url":"https://ecommons.luc.edu/bioinformatics_facpub/3","pdf_url":"https://ecommons.luc.edu/bioinformatics_facpub/3","source":{"id":"https://openalex.org/S4306402030","display_name":"Loyola eCommons (Loyola University of Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1925986","host_organization_name":"Loyola University Chicago","host_organization_lineage":["https://openalex.org/I1925986"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics Faculty Publications","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:e19cf29a80c84452be0d034a115203ca","is_oa":true,"landing_page_url":"https://doaj.org/article/e19cf29a80c84452be0d034a115203ca","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 13, Iss 1, p 62 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2462340","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3463423","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:10.1186/1471-2105-13-62","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-62","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-62","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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.4699999988079071}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309973","display_name":"Loyola University Chicago","ror":"https://ror.org/04b6x2g63"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1963936925.pdf","grobid_xml":"https://content.openalex.org/works/W1963936925.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W1489817806","https://openalex.org/W1603411458","https://openalex.org/W1692054786","https://openalex.org/W1966773394","https://openalex.org/W1989632697","https://openalex.org/W1992404702","https://openalex.org/W2004674004","https://openalex.org/W2012249377","https://openalex.org/W2017057004","https://openalex.org/W2018330825","https://openalex.org/W2018590530","https://openalex.org/W2022726657","https://openalex.org/W2024014229","https://openalex.org/W2024299495","https://openalex.org/W2025569664","https://openalex.org/W2029782419","https://openalex.org/W2030564603","https://openalex.org/W2031984001","https://openalex.org/W2032227859","https://openalex.org/W2036649644","https://openalex.org/W2042548693","https://openalex.org/W2048673910","https://openalex.org/W2051043527","https://openalex.org/W2051242197","https://openalex.org/W2051406384","https://openalex.org/W2065371606","https://openalex.org/W2066829062","https://openalex.org/W2078755055","https://openalex.org/W2080731394","https://openalex.org/W2081747108","https://openalex.org/W2082607332","https://openalex.org/W2082748330","https://openalex.org/W2084241014","https://openalex.org/W2095868955","https://openalex.org/W2096160166","https://openalex.org/W2096406964","https://openalex.org/W2103091054","https://openalex.org/W2107804881","https://openalex.org/W2122388777","https://openalex.org/W2127435852","https://openalex.org/W2135047442","https://openalex.org/W2140870757","https://openalex.org/W2142997034","https://openalex.org/W2143221412","https://openalex.org/W2144870003","https://openalex.org/W2147126179","https://openalex.org/W2148734328","https://openalex.org/W2150754067","https://openalex.org/W2151314777","https://openalex.org/W2151632575","https://openalex.org/W2157613837","https://openalex.org/W2157848631","https://openalex.org/W2160514369","https://openalex.org/W2161167739","https://openalex.org/W2162198705","https://openalex.org/W2164618276","https://openalex.org/W2166752189","https://openalex.org/W2167868583","https://openalex.org/W2168036974","https://openalex.org/W4237577688"],"related_works":["https://openalex.org/W2355920812","https://openalex.org/W2910946914","https://openalex.org/W2129444033","https://openalex.org/W2094816155","https://openalex.org/W1991670061","https://openalex.org/W2987420353","https://openalex.org/W1491897707","https://openalex.org/W2102511336","https://openalex.org/W2921764584","https://openalex.org/W1866610019"],"abstract_inverted_index":{"Comparing":[0],"species":[1,48],"and":[2,18,37,49],"strains":[3,62],"provides":[4,30],"a":[5,31,43,71,74],"comprehensive":[6],"look":[7],"at":[8],"how":[9],"codon":[10,38,58,75],"usage":[11,39,59],"has":[12],"been":[13],"shaped":[14],"over":[15],"evolutionary":[16],"time":[17],"can":[19],"elucidate":[20],"the":[21,55,61],"putative":[22],"mechanisms":[23],"behind":[24],"it.":[25],"The":[26],"Codon":[27],"Bias":[28],"Database":[29],"centralized":[32],"repository":[33],"of":[34,46,54,70,82,90],"look-up":[35],"tables":[36],"bias":[40],"measures":[41],"for":[42],"wide":[44],"variety":[45],"genera,":[47],"strains.":[50],"Through":[51],"our":[52],"analysis":[53],"variation":[56],"in":[57],"within":[60],"presently":[63],"available,":[64],"we":[65],"find":[66],"that":[67],"most":[68,77],"members":[69,81,89],"genus":[72],"have":[73],"composition":[76],"similar":[78],"to":[79],"other":[80,88],"its":[83,91],"genus,":[84],"although":[85],"not":[86],"necessarily":[87],"species.":[92]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
