{"id":"https://openalex.org/W2145163339","doi":"https://doi.org/10.1186/1471-2105-10-167","title":"Measure of synonymous codon usage diversity among genes in bacteria","display_name":"Measure of synonymous codon usage diversity among genes in bacteria","publication_year":2009,"publication_date":"2009-06-01","ids":{"openalex":"https://openalex.org/W2145163339","doi":"https://doi.org/10.1186/1471-2105-10-167","mag":"2145163339","pmid":"https://pubmed.ncbi.nlm.nih.gov/19480720"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-167","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-167","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-167","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/10.1186/1471-2105-10-167","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013235276","display_name":"Haruo Suzuki","orcid":"https://orcid.org/0000-0003-1447-6109"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]},{"id":"https://openalex.org/I112524849","display_name":"Yamagata University","ror":"https://ror.org/00xy44n04","country_code":"JP","type":"education","lineage":["https://openalex.org/I112524849"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Haruo Suzuki","raw_affiliation_strings":["Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan. haruo@g-language.org","Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan"],"affiliations":[{"raw_affiliation_string":"Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan. haruo@g-language.org","institution_ids":["https://openalex.org/I112524849"]},{"raw_affiliation_string":"Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015600215","display_name":"Rintaro Saito","orcid":"https://orcid.org/0000-0001-9084-8045"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Rintaro Saito","raw_affiliation_strings":["Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan"],"affiliations":[{"raw_affiliation_string":"Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015575713","display_name":"Masaru Tomita","orcid":"https://orcid.org/0000-0003-3423-377X"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masaru Tomita","raw_affiliation_strings":["Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan"],"affiliations":[{"raw_affiliation_string":"Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan","institution_ids":["https://openalex.org/I203951103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5013235276"],"corresponding_institution_ids":["https://openalex.org/I112524849","https://openalex.org/I203951103"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.8088,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.72611522,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"10","issue":"1","first_page":"167","last_page":"167"},"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":0.9994000196456909,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9908999800682068,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.8533512949943542},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6851054430007935},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6356298327445984},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6241709589958191},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5941332578659058},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4690946340560913},{"id":"https://openalex.org/keywords/diversity","display_name":"Diversity (politics)","score":0.439027339220047},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.4278194308280945},{"id":"https://openalex.org/keywords/synonymous-substitution","display_name":"Synonymous substitution","score":0.4219476878643036},{"id":"https://openalex.org/keywords/gc-content","display_name":"GC-content","score":0.42173904180526733},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.392875611782074},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.32262250781059265},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10334041714668274}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.8533512949943542},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6851054430007935},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6356298327445984},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6241709589958191},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5941332578659058},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4690946340560913},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.439027339220047},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.4278194308280945},{"id":"https://openalex.org/C138025448","wikidata":"https://www.wikidata.org/wiki/Q7662597","display_name":"Synonymous substitution","level":5,"score":0.4219476878643036},{"id":"https://openalex.org/C42251679","wikidata":"https://www.wikidata.org/wiki/Q933491","display_name":"GC-content","level":4,"score":0.42173904180526733},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.392875611782074},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.32262250781059265},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10334041714668274},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","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":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","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}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-10-167","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-167","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-167","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:19480720","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19480720","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:56bd96911c974296a658621fd761c0a8","is_oa":true,"landing_page_url":"https://doaj.org/article/56bd96911c974296a658621fd761c0a8","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 10, Iss 1, p 167 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2697163","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2697163","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-167","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-167","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-167","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":[{"id":"https://openalex.org/G12401395","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G2425251294","display_name":null,"funder_award_id":"Environment","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G6267471473","display_name":null,"funder_award_id":"Grant-in-Aid","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G7599130655","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G8044579487","display_name":null,"funder_award_id":"Japan","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320320909","display_name":"Keio University","ror":"https://ror.org/02kn6nx58"},{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2145163339.pdf","grobid_xml":"https://content.openalex.org/works/W2145163339.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1544273189","https://openalex.org/W1637201493","https://openalex.org/W1978294135","https://openalex.org/W1980602152","https://openalex.org/W1982026770","https://openalex.org/W1983096870","https://openalex.org/W1984116408","https://openalex.org/W1998269721","https://openalex.org/W2004146038","https://openalex.org/W2018590530","https://openalex.org/W2030564603","https://openalex.org/W2040745248","https://openalex.org/W2060158622","https://openalex.org/W2066266675","https://openalex.org/W2072284352","https://openalex.org/W2073913491","https://openalex.org/W2100911486","https://openalex.org/W2105100203","https://openalex.org/W2110372439","https://openalex.org/W2110400517","https://openalex.org/W2113824405","https://openalex.org/W2119490692","https://openalex.org/W2131245757","https://openalex.org/W2132644745","https://openalex.org/W2138210600","https://openalex.org/W2138721124","https://openalex.org/W2140211206","https://openalex.org/W2141024547","https://openalex.org/W2141524685","https://openalex.org/W2143221412","https://openalex.org/W2143412370","https://openalex.org/W2144870003","https://openalex.org/W2151632575","https://openalex.org/W2154278477","https://openalex.org/W2164618276","https://openalex.org/W2165206297","https://openalex.org/W2169303410","https://openalex.org/W2993222596","https://openalex.org/W3146979069"],"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":{"We":[0],"recommend":[1],"that":[2],"Dmean":[3],"be":[4,19],"used":[5],"to":[6,21],"measure":[7,17],"the":[8],"diversity":[9],"level":[10],"of":[11],"codon":[12],"usage":[13,29],"among":[14],"genes.":[15],"This":[16],"can":[18],"applied":[20],"other":[22],"compositional":[23],"features":[24],"such":[25],"as":[26,34],"amino":[27],"acid":[28],"and":[30],"dinucleotide":[31],"relative":[32],"abundance":[33],"a":[35],"genomic":[36],"signature.":[37]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
