{"id":"https://openalex.org/W2081746271","doi":"https://doi.org/10.1186/1471-2105-6-182","title":"Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity","display_name":"Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity","publication_year":2005,"publication_date":"2005-07-19","ids":{"openalex":"https://openalex.org/W2081746271","doi":"https://doi.org/10.1186/1471-2105-6-182","mag":"2081746271","pmid":"https://pubmed.ncbi.nlm.nih.gov/16029499"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-6-182","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-182","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-182","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/10.1186/1471-2105-6-182","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025364437","display_name":"Fran Supek","orcid":"https://orcid.org/0000-0002-7811-6711"},"institutions":[{"id":"https://openalex.org/I181343428","display_name":"University of Zagreb","ror":"https://ror.org/00mv6sv71","country_code":"HR","type":"education","lineage":["https://openalex.org/I181343428"]}],"countries":["HR"],"is_corresponding":true,"raw_author_name":"Fran Supek","raw_affiliation_strings":["Division of Biology, Department of Molecular Biology, Faculty of Science, Zagreb University, Rooseveltov trg 6, 10000 Zagreb, Croatia. fsupek@public.srce.hr","Department of Molecular Biology, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia"],"affiliations":[{"raw_affiliation_string":"Division of Biology, Department of Molecular Biology, Faculty of Science, Zagreb University, Rooseveltov trg 6, 10000 Zagreb, Croatia. fsupek@public.srce.hr","institution_ids":["https://openalex.org/I181343428"]},{"raw_affiliation_string":"Department of Molecular Biology, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia","institution_ids":["https://openalex.org/I181343428"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078029536","display_name":"Kristian Vlahovi\u010dek","orcid":"https://orcid.org/0000-0002-5705-2464"},"institutions":[{"id":"https://openalex.org/I91080651","display_name":"International Centre for Genetic Engineering and Biotechnology","ror":"https://ror.org/043bgf219","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I91080651"]},{"id":"https://openalex.org/I181343428","display_name":"University of Zagreb","ror":"https://ror.org/00mv6sv71","country_code":"HR","type":"education","lineage":["https://openalex.org/I181343428"]}],"countries":["HR","IT"],"is_corresponding":false,"raw_author_name":"Kristian Vlahovi\u010dek","raw_affiliation_strings":["Department of Molecular Biology, Division of Biology, Faculty of Science, Zagreb University, Rooseveltov trg 6, 10000, Zagreb, Croatia","Protein Structure and Bioinformatics, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012, Trieste, Italy","Protein Structure and Bioinformatics, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy","Department of Molecular Biology, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, Division of Biology, Faculty of Science, Zagreb University, Rooseveltov trg 6, 10000, Zagreb, Croatia","institution_ids":["https://openalex.org/I181343428"]},{"raw_affiliation_string":"Protein Structure and Bioinformatics, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012, Trieste, Italy","institution_ids":["https://openalex.org/I91080651"]},{"raw_affiliation_string":"Protein Structure and Bioinformatics, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy","institution_ids":["https://openalex.org/I91080651"]},{"raw_affiliation_string":"Department of Molecular Biology, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia","institution_ids":["https://openalex.org/I181343428"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5025364437"],"corresponding_institution_ids":["https://openalex.org/I181343428"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.6384,"has_fulltext":true,"cited_by_count":156,"citation_normalized_percentile":{"value":0.82404524,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"6","issue":"1","first_page":"182","last_page":"182"},"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":0.9987000226974487,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9968000054359436,"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":0.8367259502410889},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5933545827865601},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5680159330368042},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.49395090341567993},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48435768485069275},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4793761074542999},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4785255193710327},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.47606322169303894},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.46183136105537415},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.44999516010284424},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3596467673778534},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3224064111709595},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.21831470727920532},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1979566216468811}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.8367259502410889},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5933545827865601},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5680159330368042},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.49395090341567993},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48435768485069275},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4793761074542999},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4785255193710327},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.47606322169303894},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.46183136105537415},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44999516010284424},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3596467673778534},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3224064111709595},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.21831470727920532},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1979566216468811},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-6-182","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-182","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-182","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:16029499","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16029499","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:6d0a861aa4d14200b4df655ff1fc5174","is_oa":true,"landing_page_url":"https://doaj.org/article/6d0a861aa4d14200b4df655ff1fc5174","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":"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 6, Iss 1, p 182 (2005)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1199580","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1199580","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:10.1186/1471-2105-6-182","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-182","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-182","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":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2081746271.pdf","grobid_xml":"https://content.openalex.org/works/W2081746271.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W1544273189","https://openalex.org/W1815692180","https://openalex.org/W1915199010","https://openalex.org/W1969416735","https://openalex.org/W1971901785","https://openalex.org/W1972875046","https://openalex.org/W1974358663","https://openalex.org/W1974557906","https://openalex.org/W1977790594","https://openalex.org/W1987853052","https://openalex.org/W2004146038","https://openalex.org/W2004674004","https://openalex.org/W2013947447","https://openalex.org/W2015669937","https://openalex.org/W2018590530","https://openalex.org/W2019604065","https://openalex.org/W2023778561","https://openalex.org/W2027059027","https://openalex.org/W2030205072","https://openalex.org/W2031396235","https://openalex.org/W2039593299","https://openalex.org/W2042181710","https://openalex.org/W2045403483","https://openalex.org/W2045856438","https://openalex.org/W2051043527","https://openalex.org/W2056134190","https://openalex.org/W2061246785","https://openalex.org/W2065120930","https://openalex.org/W2070765702","https://openalex.org/W2075027571","https://openalex.org/W2078630432","https://openalex.org/W2100002703","https://openalex.org/W2104125532","https://openalex.org/W2107363136","https://openalex.org/W2108190214","https://openalex.org/W2110236168","https://openalex.org/W2110372439","https://openalex.org/W2113992630","https://openalex.org/W2115228331","https://openalex.org/W2125836647","https://openalex.org/W2129137649","https://openalex.org/W2132836838","https://openalex.org/W2134440848","https://openalex.org/W2135613155","https://openalex.org/W2135884205","https://openalex.org/W2144252459","https://openalex.org/W2156022009","https://openalex.org/W2158188865","https://openalex.org/W2160514369","https://openalex.org/W2164365774","https://openalex.org/W2164618276","https://openalex.org/W2165810896","https://openalex.org/W2168558559","https://openalex.org/W2169303410","https://openalex.org/W2170949754","https://openalex.org/W2410103108","https://openalex.org/W2887700135","https://openalex.org/W3146979069","https://openalex.org/W3183766709","https://openalex.org/W4213225796"],"related_works":["https://openalex.org/W4255837520","https://openalex.org/W2355920812","https://openalex.org/W106077234","https://openalex.org/W2041374557","https://openalex.org/W2081929287","https://openalex.org/W2144348650","https://openalex.org/W2132561013","https://openalex.org/W1994852842","https://openalex.org/W4246178523","https://openalex.org/W1902990570"],"abstract_inverted_index":{"We":[0],"have":[1],"established":[2],"that":[3],"MILC":[4],"is":[5],"a":[6,91,96],"generally":[7],"applicable":[8],"measure,":[9],"being":[10],"resistant":[11],"to":[12,39,89],"changes":[13],"in":[14,34,45],"gene":[15,42],"length":[16],"and":[17,21,48,62,70],"overall":[18],"nucleotide":[19],"composition,":[20],"introducing":[22],"little":[23],"noise":[24],"into":[25],"measurements.":[26],"Other":[27],"methods,":[28,68],"however,":[29],"may":[30],"also":[31],"be":[32,90],"appropriate":[33],"certain":[35],"applications.":[36],"Our":[37],"efforts":[38],"quantitatively":[40],"predict":[41],"expression":[43],"levels":[44,54],"several":[46],"prokaryotes":[47],"unicellular":[49],"eukaryotes":[50],"met":[51],"with":[52],"varying":[53],"of":[55,66],"success,":[56],"depending":[57],"on":[58],"the":[59,76],"experimental":[60],"dataset":[61],"predictor":[63],"used.":[64],"Out":[65],"all":[67],"MELP":[69],"Rainer":[71],"Merkl's":[72],"GCB":[73],"method":[74],"had":[75],"most":[77],"consistent":[78],"behaviour.":[79],"A":[80],"'reference":[81],"set'":[82],"containing":[83],"known":[84],"ribosomal":[85],"protein":[86],"genes":[87],"appears":[88],"valid":[92],"starting":[93],"point":[94],"for":[95],"codon":[97],"usage-based":[98],"expressivity":[99],"prediction.":[100]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":25},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":6}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
