{"id":"https://openalex.org/W2104029995","doi":"https://doi.org/10.1186/1471-2105-11-61","title":"Computational identification of rare codons of Escherichia coli based on codon pairs preference","display_name":"Computational identification of rare codons of Escherichia coli based on codon pairs preference","publication_year":2010,"publication_date":"2010-01-28","ids":{"openalex":"https://openalex.org/W2104029995","doi":"https://doi.org/10.1186/1471-2105-11-61","mag":"2104029995","pmid":"https://pubmed.ncbi.nlm.nih.gov/20109184"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-61","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-61","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-61","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/10.1186/1471-2105-11-61","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038604255","display_name":"Xianming Wu","orcid":"https://orcid.org/0000-0002-4825-0944"},"institutions":[{"id":"https://openalex.org/I135836153","display_name":"Shenyang Agricultural University","ror":"https://ror.org/01n7x9n08","country_code":"CN","type":"education","lineage":["https://openalex.org/I135836153"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xianming Wu","raw_affiliation_strings":["School of Biological Science and Technology, Shenyang Agricultural University, Shenyang, PR China","School of Biological Science and Technology, Shenyang Agricultural University, Shenyang, 110161, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biological Science and Technology, Shenyang Agricultural University, Shenyang, PR China","institution_ids":["https://openalex.org/I135836153"]},{"raw_affiliation_string":"School of Biological Science and Technology, Shenyang Agricultural University, Shenyang, 110161, PR China","institution_ids":["https://openalex.org/I135836153"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102717235","display_name":"Songfeng Wu","orcid":"https://orcid.org/0009-0004-6355-741X"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Songfeng Wu","raw_affiliation_strings":["State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100407488","display_name":"Dong Li","orcid":"https://orcid.org/0000-0002-8680-0468"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dong Li","raw_affiliation_strings":["State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101869831","display_name":"Jiyang Zhang","orcid":"https://orcid.org/0000-0002-4720-1657"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiyang Zhang","raw_affiliation_strings":["State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059657089","display_name":"Lin Hou","orcid":null},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Hou","raw_affiliation_strings":["State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054309071","display_name":"Jie Ma","orcid":"https://orcid.org/0000-0002-8934-922X"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Ma","raw_affiliation_strings":["State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103169758","display_name":"Wanlin Liu","orcid":"https://orcid.org/0000-0002-8641-7135"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wanlin Liu","raw_affiliation_strings":["State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100872708","display_name":"Daming Ren","orcid":null},"institutions":[{"id":"https://openalex.org/I135836153","display_name":"Shenyang Agricultural University","ror":"https://ror.org/01n7x9n08","country_code":"CN","type":"education","lineage":["https://openalex.org/I135836153"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Daming Ren","raw_affiliation_strings":["School of Biological Science and Technology, Shenyang Agricultural University, Shenyang, 110161, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biological Science and Technology, Shenyang Agricultural University, Shenyang, 110161, PR China","institution_ids":["https://openalex.org/I135836153"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100765277","display_name":"Yunping Zhu","orcid":"https://orcid.org/0000-0002-7320-7411"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yunping Zhu","raw_affiliation_strings":["State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091436402","display_name":"Fuchu He","orcid":"https://orcid.org/0000-0002-8571-2351"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Fuchu He","raw_affiliation_strings":["State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, PR China","institution_ids":["https://openalex.org/I4210149540"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5091436402","https://openalex.org/A5100765277","https://openalex.org/A5100872708"],"corresponding_institution_ids":["https://openalex.org/I135836153","https://openalex.org/I4210149540"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3734,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.6054008,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"11","issue":"1","first_page":"61","last_page":"61"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9757000207901001,"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":0.9757000207901001,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.00559999980032444,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.004999999888241291,"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":0.8042051792144775},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6565384864807129},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6469892263412476},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.576529860496521},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.5634441375732422},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4201295077800751},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.37636637687683105}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.8042051792144775},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6565384864807129},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6469892263412476},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.576529860496521},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.5634441375732422},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4201295077800751},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.37636637687683105}],"mesh":[{"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":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","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},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-11-61","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-61","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-61","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:20109184","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20109184","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:5a12ad2df3e148fa938f715e811c5f0a","is_oa":false,"landing_page_url":"https://doaj.org/article/5a12ad2df3e148fa938f715e811c5f0a","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 61 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2828438","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2828438","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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:10.1186/1471-2105-11-61","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-61","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-61","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/G158152137","display_name":null,"funder_award_id":"2006AA02A312","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4369394003","display_name":null,"funder_award_id":"30621063","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321540","display_name":"Ministry of Science and Technology of the People's Republic of China","ror":"https://ror.org/027s68j25"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2104029995.pdf"},"referenced_works_count":69,"referenced_works":["https://openalex.org/W858028742","https://openalex.org/W1527267184","https://openalex.org/W1550695177","https://openalex.org/W1586989746","https://openalex.org/W1603411458","https://openalex.org/W1965233192","https://openalex.org/W1965357949","https://openalex.org/W1976167098","https://openalex.org/W1979103958","https://openalex.org/W1981136463","https://openalex.org/W1981722151","https://openalex.org/W1988583600","https://openalex.org/W1993876559","https://openalex.org/W1994880286","https://openalex.org/W2000654639","https://openalex.org/W2004674004","https://openalex.org/W2007625667","https://openalex.org/W2011828065","https://openalex.org/W2018590530","https://openalex.org/W2023742154","https://openalex.org/W2026430354","https://openalex.org/W2028165934","https://openalex.org/W2029132648","https://openalex.org/W2034885685","https://openalex.org/W2037708869","https://openalex.org/W2037995065","https://openalex.org/W2038941962","https://openalex.org/W2039707307","https://openalex.org/W2040204069","https://openalex.org/W2040857454","https://openalex.org/W2043036449","https://openalex.org/W2044052868","https://openalex.org/W2044886732","https://openalex.org/W2046291479","https://openalex.org/W2047111341","https://openalex.org/W2051861840","https://openalex.org/W2052413864","https://openalex.org/W2060020017","https://openalex.org/W2063504601","https://openalex.org/W2064698058","https://openalex.org/W2068691391","https://openalex.org/W2073501728","https://openalex.org/W2074400089","https://openalex.org/W2074713139","https://openalex.org/W2075158468","https://openalex.org/W2080100789","https://openalex.org/W2082589219","https://openalex.org/W2103091054","https://openalex.org/W2104752637","https://openalex.org/W2113498255","https://openalex.org/W2113992630","https://openalex.org/W2114900973","https://openalex.org/W2125076649","https://openalex.org/W2128742161","https://openalex.org/W2128774203","https://openalex.org/W2132094774","https://openalex.org/W2140983831","https://openalex.org/W2147126179","https://openalex.org/W2149851570","https://openalex.org/W2156345326","https://openalex.org/W2162592907","https://openalex.org/W2164618276","https://openalex.org/W2164997719","https://openalex.org/W2165217024","https://openalex.org/W2170602689","https://openalex.org/W2412622214","https://openalex.org/W4242794150","https://openalex.org/W4255852734","https://openalex.org/W4322574976"],"related_works":["https://openalex.org/W2132060660","https://openalex.org/W2146622826","https://openalex.org/W2187207551","https://openalex.org/W2069184423","https://openalex.org/W1603543036","https://openalex.org/W4283079380","https://openalex.org/W2163703477","https://openalex.org/W2381239020","https://openalex.org/W2168467210","https://openalex.org/W1442603624"],"abstract_inverted_index":{"BACKGROUND:":[0],"Codon":[1],"bias":[2,57,87,213],"is":[3],"believed":[4],"to":[5,78,125],"play":[6],"an":[7],"important":[8],"role":[9],"in":[10,48,88,111,119,194],"the":[11,25,42,52,67,80,97,103,145,161,173,192,200,216],"control":[12],"of":[13,28,44,55,69,105,107,136,148,202,211,215,218],"gene":[14,35],"expression.":[15],"In":[16,92],"Escherichia":[17,89,93],"coli,":[18,94],"some":[19],"rare":[20,81,127,138,188,203],"codons,":[21],"which":[22,116,175,195],"can":[23,186],"limit":[24],"expression":[26,219],"level":[27],"exogenous":[29],"protein,":[30],"have":[31,40],"been":[32,60],"defined":[33,96],"by":[34,84,101,190],"engineering":[36],"operations.":[37],"Previous":[38],"studies":[39],"confirmed":[41],"existence":[43],"codon":[45,85,99,109,128,139,197,212],"pair's":[46],"preference":[47],"many":[49,135],"genomes,":[50],"but":[51],"underlying":[53],"cause":[54],"this":[56],"has":[58],"not":[59],"well":[61],"established.":[62],"Here":[63],"we":[64,95,164,185],"focus":[65],"on":[66,177],"patterns":[68],"rarely-used":[70],"synonymous":[71],"codons.":[72],"A":[73],"novel":[74],"method":[75],"was":[76,156],"introduced":[77],"identify":[79,187],"codons":[82,115,143,189,204],"merely":[83],"pair":[86],"coli.":[90],"RESULTS:":[91],"\"rare":[98],"pairs\"":[100],"calculating":[102],"frequency":[104,201],"occurrence":[106],"all":[108],"pairs":[110,140],"coding":[112],"sequences.":[113],"Rare":[114],"are":[117],"disliked":[118],"genes":[120],"could":[121,206],"make":[122],"great":[123],"contributions":[124],"forming":[126],"pairs.":[129],"Meanwhile":[130],"our":[131],"investigation":[132],"showed":[133],"that":[134,184],"these":[137],"contain":[141],"termination":[142],"and":[144,172],"recognized":[146],"sites":[147],"restriction":[149],"enzymes.":[150],"Furthermore,":[151],"a":[152,166,196,208],"new":[153],"index":[154,210],"(F(rare))":[155,205],"developed.":[157],"Through":[158],"comparison":[159],"with":[160],"classical":[162],"indices":[163,174],"found":[165],"significant":[167],"negative":[168],"correlation":[169],"between":[170],"F(rare)":[171],"depend":[176],"reference":[178],"datasets.":[179],"CONCLUSIONS:":[180],"Our":[181],"approach":[182],"suggests":[183],"studying":[191],"context":[193],"lies.":[198],"Also,":[199],"be":[207],"useful":[209],"regardless":[214],"lack":[217],"abundance":[220],"information.":[221]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
