{"id":"https://openalex.org/W4283658126","doi":"https://doi.org/10.1093/bioinformatics/btac428","title":"A unifying network modeling approach for codon optimization","display_name":"A unifying network modeling approach for codon optimization","publication_year":2022,"publication_date":"2022-06-28","ids":{"openalex":"https://openalex.org/W4283658126","doi":"https://doi.org/10.1093/bioinformatics/btac428","pmid":"https://pubmed.ncbi.nlm.nih.gov/35762943"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac428","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac428","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5110553516","display_name":"Oya Ekin Kara\u015fan","orcid":"https://orcid.org/0000-0002-3853-4003"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Oya Kara\u015fan","raw_affiliation_strings":["Department of Industrial Engineering, Bilkent University , Ankara 06800, Turkey","Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey and"],"affiliations":[{"raw_affiliation_string":"Department of Industrial Engineering, Bilkent University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey and","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055968971","display_name":"Alper \u015een","orcid":"https://orcid.org/0000-0003-1728-6538"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Alper \u015een","raw_affiliation_strings":["Department of Industrial Engineering, Bilkent University , Ankara 06800, Turkey","Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey and"],"affiliations":[{"raw_affiliation_string":"Department of Industrial Engineering, Bilkent University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey and","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023545337","display_name":"Banu Tiryaki","orcid":null},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Banu Tiryaki","raw_affiliation_strings":["Department of Industrial Engineering, Bilkent University , Ankara 06800, Turkey","Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey and"],"affiliations":[{"raw_affiliation_string":"Department of Industrial Engineering, Bilkent University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey and","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090836372","display_name":"A. Erc\u00fcment \u00c7i\u00e7ek","orcid":"https://orcid.org/0000-0001-8613-6619"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"A Ercument Cicek","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University , Ankara 06800, Turkey"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I168864056"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5055968971"],"corresponding_institution_ids":["https://openalex.org/I168864056"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6933,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.66529156,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"38","issue":"16","first_page":"3935","last_page":"3941"},"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":0.9966999888420105,"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":0.9927999973297119,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.8659420013427734},{"id":"https://openalex.org/keywords/genetic-code","display_name":"Genetic code","score":0.6754525303840637},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5052171349525452},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5037910342216492},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.47406095266342163},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.44305935502052307},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4324703812599182},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4010107219219208},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.24925965070724487},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08974912762641907}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.8659420013427734},{"id":"https://openalex.org/C10853874","wikidata":"https://www.wikidata.org/wiki/Q180618","display_name":"Genetic code","level":3,"score":0.6754525303840637},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5052171349525452},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5037910342216492},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.47406095266342163},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.44305935502052307},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4324703812599182},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4010107219219208},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.24925965070724487},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08974912762641907}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","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":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac428","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac428","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35762943","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35762943","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/111808","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/111808","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1968654669","https://openalex.org/W1984512854","https://openalex.org/W2001674944","https://openalex.org/W2013321787","https://openalex.org/W2018590530","https://openalex.org/W2022726657","https://openalex.org/W2050888933","https://openalex.org/W2063504601","https://openalex.org/W2066829062","https://openalex.org/W2069320301","https://openalex.org/W2072499238","https://openalex.org/W2112765717","https://openalex.org/W2115749923","https://openalex.org/W2116831267","https://openalex.org/W2150461743","https://openalex.org/W2157613837","https://openalex.org/W2162592907","https://openalex.org/W2164201106","https://openalex.org/W2171267841","https://openalex.org/W2172617180","https://openalex.org/W2418051327","https://openalex.org/W2562038667","https://openalex.org/W2594846953","https://openalex.org/W2941046412","https://openalex.org/W2963289339","https://openalex.org/W3006998809","https://openalex.org/W3016851473","https://openalex.org/W3021283815","https://openalex.org/W3039155556","https://openalex.org/W3108305277","https://openalex.org/W3136918052","https://openalex.org/W4205574667","https://openalex.org/W4213060235","https://openalex.org/W6786588729"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W4386881369","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W2220941019","https://openalex.org/W2102511336","https://openalex.org/W2921764584","https://openalex.org/W2368037607","https://openalex.org/W1866610019"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
