{"id":"https://openalex.org/W2953990100","doi":"https://doi.org/10.1093/bioinformatics/btaa603","title":"Network analysis of synonymous codon usage","display_name":"Network analysis of synonymous codon usage","publication_year":2020,"publication_date":"2020-06-22","ids":{"openalex":"https://openalex.org/W2953990100","doi":"https://doi.org/10.1093/bioinformatics/btaa603","mag":"2953990100","pmid":"https://pubmed.ncbi.nlm.nih.gov/32609328"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa603","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa603","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":"preprint","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1907.03351","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056455482","display_name":"Khalique Newaz","orcid":"https://orcid.org/0000-0002-1192-8360"},"institutions":[{"id":"https://openalex.org/I4210129097","display_name":"Center for Global Health","ror":"https://ror.org/02e5dc168","country_code":"US","type":"government","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934","https://openalex.org/I4210129097"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Khalique Newaz","raw_affiliation_strings":["Center for Network and Data Science","Department of Computer Science and Engineering","Eck institute for Global Health"],"affiliations":[{"raw_affiliation_string":"Center for Network and Data Science","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Eck institute for Global Health","institution_ids":["https://openalex.org/I4210129097"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030149346","display_name":"Gabriel Wright","orcid":"https://orcid.org/0000-0003-1706-0758"},"institutions":[{"id":"https://openalex.org/I4210129097","display_name":"Center for Global Health","ror":"https://ror.org/02e5dc168","country_code":"US","type":"government","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934","https://openalex.org/I4210129097"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gabriel Wright","raw_affiliation_strings":["Department of Computer Science and Engineering","Eck institute for Global Health"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Eck institute for Global Health","institution_ids":["https://openalex.org/I4210129097"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020327450","display_name":"Jacob Piland","orcid":"https://orcid.org/0009-0000-6140-7734"},"institutions":[{"id":"https://openalex.org/I4210129097","display_name":"Center for Global Health","ror":"https://ror.org/02e5dc168","country_code":"US","type":"government","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934","https://openalex.org/I4210129097"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob Piland","raw_affiliation_strings":["Center for Network and Data Science","Department of Computer Science and Engineering","Eck institute for Global Health"],"affiliations":[{"raw_affiliation_string":"Center for Network and Data Science","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Eck institute for Global Health","institution_ids":["https://openalex.org/I4210129097"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100362117","display_name":"Jun Li","orcid":"https://orcid.org/0000-0003-4353-5761"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jun Li","raw_affiliation_strings":["Department of Applied and Computational Mathematics and Statistics"],"affiliations":[{"raw_affiliation_string":"Department of Applied and Computational Mathematics and Statistics","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074774169","display_name":"Patricia L. Clark","orcid":"https://orcid.org/0000-0001-5462-8248"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patricia L Clark","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, IN 46556, USA","Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, IN 46556 (USA)"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, IN 46556, USA","institution_ids":["https://openalex.org/I107639228"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, IN 46556 (USA)","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019857186","display_name":"Scott Emrich","orcid":"https://orcid.org/0000-0002-5741-4517"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott J Emrich","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Tennessee , Knoxville, TN 37996, USA","Department of Electrical Engineering and Computer Science , University of Tennessee , Knoxville, TN 37996 , USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Tennessee , Knoxville, TN 37996, USA","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science , University of Tennessee , Knoxville, TN 37996 , USA","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042457126","display_name":"Tijana Milenkovi\u0107","orcid":"https://orcid.org/0000-0002-8023-6907"},"institutions":[{"id":"https://openalex.org/I4210129097","display_name":"Center for Global Health","ror":"https://ror.org/02e5dc168","country_code":"US","type":"government","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934","https://openalex.org/I4210129097"]},{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tijana Milenkovi\u0107","raw_affiliation_strings":["Center for Network and Data Science","Department of Computer Science and Engineering","Eck institute for Global Health","University of Notre Dame"],"affiliations":[{"raw_affiliation_string":"Center for Network and Data Science","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Eck institute for Global Health","institution_ids":["https://openalex.org/I4210129097"]},{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5056455482"],"corresponding_institution_ids":["https://openalex.org/I4210129097"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0834,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.42257662,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"36","issue":"19","first_page":"4876","last_page":"4884"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9972000122070312,"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":0.7238151431083679},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5806655883789062},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5352156162261963},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5327764749526978},{"id":"https://openalex.org/keywords/synonymous-substitution","display_name":"Synonymous substitution","score":0.5314850807189941},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47998759150505066},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.4634068012237549},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.39835983514785767},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.14040538668632507}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.7238151431083679},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5806655883789062},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5352156162261963},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5327764749526978},{"id":"https://openalex.org/C138025448","wikidata":"https://www.wikidata.org/wiki/Q7662597","display_name":"Synonymous substitution","level":5,"score":0.5314850807189941},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47998759150505066},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4634068012237549},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.39835983514785767},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.14040538668632507},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000081183","descriptor_name":"Codon Usage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081183","descriptor_name":"Codon Usage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081183","descriptor_name":"Codon Usage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btaa603","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa603","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:32609328","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32609328","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:arXiv.org:1907.03351","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1907.03351","pdf_url":"https://arxiv.org/pdf/1907.03351","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"mag:2953990100","is_oa":true,"landing_page_url":"http://export.arxiv.org/pdf/1907.03351","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7750956","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7750956","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"doi:10.48550/arxiv.1907.03351","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1907.03351","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1907.03351","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1907.03351","pdf_url":"https://arxiv.org/pdf/1907.03351","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W1593377767","https://openalex.org/W1874092228","https://openalex.org/W1965233192","https://openalex.org/W1966778471","https://openalex.org/W1968654669","https://openalex.org/W1974358663","https://openalex.org/W1974970687","https://openalex.org/W1975304761","https://openalex.org/W1984512854","https://openalex.org/W1986720579","https://openalex.org/W2008856488","https://openalex.org/W2018590530","https://openalex.org/W2022726657","https://openalex.org/W2030517878","https://openalex.org/W2031291897","https://openalex.org/W2042548693","https://openalex.org/W2055043387","https://openalex.org/W2055536178","https://openalex.org/W2058864686","https://openalex.org/W2059017497","https://openalex.org/W2059661284","https://openalex.org/W2062296203","https://openalex.org/W2070163065","https://openalex.org/W2074166146","https://openalex.org/W2074312891","https://openalex.org/W2085277871","https://openalex.org/W2087461762","https://openalex.org/W2093794723","https://openalex.org/W2094519647","https://openalex.org/W2097270746","https://openalex.org/W2101783948","https://openalex.org/W2102245393","https://openalex.org/W2103547092","https://openalex.org/W2109483063","https://openalex.org/W2110065044","https://openalex.org/W2122854841","https://openalex.org/W2130479394","https://openalex.org/W2132122858","https://openalex.org/W2139498473","https://openalex.org/W2141997506","https://openalex.org/W2143185848","https://openalex.org/W2148762636","https://openalex.org/W2149424410","https://openalex.org/W2149780759","https://openalex.org/W2153953580","https://openalex.org/W2154232977","https://openalex.org/W2156408001","https://openalex.org/W2161174387","https://openalex.org/W2164618276","https://openalex.org/W2257602426","https://openalex.org/W2413938931","https://openalex.org/W2433535207","https://openalex.org/W2566498094","https://openalex.org/W2611528178","https://openalex.org/W2743569306","https://openalex.org/W2765949636","https://openalex.org/W2785468798","https://openalex.org/W2796563271","https://openalex.org/W2903048896","https://openalex.org/W2931634967","https://openalex.org/W2951500013","https://openalex.org/W3004726194","https://openalex.org/W3021283815","https://openalex.org/W3033230306","https://openalex.org/W4235019172","https://openalex.org/W6668956976","https://openalex.org/W6684041852"],"related_works":["https://openalex.org/W3039861074","https://openalex.org/W2611528178","https://openalex.org/W2355375423","https://openalex.org/W2022726657","https://openalex.org/W3134359595","https://openalex.org/W1965233192","https://openalex.org/W1982205342","https://openalex.org/W1666616186","https://openalex.org/W1971737958","https://openalex.org/W2104029995","https://openalex.org/W2068628419","https://openalex.org/W1993038283","https://openalex.org/W2460524927","https://openalex.org/W2163282567","https://openalex.org/W2098263661","https://openalex.org/W1988419621","https://openalex.org/W2592510355","https://openalex.org/W2606419610","https://openalex.org/W2366634137","https://openalex.org/W1977531540"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
