{"id":"https://openalex.org/W2164201106","doi":"https://doi.org/10.1093/bioinformatics/btu192","title":"Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design","display_name":"Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design","publication_year":2014,"publication_date":"2014-04-10","ids":{"openalex":"https://openalex.org/W2164201106","doi":"https://doi.org/10.1093/bioinformatics/btu192","mag":"2164201106","pmid":"https://pubmed.ncbi.nlm.nih.gov/24728853"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/15/2210/48924913/bioinformatics_30_15_2210.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/15/2210/48924913/bioinformatics_30_15_2210.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052658048","display_name":"Ju Xin Chin","orcid":null},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I4210137615","display_name":"Bioprocessing Technology Institute","ror":"https://ror.org/049fnxe71","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210137615"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Ju Xin Chin","raw_affiliation_strings":["1 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and 2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and 2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I165932596","https://openalex.org/I4210137615"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015227672","display_name":"Bevan Kai-Sheng Chung","orcid":null},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I4210137615","display_name":"Bioprocessing Technology Institute","ror":"https://ror.org/049fnxe71","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210137615"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Bevan Kai-Sheng Chung","raw_affiliation_strings":["1 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and 2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and 2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I165932596","https://openalex.org/I4210137615"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011206845","display_name":"Dong\u2010Yup Lee","orcid":"https://orcid.org/0000-0003-0901-708X"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I4210137615","display_name":"Bioprocessing Technology Institute","ror":"https://ror.org/049fnxe71","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210137615"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Dong-Yup Lee","raw_affiliation_strings":["1 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and 2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138668 and 2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I165932596","https://openalex.org/I4210137615"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5011206845"],"corresponding_institution_ids":["https://openalex.org/I115228651","https://openalex.org/I165932596","https://openalex.org/I4210137615"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.7269,"has_fulltext":false,"cited_by_count":148,"citation_normalized_percentile":{"value":0.91091634,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"30","issue":"15","first_page":"2210","last_page":"2212"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9128000140190125,"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":0.9128000140190125,"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":0.015300000086426735,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.005799999926239252,"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":0.6859667301177979},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.645965039730072},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.412078857421875},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3260800838470459},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32429516315460205},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2757382392883301},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21160992980003357},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20197290182113647},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.08724856376647949}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.6859667301177979},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.645965039730072},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.412078857421875},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3260800838470459},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32429516315460205},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2757382392883301},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21160992980003357},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20197290182113647},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.08724856376647949},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0}],"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":"D005813","descriptor_name":"Genes, Synthetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005813","descriptor_name":"Genes, Synthetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005813","descriptor_name":"Genes, Synthetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btu192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/15/2210/48924913/bioinformatics_30_15_2210.pdf","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:24728853","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24728853","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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/15/2210/48924913/bioinformatics_30_15_2210.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2164201106.pdf"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1492110990","https://openalex.org/W1966252059","https://openalex.org/W1968545643","https://openalex.org/W2006607348","https://openalex.org/W2018590530","https://openalex.org/W2021099440","https://openalex.org/W2023622324","https://openalex.org/W2032265205","https://openalex.org/W2059961861","https://openalex.org/W2072499238","https://openalex.org/W2073863519","https://openalex.org/W2078755055","https://openalex.org/W2109036608","https://openalex.org/W2140486583","https://openalex.org/W2168036974","https://openalex.org/W4211125927"],"related_works":["https://openalex.org/W2366230866","https://openalex.org/W2357906747","https://openalex.org/W2372895414","https://openalex.org/W2348049494","https://openalex.org/W1992987618","https://openalex.org/W2347219288","https://openalex.org/W2366221835","https://openalex.org/W2993335797","https://openalex.org/W2072499238","https://openalex.org/W3153719477"],"abstract_inverted_index":{"SUMMARY:":[0],"Codon":[1,56],"optimization":[2,25,71,90],"has":[3],"been":[4],"widely":[5],"used":[6],"for":[7,86,160],"designing":[8],"synthetic":[9,76,112],"genes":[10],"to":[11,39,73,116,132,151,158],"improve":[12],"their":[13],"expression":[14],"in":[15],"heterologous":[16],"host":[17],"organisms.":[18],"However,":[19],"most":[20],"of":[21,167],"the":[22,49,62,68,110,128,134,138,164],"existing":[23],"codon":[24,70,89,94,98,101],"tools":[26],"consider":[27],"a":[28,34,81,161],"single":[29],"design":[30],"criterion":[31],"and/or":[32],"implement":[33],"rather":[35],"rigid":[36],"user":[37],"interface":[38,85],"yield":[40],"only":[41],"one":[42],"optimal":[43,111],"sequence,":[44],"which":[45,60,137],"may":[46],"not":[47],"be":[48,125,142],"best":[50],"solution.":[51],"Hence,":[52],"we":[53],"have":[54],"developed":[55],"Optimization":[57],"OnLine":[58],"(COOL),":[59],"is":[61,149],"first":[63],"web":[64],"tool":[65],"that":[66],"provides":[67],"multi-objective":[69],"functionality":[72],"aid":[74],"systematic":[75],"gene":[77],"design.":[78],"COOL":[79,129,148],"supports":[80],"simple":[82],"and":[83,100,108,153,156],"flexible":[84],"customizing":[87],"various":[88,117],"parameters":[91],"such":[92],"as":[93],"adaptation":[95],"index,":[96],"individual":[97],"usage":[99],"pairing.":[102],"In":[103],"addition,":[104],"users":[105,155],"can":[106,123,141],"visualize":[107],"compare":[109],"sequences":[113,122,131,140],"with":[114],"respect":[115],"fitness":[118],"measures.":[119],"User-defined":[120],"DNA":[121],"also":[124],"compared":[126],"against":[127],"optimized":[130],"show":[133],"extent":[135],"by":[136,163],"user's":[139],"further":[143],"improved.":[144],"AVAILABILITY":[145],"AND":[146],"IMPLEMENTATION:":[147],"free":[150],"academic":[152],"non-commercial":[154],"licensed":[157],"others":[159],"fee":[162],"National":[165],"University":[166],"Singapore.":[168],"Accessible":[169],"at":[170,180],"http://bioinfo.bti.a-star.edu.sg/COOL/":[171],"CONTACT:":[172],"cheld@nus.edu.sg":[173],"SUPPLEMENTARY":[174],"INFORMATION:":[175],"Supplementary":[176],"data":[177],"are":[178],"available":[179],"Bioinformatics":[181],"online.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":16},{"year":2021,"cited_by_count":25},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":20},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}