{"id":"https://openalex.org/W2020443297","doi":"https://doi.org/10.1089/10665270050081504","title":"Translation Conditional Models for Protein Coding Sequences","display_name":"Translation Conditional Models for Protein Coding Sequences","publication_year":2000,"publication_date":"2000-02-01","ids":{"openalex":"https://openalex.org/W2020443297","doi":"https://doi.org/10.1089/10665270050081504","mag":"2020443297","pmid":"https://pubmed.ncbi.nlm.nih.gov/10890400"},"language":"en","primary_location":{"id":"doi:10.1089/10665270050081504","is_oa":false,"landing_page_url":"https://doi.org/10.1089/10665270050081504","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://biblio.ugent.be/publication/125010/file/4150050.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034992828","display_name":"F. Rodolphe","orcid":null},"institutions":[{"id":"https://openalex.org/I4210116501","display_name":"D\u00e9partement G\u00e9n\u00e9tique Animale","ror":"https://ror.org/029xmsm82","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210116501"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fran\u00e7ois Rodolphe","raw_affiliation_strings":["INRA, Unit\u00e9 MIG, 78352 Jouy en Josas cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRA, Unit\u00e9 MIG, 78352 Jouy en Josas cedex, France","institution_ids":["https://openalex.org/I4210159481","https://openalex.org/I4210116501"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004202443","display_name":"Catherine Math\u00e9","orcid":"https://orcid.org/0009-0004-8018-5048"},"institutions":[{"id":"https://openalex.org/I2802017950","display_name":"Vlaams Instituut voor Biotechnologie","ror":"https://ror.org/03xrhmk39","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Catherine Math\u00e9","raw_affiliation_strings":["Vlaams Interuniversitair Instituut voor Biotechnologie, Laboratorium voor Genetika, Universiteit Gent, K.L. Ledeganckstraat 35, B-9000 GENT, Belgi\u00eb"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vlaams Interuniversitair Instituut voor Biotechnologie, Laboratorium voor Genetika, Universiteit Gent, K.L. Ledeganckstraat 35, B-9000 GENT, Belgi\u00eb","institution_ids":["https://openalex.org/I2802017950"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.08519581,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"7","issue":"1-2","first_page":"249","last_page":"260"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9890999794006348,"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":0.9890999794006348,"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":0.9746999740600586,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9700000286102295,"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/genetic-code","display_name":"Genetic code","score":0.7144590020179749},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5525116324424744},{"id":"https://openalex.org/keywords/coding-region","display_name":"Coding region","score":0.5337579846382141},{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.46070706844329834},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.459340900182724},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.45282915234565735},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.43674778938293457},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4361974895000458},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4271519184112549},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38382670283317566},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37428802251815796},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33180806040763855},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2984328866004944},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.1276775598526001},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.08932194113731384}],"concepts":[{"id":"https://openalex.org/C10853874","wikidata":"https://www.wikidata.org/wiki/Q180618","display_name":"Genetic code","level":3,"score":0.7144590020179749},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5525116324424744},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.5337579846382141},{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.46070706844329834},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.459340900182724},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.45282915234565735},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.43674778938293457},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4361974895000458},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4271519184112549},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38382670283317566},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37428802251815796},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33180806040763855},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2984328866004944},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.1276775598526001},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.08932194113731384}],"mesh":[{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","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":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","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":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1089/10665270050081504","is_oa":false,"landing_page_url":"https://doi.org/10.1089/10665270050081504","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:10890400","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/10890400","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null},{"id":"pmh:oai:archive.ugent.be:125010","is_oa":true,"landing_page_url":"http://hdl.handle.net/1854/LU-125010","pdf_url":"https://biblio.ugent.be/publication/125010/file/4150050.pdf","source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1066-5277","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"pmh:oai:archive.ugent.be:125010","is_oa":true,"landing_page_url":"http://hdl.handle.net/1854/LU-125010","pdf_url":"https://biblio.ugent.be/publication/125010/file/4150050.pdf","source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1066-5277","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2020443297.pdf","grobid_xml":"https://content.openalex.org/works/W2020443297.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1977790594","https://openalex.org/W1981053737","https://openalex.org/W1991480269","https://openalex.org/W1992404702","https://openalex.org/W2002677631","https://openalex.org/W2057814775","https://openalex.org/W2065120930","https://openalex.org/W4295030489"],"related_works":["https://openalex.org/W4386881369","https://openalex.org/W1840178582","https://openalex.org/W2028550959","https://openalex.org/W2909998738","https://openalex.org/W3009119289","https://openalex.org/W2220941019","https://openalex.org/W2377607201","https://openalex.org/W2350213167","https://openalex.org/W4379347121","https://openalex.org/W2036178416"],"abstract_inverted_index":{"A":[0],"coding":[1,9,29],"sequence":[2,8,20],"is":[3,37,70],"defined":[4,61],"as":[5],"a":[6,14,19,23,30,42,45,73,81,111],"DNA":[7],"the":[10,34,53,77],"primary":[11],"structure":[12],"of":[13,47,67],"protein":[15],"(a":[16],"polypeptide).":[17],"Such":[18],"must":[21],"satisfy":[22],"specific":[24],"constraint,":[25],"which":[26,50],"consists":[27],"in":[28,110],"functional":[31],"protein.":[32],"As":[33],"genetic":[35],"code":[36,52],"degenerated,":[38],"there":[39],"exists,":[40],"for":[41,103],"given":[43],"polypeptide,":[44],"set":[46],"synonymous":[48],"sequences":[49],"would":[51],"same":[54],"polypeptide.":[55],"Translation":[56],"conditional":[57,84],"models":[58,85,99],"are":[59],"being":[60],"on":[62,121],"such":[63],"sets.":[64],"The":[65],"aim":[66],"this":[68],"paper":[69],"to":[71,107],"give":[72],"common":[74],"formalism.":[75],"Besides":[76],"codon":[78],"bias":[79],"model,":[80],"few":[82],"other":[83],"will":[86,94,118],"be":[87,95,101,119],"defined.":[88],"Statistical":[89],"estimators":[90],"and":[91],"comparison":[92],"methods":[93],"briefly":[96],"presented.":[97],"These":[98],"can":[100],"used":[102],"gene":[104],"classification,":[105],"or":[106],"find":[108],"out,":[109],"real":[112],"sequence,":[113],"remarkable":[114],"features.":[115],"An":[116],"example":[117],"presented":[120],"Escherichia":[122],"coli":[123],"genes.":[124]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
