{"id":"https://openalex.org/W2101740440","doi":"https://doi.org/10.1093/bioinformatics/btn064","title":"Identifying trait clusters by linkage profiles: application in genetical genomics","display_name":"Identifying trait clusters by linkage profiles: application in genetical genomics","publication_year":2008,"publication_date":"2008-02-29","ids":{"openalex":"https://openalex.org/W2101740440","doi":"https://doi.org/10.1093/bioinformatics/btn064","mag":"2101740440","pmid":"https://pubmed.ncbi.nlm.nih.gov/18310620"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn064","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn064","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/7/958/49047343/bioinformatics_24_7_958.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/24/7/958/49047343/bioinformatics_24_7_958.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050414089","display_name":"Joshua N. Sampson","orcid":"https://orcid.org/0000-0003-2875-3365"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210101190","display_name":"Cancer Research And Biostatistics","ror":"https://ror.org/01575p865","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210101190"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joshua N. Sampson","raw_affiliation_strings":["1 Department of Biostatistics, University of Washington and 2Statistical Center for HIV/AIDS Research and Prevention, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biostatistics, University of Washington and 2Statistical Center for HIV/AIDS Research and Prevention, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210101190"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110086087","display_name":"Steven G. Self","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210101190","display_name":"Cancer Research And Biostatistics","ror":"https://ror.org/01575p865","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210101190"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven G. Self","raw_affiliation_strings":["1 Department of Biostatistics, University of Washington and 2Statistical Center for HIV/AIDS Research and Prevention, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biostatistics, University of Washington and 2Statistical Center for HIV/AIDS Research and Prevention, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210101190"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5050414089"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210101190"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5198,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.65588063,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"24","issue":"7","first_page":"958","last_page":"964"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5814999938011169,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5814999938011169,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.32030001282691956,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.061799999326467514,"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/linkage","display_name":"Linkage (software)","score":0.747649073600769},{"id":"https://openalex.org/keywords/trait","display_name":"Trait","score":0.7268368601799011},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.6716062426567078},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5684183835983276},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.501319169998169},{"id":"https://openalex.org/keywords/quantitative-trait-locus","display_name":"Quantitative trait locus","score":0.4958218038082123},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49310705065727234},{"id":"https://openalex.org/keywords/genetic-linkage","display_name":"Genetic linkage","score":0.41921043395996094},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.37070849537849426},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.28518763184547424},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.23915371298789978},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10745170712471008}],"concepts":[{"id":"https://openalex.org/C31266012","wikidata":"https://www.wikidata.org/wiki/Q6554340","display_name":"Linkage (software)","level":3,"score":0.747649073600769},{"id":"https://openalex.org/C106934330","wikidata":"https://www.wikidata.org/wiki/Q1971873","display_name":"Trait","level":2,"score":0.7268368601799011},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6716062426567078},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5684183835983276},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.501319169998169},{"id":"https://openalex.org/C81941488","wikidata":"https://www.wikidata.org/wiki/Q853421","display_name":"Quantitative trait locus","level":3,"score":0.4958218038082123},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49310705065727234},{"id":"https://openalex.org/C142870003","wikidata":"https://www.wikidata.org/wiki/Q843863","display_name":"Genetic linkage","level":3,"score":0.41921043395996094},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.37070849537849426},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.28518763184547424},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.23915371298789978},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10745170712471008},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btn064","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn064","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/7/958/49047343/bioinformatics_24_7_958.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:18310620","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18310620","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn064","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn064","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/7/958/49047343/bioinformatics_24_7_958.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":[{"id":"https://openalex.org/G4550466098","display_name":null,"funder_award_id":"T32DE07132","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"}],"funders":[{"id":"https://openalex.org/F4320337365","display_name":"National Institute of Dental and Craniofacial Research","ror":"https://ror.org/004a2wv92"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1480376833","https://openalex.org/W1506981339","https://openalex.org/W1835754911","https://openalex.org/W1970964234","https://openalex.org/W1975099560","https://openalex.org/W1980862193","https://openalex.org/W2051238651","https://openalex.org/W2094248448","https://openalex.org/W2100243165","https://openalex.org/W2108420379","https://openalex.org/W2117007075","https://openalex.org/W2122759946","https://openalex.org/W2135513748","https://openalex.org/W2141626473","https://openalex.org/W2148447731","https://openalex.org/W2150926065","https://openalex.org/W2152992515","https://openalex.org/W2157531820","https://openalex.org/W2163285329","https://openalex.org/W2167120442","https://openalex.org/W2320378818","https://openalex.org/W2332108399"],"related_works":["https://openalex.org/W2268117839","https://openalex.org/W2089810690","https://openalex.org/W2414021760","https://openalex.org/W1717138646","https://openalex.org/W1968966328","https://openalex.org/W4243672037","https://openalex.org/W2036087730","https://openalex.org/W2038035251","https://openalex.org/W4237074979","https://openalex.org/W3148029250"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genes":[1],"often":[2,162],"regulate":[3],"multiple":[4],"traits.":[5],"Identifying":[6],"clusters":[7],"of":[8,15,49,73,80,108],"traits":[9,99],"influenced":[10],"by":[11,56],"a":[12,121,159],"common":[13,82,101],"group":[14],"genes":[16,50,119,157],"helps":[17],"elucidate":[18],"regulatory":[19],"networks":[20],"and":[21,45,91,113],"can":[22,69,134],"improve":[23],"linkage":[24],"mapping.":[25],"METHODS:":[26],"We":[27,103],"show":[28,130,155],"that":[29,51,131,156],"the":[30,71,77,106,139],"Pearson":[31],"correlation":[32],"coefficient,":[33],"rho":[34,74,109,115,132],"L,":[35],"between":[36],"two":[37,98],"LOD":[38],"score":[39],"profiles":[40],"can,":[41],"with":[42,150],"high":[43],"specificity":[44],"sensitivity,":[46],"identify":[47],"pairs":[48],"have":[52,135],"their":[53],"transcription":[54],"regulated":[55],"shared":[57],"quantitative":[58],"trait":[59],"loci":[60],"(QTL).":[61],"Furthermore,":[62],"using":[63],"theoretical":[64],"and/or":[65],"empirical":[66],"methods,":[67],"we":[68],"approximate":[70],"distribution":[72],"L":[75,110,116,133],"under":[76],"null":[78],"hypothesis":[79],"no":[81],"QTL.":[83,102],"Therefore,":[84],"it":[85],"is":[86],"possible":[87],"to":[88,117],"calculate":[89],"P-values":[90],"false":[92],"discovery":[93],"rates":[94],"for":[95],"testing":[96],"whether":[97],"share":[100,163],"then":[104],"examine":[105],"properties":[107],"through":[111],"simulation":[112],"use":[114],"cluster":[118,161],"in":[120,144,169],"genetical":[122,145],"genomics":[123],"experiment":[124],"examining":[125],"Saccharomyces":[126],"cerevisiae.":[127],"RESULTS:":[128],"Simulations":[129],"more":[136],"power":[137],"than":[138],"clustering":[140],"methods":[141],"currently":[142],"used":[143],"genomics.":[146],"Combining":[147],"experimental":[148],"results":[149],"Gene":[151],"Ontology":[152],"(GO)":[153],"annotations":[154],"within":[158],"purported":[160],"similar":[164],"function.":[165],"SOFTWARE:":[166],"R-code":[167],"included":[168],"online":[170],"Supplementary":[171],"Material.":[172]},"counts_by_year":[],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}