{"id":"https://openalex.org/W2141437496","doi":"https://doi.org/10.1093/bioinformatics/btp693","title":"Copy number variant detection in inbred strains from short read sequence data","display_name":"Copy number variant detection in inbred strains from short read sequence data","publication_year":2009,"publication_date":"2009-12-18","ids":{"openalex":"https://openalex.org/W2141437496","doi":"https://doi.org/10.1093/bioinformatics/btp693","mag":"2141437496","pmid":"https://pubmed.ncbi.nlm.nih.gov/20022973"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp693","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp693","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/4/565/48854681/bioinformatics_26_4_565.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/4/565/48854681/bioinformatics_26_4_565.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003935660","display_name":"Jared T. Simpson","orcid":"https://orcid.org/0000-0002-2116-2602"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Jared T. Simpson","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Hinxton, CB10 1HH, UK"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, CB10 1HH, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089631924","display_name":"Rebecca E. McIntyre","orcid":"https://orcid.org/0000-0001-5291-1533"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rebecca E. McIntyre","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Hinxton, CB10 1HH, UK"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, CB10 1HH, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102865320","display_name":"David J. Adams","orcid":"https://orcid.org/0000-0001-9490-0306"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David J. Adams","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Hinxton, CB10 1HH, UK"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, CB10 1HH, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082040351","display_name":"Richard Durbin","orcid":"https://orcid.org/0000-0002-9130-1006"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard Durbin","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Hinxton, CB10 1HH, UK"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, CB10 1HH, UK","institution_ids":["https://openalex.org/I2802476451"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5003935660"],"corresponding_institution_ids":["https://openalex.org/I2802476451"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.6502,"has_fulltext":true,"cited_by_count":53,"citation_normalized_percentile":{"value":0.93452223,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"26","issue":"4","first_page":"565","last_page":"567"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9998000264167786,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9987999796867371,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.7371256351470947},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6933075189590454},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.618127167224884},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5839806795120239},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5640274286270142},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5124995708465576},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.5077346563339233},{"id":"https://openalex.org/keywords/comparative-genomic-hybridization","display_name":"Comparative genomic hybridization","score":0.4272746443748474},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4054441452026367},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.35731738805770874},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.14646023511886597},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.05942291021347046}],"concepts":[{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.7371256351470947},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6933075189590454},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.618127167224884},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5839806795120239},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5640274286270142},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5124995708465576},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.5077346563339233},{"id":"https://openalex.org/C124942203","wikidata":"https://www.wikidata.org/wiki/Q656638","display_name":"Comparative genomic hybridization","level":4,"score":0.4272746443748474},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4054441452026367},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35731738805770874},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.14646023511886597},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.05942291021347046}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"D008815","descriptor_name":"Mice, Inbred Strains","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008815","descriptor_name":"Mice, Inbred Strains","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008815","descriptor_name":"Mice, Inbred Strains","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008815","descriptor_name":"Mice, Inbred Strains","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp693","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp693","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/4/565/48854681/bioinformatics_26_4_565.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20022973","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20022973","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:pubmedcentral.nih.gov:2820678","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2820678","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp693","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp693","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/4/565/48854681/bioinformatics_26_4_565.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2141437496.pdf","grobid_xml":"https://content.openalex.org/works/W2141437496.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1598458881","https://openalex.org/W1964123743","https://openalex.org/W1969211599","https://openalex.org/W1971321176","https://openalex.org/W1971422405","https://openalex.org/W1999674531","https://openalex.org/W2009570821","https://openalex.org/W2021714239","https://openalex.org/W2035593347","https://openalex.org/W2038127858","https://openalex.org/W2051464954","https://openalex.org/W2066721762","https://openalex.org/W2077560413","https://openalex.org/W2103139723","https://openalex.org/W2112113834","https://openalex.org/W2151464048","https://openalex.org/W2155707112","https://openalex.org/W2163533231","https://openalex.org/W6655698170"],"related_works":["https://openalex.org/W2154009110","https://openalex.org/W2115134931","https://openalex.org/W2031436818","https://openalex.org/W2187207551","https://openalex.org/W2069184423","https://openalex.org/W2115701471","https://openalex.org/W2058336589","https://openalex.org/W1603543036","https://openalex.org/W2155557383","https://openalex.org/W2090795400"],"abstract_inverted_index":{"We":[0,80,120,139],"have":[1],"developed":[2],"an":[3],"algorithm":[4,83,126],"to":[5,44,63,75,129],"detect":[6,45],"copy":[7,78,110],"number":[8,111],"variants":[9,112],"(CNVs)":[10],"in":[11,41],"homozygous":[12,36],"organisms,":[13],"such":[14],"as":[15],"inbred":[16,33],"laboratory":[17],"strains":[18,97],"of":[19,59,69,94,124,146],"mice,":[20],"from":[21,90,151],"short":[22,85],"read":[23,86],"sequence":[24,60,87],"data.":[25],"Our":[26],"novel":[27],"approach":[28],"exploits":[29],"the":[30,42,57,64,67,95,102,122,147,152],"fact":[31],"that":[32,149],"mice":[34],"are":[35],"at":[37],"virtually":[38],"every":[39],"position":[40],"genome":[43],"CNVs":[46,130],"using":[47],"a":[48,144],"hidden":[49],"Markov":[50],"model":[51],"(HMM).":[52],"This":[53],"HMM":[54],"uses":[55],"both":[56],"density":[58],"reads":[61],"mapped":[62],"genome,":[65],"and":[66,99,116],"rate":[68],"apparent":[70],"heterozygous":[71],"single":[72],"nucleotide":[73],"polymorphisms,":[74],"determine":[76],"genomic":[77,135],"number.":[79],"tested":[81],"our":[82,125],"on":[84,143],"data":[88,155],"generated":[89],"re-sequencing":[91],"chromosome":[92],"17":[93],"mouse":[96],"A/J":[98,115],"CAST/EiJ":[100],"with":[101],"Illumina":[103],"platform.":[104],"In":[105],"total,":[106],"we":[107],"identified":[108,132],"118":[109],"(43":[113],"for":[114,118],"75":[117],"CAST/EiJ).":[119],"investigated":[121],"performance":[123],"through":[127],"comparison":[128],"previously":[131],"by":[133],"array-comparative":[134],"hybridization":[136],"(array":[137],"CGH).":[138],"performed":[140],"quantitative-PCR":[141],"validation":[142],"subset":[145],"calls":[148],"differed":[150],"array":[153],"CGH":[154],"sets.":[156]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":9}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}