{"id":"https://openalex.org/W2011863596","doi":"https://doi.org/10.1186/1471-2105-12-194","title":"Inference of chromosome-specific copy numbers using population haplotypes","display_name":"Inference of chromosome-specific copy numbers using population haplotypes","publication_year":2011,"publication_date":"2011-05-24","ids":{"openalex":"https://openalex.org/W2011863596","doi":"https://doi.org/10.1186/1471-2105-12-194","mag":"2011863596","pmid":"https://pubmed.ncbi.nlm.nih.gov/21605463"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-194","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-194","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-194","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-194","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091279923","display_name":"Yao\u2010Ting Huang","orcid":"https://orcid.org/0000-0001-9253-2394"},"institutions":[{"id":"https://openalex.org/I148099254","display_name":"National Chung Cheng University","ror":"https://ror.org/0028v3876","country_code":"TW","type":"education","lineage":["https://openalex.org/I148099254"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Yao-Ting Huang","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan. ythuang@cs.ccu.edu.tw","Dept. of Comput. Sci. & Inf. Eng., National Chung Cheng Univ., Chia-Yi, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan. ythuang@cs.ccu.edu.tw","institution_ids":["https://openalex.org/I148099254"]},{"raw_affiliation_string":"Dept. of Comput. Sci. & Inf. Eng., National Chung Cheng Univ., Chia-Yi, Taiwan","institution_ids":["https://openalex.org/I148099254"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111648901","display_name":"Min-Han Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I148099254","display_name":"National Chung Cheng University","ror":"https://ror.org/0028v3876","country_code":"TW","type":"education","lineage":["https://openalex.org/I148099254"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Min-Han Wu","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, 621, Taiwan","Dept. of Comput. Sci. & Inf. Eng., National Chung Cheng Univ., Chia-Yi, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, 621, Taiwan","institution_ids":["https://openalex.org/I148099254"]},{"raw_affiliation_string":"Dept. of Comput. Sci. & Inf. Eng., National Chung Cheng Univ., Chia-Yi, Taiwan","institution_ids":["https://openalex.org/I148099254"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5091279923"],"corresponding_institution_ids":["https://openalex.org/I148099254"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5825,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.71228998,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"12","issue":"1","first_page":"194","last_page":"194"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9815000295639038,"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":0.9815000295639038,"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/T10492","display_name":"Microtubule and mitosis dynamics","score":0.004000000189989805,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T10751","display_name":"Forensic and Genetic Research","score":0.003599999938160181,"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/copy-number-variation","display_name":"Copy-number variation","score":0.8355494737625122},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6578031778335571},{"id":"https://openalex.org/keywords/international-hapmap-project","display_name":"International HapMap Project","score":0.6528546214103699},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6170336008071899},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.5760594606399536},{"id":"https://openalex.org/keywords/copy-number-analysis","display_name":"Copy number analysis","score":0.5307198762893677},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.5130287408828735},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.43118393421173096},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40808647871017456},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3824900686740875},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24300438165664673},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.12328022718429565}],"concepts":[{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.8355494737625122},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6578031778335571},{"id":"https://openalex.org/C177580304","wikidata":"https://www.wikidata.org/wiki/Q1147298","display_name":"International HapMap Project","level":5,"score":0.6528546214103699},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6170336008071899},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.5760594606399536},{"id":"https://openalex.org/C166608930","wikidata":"https://www.wikidata.org/wiki/Q5169175","display_name":"Copy number analysis","level":5,"score":0.5307198762893677},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.5130287408828735},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.43118393421173096},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40808647871017456},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3824900686740875},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24300438165664673},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.12328022718429565}],"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":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","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":4,"locations":[{"id":"doi:10.1186/1471-2105-12-194","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-194","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-194","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21605463","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21605463","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:70fd4f3e5f224889a500ea1086f79eb8","is_oa":true,"landing_page_url":"https://doaj.org/article/70fd4f3e5f224889a500ea1086f79eb8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 194 (2011)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3128032","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3128032","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-194","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-194","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-194","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.6499999761581421}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2011863596.pdf","grobid_xml":"https://content.openalex.org/works/W2011863596.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1534004883","https://openalex.org/W1601503375","https://openalex.org/W1629389037","https://openalex.org/W1969271586","https://openalex.org/W1979893941","https://openalex.org/W2011671834","https://openalex.org/W2020476205","https://openalex.org/W2021714239","https://openalex.org/W2032247293","https://openalex.org/W2042004678","https://openalex.org/W2045952235","https://openalex.org/W2047361940","https://openalex.org/W2061680337","https://openalex.org/W2073552485","https://openalex.org/W2076032878","https://openalex.org/W2081872599","https://openalex.org/W2083878136","https://openalex.org/W2084708009","https://openalex.org/W2088131236","https://openalex.org/W2113980948","https://openalex.org/W2117337524","https://openalex.org/W2119279196","https://openalex.org/W2123431154","https://openalex.org/W2139747296","https://openalex.org/W2144644150","https://openalex.org/W2149757018","https://openalex.org/W2150271406","https://openalex.org/W2150284179","https://openalex.org/W2155707112","https://openalex.org/W2156866331","https://openalex.org/W2159091117","https://openalex.org/W2164971951","https://openalex.org/W2168046000","https://openalex.org/W3139230464"],"related_works":["https://openalex.org/W2036715394","https://openalex.org/W1505676121","https://openalex.org/W3031751940","https://openalex.org/W2468405568","https://openalex.org/W2014606320","https://openalex.org/W3161440814","https://openalex.org/W2474139959","https://openalex.org/W2206749611","https://openalex.org/W2129637418","https://openalex.org/W2089535743"],"abstract_inverted_index":{"BACKGROUND:":[0],"Using":[1],"microarray":[2,167],"and":[3,62,103,115],"sequencing":[4,169],"platforms,":[5],"a":[6,26,175],"large":[7],"number":[8,11,176,196],"of":[9,48,56,91,139,144,162,177,185,194],"copy":[10,39,44,67,85,93,131,145,164,195],"variations":[12],"(CNVs)":[13],"have":[14],"been":[15],"identified":[16],"in":[17,124,155,210],"humans.":[18],"In":[19],"practice,":[20],"because":[21],"our":[22,111],"human":[23],"genome":[24],"is":[25,113,188],"diploid,":[27],"these":[28],"platforms":[29,170],"are":[30,98,106,133,150],"limited":[31],"to":[32,100,190],"or":[33,168],"more":[34],"accurate":[35,114],"for":[36,82,152,202],"detecting":[37],"total":[38],"numbers":[40,45,68,86,132,146,165],"rather":[41],"than":[42],"chromosome-specific":[43,84,130,163],"at":[46,147,198],"each":[47,92],"the":[49,54,117,122,128,137,183,192,203],"two":[50],"homologous":[51],"chromosomes.":[52],"Nevertheless,":[53],"analysis":[55],"linkage":[57],"disequilibrium":[58],"(LD)":[59],"between":[60],"CNVs":[61,204],"SNPs":[63,209],"indicates":[64,109],"that":[65,110,182],"distinct":[66],"often":[69,172],"sit":[70],"on":[71],"their":[72],"own":[73],"background":[74,89,186],"haplotypes.":[75],"RESULTS:":[76],"We":[77],"propose":[78],"new":[79],"computational":[80],"models":[81],"inferring":[83],"by":[87,174],"distinguishing":[88],"haplotypes":[90,187],"number.":[94],"The":[95,142,160],"formulated":[96],"problems":[97],"shown":[99],"be":[101],"NP-hard":[102],"approximation/heuristic":[104],"algorithms":[105],"developed.":[107],"Simulation":[108],"method":[112],"outperforms":[116],"existing":[118],"approach.":[119],"By":[120],"testing":[121],"program":[123],"60":[125],"parent-offspring":[126],"trios,":[127],"inferred":[129],"highly":[134],"consistent":[135],"with":[136,208],"law":[138],"Mendelian":[140],"inheritance.":[141],"distributions":[143],"chromosomal":[148],"level":[149],"provided":[151],"270":[153],"individuals":[154],"three":[156],"HapMap":[157],"panels.":[158],"CONCLUSIONS:":[159],"estimation":[161,197],"using":[166],"was":[171],"confounded":[173],"factors.":[178],"This":[179],"study":[180],"showed":[181],"integration":[184],"able":[189],"improve":[191],"accuracies":[193],"chromosome":[199],"level,":[200],"especially":[201],"having":[205],"strong":[206],"LD":[207],"proximity.":[211]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
