{"id":"https://openalex.org/W350152004","doi":null,"title":"Efficient algorithms for human genetic variation detection using high-throughput sequencing techniques","display_name":"Efficient algorithms for human genetic variation detection using high-throughput sequencing techniques","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W350152004","mag":"350152004"},"language":"en","primary_location":{"id":"mag:350152004","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/content/qt73s9p1df/qt73s9p1df.pdf?t=me7i2n","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009368988","display_name":"Eleazar Eskin","orcid":"https://orcid.org/0000-0003-1149-4758","observed_orcids":["https://orcid.org/0000-0003-1149-4758"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eleazar Eskin","raw_affiliation_strings":["University of California\u2013Los Angeles"],"raw_orcid":"https://orcid.org/0000-0003-1149-4758","affiliations":[{"raw_affiliation_string":"University of California\u2013Los Angeles","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023085024","display_name":"Dan He","orcid":"https://orcid.org/0000-0001-9064-566X","observed_orcids":["https://orcid.org/0000-0001-9064-566X"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dan He","raw_affiliation_strings":["University of California\u2013Los Angeles"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California\u2013Los Angeles","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0188289,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9384999871253967,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9384999871253967,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.04270000010728836,"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/T11269","display_name":"Algorithms and Data Compression","score":0.0032999999821186066,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/human-genetic-variation","display_name":"human genetic variation","score":0.9110000133514404},{"id":"https://openalex.org/keywords/haplotype-inference","display_name":"haplotype inference","score":0.8870000243186951},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphisms","display_name":"single nucleotide polymorphisms","score":0.890999972820282},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"copy number variation","score":0.699999988079071},{"id":"https://openalex.org/keywords/structural-variants","display_name":"structural variants","score":0.7129999995231628},{"id":"https://openalex.org/keywords/sequencing-errors","display_name":"sequencing errors","score":0.6930000185966492},{"id":"https://openalex.org/keywords/multiplexing","display_name":"multiplexing","score":0.5289999842643738},{"id":"https://openalex.org/keywords/rare-variant-detection","display_name":"rare variant detection","score":0.6650000214576721},{"id":"https://openalex.org/keywords/genotype-imputation","display_name":"genotype imputation","score":0.7250000238418579},{"id":"https://openalex.org/keywords/microarray-genotyping","display_name":"microarray genotyping","score":0.8199999928474426},{"id":"https://openalex.org/keywords/linear-programming","display_name":"linear programming","score":0.5529999732971191},{"id":"https://openalex.org/keywords/maxsat","display_name":"MaxSAT","score":0.7850000262260437},{"id":"https://openalex.org/keywords/hidden-markov-models","display_name":"hidden Markov models","score":0.8159999847412109},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"dynamic programming","score":0.8019999861717224},{"id":"https://openalex.org/keywords/computational-complexity","display_name":"computational complexity","score":0.35100001096725464}],"concepts":[{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.6360719203948975},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.5792779326438904},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5568069815635681},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5143460035324097},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.503750741481781},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49609312415122986},{"id":"https://openalex.org/C44432683","wikidata":"https://www.wikidata.org/wiki/Q17145705","display_name":"Haplotype estimation","level":5,"score":0.4925740361213684},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.4907170534133911},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48794955015182495},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.4843538999557495},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4780619442462921},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4707259237766266},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.449752539396286},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4366312026977539},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.4129672646522522},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.3675081133842468},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3644304871559143},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18816149234771729},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.11144256591796875},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.09531530737876892},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.08277374505996704}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:350152004","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/content/qt73s9p1df/qt73s9p1df.pdf?t=me7i2n","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W111132822","https://openalex.org/W180925943","https://openalex.org/W1608204591","https://openalex.org/W1775352280","https://openalex.org/W1790474971","https://openalex.org/W1866835760","https://openalex.org/W1875901059","https://openalex.org/W1965464420","https://openalex.org/W1966938977","https://openalex.org/W1971321176","https://openalex.org/W1974646727","https://openalex.org/W1975087248","https://openalex.org/W1981509058","https://openalex.org/W1989568035","https://openalex.org/W2000586119","https://openalex.org/W2005129098","https://openalex.org/W2013221974","https://openalex.org/W2014606320","https://openalex.org/W2024528333","https://openalex.org/W2029376095","https://openalex.org/W2032247293","https://openalex.org/W2041947570","https://openalex.org/W2046601740","https://openalex.org/W2047440448","https://openalex.org/W2051464954","https://openalex.org/W2066371818","https://openalex.org/W2070359206","https://openalex.org/W2071221560","https://openalex.org/W2073868508","https://openalex.org/W2087036932","https://openalex.org/W2090144921","https://openalex.org/W2096313830","https://openalex.org/W2101342813","https://openalex.org/W2102095995","https://openalex.org/W2103647262","https://openalex.org/W2110755408","https://openalex.org/W2110772696","https://openalex.org/W2112113834","https://openalex.org/W2113649367","https://openalex.org/W2115480698","https://openalex.org/W2116753165","https://openalex.org/W2118653712","https://openalex.org/W2121211805","https://openalex.org/W2124514351","https://openalex.org/W2124734937","https://openalex.org/W2127710810","https://openalex.org/W2128114769","https://openalex.org/W2129326667","https://openalex.org/W2129795133","https://openalex.org/W2132971754","https://openalex.org/W2139747296","https://openalex.org/W2140869203","https://openalex.org/W2141437496","https://openalex.org/W2142642738","https://openalex.org/W2142707529","https://openalex.org/W2144644150","https://openalex.org/W2149681218","https://openalex.org/W2149791927","https://openalex.org/W2151751911","https://openalex.org/W2152559981","https://openalex.org/W2154431984","https://openalex.org/W2161689016","https://openalex.org/W2162927194","https://openalex.org/W2164971951","https://openalex.org/W2166501262","https://openalex.org/W2296616510","https://openalex.org/W7095308132"],"related_works":["https://openalex.org/W2140743149","https://openalex.org/W2020476205","https://openalex.org/W2110772696","https://openalex.org/W2114302801","https://openalex.org/W2756260525","https://openalex.org/W2767259410","https://openalex.org/W1790474971","https://openalex.org/W7100727667","https://openalex.org/W2901416809","https://openalex.org/W1579697098"],"abstract_inverted_index":{"High-throughput":[0],"sequencing":[1,9,28,43,144,235,304],"(HTS)":[2],"technologies":[3,51,305],"are":[4,17,38,120,158,240,254,269,342,347,359],"one":[5],"type":[6],"of":[7,48,93,100,111,116,127,131,143,150,171,214,251,320,322,339,364,375],"genome":[8,27,245],"techniques":[10,184],"where":[11,233,267],"short":[12],"DNA":[13,317,340,376],"segments,":[14],"or":[15,19,102,318,353],"reads,":[16],"sequenced":[18],"sampled":[20],"from":[21,86,164,199,238],"genome.":[22],"Compared":[23],"with":[24,73,161,402],"the":[25,42,74,94,98,109,141,151,162,172,196,234,249,259,274,289,307,316,345,362,373],"traditional":[26],"techniques,":[29],"they":[30,37],"have":[31,52,211,331],"advantages":[32],"such":[33,124],"as":[34,108,125],"low-cost":[35],"and":[36,146,189,204,216,226,246,273,295,344,387,390,397,405],"able":[39,392],"to":[40,45,61,154,177,194,224,242,261,279,292,361,393],"parallelize":[41],"process":[44],"produce":[46],"millions":[47],"reads.":[49],"These":[50,356],"been":[53,332],"widely":[54],"used":[55],"in":[56,97,137,205,229,270,298,303,314,334],"many":[57],"important":[58,121],"problems":[59,72,123],"related":[60],"human":[62,69,83,118,132],"genetic":[63,70,128],"variations.":[64],"We":[65,180,218,367],"mainly":[66],"target":[67],"three":[68],"variation":[71],"reads":[75,236,275],"generated":[76,237],"by":[77,89],"HTS.":[78],"\r\nIt":[79],"is":[80,96,140,153,175,288,391],"well-known":[81],"that":[82],"individuals":[84,323],"differ":[85],"each":[87,114],"other":[88],"0.1%.":[90],"The":[91,380],"majority":[92],"differences":[95],"form":[99],"SNPs,":[101],"Single":[103],"Nucleotide":[104],"Polymophisms.":[105],"Haplotypes,":[106],"defined":[107],"sequences":[110],"SNPs":[112,401],"on":[113],"chromosome":[115],"a":[117,147,165,182,243,252,262,336,369,384],"genome,":[119],"for":[122,309,372],"imputation":[126],"variants,":[129],"relatedness":[130],"individuals,":[133],"etc.":[134],"A":[135,327],"difficulty":[136],"haplotype":[138,173],"inference":[139],"presence":[142,250],"errors":[145],"natural":[148],"formulation":[149,170],"problem":[152,197,266],"infer":[155],"haplotypes":[156],"which":[157,315,335],"most":[159],"consistent":[160],"data":[163],"combinatorial":[166],"perspective.":[167],"Unfortunately,":[168],"this":[169],"assembly":[174],"known":[176],"be":[178,277,325],"NP-hard.":[179],"proposed":[181,220],"few":[183,328],"including":[185],"dynamic":[186],"programming,":[187],"MaxSAT":[188],"Hidden":[190],"Markov":[191],"Model":[192],"(HMM)":[193],"solve":[195],"optimally":[198],"different":[200],"perspectives.":[201],"\r\nStructural":[202],"variations":[203],"particular":[206],"Copy":[207],"Number":[208],"Variations":[209],"(CNV)":[210],"dramatic":[212],"effects":[213],"disease":[215],"traits.":[217],"first":[219,290],"an":[221],"efficient":[222],"algorithm":[223,260,371,382],"detect":[225],"reconstruct":[227,296],"CNVs":[228,268,297],"unique":[230],"genomic":[231],"regions,":[232],"HTS":[239],"mapped":[241,278],"reference":[244],"signatures":[247],"indicating":[248],"CNV":[253],"identified.":[255],"Then":[256],"we":[257],"extend":[258],"much":[263],"more":[264],"challenging":[265],"repeat-rich":[271,299],"regions":[272],"may":[276],"multiple":[280],"mapping":[281],"positions.":[282],"To":[283],"our":[284,286],"knowledge,":[285],"method":[287],"attempt":[291],"both":[293,395],"identify":[294],"regions.":[300],"\r\nRecent":[301],"advances":[302],"set":[306],"stage":[308],"large":[310],"population":[311],"based":[312],"studies,":[313],"RNA":[319],"thousands":[321],"will":[324],"sequenced.":[326],"multiplexing":[329,378],"schemes":[330],"suggested,":[333],"small":[337],"number":[338],"pools":[341,377],"sequenced,":[343],"results":[346],"then":[348],"deconvoluted":[349],"using":[350],"compressed":[351],"sensing":[352],"similar":[354],"approaches.":[355],"methods,":[357],"however,":[358],"limited":[360],"detection":[363],"rare":[365],"variants.":[366],"provide":[368],"new":[370],"deconvolution":[374],"schemes.":[379],"presented":[381],"utilizes":[383],"likelihood":[385],"model":[386],"linear":[388],"programming":[389],"genotype":[394],"low":[396],"high":[398],"allele":[399],"frequency":[400],"microarray":[403],"genotyping":[404],"imputation.":[406]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}