{"id":"https://openalex.org/W2471838566","doi":"https://doi.org/10.1093/bioinformatics/btw409","title":"An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing data","display_name":"An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing data","publication_year":2016,"publication_date":"2016-07-04","ids":{"openalex":"https://openalex.org/W2471838566","doi":"https://doi.org/10.1093/bioinformatics/btw409","mag":"2471838566","pmid":"https://pubmed.ncbi.nlm.nih.gov/27378300"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw409","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw409","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3240/7889696/btw409.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/32/21/3240/7889696/btw409.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053273910","display_name":"Gongyi Huang","orcid":"https://orcid.org/0009-0005-0819-0480"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gongyi Huang","raw_affiliation_strings":["1 School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100747409","display_name":"Shaoli Wang","orcid":"https://orcid.org/0000-0001-9865-2442"},"institutions":[{"id":"https://openalex.org/I181679659","display_name":"Shanghai University of Finance and Economics","ror":"https://ror.org/00wtvfq62","country_code":"CN","type":"education","lineage":["https://openalex.org/I181679659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaoli Wang","raw_affiliation_strings":["2 School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai 200433, China","3 Shanghai Key Laboratory of Financial Information Technology, Shanghai University of Finance and Economics, Shanghai 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai 200433, China","institution_ids":["https://openalex.org/I181679659"]},{"raw_affiliation_string":"3 Shanghai Key Laboratory of Financial Information Technology, Shanghai University of Finance and Economics, Shanghai 200433, China","institution_ids":["https://openalex.org/I181679659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100329544","display_name":"Xueqin Wang","orcid":"https://orcid.org/0000-0001-5205-9950"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueqin Wang","raw_affiliation_strings":["1 School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China","4 South China Center for Statistical Science, Sun Yat-sen University, Guangzhou 510275, China","5 Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"4 South China Center for Statistical Science, Sun Yat-sen University, Guangzhou 510275, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"5 Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103136437","display_name":"Na You","orcid":"https://orcid.org/0000-0001-8014-7229"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Na You","raw_affiliation_strings":["1 School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China","4 South China Center for Statistical Science, Sun Yat-sen University, Guangzhou 510275, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"4 South China Center for Statistical Science, Sun Yat-sen University, Guangzhou 510275, China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5103136437"],"corresponding_institution_ids":["https://openalex.org/I157773358"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1572,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.83049616,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"32","issue":"21","first_page":"3240","last_page":"3245"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.85589998960495,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.85589998960495,"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/T10751","display_name":"Forensic and Genetic Research","score":0.023900000378489494,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.022199999541044235,"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/bayes-theorem","display_name":"Bayes' theorem","score":0.7673711776733398},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6614747643470764},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.497609406709671},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48855265974998474},{"id":"https://openalex.org/keywords/sample-size-determination","display_name":"Sample size determination","score":0.4529891312122345},{"id":"https://openalex.org/keywords/word-error-rate","display_name":"Word error rate","score":0.45234787464141846},{"id":"https://openalex.org/keywords/statistical-power","display_name":"Statistical power","score":0.44707435369491577},{"id":"https://openalex.org/keywords/snp-genotyping","display_name":"SNP genotyping","score":0.41276708245277405},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.28537118434906006},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.2565605044364929},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.2459731101989746},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21552953124046326},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18618115782737732},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15908148884773254},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11807611584663391}],"concepts":[{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.7673711776733398},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6614747643470764},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.497609406709671},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48855265974998474},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.4529891312122345},{"id":"https://openalex.org/C40969351","wikidata":"https://www.wikidata.org/wiki/Q3516228","display_name":"Word error rate","level":2,"score":0.45234787464141846},{"id":"https://openalex.org/C96608239","wikidata":"https://www.wikidata.org/wiki/Q1199823","display_name":"Statistical power","level":2,"score":0.44707435369491577},{"id":"https://openalex.org/C163691529","wikidata":"https://www.wikidata.org/wiki/Q7391886","display_name":"SNP genotyping","level":5,"score":0.41276708245277405},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.28537118434906006},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.2565605044364929},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.2459731101989746},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21552953124046326},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18618115782737732},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15908148884773254},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11807611584663391},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw409","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw409","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3240/7889696/btw409.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:27378300","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27378300","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:open-archive.highwire.org:bioinfo:32/21/3240","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/21/3240","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw409","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw409","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3240/7889696/btw409.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":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1510659740","https://openalex.org/W1824047490","https://openalex.org/W1967639437","https://openalex.org/W2005129098","https://openalex.org/W2006145698","https://openalex.org/W2009660843","https://openalex.org/W2015022780","https://openalex.org/W2020154367","https://openalex.org/W2055650752","https://openalex.org/W2060683621","https://openalex.org/W2108234281","https://openalex.org/W2108409892","https://openalex.org/W2110514036","https://openalex.org/W2115244190","https://openalex.org/W2121150886","https://openalex.org/W2124960286","https://openalex.org/W2127515057","https://openalex.org/W2149377910","https://openalex.org/W2161724277","https://openalex.org/W2168133698","https://openalex.org/W2285497499","https://openalex.org/W2949138186","https://openalex.org/W3101330071","https://openalex.org/W3103154150"],"related_works":["https://openalex.org/W2137338763","https://openalex.org/W1998128037","https://openalex.org/W2033396143","https://openalex.org/W53693348","https://openalex.org/W2098771161","https://openalex.org/W1978124765","https://openalex.org/W1990163070","https://openalex.org/W2100908124","https://openalex.org/W3192724178","https://openalex.org/W2049692116"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,106,152],"development":[2],"of":[3,37,40,108],"next":[4],"generation":[5],"sequencing":[6,30,62],"technology":[7],"provides":[8],"an":[9,96],"efficient":[10],"and":[11,43,83,92,116,130],"powerful":[12],"approach":[13],"to":[14,27,46,59,75,101],"rare":[15],"variant":[16],"detection.":[17,67],"To":[18],"identify":[19],"genetic":[20],"variations,":[21],"the":[22,29,34,38,44,52,61,77,85,103,132,136,158],"essential":[23],"question":[24],"is":[25,56,99,112,121,155],"how":[26],"quantity":[28],"error":[31,63],"rate":[32,64],"in":[33,157],"data.":[35],"Because":[36],"advantage":[39],"easy":[41],"implementation":[42],"ability":[45],"integrate":[47],"data":[48,118,172],"from":[49,135,166],"different":[50],"sources,":[51],"empirical":[53,86],"Bayes":[54,87],"method":[55,88,111,125],"popularly":[57],"employed":[58],"estimate":[60,102],"for":[65,89],"SNP":[66,93],"RESULTS:":[68],"We":[69],"propose":[70],"a":[71],"novel":[72],"statistical":[73],"model":[74,104],"fit":[76],"observed":[78],"non-reference":[79],"allele":[80],"frequency":[81],"data,":[82],"utilize":[84],"both":[90],"genotyping":[91],"detection,":[94],"where":[95],"ECM":[97,137],"algorithm":[98,154],"implemented":[100],"parameters.":[105],"performance":[107],"our":[109,124],"proposed":[110,153],"investigated":[113],"via":[114],"simulations":[115],"real":[117],"analysis.":[119],"It":[120],"shown":[122],"that":[123],"makes":[126],"less":[127],"genotype-call":[128],"errors,":[129],"with":[131,144],"parameter":[133],"estimates":[134],"algorithm,":[138],"it":[139],"attains":[140],"high":[141],"detection":[142],"power":[143],"FDR":[145],"being":[146],"well":[147],"controlled.":[148],"AVAILABILITY":[149],"AND":[150],"IMPLEMENTATION:":[151],"wrapped":[156],"R":[159],"package":[160],"ebGenotyping,":[161],"which":[162],"can":[163],"be":[164],"downloaded":[165],"http://cran.r-project.org/web/packages/ebGenotyping/":[167],"CONTACT:":[168],"youn@mail.sysu.edu.cnSupplementary":[169],"information:":[170],"Supplementary":[171],"are":[173],"available":[174],"at":[175],"Bioinformatics":[176],"online.":[177]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}