{"id":"https://openalex.org/W2149377910","doi":"https://doi.org/10.1093/bioinformatics/btq526","title":"SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies","display_name":"SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies","publication_year":2010,"publication_date":"2010-09-21","ids":{"openalex":"https://openalex.org/W2149377910","doi":"https://doi.org/10.1093/bioinformatics/btq526","mag":"2149377910"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq526","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq526","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/22/2803/16895830/btq526.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"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/22/2803/16895830/btq526.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083429290","display_name":"Eden R. Martin","orcid":"https://orcid.org/0000-0002-4035-9152"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]},{"id":"https://openalex.org/I4210131692","display_name":"Dr. John T. Macdonald Foundation","ror":"https://ror.org/02vawgn43","country_code":"US","type":"other","lineage":["https://openalex.org/I4210131692"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"E. R. Martin","raw_affiliation_strings":["John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA"],"affiliations":[{"raw_affiliation_string":"John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA","institution_ids":["https://openalex.org/I4210131692","https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078501767","display_name":"Daniel D. Kinnamon","orcid":"https://orcid.org/0000-0002-0867-5227"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]},{"id":"https://openalex.org/I4210131692","display_name":"Dr. John T. Macdonald Foundation","ror":"https://ror.org/02vawgn43","country_code":"US","type":"other","lineage":["https://openalex.org/I4210131692"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. D. Kinnamon","raw_affiliation_strings":["John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA"],"affiliations":[{"raw_affiliation_string":"John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA","institution_ids":["https://openalex.org/I4210131692","https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088560327","display_name":"Michael A. Schmidt","orcid":null},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]},{"id":"https://openalex.org/I4210131692","display_name":"Dr. John T. Macdonald Foundation","ror":"https://ror.org/02vawgn43","country_code":"US","type":"other","lineage":["https://openalex.org/I4210131692"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. A. Schmidt","raw_affiliation_strings":["John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA"],"affiliations":[{"raw_affiliation_string":"John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA","institution_ids":["https://openalex.org/I4210131692","https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057364983","display_name":"Eric Powell","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131692","display_name":"Dr. John T. Macdonald Foundation","ror":"https://ror.org/02vawgn43","country_code":"US","type":"other","lineage":["https://openalex.org/I4210131692"]},{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"E. H. Powell","raw_affiliation_strings":["John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA"],"affiliations":[{"raw_affiliation_string":"John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA","institution_ids":["https://openalex.org/I4210131692","https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112060032","display_name":"Stephan Z\u00fcchner","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131692","display_name":"Dr. John T. Macdonald Foundation","ror":"https://ror.org/02vawgn43","country_code":"US","type":"other","lineage":["https://openalex.org/I4210131692"]},{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Zuchner","raw_affiliation_strings":["John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA"],"affiliations":[{"raw_affiliation_string":"John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA","institution_ids":["https://openalex.org/I4210131692","https://openalex.org/I145608581"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024991056","display_name":"Richard Morris","orcid":"https://orcid.org/0000-0001-7240-4563"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]},{"id":"https://openalex.org/I4210131692","display_name":"Dr. John T. Macdonald Foundation","ror":"https://ror.org/02vawgn43","country_code":"US","type":"other","lineage":["https://openalex.org/I4210131692"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. W. Morris","raw_affiliation_strings":["John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA"],"affiliations":[{"raw_affiliation_string":"John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA","institution_ids":["https://openalex.org/I4210131692","https://openalex.org/I145608581"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5083429290"],"corresponding_institution_ids":["https://openalex.org/I145608581","https://openalex.org/I4210131692"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.9738,"has_fulltext":true,"cited_by_count":76,"citation_normalized_percentile":{"value":0.91559605,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"26","issue":"22","first_page":"2803","last_page":"2810"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9994000196456909,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9994000196456909,"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":0.9979000091552734,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973999857902527,"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/genotype","display_name":"Genotype","score":0.6065974235534668},{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.5550522804260254},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4661238193511963},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45552003383636475},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.41409873962402344},{"id":"https://openalex.org/keywords/a-priori-and-a-posteriori","display_name":"A priori and a posteriori","score":0.41308659315109253},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.35541391372680664},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34256982803344727},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.34003520011901855},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33797961473464966},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2781083881855011},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.231736958026886},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22366788983345032},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09426847100257874}],"concepts":[{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.6065974235534668},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.5550522804260254},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4661238193511963},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45552003383636475},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.41409873962402344},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.41308659315109253},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.35541391372680664},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34256982803344727},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.34003520011901855},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33797961473464966},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2781083881855011},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.231736958026886},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22366788983345032},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09426847100257874},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btq526","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq526","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/22/2803/16895830/btq526.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":"pmh:oai:pubmedcentral.nih.gov:2971572","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2971572","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq526","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq526","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/22/2803/16895830/btq526.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":[{"id":"https://openalex.org/G2253936839","display_name":null,"funder_award_id":"NS065712","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3799965259","display_name":null,"funder_award_id":"U54NS065712","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2149377910.pdf","grobid_xml":"https://content.openalex.org/works/W2149377910.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1566107011","https://openalex.org/W1974498322","https://openalex.org/W1998487261","https://openalex.org/W1999592462","https://openalex.org/W2036210716","https://openalex.org/W2044758663","https://openalex.org/W2049633694","https://openalex.org/W2082318627","https://openalex.org/W2090430326","https://openalex.org/W2098207011","https://openalex.org/W2112113834","https://openalex.org/W2124960286","https://openalex.org/W2136796229","https://openalex.org/W2141413821","https://openalex.org/W2149791927","https://openalex.org/W2167635362","https://openalex.org/W2799002609","https://openalex.org/W2988522900","https://openalex.org/W4210345393","https://openalex.org/W4251911815","https://openalex.org/W7048738093"],"related_works":["https://openalex.org/W1974056099","https://openalex.org/W2386077341","https://openalex.org/W563589758","https://openalex.org/W5922282","https://openalex.org/W2954004777","https://openalex.org/W2949638731","https://openalex.org/W2951102138","https://openalex.org/W62490179","https://openalex.org/W4299447939","https://openalex.org/W2117545158"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Next-generation":[2],"sequencing":[3,226],"presents":[4],"several":[5],"statistical":[6],"challenges,":[7],"with":[8,130],"one":[9],"of":[10,48,65,127],"the":[11,49,89,95,116,137,144,186,224],"most":[12],"fundamental":[13],"being":[14],"determining":[15],"an":[16,99,121,191,211],"individual's":[17],"genotype":[18,32,75,141],"from":[19,136,190,205,237],"multiple":[20],"aligned":[21],"short":[22],"read":[23],"sequences":[24],"at":[25,252],"a":[26,40,45,81,107,125],"position.":[27],"Some":[28],"simple":[29],"approaches":[30,169],"for":[31,124,232],"calling":[33,39],"apply":[34,174],"fixed":[35],"filters,":[36],"such":[37,58],"as":[38,59,162,164],"heterozygote":[41],"if":[42],"more":[43],"than":[44,103,167],"specified":[46],"percentage":[47],"reads":[50],"have":[51],"variant":[52],"nucleotide":[53],"calls.":[54],"Other":[55],"genotype-calling":[56,83,216],"methods,":[57,91],"MAQ":[60],"and":[61,143,153,170,184,214,229],"SOAPsnp,":[62],"are":[63,250],"implementations":[64],"Bayes":[66],"classifiers":[67],"in":[68,86,98,158,180,200,223],"that":[69,155,196,203,218],"they":[70],"classify":[71],"genotypes":[72,189],"using":[73,150],"posterior":[74,96],"probabilities.":[76],"Results:":[77],"Here,":[78],"we":[79,112],"propose":[80],"novel":[82],"algorithm":[84,119],"that,":[85],"contrast":[87],"to":[88,120,139,176,188],"other":[90],"estimates":[92],"parameters":[93],"underlying":[94],"probabilities":[97,142],"adaptive":[100],"way":[101],"rather":[102],"arbitrarily":[104],"specifying":[105],"them":[106],"priori.":[108],"The":[109],"algorithm,":[110],"which":[111],"call":[113],"SeqEM,":[114],"applies":[115],"well-known":[117],"Expectation-Maximization":[118],"appropriate":[122],"likelihood":[123],"sample":[126,138],"unrelated":[128],"individuals":[129,183],"next-generation":[131,225],"sequence":[132,178],"data,":[133],"leveraging":[134],"information":[135],"estimate":[140],"nucleotide-read":[145],"error":[146,160],"rate.":[147],"We":[148,172],"demonstrate":[149],"analytic":[151],"calculations":[152],"simulations":[154],"SeqEM":[156,175,197,209,233],"results":[157,187],"genotype-call":[159],"rates":[161],"small":[163],"or":[165],"smaller":[166],"filtering":[168],"MAQ.":[171],"also":[173],"exome":[177],"data":[179,202,249],"eight":[181],"related":[182],"compare":[185],"Illumina":[192],"SNP":[193],"array,":[194],"showing":[195],"behaves":[198],"well":[199],"real":[201],"deviates":[204],"idealized":[206],"assumptions.":[207],"Conclusion:":[208],"offers":[210],"improved,":[212],"robust":[213],"flexible":[215],"approach":[217],"can":[219],"be":[220],"widely":[221],"applied":[222],"studies.":[227],"Availability":[228],"implementation:":[230],"Software":[231,242],"is":[234],"freely":[235],"available":[236,251],"our":[238],"website:":[239],"www.hihg.org":[240],"under":[241],"Download.":[243],"Contact:":[244],"emartin1@med.miami.edu":[245],"Supplementary":[246,248],"information:":[247],"Bioinformatics":[253],"online.":[254]},"counts_by_year":[{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":7}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
