{"id":"https://openalex.org/W4323811264","doi":"https://doi.org/10.1093/bioinformatics/btad127","title":"SLEMM: million-scale genomic predictions with window-based SNP weighting","display_name":"SLEMM: million-scale genomic predictions with window-based SNP weighting","publication_year":2023,"publication_date":"2023-03-01","ids":{"openalex":"https://openalex.org/W4323811264","doi":"https://doi.org/10.1093/bioinformatics/btad127"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad127","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad127","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad127/49633039/btad127.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad127/49633039/btad127.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030854920","display_name":"Jian Cheng","orcid":"https://orcid.org/0000-0002-7560-068X"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jian Cheng","raw_affiliation_strings":["Department of Animal Science, North Carolina State University , Raleigh, NC 27695, United States"],"affiliations":[{"raw_affiliation_string":"Department of Animal Science, North Carolina State University , Raleigh, NC 27695, United States","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049846480","display_name":"Christian Maltecca","orcid":"https://orcid.org/0000-0002-9996-4680"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christian Maltecca","raw_affiliation_strings":["Department of Animal Science, North Carolina State University , Raleigh, NC 27695, United States"],"affiliations":[{"raw_affiliation_string":"Department of Animal Science, North Carolina State University , Raleigh, NC 27695, United States","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010725845","display_name":"P.M. VanRaden","orcid":"https://orcid.org/0000-0002-9123-7278"},"institutions":[{"id":"https://openalex.org/I1312222531","display_name":"Agricultural Research Service","ror":"https://ror.org/02d2m2044","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul M VanRaden","raw_affiliation_strings":["Animal Genomics and Improvement Laboratory, USDA-ARS , Beltsville, MD 20705, United States"],"affiliations":[{"raw_affiliation_string":"Animal Genomics and Improvement Laboratory, USDA-ARS , Beltsville, MD 20705, United States","institution_ids":["https://openalex.org/I1312222531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043833054","display_name":"Jeffrey R. O\u2019Connell","orcid":"https://orcid.org/0000-0002-7046-6688"},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey R O'Connell","raw_affiliation_strings":["Department of Medicine, University of Maryland School of Medicine , Baltimore, MD 21201, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Maryland School of Medicine , Baltimore, MD 21201, United States","institution_ids":["https://openalex.org/I126744593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100747288","display_name":"Li Ma","orcid":"https://orcid.org/0000-0003-1038-1081"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li Ma","raw_affiliation_strings":["Department of Animal and Avian Sciences, University of Maryland , College Park, MD 20742, United States"],"affiliations":[{"raw_affiliation_string":"Department of Animal and Avian Sciences, University of Maryland , College Park, MD 20742, United States","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052188681","display_name":"Jicai Jiang","orcid":"https://orcid.org/0000-0001-6890-7539"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jicai Jiang","raw_affiliation_strings":["Department of Animal Science, North Carolina State University , Raleigh, NC 27695, United States"],"affiliations":[{"raw_affiliation_string":"Department of Animal Science, North Carolina State University , Raleigh, NC 27695, United States","institution_ids":["https://openalex.org/I137902535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5052188681"],"corresponding_institution_ids":["https://openalex.org/I137902535"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.4483,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.96852112,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"39","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10594","display_name":"Genetic and phenotypic traits in livestock","score":1.0,"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/T10594","display_name":"Genetic and phenotypic traits in livestock","score":1.0,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9966999888420105,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/best-linear-unbiased-prediction","display_name":"Best linear unbiased prediction","score":0.6741975545883179},{"id":"https://openalex.org/keywords/weighting","display_name":"Weighting","score":0.6265643239021301},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.5330520868301392},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5149796605110168},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4350385367870331},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.428505003452301},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.41753843426704407},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41029587388038635},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3764411211013794},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3682006895542145},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.31097692251205444},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2764560580253601},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.25645869970321655},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.215349018573761},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21185249090194702},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.13540682196617126},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.12892240285873413},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07822313904762268},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.07652983069419861}],"concepts":[{"id":"https://openalex.org/C103545067","wikidata":"https://www.wikidata.org/wiki/Q796265","display_name":"Best linear unbiased prediction","level":3,"score":0.6741975545883179},{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.6265643239021301},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.5330520868301392},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5149796605110168},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4350385367870331},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.428505003452301},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.41753843426704407},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41029587388038635},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3764411211013794},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3682006895542145},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.31097692251205444},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2764560580253601},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.25645869970321655},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.215349018573761},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21185249090194702},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.13540682196617126},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.12892240285873413},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07822313904762268},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.07652983069419861},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C126838900","wikidata":"https://www.wikidata.org/wiki/Q77604","display_name":"Radiology","level":1,"score":0.0},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btad127","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad127","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad127/49633039/btad127.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10039786","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10039786","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10039786/pdf/btad127.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad127","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad127","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad127/49633039/btad127.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2113439094","display_name":null,"funder_award_id":"2020-67015-31398","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G3615615310","display_name":null,"funder_award_id":"2021-67015-33409","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G5082646809","display_name":null,"funder_award_id":"2021-67015","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G6836947205","display_name":null,"funder_award_id":"2021-67015","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G6939483916","display_name":null,"funder_award_id":"1023267","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G7149858532","display_name":null,"funder_award_id":"2020-67015-31398","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G8420118621","display_name":null,"funder_award_id":"2021-67015-33409","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4323811264.pdf"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1619352775","https://openalex.org/W1844405070","https://openalex.org/W1928998639","https://openalex.org/W1966775465","https://openalex.org/W2001675230","https://openalex.org/W2019961888","https://openalex.org/W2067715889","https://openalex.org/W2077763475","https://openalex.org/W2101272289","https://openalex.org/W2110787179","https://openalex.org/W2128343509","https://openalex.org/W2140319434","https://openalex.org/W2150468137","https://openalex.org/W2163953557","https://openalex.org/W2164056841","https://openalex.org/W2166033750","https://openalex.org/W2188707104","https://openalex.org/W2342367770","https://openalex.org/W2345958530","https://openalex.org/W2511378584","https://openalex.org/W2617742891","https://openalex.org/W2624742489","https://openalex.org/W2800666211","https://openalex.org/W2808382008","https://openalex.org/W2914532656","https://openalex.org/W2931025368","https://openalex.org/W2936556724","https://openalex.org/W2938632242","https://openalex.org/W2950565052","https://openalex.org/W2964847782","https://openalex.org/W3036465674","https://openalex.org/W3131140676","https://openalex.org/W3181602837","https://openalex.org/W3185412568","https://openalex.org/W3187415957","https://openalex.org/W3205241549","https://openalex.org/W4288694737","https://openalex.org/W6636211426","https://openalex.org/W6684419525","https://openalex.org/W6739529650","https://openalex.org/W6751279692","https://openalex.org/W6752403626","https://openalex.org/W6759102444","https://openalex.org/W6761360123","https://openalex.org/W6761452685","https://openalex.org/W6761648689","https://openalex.org/W6779793095","https://openalex.org/W6798751038"],"related_works":["https://openalex.org/W2164855536","https://openalex.org/W1997352593","https://openalex.org/W1986074241","https://openalex.org/W2143489661","https://openalex.org/W4231523199","https://openalex.org/W3016573916","https://openalex.org/W4281711902","https://openalex.org/W3206555169","https://openalex.org/W2082443386","https://openalex.org/W2121150886"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"The":[2,186],"amount":[3],"of":[4,47,57,103,128],"genomic":[5,17,104,175],"data":[6],"is":[7,19,188],"increasing":[8],"exponentially.":[9],"Using":[10],"many":[11],"genotyped":[12,130],"and":[13,84,113,116,155,184],"phenotyped":[14],"individuals":[15,154],"for":[16,28,52,167],"prediction":[18,105,136],"appealing":[20],"yet":[21],"challenging.":[22],"Results":[23],"We":[24,60,119],"present":[25],"SLEMM":[26,41,66,90,161,171],"(short":[27],"Stochastic-Lanczos-Expedited":[29],"Mixed":[30],"Models),":[31],"a":[32,55,101],"new":[33],"software":[34,187],"tool,":[35],"to":[36,67,142,151,181],"address":[37],"the":[38,48,96,122,144],"computational":[39,168],"challenge.":[40],"builds":[42],"on":[43,73,149],"an":[44,178],"efficient":[45],"implementation":[46,185],"stochastic":[49],"Lanczos":[50],"algorithm":[51],"REML":[53],"in":[54,65,81],"framework":[56],"mixed":[58],"models.":[59,118],"further":[61],"implement":[62],"SNP":[63,92],"weighting":[64,93],"improve":[68],"its":[69],"predictions.":[70],"Extensive":[71],"analyses":[72,148],"seven":[74],"public":[75],"datasets,":[76],"covering":[77],"19":[78],"polygenic":[79],"traits":[80,127],"three":[82,85],"plant":[83],"livestock":[86],"species,":[87],"showed":[88,159],"that":[89,139,160],"with":[91,177],"had":[94,133],"overall":[95,134],"best":[97],"predictive":[98],"ability":[99],"among":[100],"variety":[102],"methods":[106,123],"including":[107],"GCTA\u2019s":[108],"empirical":[109],"BLUP,":[110],"BayesR,":[111],"KAML,":[112],"LDAK\u2019s":[114],"BOLT":[115],"BayesR":[117],"also":[120],"compared":[121],"using":[124],"nine":[125],"dairy":[126],"\u223c300k":[129],"cows.":[131],"All":[132],"similar":[135],"accuracies,":[137],"except":[138],"KAML":[140],"failed":[141],"process":[143],"data.":[145],"Additional":[146],"simulation":[147],"up":[150],"3":[152],"million":[153,157],"1":[156],"SNPs":[158],"was":[162],"advantageous":[163],"over":[164],"counterparts":[165],"as":[166],"performance.":[169],"Overall,":[170],"can":[172],"do":[173],"million-scale":[174],"predictions":[176],"accuracy":[179],"comparable":[180],"BayesR.":[182],"Availability":[183],"available":[189],"at":[190],"https://github.com/jiang18/slemm.":[191]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
