{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T02:47:57Z","timestamp":1769309277256,"version":"3.49.0"},"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2016,5,25]],"date-time":"2016-05-25T00:00:00Z","timestamp":1464134400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000153","name":"Division of Biological Infrastructure","doi-asserted-by":"publisher","award":["1458597"],"award-info":[{"award-number":["1458597"]}],"id":[{"id":"10.13039\/100000153","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000153","name":"Division of Biological Infrastructure","doi-asserted-by":"publisher","award":["1458515"],"award-info":[{"award-number":["1458515"]}],"id":[{"id":"10.13039\/100000153","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004925","type":"journal-article","created":{"date-parts":[[2016,5,25]],"date-time":"2016-05-25T17:34:29Z","timestamp":1464197669000},"page":"e1004925","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":25,"title":["PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies"],"prefix":"10.1371","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8106-3553","authenticated-orcid":false,"given":"Wenchao","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinbin","family":"Dai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qishan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shizhong","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick X.","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2016,5,25]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1093\/bioinformatics\/btu727","article-title":"eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathways","volume":"31","author":"M Kang","year":"2015","journal-title":"Bioinformatics"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1093\/genetics\/39.6.859","article-title":"AN EXTENSION OF THE CONCEPT OF PARTITIONING HEREDITARY VARIANCE FOR ANALYSIS OF COVARIANCES AMONG RELATIVES WHEN EPISTASIS IS PRESENT","volume":"39","author":"CC Cockerham","year":"1954","journal-title":"Genetics"},{"key":"ref3","article-title":"Genetic variation and disease: GWAS","volume":"1","author":"K Norrgard","year":"2008","journal-title":"Nature Education"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"e154","DOI":"10.1038\/tp.2012.80","article-title":"Epistasis network centrality analysis yields pathway replication across two GWAS cohorts for bipolar disorder","volume":"2","author":"A Pandey","year":"2012","journal-title":"Transl Psychiatry"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/nrg1407","article-title":"Epistasis: too often neglected in complex trait studies?","volume":"5","author":"O Carlborg","year":"2004","journal-title":"Nat Rev Genet"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1038\/nrg2809","article-title":"Missing heritability and strategies for finding the underlying causes of complex disease","volume":"11","author":"EE Eichler","year":"2010","journal-title":"Nat Rev Genet"},{"key":"ref7","article-title":"Unraveling Additive from Non-Additive Effects Using Genomic Relationship Matrices","author":"PR Mu\u00f1oz","year":"2014","journal-title":"Genetics"},{"key":"ref8","doi-asserted-by":"crossref","unstructured":"Kempthorne O (1954) The Correlation between Relatives in a Random Mating Population. 103\u2013113 p.","DOI":"10.1098\/rspb.1954.0056"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"e1000008","DOI":"10.1371\/journal.pgen.1000008","article-title":"Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits","volume":"4","author":"WG Hill","year":"2008","journal-title":"PLoS Genet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1093\/genetics\/143.3.1437","article-title":"Design III With Marker Loci","volume":"143","author":"CC Cockerham","year":"1996","journal-title":"Genetics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1093\/genetics\/160.3.1243","article-title":"Modeling Epistasis of Quantitative Trait Loci Using Cockerham's Model","volume":"160","author":"C-H Kao","year":"2002","journal-title":"Genetics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1017\/S0016672301005511","article-title":"Mapping quantitative trait loci with epistatic effects","volume":"79","author":"N YI","year":"2002","journal-title":"Genetics Research"},{"key":"ref13","first-page":"9","article-title":"An Empirical Bayes Method for Estimating Epistatic Effects of Quantitative Trait Loci","volume":"63","author":"S Xu","year":"2007","journal-title":"Biometrics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1955","DOI":"10.1534\/genetics.106.066571","article-title":"Genomewide Analysis of Epistatic Effects for Quantitative Traits in Barley","volume":"175","author":"S Xu","year":"2007","journal-title":"Genetics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.1534\/genetics.107.082867","article-title":"Quantitative Trait Loci Mapping and The Genetic Basis of Heterosis in Maize and Rice","volume":"180","author":"AAF Garcia","year":"2008","journal-title":"Genetics"},{"key":"ref16","article-title":"Mapping Quantitative Trait Loci by Controlling Polygenic Background Effects","author":"S Xu","year":"2013","journal-title":"Genetics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"12456","DOI":"10.1073\/pnas.1413750111","article-title":"Predicting hybrid performance in rice using genomic best linear unbiased prediction","volume":"111","author":"S Xu","year":"2014","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"10578","DOI":"10.1073\/pnas.1005931107","article-title":"Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing","volume":"107","author":"W Xie","year":"2010","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"e17595","DOI":"10.1371\/journal.pone.0017595","article-title":"Gains in QTL Detection Using an Ultra-High Density SNP Map Based on Population Sequencing Relative to Traditional RFLP\/SSR Markers","volume":"6","author":"H Yu","year":"2011","journal-title":"PLoS ONE"},{"key":"ref20","author":"C Sanderson","year":"2010"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1137\/0916069","article-title":"A Limited Memory Algorithm for Bound Constrained Optimization","volume":"16","author":"RH Byrd","year":"1995","journal-title":"SIAM Journal on Scientific Computing"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1145\/279232.279236","article-title":"Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization","volume":"23","author":"Zhu RHB Ciyou","year":"1997","journal-title":"ACM Transactions on Mathematical Software"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.1093\/genetics\/162.4.1885","article-title":"Genetic Dissection of an Elite Rice Hybrid Revealed That Heterozygotes Are Not Always Advantageous for Performance","volume":"162","author":"JP Hua","year":"2002","journal-title":"Genetics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"2574","DOI":"10.1073\/pnas.0437907100","article-title":"Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid","volume":"100","author":"J Hua","year":"2003","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"15847","DOI":"10.1073\/pnas.1214141109","article-title":"Genetic composition of yield heterosis in an elite rice hybrid","volume":"109","author":"G Zhou","year":"2012","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"2633","DOI":"10.1093\/bioinformatics\/btm308","article-title":"TASSEL: software for association mapping of complex traits in diverse samples","volume":"23","author":"PJ Bradbury","year":"2007","journal-title":"Bioinformatics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.ajhg.2010.11.011","article-title":"GCTA: A Tool for Genome-wide Complex Trait Analysis","volume":"88","author":"J Yang","journal-title":"The American Journal of Human Genetics"},{"key":"ref28","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"CCC Chang","year":"2015","journal-title":"GigaScience"},{"key":"ref29","article-title":"Zhao PX GPLEXUS: Enabling Genome-scale Gene Association Network Reconstruction and Analysis for Very Large-scale Expression Data","author":"J Li","journal-title":"Nucleic Acids Research Under review"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1534\/genetics.113.155309","article-title":"Genetic Mapping and Genomic Selection Using Recombination Breakpoint Data","volume":"195","author":"S Xu","year":"2013","journal-title":"Genetics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1534\/genetics.115.179945","article-title":"A Random-Model Approach to QTL Mapping in Multiparent Advanced Generation Intercross (MAGIC) Populations","volume":"202","author":"J Wei","year":"2016","journal-title":"Genetics"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004925","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,30]],"date-time":"2022-06-30T13:53:49Z","timestamp":1656597229000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004925"}},"subtitle":[],"editor":[{"given":"Paul P","family":"Gardner","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,5,25]]},"references-count":31,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2016,5,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004925","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,5,25]]}}}