{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T15:25:24Z","timestamp":1759332324881},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/1471-2105-16-s1-s10","type":"journal-article","created":{"date-parts":[[2015,6,18]],"date-time":"2015-06-18T18:01:52Z","timestamp":1434650512000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Data-driven encoding for quantitative genetic trait prediction"],"prefix":"10.1186","volume":"16","author":[{"given":"Dan","family":"He","sequence":"first","affiliation":[]},{"given":"Zhanyong","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Laxmi","family":"Parida","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,2,18]]},"reference":[{"key":"6901_CR1","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1093\/genetics\/157.4.1819","volume":"157","author":"THE Meuwissen","year":"2001","unstructured":"Meuwissen THE, Hayes BJ, Goddard ME: Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001, 157: 1819-1829.","journal-title":"Genetics"},{"issue":"2","key":"6901_CR2","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bfgp\/elq001","volume":"9","author":"J-L Jannink","year":"2010","unstructured":"Jannink J-L, Lorenz AJ, Iwata H: Genomic selection in plant breeding: from theory to practice. Briefings in Functional Genomics. 2010, 9 (2): 166-177. 10.1093\/bfgp\/elq001.","journal-title":"Briefings in Functional Genomics"},{"issue":"1","key":"6901_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.2135\/cropsci2008.08.0512","volume":"49","author":"EL Heffner","year":"2009","unstructured":"Heffner EL, Sorrells ME, Jannink J-L: Genomic selection for crop improvement. Crop Science. 2009, 49 (1): 1-12. 10.2135\/cropsci2008.08.0512.","journal-title":"Crop Science"},{"issue":"2","key":"6901_CR4","doi-asserted-by":"publisher","first-page":"391","DOI":"10.2135\/cropsci2007.04.0191","volume":"48","author":"Y Xu","year":"2008","unstructured":"Xu Y, Crouch JH: Marker-assisted selection in plant breeding: from publications to practice. Crop Science. 2008, 48 (2): 391-407. 10.2135\/cropsci2007.04.0191.","journal-title":"Crop Science"},{"issue":"3","key":"6901_CR5","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1093\/genetics\/124.3.743","volume":"124","author":"R Lande","year":"1990","unstructured":"Lande R, Thompson R: Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics. 1990, 124 (3): 743-756.","journal-title":"Genetics"},{"issue":"2","key":"6901_CR6","doi-asserted-by":"publisher","first-page":"433","DOI":"10.3168\/jds.2008-1646","volume":"92","author":"B Hayes","year":"2009","unstructured":"Hayes B, Bowman P, Chamberlain A, Goddard M: Genomic selection in dairy cattle: Progress and challenges. Journal of Dairy Science. 2009, 92 (2): 433-443. 10.3168\/jds.2008-1646.","journal-title":"Journal of Dairy Science"},{"issue":"2","key":"6901_CR7","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1534\/genetics.112.141473","volume":"192","author":"R Rincent","year":"2012","unstructured":"Rincent R, Nicolas S, Altmann T, Brunel D, Revilla P, Rodriguez VM, Moreno-Gonzalez J, Melchinger A, Bauer E, et al: Maximizing the reliability of genomic selection by optimizing the calibration set of reference individuals: Comparison of methods in two diverse groups of maize inbreds (zea mays l.). Genetics. 2012, 192 (2): 715-728. 10.1534\/genetics.112.141473.","journal-title":"Genetics"},{"issue":"4","key":"6901_CR8","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1534\/g3.111.001453","volume":"2","author":"MA Cleveland","year":"2012","unstructured":"Cleveland MA, Hickey JM, Forni S: A common dataset for genomic analysis of livestock populations. G3: Genes--Genomes--Genetics. 2012, 2 (4): 429-435.","journal-title":"G3: Genes--Genomes--Genetics"},{"key":"6901_CR9","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1017\/S0016672399004462","volume":"75","author":"JC Whittaker","year":"2000","unstructured":"Whittaker JC, Thompson R, Denham MC: Marker-assisted selection using ridge regression. Genet Res. 2000, 75: 249-252. 10.1017\/S0016672399004462.","journal-title":"Genet Res"},{"issue":"11","key":"6901_CR10","doi-asserted-by":"publisher","first-page":"4414","DOI":"10.3168\/jds.2007-0980","volume":"91","author":"P VanRaden","year":"2008","unstructured":"VanRaden P: Efficient methods to compute genomic predictions. Journal of dairy science. 2008, 91 (11): 4414-4423. 10.3168\/jds.2007-0980.","journal-title":"Journal of dairy science"},{"issue":"4","key":"6901_CR11","doi-asserted-by":"crossref","first-page":"2389","DOI":"10.1534\/genetics.107.081190","volume":"177","author":"D Habier","year":"2007","unstructured":"Habier D, Fernando R, Dekkers J: The impact of genetic relationship information on genome-assisted breeding values. Genetics. 2007, 177 (4): 2389-2397.","journal-title":"Genetics"},{"key":"6901_CR12","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","volume":"58","author":"R Tibshirani","year":"1994","unstructured":"Tibshirani R: Regression shrinkage and selection via the lasso. Journal of the Royal Statistical Society, Series B. 1994, 58: 267-288.","journal-title":"Journal of the Royal Statistical Society, Series B"},{"key":"6901_CR13","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1137\/S1064827596304010","volume":"20","author":"SS Chen","year":"1998","unstructured":"Chen SS, Donoho DL, Saunders A: Atomic decomposition by basis pursuit. SIAM Journal on Scientific Computing. 1998, 20: 33-61. 10.1137\/S1064827596304010.","journal-title":"SIAM Journal on Scientific Computing"},{"issue":"2","key":"6901_CR14","doi-asserted-by":"publisher","first-page":"544","DOI":"10.2527\/jas.2009-2064","volume":"88","author":"K Kizilkaya","year":"2010","unstructured":"Kizilkaya K, Fernando R, Garrick D: Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. Journal of animal science. 2010, 88 (2): 544-551. 10.2527\/jas.2009-2064.","journal-title":"Journal of animal science"},{"issue":"1","key":"6901_CR15","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1017\/S0016672310000534","volume":"93","author":"A Legarra","year":"2011","unstructured":"Legarra A, Robert-Grani\u00e9 C, Croiseau P, Guillaume F, Fritz S, et al: Improved lasso for genomic selection. Genetics research. 2011, 93 (1): 77-10.1017\/S0016672310000534.","journal-title":"Genetics research"},{"key":"6901_CR16","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1198\/016214508000000337","volume":"103","author":"T Park","year":"2008","unstructured":"Park T, Casella G: The bayesian lasso. Journal of the American Statistical Association. 2008, 103: 681-686. 10.1198\/016214508000000337.","journal-title":"Journal of the American Statistical Association"},{"key":"6901_CR17","volume-title":"PhD thesis","author":"JR Kilpatrick","year":"2009","unstructured":"Kilpatrick JR: Methods for detecting multi-locus genotype-phenotype association. PhD thesis. 2009, RICE UNIVERSITY"},{"key":"6901_CR18","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1111\/j.1467-9868.2005.00532.x","volume":"68","author":"M Yuan","year":"2006","unstructured":"Yuan M, Yuan M, Lin Y, Lin Y: Model selection and estimation in regression with grouped variables. Journal of the Royal Statistical Society, Series B. 2006, 68: 49-67. 10.1111\/j.1467-9868.2005.00532.x.","journal-title":"Journal of the Royal Statistical Society, Series B"},{"key":"6901_CR19","volume-title":"Journal of the Royal Statistical Society, Series B","author":"L Meier","year":"2008","unstructured":"Meier L, Geer SVD, B\u00fchlmann P, Z\u00fcrich ETH: The group lasso for logistic regression. Journal of the Royal Statistical Society, Series B. 2008"},{"key":"6901_CR20","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1080\/00401706.1970.10488634","volume":"12","author":"AE Hoerl","year":"1970","unstructured":"Hoerl AE, Kennard RW: Ridge regression: Biased estimation for nonorthogonal problems. Technometrics. 1970, 12: 55-67. 10.1080\/00401706.1970.10488634.","journal-title":"Technometrics"},{"key":"6901_CR21","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1111\/j.1467-9868.2005.00503.x","volume":"67","author":"H Zou","year":"2005","unstructured":"Zou H, Hastie T: Regularization and variable selection via the elastic net. Journal of the Royal Statistical Society, Series B. 2005, 67: 301-320. 10.1111\/j.1467-9868.2005.00503.x.","journal-title":"Journal of the Royal Statistical Society, Series B"},{"issue":"1","key":"6901_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v033.i01","volume":"33","author":"J Friedman","year":"2010","unstructured":"Friedman J, Hastie T, Tibshirani R: Regularization paths for generalized linear models via coordinate descent. Journal of Statistical Software. 2010, 33 (1): 1-22.","journal-title":"Journal of Statistical Software"},{"key":"6901_CR23","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1093\/genetics\/157.4.1819","volume":"157","author":"THE Meuwissen","year":"2001","unstructured":"Meuwissen THE, Hayes BJ, Goddard ME: Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001, 157: 1819-1829.","journal-title":"Genetics"},{"key":"6901_CR24","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511755453","volume-title":"Semiparametric Regression. Cambridge Series in Statistical and Probabilistic Mathematics","author":"D Ruppert","year":"2003","unstructured":"Ruppert D, Wand MP, Carroll RJ: Semiparametric Regression. Cambridge Series in Statistical and Probabilistic Mathematics. 2003, Cambridge University Press, New York, NY"},{"key":"6901_CR25","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1145\/130385.130401","volume-title":"Proceedings of the 5th Annual ACM workshop on computational learning theory","author":"BE Boser","year":"1992","unstructured":"Boser BE, et al: A training algorithm for optimal margin classifiers. Proceedings of the 5th Annual ACM workshop on computational learning theory. 1992, ACM Press, 144-152."},{"key":"6901_CR26","first-page":"147","volume-title":"Advances in Neural Information Processing Systems","author":"I Guyon","year":"1993","unstructured":"Guyon I, Boser B, Vapnik V: Automatic capacity tuning of very large vc-dimension classifiers. Advances in Neural Information Processing Systems. 1993, Morgan Kaufmann, 147-155."},{"key":"6901_CR27","first-page":"273","volume-title":"Machine Learning","author":"C Cortes","year":"1995","unstructured":"Cortes C, Vapnik V: Support-vector networks. Machine Learning. 1995, 273-297."},{"key":"6901_CR28","volume-title":"Support Vector Learning","author":"B Sch\u00f6lkopf","year":"1997","unstructured":"Sch\u00f6lkopf B: Support Vector Learning. 1997, [http:\/\/www.kernel-machines.org]"},{"key":"6901_CR29","first-page":"281","volume-title":"Advances in Neural Information Processing Systems 9","author":"V Vapnik","year":"1996","unstructured":"Vapnik V, Golowich SE, Smola A: Support vector method for function approximation, regression estimation, and signal processing. Advances in Neural Information Processing Systems 9. 1996, MIT Press, 281-287."},{"issue":"3","key":"6901_CR30","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1023\/B:STCO.0000035301.49549.88","volume":"14","author":"AJ Smola","year":"2004","unstructured":"Smola AJ, Sch\u00f6lkopf B: A tutorial on support vector regression. Statistics and Computing. 2004, 14 (3): 199-222. doi:10.1023\/B:STCO.0000035301.49549.88","journal-title":"Statistics and Computing"},{"issue":"1","key":"6901_CR31","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1002\/gepi.20360","volume":"33","author":"KA Pattin","year":"2009","unstructured":"Pattin KA, White BC, Barney N, Gui J, Nelson HH, Kelsey KT, Andrew AS, Karagas MR, Moore JH: A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction. Genetic epidemiology. 2009, 33 (1): 87-94. 10.1002\/gepi.20360.","journal-title":"Genetic epidemiology"},{"issue":"4","key":"6901_CR32","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1038\/ng1537","volume":"37","author":"J Marchini","year":"2005","unstructured":"Marchini J, Donnelly P, Cardon LR: Genome-wide strategies for detecting multiple loci that influence complex diseases. Nature genetics. 2005, 37 (4): 413-417. 10.1038\/ng1537.","journal-title":"Nature genetics"},{"issue":"9","key":"6901_CR33","doi-asserted-by":"publisher","first-page":"1439","DOI":"10.1002\/sim.1749","volume":"23","author":"NR Cook","year":"2004","unstructured":"Cook NR, Zee RY, Ridker PM: Tree and spline based association analysis of gene-gene interaction models for ischemic stroke. Statistics in medicine. 2004, 23 (9): 1439-1453. 10.1002\/sim.1749.","journal-title":"Statistics in medicine"},{"issue":"4","key":"6901_CR34","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1093\/bioinformatics\/btn652","volume":"25","author":"C Yang","year":"2009","unstructured":"Yang C, He Z, Wan X, Yang Q, Xue H, Yu W: Snpharvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies. Bioinformatics. 2009, 25 (4): 504-511. 10.1093\/bioinformatics\/btn652.","journal-title":"Bioinformatics"},{"issue":"9","key":"6901_CR35","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.1038\/ng2110","volume":"39","author":"Y Zhang","year":"2007","unstructured":"Zhang Y, Liu JS: Bayesian inference of epistatic interactions in case-control studies. Nature genetics. 2007, 39 (9): 1167-1173. 10.1038\/ng2110.","journal-title":"Nature genetics"},{"issue":"4","key":"6901_CR36","doi-asserted-by":"publisher","first-page":"33531","DOI":"10.1371\/journal.pone.0033531","volume":"7","author":"G Fang","year":"2012","unstructured":"Fang G, Haznadar M, Wang W, Yu H, Steinbach M, Church TR, Oetting WS, Van Ness B, Kumar V: High-order snp combinations associated with complex diseases: efficient discovery, statistical power and functional interactions. PloS one. 2012, 7 (4): 33531-10.1371\/journal.pone.0033531.","journal-title":"PloS one"},{"issue":"12","key":"6901_CR37","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1093\/bioinformatics\/btq186","volume":"26","author":"X Zhang","year":"2010","unstructured":"Zhang X, Huang S, Zou F, Wang W: Team: efficient two-locus epistasis tests in human genome-wide association study. Bioinformatics. 2010, 26 (12): 217-227. 10.1093\/bioinformatics\/btq186.","journal-title":"Bioinformatics"},{"issue":"4","key":"6901_CR38","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1145\/1852102.1852106","volume":"28","author":"W Webber","year":"2010","unstructured":"Webber W, Moffat A, Zobel J: A similarity measure for indefinite rankings. ACM Transactions on Information Systems (TOIS). 2010, 28 (4): 20-","journal-title":"ACM Transactions on Information Systems (TOIS)"},{"key":"6901_CR39","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1038\/ncomms1467","volume":"2","author":"K Zhao","year":"2011","unstructured":"Zhao K, Tung C-W, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, et al: Genome-wide association mapping reveals a rich genetic architecture of complex traits in oryza sativa. Nature communications. 2011, 2: 467-","journal-title":"Nature communications"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-16-S1-S10.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,9]],"date-time":"2024-06-09T15:56:52Z","timestamp":1717948612000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-16-S1-S10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,2,18]]},"references-count":39,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["6901"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-16-s1-s10","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,2,18]]},"assertion":[{"value":"18 February 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S10"}}