An evaluation of machine-learning for predicting phenotype: studies in yeast, rice, and wheat

From genome-wide associations to candidate causal variants by statistical fine-mapping

(2018) Daniel J. Schaid et al.   NATURE REVIEWS GENETICS

Prediction of treatment response in rheumatoid arthritis patients using genome‐wide SNP data

(2018) Svetlana Cherlin et al.   GENETIC EPIDEMIOLOGY

Meta-QSAR: a large-scale application of meta-learning to drug design and discovery

(2017) Ivan Olier et al.   MACHINE LEARNING

MTG2: an efficient algorithm for multivariate linear mixed model analysis based on genomic information: Table 1.

(2016) S. H. Lee et al.   BIOINFORMATICS

Do little interactions get lost in dark random forests?

(2016) Marvin N. Wright et al.   BMC BIOINFORMATICS

Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets

(2016) Michael K. K. Leung et al.   PROCEEDINGS OF THE IEEE

Detecting gene-gene interactions using a permutation-based random forest method

(2016) Jing Li et al.   BioData Mining

Genetic studies of body mass index yield new insights for obesity biology

(2015) Adam E. Locke et al.   NATURE

Efficient Bayesian mixed-model analysis increases association power in large cohorts

(2015) Po-Ru Loh et al.   NATURE GENETICS

A gene-based association method for mapping traits using reference transcriptome data

(2015) Eric R Gamazon et al.   NATURE GENETICS

Efficient set tests for the genetic analysis of correlated traits

(2015) Francesco Paolo Casale et al.   NATURE METHODS

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

(2015) Jennifer Spindel et al.   PLoS Genetics

The identification of complex interactions in epidemiology and toxicology: a simulation study of boosted regression trees

(2014) Erik Lampa et al.   Environmental Health

MultiBLUP: improved SNP-based prediction for complex traits

(2014) Doug Speed et al.   GENOME RESEARCH

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

Efficient multivariate linear mixed model algorithms for genome-wide association studies

(2014) Xiang Zhou et al.   NATURE METHODS

Detecting epistasis in human complex traits

(2014) Wen-Hua Wei et al.   NATURE REVIEWS GENETICS

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

The Construction of Risk Prediction Models Using GWAS Data and Its Application to a Type 2 Diabetes Prospective Cohort

(2014) Daichi Shigemizu et al.   PLoS One

Genomic selection: genome-wide prediction in plant improvement

(2014) Zeratsion Abera Desta et al.   TRENDS IN PLANT SCIENCE

Further Improvements to Linear Mixed Models for Genome-Wide Association Studies

(2014) Christian Widmer et al.   Scientific Reports

Regularized Machine Learning in the Genetic Prediction of Complex Traits

(2014) Sebastian Okser et al.   PLoS Genetics

Finding the sources of missing heritability in a yeast cross

(2013) Joshua S. Bloom et al.   NATURE

Epistasis and quantitative traits: using model organisms to study gene–gene interactions

(2013) Trudy F. C. Mackay   NATURE REVIEWS GENETICS

Pitfalls of predicting complex traits from SNPs

(2013) Naomi R. Wray et al.   NATURE REVIEWS GENETICS

Imputation of Unordered Markers and the Impact on Genomic Selection Accuracy

(2013) Jessica E. Rutkoski et al.   G3-Genes Genomes Genetics

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

(2013) Xiang Zhou et al.   PLoS Genetics

Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding

(2012) G. de los Campos et al.   GENETICS

Use of support vector machines for disease risk prediction in genome-wide association studies: Concerns and opportunities

(2012) Florian Mittag et al.   HUMAN MUTATION

A mixed-model approach for genome-wide association studies of correlated traits in structured populations

(2012) Arthur Korte et al.   NATURE GENETICS

Overview of LASSO-related penalized regression methods for quantitative trait mapping and genomic selection

(2012) Zitong Li et al.   THEORETICAL AND APPLIED GENETICS

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

(2012) Jesse Poland et al.   Plant Genome

Estimating Missing Heritability for Disease from Genome-wide Association Studies

(2011) Sang Hong Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Bayesian variable selection regression for genome-wide association studies and other large-scale problems

(2011) Yongtao Guan et al.   Annals of Applied Statistics

Extension of the bayesian alphabet for genomic selection

(2011) David Habier et al.   BMC BIOINFORMATICS

Genomic selection in plant breeding: from theory to practice

(2011) J.-L. Jannink et al.   Briefings in Functional Genomics

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Data mining approaches for genome-wide association of mood disorders

(2011) Mehdi Pirooznia et al.   PSYCHIATRIC GENETICS

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

(2011) Jeffrey B. Endelman   Plant Genome

Genome-wide association studies in plants: the missing heritability is in the field

(2011) Benjamin Brachi et al.   GENOME BIOLOGY

Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics

(2010) B. E. Stranger et al.   GENETICS

Genome-wide association and genomic selection in animal breedingThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Ben Hayes et al.   GENOME

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Mixed linear model approach adapted for genome-wide association studies

(2010) Zhiwu Zhang et al.   NATURE GENETICS

New approaches to population stratification in genome-wide association studies

(2010) Alkes L. Price et al.   NATURE REVIEWS GENETICS

Machine learning in genome-wide association studies

(2009) Silke Szymczak et al.   GENETIC EPIDEMIOLOGY

Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree

(2009) G. de los Campos et al.   GENETICS

The Genetic Architecture of Maize Flowering Time

(2009) E. S. Buckler et al.   SCIENCE

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

Efficient Methods to Compute Genomic Predictions

(2008) P.M. VanRaden   JOURNAL OF DAIRY SCIENCE

Large-scale multiple testing under dependence

(2008) Wenguang Sun et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY