A Guide for Using Deep Learning for Complex Trait Genomic Prediction

Deep learning and process understanding for data-driven Earth system science

(2019) Markus Reichstein et al.   NATURE

mACPpred: A Support Vector Machine-Based Meta-Predictor for Identification of Anticancer Peptides

(2019) Vinothini Boopathi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Crop Yield Prediction Using Deep Neural Networks

(2019) Saeed Khaki et al.   Frontiers in Plant Science

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential

(2018) Steven T Hill et al.   NUCLEIC ACIDS RESEARCH

A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data

(2018) Benjamin J. Ainscough et al.   NATURE GENETICS

A primer on deep learning in genomics

(2018) James Zou et al.   NATURE GENETICS

Multi-environment Genomic Prediction of Plant Traits Using Deep Learners with Dense Architecture

(2018) Abelardo Montesinos-López et al.   G3-Genes Genomes Genetics

A Benchmarking Between Deep Learning, Support Vector Machine and Bayesian Threshold Best Linear Unbiased Prediction for Predicting Ordinal Traits in Plant Breeding

(2018) Osval A. Montesinos-López et al.   G3-Genes Genomes Genetics

Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding

(2018) Dario Grattapaglia et al.   Frontiers in Plant Science

Accuracy of genomic prediction using imputed whole-genome sequence data in white layers

(2016) M. Heidaritabar et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Comparison of Feature Selection Techniques in Machine Learning for Anatomical Brain MRI in Dementia

(2016) Jussi Tohka et al.   NEUROINFORMATICS

Deep Learning for Population Genetic Inference

(2016) Sara Sheehan et al.   PLoS Computational Biology

Deep learning

(2015) Yann LeCun et al.   NATURE

Genome-Wide Regression and Prediction with the BGLR Statistical Package

(2014) P. Perez et al.   GENETICS

Machine learning methods and predictive ability metrics for genome-wide prediction of complex traits

(2014) Oscar González-Recio et al.   Livestock Science

Priors in Whole-Genome Regression: The Bayesian Alphabet Returns

(2013) D. Gianola   GENETICS

Comparison Between Linear and Non-parametric Regression Models for Genome-Enabled Prediction in Wheat

(2012) Paulino Pérez-Rodríguez et al.   G3-Genes Genomes Genetics

Predicting complex quantitative traits with Bayesian neural networks: a case study with Jersey cows and wheat

(2011) Daniel Gianola et al.   BMC GENETICS

To Explain or to Predict?

(2011) Galit Shmueli   STATISTICAL SCIENCE

Accurate Prediction of Genetic Values for Complex Traits by Whole-Genome Resequencing

(2010) T. Meuwissen et al.   GENETICS

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

(2010) Jian Yang et al.   NATURE GENETICS

Predicting genetic predisposition in humans: the promise of whole-genome markers

(2010) Gustavo de los Campos et al.   NATURE REVIEWS GENETICS

Efficient Methods to Compute Genomic Predictions

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