A deep convolutional neural network approach for predicting phenotypes from genotypes

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives

(2017) José Crossa et al.   TRENDS IN PLANT SCIENCE

Genomic Selection Accuracy using Multifamily Prediction Models in a Wheat Breeding Program

(2017) Elliot L. Heffner et al.   Plant Genome

Advances and Challenges in Genomic Selection for Disease Resistance

(2016) Jesse Poland et al.   Annual Review of Phytopathology

DeepChrome: deep-learning for predicting gene expression from histone modifications

(2016) Ritambhara Singh et al.   BIOINFORMATICS

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

Bulked sample analysis in genetics, genomics and crop improvement

(2016) Cheng Zou et al.   PLANT BIOTECHNOLOGY JOURNAL

Exciting journey of 10 years from genomes to fields and markets: Some success stories of genomics-assisted breeding in chickpea, pigeonpea and groundnut

(2016) Rajeev K Varshney   PLANT SCIENCE

Optimum breeding strategies using genomic selection for hybrid breeding in wheat, maize, rye, barley, rice and triticale

(2016) Jose J. Marulanda et al.   THEORETICAL AND APPLIED GENETICS

Genomic selection for wheat traits and trait stability

(2016) Mao Huang et al.   THEORETICAL AND APPLIED GENETICS

PEDLA: predicting enhancers with a deep learning-based algorithmic framework

(2016) Feng Liu et al.   Scientific Reports

Cross-Validation Without Doing Cross-Validation in Genome-Enabled Prediction

(2016) D. Gianola et al.   G3-Genes Genomes Genetics

Genomic Prediction of Gene Bank Wheat Landraces

(2016) José Crossa et al.   G3-Genes Genomes Genetics

Genome-Enabled Prediction Models for Yield Related Traits in Chickpea

(2016) Manish Roorkiwal et al.   Frontiers in Plant Science

Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding

(2016) Javaid A. Bhat et al.   Frontiers in Genetics

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

(2016) Sheng Wang et al.   Scientific Reports

EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm

(2016) Seong Gon Kim et al.   Scientific Reports

Comparison of methods used to identify superior individuals in genomic selection in plant breeding

(2015) L.L. Bhering et al.   GENETICS AND MOLECULAR RESEARCH

Deep learning

(2015) Yann LeCun et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

A deep learning framework for modeling structural features of RNA-binding protein targets

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

A Ranking Approach to Genomic Selection

(2015) Mathieu Blondel et al.   PLoS One

Prediction of malting quality traits in barley based on genome-wide marker data to assess the potential of genomic selection

(2015) Malthe Schmidt et al.   THEORETICAL AND APPLIED GENETICS

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

Improving Protein Fold Recognition by Deep Learning Networks

(2015) Taeho Jo et al.   Scientific Reports

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Genomic selection: genome-wide prediction in plant improvement

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

Genome-Wide Prediction of Traits with Different Genetic Architecture Through Efficient Variable Selection

(2013) V. Wimmer et al.   GENETICS

Does genomic selection have a future in plant breeding?

(2013) Elisabeth Jonas et al.   TRENDS IN BIOTECHNOLOGY

Comparison of whole-genome prediction models for traits with contrasting genetic architecture in a diversity panel of maize inbred lines

(2012) Christian Riedelsheimer et al.   BMC GENOMICS

Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine (Pinus taeda L.)

(2012) M. F. R. Resende et al.   GENETICS

Genomic selection in plant breeding: from theory to practice

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

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

(2011) Jeffrey B. Endelman   Plant Genome

Detection and use of QTL for complex traits in multiple environments

(2010) Fred A van Eeuwijk et al.   CURRENT OPINION IN PLANT BIOLOGY

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

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

Efficient Methods to Compute Genomic Predictions

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