A review of deep learning applications for genomic selection

Exploring Deep Learning for Complex Trait Genomic Prediction in Polyploid Outcrossing Species

(2020) Laura M. Zingaretti et al.   Frontiers in Plant Science

Sparse Convolutional Neural Networks for Genome-Wide Prediction

(2020) Patrik Waldmann et al.   Frontiers in Genetics

Role of New Plant Breeding Technologies for Food Security and Sustainable Agricultural Development

(2020) Matin Qaim   Applied Economic Perspectives and Policy

On to the next chapter for crop breeding: Convergence with data science

(2020) Elhan S. Ersoz et al.   CROP SCIENCE

Genomic prediction of sugar content and cane yield in sugar cane clones in different stages of selection in a breeding program, with and without pedigree information

(2020) Emily Deomano et al.   MOLECULAR BREEDING

Predicting yield performance of parents in plant breeding: A neural collaborative filtering approach

(2020) Saeed Khaki et al.   PLoS One

Comparison of genome-wide and phenotypic selection indices in maize

(2019) Gustavo Vitti Môro et al.   EUPHYTICA

Deep learning outperformed 136 of 157 dermatologists in a head-to-head dermoscopic melanoma image classification task

(2019) Titus J. Brinker et al.   EUROPEAN JOURNAL OF CANCER

Crop Yield Prediction Using Deep Neural Networks

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

De novo genome assembly of the white-spotted flower chafer (Protaetia brevitarsis)

(2019) Kui Wang et al.   GigaScience

Differentiating between morphologically similar species in genus Cinnamomum (Lauraceae) using deep convolutional neural networks

(2019) Hao-Wen Yang et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

A Guide for Using Deep Learning for Complex Trait Genomic Prediction

(2019) Pérez-Enciso et al.   Genes

DeepCount: In-Field Automatic Quantification of Wheat Spikes Using Simple Linear Iterative Clustering and Deep Convolutional Neural Networks

(2019) Pouria Sadeghi-Tehran et al.   Frontiers in Plant Science

Phenotype Prediction and Genome-Wide Association Study Using Deep Convolutional Neural Network of Soybean

(2019) Yang Liu et al.   Frontiers in Genetics

Deep Kernel and Deep Learning for Genome-Based Prediction of Single Traits in Multienvironment Breeding Trials

(2019) José Crossa et al.   Frontiers in Genetics

Seed-per-pod estimation for plant breeding using deep learning

(2018) L.C. Uzal et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Deep learning in agriculture: A survey

(2018) Andreas Kamilaris et al.   COMPUTERS AND ELECTRONICS IN AGRICULTURE

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

(2018) Rajeev K Varshney et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genomic selection for grain yield and quality traits in durum wheat

(2018) Jemanesh K. Haile et al.   MOLECULAR BREEDING

Statistical and Machine Learning forecasting methods: Concerns and ways forward

(2018) Spyros Makridakis et al.   PLoS One

An explainable deep machine vision framework for plant stress phenotyping

(2018) Sambuddha Ghosal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Prediction in a Multiploid Crop: Genotype by Environment Interaction and Allele Dosage Effects on Predictive Ability in Banana

(2018) Moses Nyine et al.   Plant Genome

Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection

(2018) Michel S. McElroy et al.   Frontiers in Plant Science

Pheno-Deep Counter: a unified and versatile deep learning architecture for leaf counting

(2018) Mario Valerio Giuffrida et al.   PLANT JOURNAL

A deep convolutional neural network approach for predicting phenotypes from genotypes

(2018) Wenlong Ma et al.   PLANTA

Deep Learning for Plant Stress Phenotyping: Trends and Future Perspectives

(2018) Asheesh Kumar Singh et al.   TRENDS IN PLANT SCIENCE

Detection and analysis of wheat spikes using Convolutional Neural Networks

(2018) Md Mehedi Hasan et al.   Plant Methods

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

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

Portfolio optimization for seed selection in diverse weather scenarios

(2017) Oskar Marko et al.   PLoS One

Use of Genomic Estimated Breeding Values Results in Rapid Genetic Gains for Drought Tolerance in Maize

(2017) B.S. Vivek et al.   Plant Genome

Genomic Selection in Dairy Cattle: The USDA Experience

(2017) George R. Wiggans et al.   Annual Review of Animal Biosciences

Deep machine learning provides state-of-the-art performance in image-based plant phenotyping

(2017) Michael P. Pound et al.   GigaScience

Genome-enabled prediction using probabilistic neural network classifiers

(2016) Juan Manuel González-Camacho et al.   BMC GENOMICS

Genomic Selection Performs Similarly to Phenotypic Selection in Barley

(2016) Ahmad H. Sallam et al.   CROP SCIENCE

Short communication: Use of genomic and metabolic information as well as milk performance records for prediction of subclinical ketosis risk via artificial neural networks

(2015) A. Ehret et al.   JOURNAL OF DAIRY SCIENCE

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

Priors in Whole-Genome Regression: The Bayesian Alphabet Returns

(2013) D. Gianola   GENETICS

Genomic prediction in CIMMYT maize and wheat breeding programs

(2013) J Crossa et al.   HEREDITY

Machine Learning Prediction of Cancer Cell Sensitivity to Drugs Based on Genomic and Chemical Properties

(2013) Michael P. Menden et al.   PLoS One

Accelerating Improvement of Livestock with Genomic Selection

(2013) Theo Meuwissen et al.   Annual Review of Animal Biosciences

Genome-wide selection in cassava

(2012) Eder Jorge de Oliveira et al.   EUPHYTICA

Genome-enabled prediction of genetic values using radial basis function neural networks

(2012) J. M. González-Camacho et al.   THEORETICAL AND APPLIED 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

A Common Dataset for Genomic Analysis of Livestock Populations

(2012) Matthew A. Cleveland et al.   G3-Genes Genomes Genetics

Extension of the bayesian alphabet for genomic selection

(2011) David Habier et al.   BMC BIOINFORMATICS

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

(2011) Daniel Gianola et al.   BMC GENETICS

Accelerating the domestication of forest trees in a changing world

(2011) Antoine Harfouche et al.   TRENDS IN PLANT SCIENCE

Additive Genetic Variability and the Bayesian Alphabet

(2009) D. Gianola et al.   GENETICS