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

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry

(2019) Marivi Colle et al.   GigaScience

New Deep Learning Genomic-Based Prediction Model for Multiple Traits with Binary, Ordinal, and Continuous Phenotypes

(2019) Osval A. Montesinos-López et al.   G3-Genes Genomes Genetics

Genomic Prediction of Autotetraploids; Influence of Relationship Matrices, Allele Dosage, and Continuous Genotyping Calls in Phenotype Prediction

(2019) Ivone de Bem Oliveira et al.   G3-Genes Genomes Genetics

Hyperparameter optimization of deep neural network using univariate dynamic encoding algorithm for searches

(2019) YoungJun Yoo   KNOWLEDGE-BASED SYSTEMS

Performance evaluation of deep neural ensembles toward malaria parasite detection in thin-blood smear images

(2019) Sivaramakrishnan Rajaraman et al.   PeerJ

Genomic Selection with Allele Dosage in Panicum maximum Jacq.

(2019) Letícia A. de C. Lara et al.   G3-Genes Genomes Genetics

A Guide for Using Deep Learning for Complex Trait Genomic Prediction

(2019) Pérez-Enciso et al.   Genes

How can a high-quality genome assembly help plant breeders?

(2019) Juliana Benevenuto et al.   GigaScience

Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles

(2019) Nguyen Quoc Khanh Le et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Improving grain yield, stress resilience and quality of bread wheat using large-scale genomics

(2019) Philomin Juliana et al.   NATURE GENETICS

Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato

(2018) Jeffrey B. Endelman et al.   GENETICS

Historical Datasets Support Genomic Selection Models for the Prediction of Cotton Fiber Quality Phenotypes Across Multiple Environments

(2018) Washington Gapare et al.   G3-Genes Genomes Genetics

Genomic Selection for Late Blight and Common Scab Resistance in Tetraploid Potato ( Solanum tuberosum )

(2018) Felix Enciso-Rodriguez et al.   G3-Genes Genomes Genetics

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

Tools for Genetic Studies in Experimental Populations of Polyploids

(2018) Peter M. Bourke et al.   Frontiers in Plant Science

Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato

(2018) Jeffrey B. Endelman et al.   GENETICS

Deep phenotyping: deep learning for temporal phenotype/genotype classification

(2018) Sarah Taghavi Namin 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

Multi-trait, Multi-environment Deep Learning Modeling for Genomic-Enabled Prediction of Plant Traits

(2018) Osval A. Montesinos-Lopez 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

A Low Resolution Epistasis Mapping Approach To Identify Chromosome Arm Interactions in Allohexaploid Wheat

(2018) Nicholas Santantonio et al.   G3-Genes Genomes Genetics

pSBVB: A Versatile Simulation Tool To Evaluate Genomic Selection in Polyploid Species

(2018) Laura Zingaretti et al.   G3-Genes Genomes Genetics

Linearized sigmoidal activation: A novel activation function with tractable non-linear characteristics to boost representation capability

(2018) Vivek Singh Bawa et al.   EXPERT SYSTEMS WITH APPLICATIONS

SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation

(2017) Vijay Badrinarayanan et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Genomic Selection in Dairy Cattle: The USDA Experience

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

An experimental validation of genomic selection in octoploid strawberry

(2017) Salvador A Gezan et al.   Horticulture Research

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

(2016) Jun Hong et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Efficiency of genomic selection for tomato fruit quality

(2016) Janejira Duangjit et al.   MOLECULAR BREEDING

Improving Genetic Gain with Genomic Selection in Autotetraploid Potato

(2016) Anthony T. Slater et al.   Plant Genome

AGHmatrix: R Package to Construct Relationship Matrices for Autotetraploid and Diploid Species: A Blueberry Example

(2016) Rodrigo R. Amadeu et al.   Plant Genome

Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

(2015) Nahla V Bassil et al.   BMC GENOMICS

Lights, camera, action: high-throughput plant phenotyping is ready for a close-up

(2015) Noah Fahlgren et al.   CURRENT OPINION IN PLANT BIOLOGY

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

HyperART: non-invasive quantification of leaf traits using hyperspectral absorption-reflectance-transmittance imaging

(2015) Sergej Bergsträsser et al.   Plant Methods

Genetic improvement of Pacific white shrimp [Penaeus (Litopenaeus) vannamei]: perspectives for genomic selection

(2015) Héctor Castillo-Juárez et al.   Frontiers in Genetics

Accounting for Genetic Architecture Improves Sequence Based Genomic Prediction for a Drosophila Fitness Trait

(2015) Ulrike Ober et al.   PLoS One

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

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

(2014) H. Y. Xiong et al.   SCIENCE

Priors in Whole-Genome Regression: The Bayesian Alphabet Returns

(2013) D. Gianola   GENETICS

On the Additive and Dominant Variance and Covariance of Individuals Within the Genomic Selection Scope

(2013) Z. G. Vitezica et al.   GENETICS

Genomic prediction in CIMMYT maize and wheat breeding programs

(2013) J Crossa et al.   HEREDITY

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement

(2013) Joshua N. Cobb et al.   THEORETICAL AND APPLIED GENETICS

Genomic Prediction in Maize Breeding Populations with Genotyping-by-Sequencing

(2013) José Crossa et al.   G3-Genes Genomes Genetics

Accelerating Improvement of Livestock with Genomic Selection

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

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

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

Genomic Prediction in Animals and Plants: Simulation of Data, Validation, Reporting, and Benchmarking

(2012) H. D. Daetwyler et al.   GENETICS

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

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

Semi-parametric genomic-enabled prediction of genetic values using reproducing kernel Hilbert spaces methods

(2010) GUSTAVO DE LOS CAMPOS et al.   Genetics Research

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

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

Reproducing kernel Hilbert spaces regression: A general framework for genetic evaluation1

(2009) G. de los Campos et al.   JOURNAL OF ANIMAL SCIENCE

Reproducing Kernel Hilbert Spaces Regression Methods for Genomic Assisted Prediction of Quantitative Traits

(2008) D. Gianola et al.   GENETICS

Efficient Methods to Compute Genomic Predictions

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