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

Combining QTL-seq and linkage mapping to fine map a wild soybean allele characteristic of greater plant height

(2018) Xiaoli Zhang et al.   BMC GENOMICS

Prediction of Protein Backbone Torsion Angles Using Deep Residual Inception Neural Networks

(2018) Chao Fang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A One-Penny Imputed Genome from Next-Generation Reference Panels

(2018) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A deep convolutional neural network approach for predicting phenotypes from genotypes

(2018) Wenlong Ma et al.   PLANTA

Capsule network for protein post-translational modification site prediction

(2018) Duolin Wang et al.   BIOINFORMATICS

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

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

Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population

(2017) Alencar Xavier et al.   G3-Genes Genomes Genetics

Genetic Characterization of the Soybean Nested Association Mapping Population

(2017) Qijian Song et al.   Plant Genome

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

Optimizing Training Population Size and Genotyping Strategy for Genomic Prediction Using Association Study Results and Pedigree Information. A Case of Study in Advanced Wheat Breeding Lines

(2017) Fabio Cericola et al.   PLoS One

Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans

(2016) A. Xavier et al.   BMC BIOINFORMATICS

DL-ADR: a novel deep learning model for classifying genomic variants into adverse drug reactions

(2016) Zhaohui Liang et al.   BMC Medical Genomics

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

How far from the SNP may the causative genes be?

(2016) Aharon Brodie et al.   NUCLEIC ACIDS RESEARCH

Assessing Predictive Properties of Genome-Wide Selection in Soybeans

(2016) Alencar Xavier et al.   G3-Genes Genomes Genetics

A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies

(2015) Juexin Wang et al.   BMC GENOMICS

Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean

(2015) Silvas J Prince et al.   BMC GENOMICS

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

(2015) Matt Spencer et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

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

(2015) Jian Zhou 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

A genome-wide association study of seed protein and oil content in soybean

(2014) Eun-Young Hwang et al.   BMC GENOMICS

Analysis of flooding-responsive proteins localized in the nucleus of soybean root tips

(2014) Setsuko Komatsu et al.   MOLECULAR BIOLOGY REPORTS

Analysis of Soybean Root Proteins Affected by Gibberellic Acid Treatment Under Flooding Stress

(2014) Myeong Oh et al.   PROTEIN AND PEPTIDE LETTERS

Genomic selection prediction accuracy in a perennial crop: case study of oil palm (Elaeis guineensis Jacq.)

(2014) David Cros et al.   THEORETICAL AND APPLIED GENETICS

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding

(2013) Trupti Joshi et al.   NUCLEIC ACIDS RESEARCH

Imputation of Unordered Markers and the Impact on Genomic Selection Accuracy

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

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics

(2012) Trupti Joshi et al.   BMC GENOMICS

Comprehensive analysis of endoplasmic reticulum-enriched fraction in root tips of soybean under flooding stress using proteomics techniques

(2012) Setsuko Komatsu et al.   Journal of Proteomics

Comparative Genomic Analysis of Soybean Flowering Genes

(2012) Chol-Hee Jung et al.   PLoS One

MissForest--non-parametric missing value imputation for mixed-type data

(2011) D. J. Stekhoven et al.   BIOINFORMATICS

Genomic selection in plant breeding: from theory to practice

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

Accuracy of genomic selection in European maize elite breeding populations

(2011) Yusheng Zhao et al.   THEORETICAL AND APPLIED GENETICS

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

(2011) Jeffrey B. Endelman   Plant Genome

From sulfur to homoglutathione: thiol metabolism in soybean

(2010) Hankuil Yi et al.   AMINO ACIDS

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

Genomic-Enabled Prediction Based on Molecular Markers and Pedigree Using the Bayesian Linear Regression Package in R

(2010) Paulino Pérez et al.   Plant Genome

Markov clustering versus affinity propagation for the partitioning of protein interaction graphs

(2009) James Vlasblom et al.   BMC BIOINFORMATICS

Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle

(2009) KLARA L. VERBYLA et al.   Genetics Research

SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies

(2009) Zongli Xu et al.   NUCLEIC ACIDS RESEARCH

SoyBase, the USDA-ARS soybean genetics and genomics database

(2009) David Grant et al.   NUCLEIC ACIDS RESEARCH

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics