Zhiwu Zhang

Deep learning based genomic breeding of pest-resistant grapevine

This study uses deep learning and genome-wide association studies to identify pest-resistant genes in grapevine, achieving high accuracy in predicting pest damage.

Trait Association and Prediction Through Integrative K-mer Analysis

This study uses k-mer GWAS to identify genetic associations with maize traits and shows comparable prediction accuracy to SNP-based methods.

Streamline unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes

The paper develops BRIDGEcereal, a web tool using unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes, demonstrating its use in wheat candidate genes.

Comparison of Single-Trait and Multi-Trait Genome-Wide Association Models and Inclusion of Correlated Traits in the Dissection of the Genetic Architecture of a Complex Trait in a Breeding Program

This study compares single-trait and multi-trait GWAS models to dissect the genetic architecture of seedling emergence in wheat, finding that multi-trait models identify more large-effect markers.

GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction

GAPIT Version 3 introduces multiple loci test methods and improved GP/GS methods to enhance statistical power and prediction accuracy for genomic association and prediction.

Chromosomal Characteristics of Salt Stress Heritable Gene Expression in the Rice Genome

The paper examines heritable gene expression under salt stress in rice, identifying condition-specific heritable genes and their chromosomal distribution patterns.

GridFree: A Python Package of Image Analysis for Interactive Grain Counting and Measuring

GridFree is a Python software package that automates grain counting and measurement using unsupervised machine learning, achieving lower error rates than existing tools across multiple crops.

Whole-Genome Sequencing on 220 Alfalfa (Medicago sativa L.) Accessions Identified Association of DREB1C Gene with Fall Dormancy Height

The paper uses whole-genome sequencing on 220 alfalfa accessions to identify SNPs associated with fall dormancy height, finding a SNP linked to the DREB1C gene.

rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated tool for Genome-Wide Association Study

rMVP improves GWAS computation by offering memory efficiency, visualization tools, and parallel acceleration for faster and more scalable analysis.

Ten Genetic Loci Identified for Milk Yield, Fat, and Protein in Holstein Cattle

This study identifies ten genetic loci associated with milk yield, fat, and protein traits in Holstein cattle using GWAS and FarmCPU method.

BLINK: A Package for Next Level of Genome Wide Association Studies with Both Individuals and Markers in Millions

BLINK improves statistical power and reduces computing time for GWAS by replacing FarmCPU's bin method with Bayesian information criteria and linkage disequilibrium information.

A large scale joint analysis of flowering time reveals independent temperate adaptations in maize

This study identifies independent temperate adaptations in maize flowering time across different populations using GWAS and machine learning.