Jianwei Zhang

The paper introduces POPPIN, an experimentally verified PPI database for rice, containing over 150,451 PPI-related entries and functional annotations.

LightAlign is a lightweight HiFi read aligner that reduces memory usage for genome assembly in resource-constrained settings.

The paper presents 11 new chromosome-level genome assemblies of Oryza species, revealing core genome conservation and subgenome plasticity, and highlights implications for crop improvement.

The paper develops a pan-gene catalogue for Asian cultivated rice by creating a reference panel of 16 cultivars and identifying core and cultivar-specific genes.

This paper identifies and validates the Rpt5 gene in barley, which encodes a receptor-like protein providing broad resistance to net form net blotch caused by Pyrenophora teres f. teres.

The paper identifies a single hybrid susceptibility locus in barley for a pathogen, mapped to a pentatricopeptide repeat-containing protein gene.

DEGAP fills gaps in genome assemblies using HiFi reads to improve accuracy and length, offering modes to eliminate or shorten gaps in complex regions.

The paper presents an HPC-based workflow for genome variant calling using GATK, demonstrating SNP detection in four plant species and identifying novel SNPs in rice.

The paper introduces RGI, a pan-genome database for Asian rice, integrating 16 reference genomes and transcriptome data to provide gene information and visualization tools.

The paper constructs a pan-genome inversion index for Asian rice using 16 genomes and finds a high inversion rate with functional implications.

The paper uses Ribo-seq and RNA-seq to analyze translational regulation and allele-specific translation efficiency in rice across tissues.

The paper presents a high-quality genome assembly of the soybean cultivar JD17 and identifies genetic variations compared to other soybean genomes.

The paper presents two gap-free rice genomes, revealing centromere structure and gene expression insights.

This paper presents a chromosome-scale genome assembly of Brassica juncea, revealing differences between its A and B genomes.

The paper generates 12 new high-quality rice reference genomes to expand the genetic diversity coverage of cultivated rice, forming a comprehensive pan-genome resource with 16 reference sequences.