Zhigui Bao

EDTA v2 improves transposable element annotation in animal genomes by adding LINE/SINE detection and enhancing scalability and speed.

This study uses genome and transcriptomic analyses of oat species to show that polyploidy creates functional redundancy, buffering mutations but hindering beneficial allele fixation, and proposes breeding strategies to overcome these challenges.

This study analyzes mitochondrial and chloroplast genomes of Arabidopsis thaliana to show that large repeats correlate with geography and phenotypes, and identify novel ORFs potentially from horizontal gene transfer.

The paper curates and presents a collection of long-read genome assemblies for Arabidopsis thaliana accessions to enhance plant genome research.

Gretl evaluates genome graphs to identify genetic variation patterns and improve analysis of complex genomic data.

Gfa2bin converts genome graphs to pan-genomic genotypes for GWAS, identifying additional associations with higher significance than SNP-based approaches in Arabidopsis thaliana.

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

TIPPo assembles organellar genomes using HiFi data without reference genomes or nuclear information, achieving complete chloroplast assemblies and improved mitochondrial results compared to existing tools.