Baoxing Song

This study uses ESM2 to identify beneficial genetic variants in a Sorghum bicolor diversity panel by analyzing PRC scores and their association with agronomic traits.

This study uses landrace diversity in wheat to identify genetic resources for climate resilience and improved traits, providing a framework for crop improvement.

The paper analyzes transposable elements and structural variation in maize genomes, finding that deletions of transposable elements contribute more to genomic differences than insertions.

This study quantifies the fitness costs of transposable elements in maize by analyzing TE content across thousands of inbred lines and linking TE accumulation to reduced grain yield.

The paper introduces the Practical Haplotype Graph (PHG) platform for storing and using pangenomes, demonstrating its effectiveness in imputing genomes from low-coverage data in crops like maize.

This study investigates how heritable transcriptomic variation contributes to maize adaptation to temperate environments through eQTLs, sQTLs, and gene expression patterns.

AnchorWave improves genome alignment for genomes with high diversity, structural polymorphism, and whole-genome duplication by using a duplication-informed algorithm and gap cost strategy.

The paper develops a multiple genome alignment workflow for plants, showing that k-mer masking and parameter tuning improve alignment of functional regions.

GEAN improves gene structure annotation lift over from a reference genome to newly sequenced individuals by addressing alignment inconsistencies through a weighted dynamic programming algorithm.