Yu Xu

OneGenome-Rice (OGR) is a genomic foundation model for rice pre-trained on 422 genomes, outperforming existing models in 11 tasks and enabling downstream applications like trait analysis and gene expression prediction.

The paper develops LTR_Stream to cluster LTR-RTs in Papaver species, revealing complex interactions between retrotransposons and the host genome, including effects of allopolyploidization.

MSIsensor-RNA detects microsatellite instability from bulk and single-cell gene expression data, showing favorable performance across multiple platforms.

The paper presents a high-quality Arabidopsis thaliana genome assembly using long-read sequencing and Hi-C data, resolving previously missing regions and centromeres.

This study evaluates the BGISEQ-500 platform for whole exome sequencing, finding it comparable to Hiseq4000 in SNP detection and slightly better in indel detection.