Peng Jia

The paper shows that somatic variants' transcriptomic impact depends on cellular context, not just sequence, using single-cell transcriptomics and new tools.

MEIsensor detects and classifies mobile element insertions from long-read sequencing data, outperforming existing tools in accuracy and efficiency, especially for complex insertions.

The paper presents a telomere-to-telomere diploid reference genome for the Chinese Quartet, improving centromere structure annotation and enabling population-specific structural variant analysis.

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.

Pindel-TD detects tandem duplications with high precision and recall using a pattern growth approach, outperforming existing methods on simulated and real data.

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

This study generates haplotype-resolved assemblies and a variant benchmark for a Chinese monozygotic twin quartet using advanced sequencing and computational methods.

This paper introduces Quartet DNA reference materials to comprehensively evaluate germline variant calling accuracy across the genome, including difficult regions and batch effects.

This study compares read-based and assembly-based strategies for detecting structural variants using long-read data and finds that assembly-based methods are more consistent with sufficient coverage, while read-based methods offer higher sensitivity at lower coverage.

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

MSIsensor-pro detects microsatellite instability without matched normal samples, outperforming existing methods in accuracy and speed.