Peng Jia

Cellular context shapes the transcriptomic impact of somatic variants

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

MEIsensor: a deep-learning method for mobile element insertion discovery

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

A Telomere-to-Telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet

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.

Deciphering complex interactions between LTR retrotransposons and three Papaver species using LTR_Stream

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: a tandem duplication detector based on a pattern growth approach

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: microsatellite instability detection for bulk and single-cell gene expression data

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

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

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

Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance

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

Comparison and benchmark of long-read based structural variant detection strategies

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.

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

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: fast, accurate and matched-normal-sample-free detection of microsatellite instability

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