Xiaofei Yang

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.

The paper analyzes centromere diversity across hundreds of human genomes using HiFi sequencing and a novel HOR annotation pipeline, identifying 23 HORs with significant copy number variation and three centromere genotypes on chromosomes 5, 8, and 17.

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.

HiCAT automatically annotates centromere structure using hierarchical tandem repeat mining, improving continuity and revealing fine structures in human and Arabidopsis genomes.

The paper presents a high coverage whole genome sequencing resource of 3,202 samples, including 602 trios, generated from the expanded 1000 Genomes Project.

JAX-CNV is a whole genome sequencing-based algorithm for copy number variant detection, achieving 100% recall and 4% false discovery rate in clinical validation.

The paper uses long-read sequencing to identify HBV integration-driven genome rearrangements in HCC and links them to immune and metabolic dysfunction.

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

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

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