Qihui Zhu

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

The paper presents long-read assemblies of 43 diverse human Y chromosomes, revealing extensive structural complexity and variation across 180,000 years of evolution.

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 identifies recurrent inversions in human genomes and links them to genomic disorders through mutational recurrence and structural diversity.

SvAnna predicts pathogenicity of structural variants in long-read sequencing data by integrating transcript and regulatory annotations with clinical phenotype data, achieving high accuracy in prioritizing pathogenic variants.

The paper develops a repeat-pangenome graph to analyze VNTR variation across populations and identifies population-specific VNTRs and expression quantitative trait loci.

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.

The paper compares structural variant detection using short-read and long-read sequencing in three trios, showing lrWGS finds more SVs but srWGS has high concordance in non-repetitive regions.

The paper introduces TeXP, a method to distinguish pervasive transcription from autonomous LINE-1 activity, revealing LINE-1 activity in many healthy somatic cells and its correlation with cell turnover.

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

This study quantifies intratumoral subclone dynamics in breast cancer xenografts, revealing a treatable ecology where subclone ratios predict treatment response.