Ying Zhou

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

The paper analyzes expression and splicing quantitative trait loci (e/sQTL) across multiple tissues in the TOPMed dataset and finds that secondary e/sQTL signals are still discoverable, with many GWAS signals colocalizing with these e/sQTL.

FuFiHLA is a tool for full-field HLA typing from long-read data, achieving high accuracy in allele typing and consensus sequence construction.

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 shows that TAF-12 is required for piRNA transcription in C. elegans by recruiting transcription factors and machinery to H3K27me3-enriched regions.

The paper introduces Immuannot, a tool for annotating HLA and KIR genes in long-read assemblies, identifying novel alleles and haplotype structures.

The paper develops PACER to infer clonal expansion rates from single timepoint data and identifies TCL1A activation as a mediator of clonal hematopoiesis fitness.

The paper systematically characterizes chromodomain proteins in C. elegans, identifying CEC-5 as an H3K9me1/2 reader that regulates aging through interactions with MET-2.

This study uses whole-genome sequencing to analyze mosaic chromosomal alterations across diverse ancestries, finding higher rates in certain populations and associations with germline variants.

The paper quantifies similarity in causal effects across local ancestries in admixed individuals and finds high genetic correlation (radmix=0.95) within individuals.

The paper develops a cost-effective sequencing assay to detect clonal hematopoiesis and shows that most clonal mutations expand over time in longitudinal samples.

The paper introduces hap-IBD, a fast and accurate method for detecting IBD segments in large-scale genotype data, outperforming existing methods in speed and accuracy.

The paper introduces Beagle 5.0, a genotype imputation method that significantly reduces computational cost compared to existing methods while maintaining similar accuracy.