Yanan Chu

A T2T Benchmark Reveals How Reference Choice Shapes Human Genome Interpretation

This paper benchmarks how reference genome choice affects human genome interpretation by comparing T2T references and finding ancestry-matched references provide more accurate variant discovery.

A complete diploid human genome benchmark for personalized genomics

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.

Approaching an Error-Free Diploid Human Genome Using a Support-Based Validation Framework

The paper introduces a support-based validation framework to correct assembly errors in diploid genomes using independent sequencing evidence.

Enhancing Variant Calling in Whole Exome Sequencing (WES) Data Using Population-Matched Reference Genomes

This study evaluates the impact of population-specific reference genomes on variant calling in WES data from Chinese tumor samples, finding improved accuracy with the YAO reference.

T2T-YAO: a Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese

The paper presents T2T-YAO, a telomere-to-telomere diploid reference genome for a Han Chinese male, offering improved haplotype resolution and genetic diversity compared to T2T-CHM13.

Gene-centric intra- and inter-clade recombination in a context of Escherichia coli subpopulations

The paper analyzes recombination patterns in Escherichia coli genomes to show extensive intra-clade recombination and reduced inter-clade recombination, establishing genetic barriers between subpopulations.