Kai Ye

The paper presents a complete, gapless telomere-to-telomere Y chromosome assembly from the Chinese Quartet, improving genomic reference quality for East Asian populations.

The paper presents 320 nearly-complete East Asian genome assemblies, revealing new genetic diversity and structural variations not present in existing global pangenomes.

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

This study uses Hi-C data from 1,025 species to trace the evolution of 3D genome architecture, revealing distinct patterns in global folding and checkerboard structures across different lineages.

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

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.

Swave identifies structural variants from pangenome graphs, revealing complex SV patterns and pathogenic variants in human populations.

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.

NextPolish2 improves genome accuracy by fixing base errors in HiFi assemblies without overcorrections or haplotype switch errors.

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

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

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

NextDenovo corrects noisy Nanopore reads faster and more accurately than Canu and Necat; its maize and 35 human-genome assemblies are more contiguous, with fewer misassemblies, than Flye's.

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

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.

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.

This study characterizes structural variants in Fusarium graminearum, showing their prevalence and functional relevance in pangenome evolution and fungal virulence.

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

The paper improves the genome assembly of Fusarium oxysporum strain Fo5176 and expands its use as a model system for studying plant-fungal interactions.

The paper presents a chromosome-level genome assembly of Fusarium oxysporum strain Fo47, highlighting its unique genomic features and potential for studying plant interactions.

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

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 identifies novel HPE genes and oligogenic inheritance patterns in holoprosencephaly by integrating clinical data with exome sequencing and gene prioritization.