Charles Lee

The paper develops k-mer-based tools to measure Yq12 heterochromatin size from sequencing data without complete assemblies, revealing population-scale variation and transcription in testis.

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

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

The paper identifies a Denisovan-derived Alu insertion in OCA2 associated with increased pigmentation in Melanesians and demonstrates its functional impact in melanocytes.

The paper develops a minimally invasive workflow to recover biological signatures from Renaissance-era artifacts, revealing microbial biomes and Y-chromosome markers linked to historical handling and conservation.

This study identifies satellite DNA fragility and ecDNA oncogene amplification in canine osteosarcomas using long-read sequencing, revealing genomic instability mechanisms relevant to human cancer.

The paper identifies structural variants at CTCF loop anchors that influence alternative splicing by disrupting chromatin looping in mouse ESCs.

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 uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

The paper analyzes segmental duplications in human genomes using long-read sequencing, identifying structurally polymorphic events and novel genes associated with copy number variation.

The paper identifies 56 recent functional variants in modern humans, 24 linked to brain functions and skull morphology, which did not introgress into Neanderthals.

The paper develops a Hi-C analysis pipeline to catalog TADs and loops in human genomes and quantifies the impact of SVs on chromatin structure and gene expression.

The paper resolves the amylase locus at nucleotide resolution in modern and ancient humans, showing AMY1 copy number variation predated agriculture and was driven by recombination.

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

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 investigates the 3q29 genomic region, identifying novel haplotypes and breakpoint segments associated with deletion and duplication syndromes, and categorizes cases into distinct classes.

novoRNABreak detects novel splice junctions and fusion transcripts in cancer RNA-seq data with high sensitivity and efficiency.

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.

This paper presents a fully phased de novo genome assembly of an individual using Strand-seq and HiFi reads, achieving high accuracy and contiguity with low switch error rates.

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.