Katherine M. Munson

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper uses Fiber-seq to show that regional centromeres have dichromatin organization, with accessible and compacted chromatin, which is conserved across species despite DNA sequence differences.

Pooling Fiber-seq gDNA with concatenated MAS-Seq cDNA in one PacBio run gives phased genome, methylome, chromatin, and transcriptome, exposing four gene disruptions from one X;13 translocation.

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 investigates the expansion, selection, and hypervariability of the TBC1D3 gene family in humans using long-read sequencing data, revealing multiple duplications, copy number variation, and expression patterns.

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.

This study characterizes structural and genetic diversity in MUC5AC and MUC5B using long-read sequencing, revealing haplotype variation and evolutionary patterns across human and nonhuman primate populations.

This study uses targeted Fiber-seq to analyze the chromatin impact of mosaic variants, showing that pathogenic DMPK CTG expansions disrupt regulatory elements and that base editing can alter chromatin accessibility.

The paper introduces FIRE to comprehensively map haplotype-selective chromatin accessibility in diploid human genomes, revealing somatic epimutations that contribute to non-genetic chromatin alterations.

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.

A second complete human centromere set (CHM1) plus 31 nonhuman primate centromeres reveals extensive α-satellite higher-order repeat variation, kinetochore repositioning, and saltatory emergence of new repeats.

The paper identifies structurally divergent regions in primate genomes and quantifies the impact of structural variants across multiple species.

This study compares variant calling precision and recall of Oxford Nanopore and PacBio HiFi platforms across different sequence coverages.

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 the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

The paper assesses SNVs within human segmental duplications, finding increased mutation rates and interlocus gene conversion, along with distinct mutational spectra.

The paper presents a comprehensive analysis of segmental duplications in a complete human genome, revealing their distribution, variation, and evolutionary significance.

The paper reports a de novo alpha satellite DNA insertion near an ancestral centromere, showing it lacks centromeric functionality and does not disrupt genes or methylation.

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.

FALCON-Phase uses long-read sequencing and Hi-C data to create phased diploid genome assemblies, achieving high accuracy in non-human species but lower accuracy in humans.

This paper completes the linear assembly of human chromosome 8, resolves long-standing gaps, and analyzes the evolutionary history of its centromeric regions across great apes.

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.

This paper introduces targeted long-read sequencing to identify complex structural variants and disease-causing mutations missed by conventional methods, improving diagnostic accuracy in genetic disorders.

The paper presents an optimized PromethION nanopore sequencing method and new computational tools for efficient human genome assembly, achieving high accuracy and speed.