Kendra Hoekzema

The paper presents an updated reference genome for the naked mole-rat, identifying gene losses and gains linked to its unique physiological traits.

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 uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

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

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 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.

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.

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 identifies ultra-rare inherited mutations that are younger and preferentially transmitted to autism probands, revealing novel candidate genes and functional networks.

The paper investigates how BOLA2 duplication in chromosome 16p11.2 affects iron homeostasis and anemia risk in autism patients, finding associations with anemia and iron deficiency.