Kendra Hoekzema

The paper presents a telomere-to-telomere genome assembly of the naked mole-rat and compares it with a related species to identify gene losses and duplications associated with unique traits.

This study benchmarks saliva-derived DNA against blood for long-read sequencing in autism, showing comparable variant detection despite nonhuman DNA contamination.

The paper shows that structural variants from donor-specific assemblies influence chromatin contact divergence in humans, with many SVs linked to regulatory contexts and expression variation.

The paper identifies distinct mechanisms of CNV formation at the human 15q13.3 locus, showing that non-allelic homologous recombination is the primary mechanism, influenced by inversion polymorphisms and population-specific susceptibility.

The paper characterizes chromosome 21 centromeres in a family with recurrent Trisomy 21, identifying a diffuse hypomethylation pattern linked to maternal age-related risk.

The paper investigates sex-specific penetrance in PILBOS, showing male overrepresentation and androgen-mediated sexual dimorphism through genetic and mouse model studies.

The paper constructs a high-resolution human pangenome structural variant resource, identifies disease-associated SVs, and demonstrates its utility in filtering variants from probands and associating SVs with traits in a large cohort.

The paper identifies and characterizes human protein-coding duplicated genes using long-read genomic and transcriptomic data, revealing new gene models and constraint patterns.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

The paper investigates mutation and recombination patterns in human acrocentric chromosome short arms using multiple sequencing technologies and a four-generation pedigree.

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

The paper sequences chromosome 21 centromeres in Down syndrome families, finding extreme size asymmetry in some cases and suggesting it may be a genetic risk factor.

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

This study presents a pan-pangenome of humans, chimpanzees, and bonobos, revealing structural variation, selection patterns, and adaptations related to immunity and malaria resistance.

The paper analyzes centromere evolution in lemurs using long-read sequencing, finding rapid sequence turnover and distinct centromeric repeats across species.

This study identifies genomic factors influencing tandem repeat mutagenesis using long-read sequencing in a large family, finding that de novo mutations are more common at longer, uninterrupted, and heterozygous loci.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

MitoScope is a long-read sequencing workflow for mitochondrial genome analysis that improves sensitivity and precision in variant detection and NUMT profiling.

The paper identifies a segmental duplication-mediated deletion causing neocentromere formation in orangutans by analyzing structural and epigenetic variation.

The paper characterizes the genetic diversity and regulatory features of human-specific NOTCH2NL duplications using long-read sequencing and organoid models.

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

The paper identifies a segmental duplication that drives position effect expression of TBC1D3 in the human brain, explaining its high structural heterozygosity.

The paper investigates how neocentromeres reshape chromatin and identifies conserved features of native centromeres using haplotype-resolved assemblies and multi-omics data.

The paper maps somatic mutation burden and functional impact across the cancer genome using telomere-to-telomere sequencing, revealing novel mutation hotspots and regulatory rewiring mechanisms.

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

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 long-read sequencing to analyze de novo mutations in autism families, finding higher mutation rates in repetitive DNA and a paternal bias in postzygotic mutations.

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