William T. Harvey

The paper presents GAIA, a global atlas of immune alleles, showing that underrepresented groups have more diverse alleles needed for vaccine design than Northwest European groups.

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.

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

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 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 analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

The paper characterizes the structural variation and diversification of the NPIP gene family in humans using long-read sequencing and identifies evidence of positive selection and novel gene models.

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.

SVbyEye is an open-source R package that visualizes and annotates structural variation between genome assemblies using PAF alignments.

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.

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

CDR-Finder identifies hypomethylated regions in centromeres using long-read sequencing data and generates BED files and plots for analysis.

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.

Graphasing uses Strand-seq and assembly graphs to produce chromosome-scale haplotypes without parental data or intermediate steps.

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.

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.

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 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 analyzes gaps and structural variants in phased human genome assemblies, identifying issues with contig ends, misorientations, and large-scale insertions and deletions.

The paper identifies and categorizes large-scale genomic differences between the T2T-CHM13 and GRCh38 human genome assemblies, highlighting their implications for disease and evolution.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper analyzes inversion polymorphisms in a complete human genome assembly, showing improved detection and orientation accuracy with the T2T reference compared to GRCh38.

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