Glenn Hickey

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

The paper introduces Centrolign, a tool for aligning centromeric regions, revealing mutation dynamics and enabling variant calling in human centromeres.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

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 generates and characterizes a custom genome assembly for the KOLF2.1J iPSC line to improve genomic analysis accuracy compared to standard references.

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 presents T2T reference genomes from a multi-generational pedigree to study genetic and epigenetic inheritance across the complete genome.

The paper updates Giraffe to map both long and short reads to large pangenome graphs, showing improved speed and accuracy compared to existing tools.

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.

This paper introduces pangenome-aware DeepVariant, a variant caller that improves accuracy by using a pangenome reference, outperforming linear-reference-based DeepVariant by up to 25.5%.

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 introduces tools to efficiently index and query annotations in pangenome graphs using GAF format, demonstrating applications on human pangenome data.

The paper introduces a personalized pangenome approach to improve short-read mapping and variant calling by reducing reference bias and errors.

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 proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

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.

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

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 introduces Giraffe, a pangenome mapper that improves genotyping of SNVs, indels, and SVs in 5,202 human genomes using the vg toolkit.

The paper introduces two C++ libraries for efficient manipulation of pangenomic graphs, showing improved performance over existing tools.

The paper demonstrates that variation graphs using the vg toolkit improve structural variant genotyping compared to traditional methods and VCF-based catalogs.

The paper improves the Cactus multiple-genome aligner to handle large numbers of vertebrate genomes with high accuracy and better orthology resolution.

The paper introduces vg, a toolkit for creating and using variation graphs as genome references, improving read mapping and variant calling accuracy over linear references.