Glenn Hickey

GBZ-base and GAF-base: Indexed pangenome file formats

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

Pangenome alignment reveals global diversity and evolution of human centromeric regions

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

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

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: A global reference genome resource

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

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

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

The complete genome of the KOLF2.1J reference iPSC line

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

Pangenome discovery of missing autism variants

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.

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

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

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe

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

Complex genetic variation in nearly complete human genomes

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.

Pangenome-aware DeepVariant

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%.

Complete sequencing of ape genomes

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.

Efficient indexing and querying of annotations in a pangenome graph

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

Personalized Pangenome References

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

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

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.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

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

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

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.

A Draft Human Pangenome Reference

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

Recombination between heterologous human acrocentric chromosomes

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

Integrating gene annotation with orthology inference at scale

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

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

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

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

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

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

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

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

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.

Gaps and complex structurally variant loci in phased genome assemblies

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

Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit

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

Succinct dynamic variation graphs

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

Genotyping structural variants in pangenome graphs using the vg toolkit

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

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

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

Sequence variation aware genome references and read mapping with the variation graph toolkit

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.