Ira M. Hall

This paper identifies 23 candidate causal genes for critical COVID-19 by integrating severity-stratified, longitudinal cis-eQTL mapping with GWAS signals from 1,031 patients.

This paper develops a pangenome-based method to improve trait association and genomic prediction by capturing complex genetic variation missed by traditional approaches.

The paper introduces LOCATER, a genealogy-based method that improves trait association power by leveraging haplotype diversity and allelic heterogeneity, identifying novel associations and recovering known loci in a Finnish cohort.

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

LongcallD jointly calls and phases small, structural, and mosaic variants from long reads, improving SV discovery and mosaic variant accuracy.

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 introduces LOCATER, a method to test genealogical trees for association with traits, showing improved power over traditional methods in detecting allelic heterogeneity.

The paper introduces vsdistill, a method for improving power in genomics by distilling variant sets, and demonstrates its effectiveness through simulations and UK Biobank analysis.

This paper links CAD GWAS variants to causal genes in SMCs using single-cell chromatin accessibility and Hi-C data, creating a scV2E2G map for disease mechanism discovery.

The paper develops a method to infer compound heterozygosity from exome sequencing data, achieving high accuracy in phasing rare variants for recessive disease diagnosis.

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

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

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

This study identifies 303 novel genetic signals associated with plasma metabolites in Finnish men, revealing biological insights into disease mechanisms.

The paper describes AnVIL, a cloud-based platform that enables genomic data analysis without data transfer, improving security, scalability, and collaboration.

The paper identifies structural variants as a major source of gene expression differences, showing they affect multiple genes and have broader expression effects than SNVs or indels.

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

This study identifies 31 genome-wide significant associations between structural variations and cardiometabolic traits in Finns, including two novel loci with strong phenotypic effects.

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

The paper presents a gapless, telomere-to-telomere assembly of the human X chromosome using ultra-long-read nanopore sequencing and complementary technologies.

The paper identifies distinct regulatory patterns and trait associations of lncRNA genes compared to protein-coding genes across human tissues.

svtools enables population-scale structural variation analysis by providing a fast, scalable toolkit and cloud pipeline for high-quality SV mapping across thousands of human genomes.

Exome sequencing in Finnish populations identifies rare trait-associated alleles with higher frequencies and geographical clustering, revealing 30 novel associations with quantitative traits.

The paper maps and characterizes structural variants in 17,795 human genomes, revealing their frequency, impact, and relationship to gene dosage and regulatory elements.

The paper defines functional equivalence standards for genome sequencing pipelines to enable harmonized variant calling across diverse datasets with minimal batch effects.

The paper develops S-PrediXcan to compute gene expression associations from GWAS summary data and applies it to 44 GTEx tissues and 100+ phenotypes, finding tissue-specific effects and colocalized associations.