Erik P. Garrison

The paper identifies evolutionary processes in acrocentric chromosomes of great apes, including repeat enrichment, inversion, and gene family amplification, with implications for human genomic instability.

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.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

The paper analyzes subtelomeric regions across 465 human genomes to show widespread sequence exchange and recombination, revealing a population-scale pattern of concerted evolution.

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

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

The paper introduces PBML, an algorithm for efficiently detecting long-range shared ancestry tracts in large haplotype panels by filtering short, uninformative matches.

This paper introduces adaptive tracepoints for compressing pangenome alignments, achieving significant compression ratios while maintaining alignment accuracy.

COSIGT improves genotyping accuracy at low sequencing depths by matching coverage patterns to pangenome haplotypes using cosine similarity, enabling population-scale analysis of complex variation.

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.

This paper introduces pangenome-informed language models for generating synthetic DNA sequences, showing improved efficiency and quality over classical methods.

The paper analyzes structural variants in three North American jay species using pangenome tools and long-read assemblies, revealing rapid genome evolution and population size effects on SV dynamics.

The paper presents a mouse pangenome with 17 strains, resolving structural complexity and improving RNA-Seq analysis by identifying non-reference genes and VNTR polymorphisms.

This study assembles human Robertsonian chromosomes, identifies a common breakpoint and centromere epigenetic changes, and explores structural features enabling their formation.

GNQA, a retrieval-augmented GPT question-answering system over 3000 GeneNetwork, aging and diabetes papers, cites source paragraphs; RAGAS rated answer relevance above human thumbs-up ratings (89% vs 76%).

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.

This paper uses rare k-mers to identify centromere haplogroups in human populations and cancer translocations, revealing structural diversity and translocation mechanisms.

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.

This study constructs a rat pangenome from linked-read data to enhance variant discovery and genotype-phenotype mapping in recombinant inbred strains.

Panacus quantifies core genome size and pangenome growth from pangenome graphs, processing large datasets efficiently.

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

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 nf-core/pangenome, a scalable and reference-unbiased pipeline for constructing pangenome graphs, achieving faster performance than PGGB on large datasets.

The paper investigates epigenetic regulation of rDNA arrays, showing DNA methylation controls their activity and inheritance across generations.

This study examines amylase structural haplotypes in humans, finding increased copy numbers in agricultural populations and evidence of recent selection over the last 12,000 years.

The paper presents an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

This study constructs a super-pangenome of North American wild grape species to capture genetic diversity and identify loci associated with adaptive traits like salt tolerance.