Peter A. Audano

This study uses long-read whole genome sequencing and pangenomes to identify novel variants and pathogenic findings in neurodevelopmental disorder cases from underrepresented populations.

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

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.

The paper identifies SD-mediated rearrangements in mouse genomes using long-read sequencing and other methods, revealing their impact on gene content and function.

The paper identifies a novel de novo PAK2 variant in a patient with Knobloch syndrome type 2, supporting PAK2's role in the disorder and expanding its clinical features.

The paper develops a new method to detect complex structural variants in large genomic regions, revealing previously undetectable structures and improving breakpoint accuracy.

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.

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.

The paper identifies structurally divergent regions in primate genomes and quantifies the impact of structural variants across multiple species.

The paper compares short-read and long-read sequencing in the All of Us initiative, finding HiFi reads provide the most accurate variant calling and presents a cloud-based pipeline for long-read analysis.

The paper identifies ancestral bias in structural variant breakpoint placement, showing that small allelic variants contribute to inconsistent breakpoint locations across haplotypes.

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 identifies structural variants in 20 mouse strains using long-read sequencing, revealing transposable elements' role in chromatin remodeling and gene expression in mESCs.

The paper identifies transposable element-mediated rearrangements (TEMRs) in human genomes, showing they are enriched in genic regions and can create risk alleles.

PanGenie improves variant calling by using a pangenome reference and k-mer counts, achieving higher accuracy and speed compared to traditional methods.

The paper identifies recurrent inversions in human genomes and links them to genomic disorders through mutational recurrence and structural diversity.

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.

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

This paper presents a fully phased de novo genome assembly of an individual using Strand-seq and HiFi reads, achieving high accuracy and contiguity with low switch error rates.

The paper compares structural variant detection using short-read and long-read sequencing in three trios, showing lrWGS finds more SVs but srWGS has high concordance in non-repetitive regions.

This study compares HiFi and CLR long-read sequencing for human genome assembly, finding HiFi provides better continuity and accuracy in complex regions but not centromeres or segmental duplications.

The paper presents a high-quality long-read genome assembly of the Chinese rhesus macaque and identifies ape-specific structural variants.

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

The paper introduces Kestrel, a k-mer-based variant caller that avoids mapping, assembly, and de Bruijn graphs, achieving high concordance with assembled contigs in Streptococcus pneumoniae.