Richard Michael Durbin

The paper introduces a method to identify transposable element families using pangenome polymorphisms and presents a tool called pantera that effectively detects TE families with high sensitivity and accuracy.

The paper uses a pangenomic approach to analyze Lake Malawi cichlid genomes, revealing extensive structural variation driven by transposable elements.

This study analyzes ancient genomes from Bahrain to reveal population history and malaria adaptation, identifying the G6PD Mediterranean mutation's rise in frequency around 5-6 kya.

MCHelper automates transposable element library curation across species, improving quality and reducing redundancy and false positives.

This paper introduces a deep learning tool for phenotyping 3D micro-CT data to support genetic analysis of morphological traits in fish.

The paper introduces Gamma-SMC, a method for fast genome-wide inference of pairwise coalescence times, showing it is >14 times faster than existing methods.

MitoHiFi assembles mitochondrial genomes from PacBio HiFi reads, identifying heteroplasmy variants and excluding nuclear contaminants, and has been used to assemble 374 mitochondrial genomes.

The paper generates and analyzes genome assemblies for 24 Antarctic notothenioid fish species to study cold adaptations, identifying genomic changes related to antifreeze proteins and haemoglobin loss.

This study uses long-read sequencing to analyze 88 Lepidoptera genomes, identifying genomic signatures linked to conservation concerns like low heterozygosity and high inbreeding.

This paper introduces a new local ancestry inference method that addresses complex population histories by using machine learning on tree sequences and path ancestry, showing improved performance over existing tools.

YaHS, a C command-line Hi-C scaffolder, normalises inter-contig contacts by intra-contig medians, yielding more contiguous, accurate chromosome-scale scaffolds than SALSA2 and pin_hic.

The paper investigates epigenetic divergence in two ecomorphs of Astatotilapia calliptera, finding methylome differences linked to ecological adaptation and showing that these differences can be inherited across generations.

The paper evaluates new vertebrate genome assemblies from the VGP against previous references, finding significant improvements in completeness and accuracy.

The paper analyzes genomic variation in hiPSCs derived from skin and blood, finding high mutation rates in fibroblast-derived lines and frequent BCOR mutations in blood-derived lines.

This paper introduces Asset, a tool to evaluate genome assemblies using long-range data, demonstrating its ability to detect structural misassemblies in human, goat, and fish genomes.

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 paper develops an automated workflow to place ancient DNA sequences into reference phylogenies, using a parsimony and likelihood-based approach, and applies it to Y-chromosomal data.

The paper examines methylome and transcriptome divergence in Lake Malawi cichlid fishes, finding links between epigenetic changes and ecological adaptation.

The paper develops a pipeline for mitochondrial genome assembly and identifies errors and novel duplications in reference mitogenomes.

The paper presents a high-quality chromosome-level genome assembly of the Black Soldier Fly and identifies genomic features and inbreeding patterns in a lab population.

This study shows that aligning ancient DNA data to variation graphs reduces reference bias and improves indel detection compared to traditional linear reference methods.

The paper characterizes proteome variation across 202 human iPSC lines, identifies 700 pQTLs, and links pQTLs to disease-associated GWAS variants.

The paper presents a haplotype-resolved genome assembly for the wood tiger moth using trio binning, revealing population structure insights.

This study presents 929 high-coverage human genome sequences from 54 populations, revealing new insights into genetic variation and population history.

The paper uses single-cell RNA-seq of differentiating iPS cells from 125 donors to identify expression quantitative trait loci influencing gene expression during endoderm differentiation.

The paper introduces a tool to identify and remove haplotypic duplication in genome assemblies, improving continuity and completeness.

Souporcell clusters single-cell RNAseq data using genetic variants to accurately assign genotypes, detect doublets, and estimate ambient RNA without reference genotypes.

The paper introduces haplotype-aware graph indexes to improve the representation of genetic variation in variation graphs.

This paper analyzes ancient genomes from northeastern Siberia to reveal complex population migrations and admixture events over the past 40,000 years.

The paper introduces a pedigree-graph-based method for haplotype-aware de novo assembly of related individuals using Illumina and PacBio data, achieving chromosomal-scale phased assemblies with low coverage.