Richard Michael Durbin

Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations

This study presents the first comprehensive phylogenomic analysis of Cypriniformes, establishing a robust backbone topology and identifying unresolved conflicts in evolutionary relationships.

Efficient and precise discovery of LTR-retrotransposon families using HiRepEat

The paper introduces HiRepEat, a method for efficiently discovering and clustering LTR-retrotransposon families across genomes, showing results on vertebrate and Drosophila genomes.

Near-complete genomes for nine haplochromine cichlid fishes reveal a novel centromeric satellite structure organised around a pair of inverted elements

The paper presents nine T2T genomes of Lake Malawi cichlids, revealing a novel centromeric satellite structure with inverted elements and potential implications for speciation.

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

The relationship of genetic diversity and inbreeding to extinction risk across over 500 vertebrate diploid genomes

The paper analyzes genetic diversity and inbreeding in 512 vertebrate genomes to assess their relationship with extinction risk, finding ecological factors are stronger predictors than genetic measures.

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.

A run-length-compressed skiplist data structure for dynamic GBWTs supports time and space efficient pangenome operations over syncmers

340 dipteran genomes reveal the origin of Muller elements and sex chromosomes in Diptera

The paper reconstructs ancestral linkage groups in 340 dipteran genomes to study chromosome evolution, finding conserved groups in Nematoceran lineages and chromosomal fissions in Brachycera.

A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.

The paper presents a new phased assembly of the Antarctic spiny plunderfish and identifies genomic features linked to cold adaptation in notothenioids.

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.

Cryptic diversity and impacts of domestication in the Black Soldier Fly (Hermetia illucens)

The paper analyzes whole genome sequences of Black Soldier Fly populations to reveal cryptic genetic diversity and the impacts of domestication on genetic variation.

Genetic architecture of cichlid brain morphology

The paper investigates the genetic architecture of brain morphology in cichlid fish, showing modular genetic control of brain components and weaker genetic correlations in hybrids.

The genomics of convergent adaptation to intertidal gravel beaches in Mediterranean clingfishes

This study investigates genomic convergence in Mediterranean clingfishes adapting to intertidal gravel beaches, finding no large-scale convergence but identifying candidate regions associated with morphological traits.

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.

Somatic and germline mutational processes across the tree of life

This study identifies somatic and germline mutational signatures across 661 species, revealing greater diversity than in human samples, likely due to environmental or biological factors.

fgf8a signalling shapes brain divergence between Malawi cichlids

This study identifies fgf8a as a key gene driving brain divergence in Lake Malawi cichlids through species-specific enhancer elements and functional experiments.

Environmental DNA Reveals Reykjavik's Human and Ecological History

This study uses environmental DNA from Lake Tjornin to challenge the narrative of Norse-induced environmental collapse in Reykjavik, showing dynamic human-environment interactions shaped by both cultural practices and external stressors.

Genomic diversity of the African malaria vector Anopheles funestus

The paper analyzes genomic diversity in Anopheles funestus across Africa, identifying genetic variation, adaptation signals, and conservation of a gene drive target.

Oatk: a de novo assembly tool for complex plant organelle genomes

Oatk combines a sparse syncmer assembler, profile HMM gene databases and graph path search to assemble plastomes and mitogenomes from HiFi reads for 195 plant species.

Pangenome-guided sequence assembly via binary optimisation

This paper introduces a pangenome-guided sequence assembly framework that reduces contigs in complex regions using graph traversal optimisation, with potential for quantum computing implementation.

Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing

Hi-reComb estimates recombination maps from bulk gamete Hi-C data, showing accurate results in fish sperm and enabling structural variant analysis.

Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation

The paper analyzes 1,375 Malawi cichlid genomes to show that sex-linked chromosomal inversions drive adaptive speciation through introgression and selection on neuro-sensory, physiological, and reproductive genes.

Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses

The paper introduces efficient algorithms for fine-scale local ancestry inference using haplotypes, revealing recent selection on immune-related genomic regions in the UK Biobank.

A structured coalescent model reveals deep ancestral structure shared by all modern humans

The paper uses a coalescent model to show that all modern humans share deep ancestral structure from two populations that admixed ~300k years ago, with the minority ancestry linked to deleterious effects and majority ancestry linked to archaic human divergence.

FastGA: Fast Genome Alignment

FastGA aligns genomes significantly faster than existing methods while maintaining sensitivity and efficiently storing alignments.

Deep coalescent history of the hominin lineage

The paper extends coalescent-based inference to deep time scales using high-quality genome assemblies, revealing a population size peak in humans, chimpanzees, and bonobos around 3-6 million years ago.

The Hypolimnas misippus genome supports a common origin of the W chromosome in Lepidoptera

The paper presents genome assemblies of two Hypolimnas species and analyzes the evolution of W chromosomes in Lepidoptera, suggesting a common origin despite conflicting hypotheses.

Insights into non-crossover recombination from long-read sperm sequencing

The paper uses long-read sperm sequencing to analyze non-crossover recombination events, finding variation in recombination rates and distinct mechanisms for non-crossover gene conversions.

Identification of transposable element families from pangenome polymorphisms

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.

Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria

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.