Aylwyn Scally

Statistical inference of virus evolution using ancestral recombination graphs

This paper develops ARG-based methods to analyze virus evolution, showing EBV coalesces predominantly inter-host and revealing gene-level selective structure.

Landscape of parental postzygotic mutations in >11,000 rare disease trios

The paper identifies 1,015 high-confidence postzygotic mutations in 12,015 parent-offspring trios, showing they contribute to clinical phenotypes and can be detected from standard sequencing data.

Population-scale inheritance analysis of 858,635 individuals reveals North Sea migration from the Middle Ages to the Industrial Revolution

The paper uses genetic data from Denmark and Britain to infer historical North Sea migrations from the Middle Ages to the Industrial Revolution, identifying distinct population patterns and migration trends.

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.

The impact of ancestral, environmental and genetic influences on germline de novo mutation rates and spectra

This study examines how ancestry and environmental factors influence de novo mutation rates and spectra in a large whole-genome sequenced cohort, finding ancestry-related effects and a link between tobacco smoke exposure and increased mutation rates.

Deciphering the role of germline complex de novo structural variations in rare disorders

This study identifies de novo structural variants in a large cohort of rare disease patients, highlighting their prevalence and potential pathogenicity.

NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naive pluripotent stem cells

The paper shows NANOGP1, a duplicate of NANOG, has partial functional conservation in human naive pluripotent stem cells, contributing to pluripotency but not maintaining undifferentiated status.

Heritability of de novo germline mutation reveals a contribution from paternal but not maternal genetic factors

The paper estimates SNP heritability of de novo mutations in offspring using the 100k Genomes Project cohort, finding paternal but not maternal genetic contributions.

Short-range template switching in great ape genomes explored using a pair hidden Markov model

The paper introduces a pair hidden Markov model to detect short-range template switch mutations in great ape genomes and shows their prevalence in evolutionary history.

Insights into human genetic variation and population history from 929 diverse genomes

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

Detecting archaic introgression without archaic reference genomes

The paper introduces a method to detect archaic introgression in genomes without archaic reference genomes, finding more Denisovan admixture and differences in admixture timing in Papuans.

Inference of candidate germline mutator loci in humans from genome-wide haplotype data

The paper identifies candidate germline mutator loci in humans by analyzing haplotype data and de novo mutation rates, finding support for two loci near DNA repair genes.

A direct multi-generational estimate of the human mutation rate from autozygous segments seen in thousands of parentally related individuals

The paper estimates the human mutation rate using autozygous segments from 3,222 British-Pakistani individuals, finding a lower mutation rate than previous estimates and population-specific mutational patterns.