Oliver G. Pybus

This study tracks the emergence and molecular evolution of H5N1 influenza viruses in U.S. dairy cattle, identifying increased mutation rates and positive selection after spillover from birds.

This study uses target enrichment sequencing to assess viral load and diversity in wildlife samples, showing a log-linear relationship between spike-in concentration and read depth.

This study develops and compares three novel landscape phylogeographic methods to assess environmental impacts on viral spread, providing guidelines for their use and open-source tools for viral epidemiology research.

The paper investigates how much Pango lineage information can be inferred from SARS-CoV-2 spike gene sequences and introduces the concept of lineage sets for classification.

The paper introduces a computationally efficient birth-death model that integrates phylogenetic and epidemiological data to estimate transmission dynamics and unreported infections.

This paper evaluates how much smoothing priors affect demographic estimates in Bayesian phylogenetics and introduces a statistic to measure their impact.

The paper identifies a deletion mutation in the spike protein of SARS-CoV-2 and examines its presence in clinical and in vitro samples, suggesting potential implications for viral replication and vaccine development.

This paper introduces a new method to jointly estimate population size and sampling intensity dynamics from molecular sequences, showing improved accuracy over existing methods.

MESSI infers coevolution rates of base-pairing interactions in nucleic acid sequences and identifies functionally important substructures.

This study identifies a new DENV2 lineage replacement in Brazil using portable genomic surveillance, detecting its introduction from the Caribbean in 2014.

The paper introduces a multifurcating skyline plot to estimate effective population size through time from time-scaled multifurcating phylogenies, validated on simulated data and applied to Ebola virus sequences.

The paper optimizes an rRT-PCR assay for Ecuadorian OROV lineage, identifying five additional cases in febrile patients.

This paper develops a robust experimental design framework for coalescent model inference by proving that logarithmic parameter transformation and uniform distribution of coalescent events minimises estimation uncertainty.

This paper introduces the Bayesian Snyder filter for estimating birth-death process parameters from phylogenies, showing it is mean square error optimal and comparable to existing methods.

This paper describes a method to sequence Zika and other virus genomes directly from clinical samples using multiplex PCR and portable sequencing technologies, achieving complete genomes in 1-2 days.

The paper uses ZIKV genomes to estimate the origin and spread of Zika virus in Brazil and the Americas, providing a timeframe for baseline microcephaly rates.