Papers

Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity

Forde et al. (2021) bioRxiv


Mutations that adapt SARS-CoV-2 to mustelid hosts do not increase fitness in the human airway

Zhou et al. (2021) bioRxiv


Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination

Davis et al. (2021) medRxiv


Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and impact on B.1.1.7

Meng et al. (2021) Cell Rep


SARS-CoV-2 variants, spike mutations and immune escape

2021harvey

Harvey et al. (2021) Nat Rev Microbiol


Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

2021_collier

Collier et al. (2021) Nature


Genetic determinants of receptor-binding preference and zoonotic potential of H9N2 avian influenza viruses

2020peacock

Peacock et al. (2021) J Virol


Different environmental gradients associated to the spatiotemporal and genetic pattern of the H5N8 highly pathogenic avian influenza outbreaks in poultry in Italy

2020scholmacchia

Scolamacchia et al. (2021) Transbound Emerg Dis


Spatiotemporal reconstruction and transmission dynamics during the 2016-17 H5N8 highly pathogenic avian influenza epidemic in Italy

2019harvey

Harvey et al. (2021) Transbound Emerg Dis


Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70

2020kemp

Kemp et al. (2020) bioRxiv


Genetic basis of antigenic variation of SAT3 foot-and-mouth disease virus

2020maake

Maake et al. (2020) Front Vet Sci


Genomic and immunogenic protein diversity of Erysipelothrix rhusiopathiae isolated from pigs in Great Britain: implications for vaccine protection

webpost

Forde et al. (2020) Front Microbiol


Improving the identification of antigenic sites in the H1N1 influenza virus through accounting for the experimental structure in a sparse hierarchical Bayesian model

davies2017b

Davies et al. (2019) J Royal Stat Soc C


The molecular basis of antigenic variation among A(H9N2) avian influenza viruses

2018peacockN

Peacock et al. (2018) Emerg Microbes Infect


Integrating patient and whole genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses

goldstein2017

Goldstein et al. (2017) Microb Genom


A sparse hierarchical Bayesian model for detecting relevant antigenic sites in virus evolution

Davies2017

Davies et al. (2017) Comput Stat


Identification of low- and high-impact hemagglutinin amino acid substitutions that drive antigenic drift of influenza A(H1N1) viruses

harvey2016

Harvey et al. (2016) PLOS Pathog


Tracking the antigenic evolution of foot-and-mouth disease virus

reeve2016

Reeve et al. (2016) PLOS ONE


Selecting random effect components in a sparse hierarchical Bayesian model for identifying antigenic variability

davies2016

Davies et al. (2016) In: Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2015. Lecture Notes in Computer Science


 Sparse Bayesian variable selection for the identification of antigenic variability in the foot-and-mouth disease virus

davies2014

Davies et al. (2014) JMLR Workshop Conf Proc