Oliver Pybus - Selected Publications#

McCrone et al. (2022) Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature 610:154–160

Hill et al. (2022) Impact of host age on viral and bacterial communities in a waterbird population. The ISME Journal 17:215–226

Attwood et al. (2022) Phylogenetic and phylodynamic approaches to understanding and combating the SARS-CoV-2 pandemic. Nature Reviews Genetics 23:547–562

du Plessis et al. (2021) Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science 371:708–12

Kraemer et al. (2021) Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science 373:889–95

Stadler et al. (2021) Phylodynamics for cell biologists. Science 371:eaah6266

Saad-Roy et al. (2021) Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes. Science 372:363-70

Parag et al. (2020) Jointly inferring the dynamics of population size and sampling intensity from molecular sequences. Molecular Biology & Evolution 37:2414–29

Yang et al. (2020) Assessing the role of live poultry trade in community-structured transmission of avian influenza in China. Proceedings of the National Academy of Sciences USA 117:5949-54

Kraemer et al. (2020) The effect of human mobility and control measures on the COVID-19 epidemic in China. Science 368:493–7

Escalera-Zamudio et al. (2020) Parallel evolution in the emergence of highly pathogenic avian influenza A viruses. Nature Communications 11:5511

Rambaut et al. (2020) A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology 5:1403–07

Lu et al. (2020) Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China. Cell 181:997-1003

Hoehn et al. (2019) Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination. Proceedings of the National Academy of Sciences USA 116:22664–72

Hill et al. (2019) Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population. Philosophical Transactions of the Royal Society B 374: 20180259

Faria et al. (2018) Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science 361:894–99

Thézé et al. (2018) Genomic epidemiology reconstructs the introduction and spread of Zika virus in central America and Mexico. Cell Host & Microbe 23:855–64

Lu et al. (2018) Molecular evolution, diversity and adaptation of H7N9 viruses in China during 2013-2017. Emerging Infectious Diseases 24:1795–805

Parag & Pybus (2018) Exact Bayesian inference for phylogenetic birth-death models. Bioinformatics 34:3638–45

Faria et al. (2017) Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546:406–10

Dellicour et al. (2017) Using viral gene sequences to compare and explain the heterogeneous spatial dynamics of virus epidemics. Molecular Biology & Evolution 34:2563–71

Hoehn et al. (2017) A phylogenetic codon substitution model for antibody lineages. Genetics 206:417–27