GENIE: estimating demographic history from molecular phylogenies. - Oliver G. Pybus; Andrew Rambaut (Bioinform., 2002)

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics. - Philippe Lemey; Sergei L. Kosakovsky Pond; Alexei J. Drummond; Oliver G. Pybus; Beth Shapiro; Helena Barroso; Nuno Taveira; Andrew Rambaut (PLoS Comput. Biol., 2007)

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. - Luiz Carlos Júnior Alcântara; Sharon Cassol; Pieter Libin; Koen Deforche; Oliver G. Pybus; Marc Van Ranst; Bernardo Galvão-Castro; Anne-Mieke Vandamme; Tulio de Oliveira (Nucleic Acids Res., 2009)

Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics. - Gkikas Magiorkinis; Vana Sypsa; Emmanouil Magiorkinis; Dimitrios Paraskevis; Antigoni Katsoulidou; Robert Belshaw; Christophe Fraser; Oliver George Pybus; Angelos Hatzakis (PLoS Comput. Biol., 2013)

SERAPHIM: studying environmental rasters and phylogenetically informed movements. - Simon Dellicour; Rebecca Rose; Nuno R. Faria; Philippe Lemey; Oliver G. Pybus (Bioinform., 2016)

Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data. - Simon Dellicour; Rebecca Rose; Oliver G. Pybus (BMC Bioinform., 2016)

Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection. - Jayna Raghwani; Samir Bhatt; Oliver G. Pybus (PLoS Comput. Biol., 2016)

Virus genomes reveal factors that spread and sustained the Ebola epidemic. - Gytis Dudas; Luiz Max Carvalho; Trevor Bedford; Andrew J. Tatem; Guy Baele; Nuno R. Faria; Daniel J. Park; Jason T. Ladner; Armando Arias; Danny Asogun; Filip Bielejec; Sarah L. Caddy; et al. (Nat., 2017)

Establishment and cryptic transmission of Zika virus in Brazil and the Americas. - Nuno R. Faria; Joshua Quick; I. M. Claro; Julien Thézé; J. G. de Jesus; Marta Giovanetti; Moritz U. G. Kraemer; S. C. Hill; Allison Black; A. C. Da Costa; L. C. Franco; S. P. Silva; et al. (Nat., 2017)

Exact Bayesian inference for phylogenetic birth-death models. - Kris V. Parag; Oliver G. Pybus (Bioinform., 2018)

Phylogenetic analysis of migration, differentiation, and class switching in B cells. - Kenneth B. Hoehn; Oliver G. Pybus; Steven H. Kleinstein (PLoS Comput. Biol., 2022)

A computationally tractable birth-death model that combines phylogenetic and epidemiological data. - Alexander Eugene Zarebski; Louis du Plessis; Kris V. Parag; Oliver George Pybus (PLoS Comput. Biol., 2022)

Artificial intelligence for modelling infectious disease epidemics. - Moritz U. G. Kraemer; Joseph L.-H. Tsui; Serina Chang; Spyros Lytras; Mark P. Khurana; Samantha Vanderslott; Sumali Bajaj; Neil Scheidwasser; Jacob Liam Curran-Sebastian; Elizaveta Semenova; Mengyan Zhang; H. Juliette T. Unwin; et al. (Nat., 2025)