Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model. - Edward B. Baskerville; Andy P. Dobson; Trevor Bedford; Stefano Allesina; T. Michael Anderson; Mercedes Pascual (PLoS Comput. Biol., 2011)

Viral Phylodynamics. - Erik M. Volz; Katia Koelle; Trevor Bedford (PLoS Comput. Biol., 2013)

Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. - Michael J. Landis; Trevor Bedford (Bioinform., 2014)

nextflu: real-time tracking of seasonal influenza virus evolution in humans. - Richard A. Neher; Trevor Bedford (Bioinform., 2015)

Global circulation patterns of seasonal influenza viruses vary with antigenic drift. - Trevor Bedford; Steven Riley; Ian G. Barr; Shobha Broor; Mandeep Chadha; Nancy J. Cox; Rodney S. Daniels; C. Palani Gunasekaran; Aeron C. Hurt; Anne Kelso; Alexander Klimov; Nicola S. Lewis; et al. (Nat., 2015)

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference. - Michael D. Karcher; Julia A. Palacios; Trevor Bedford; Marc A. Suchard; Vladimir N. Minin (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)

Lorenzo-Redondo et al. reply. - Ramon Lorenzo-Redondo; Helen R. Fryer; Trevor Bedford; Eun-Young Kim; John A. C. Archer; Sergei L. Kosakovsky Pond; Yoon-Seok Chung; Sudhir Penugonda; Jeffrey G. Chipman; Courtney V. Fletcher; Timothy W. Schacker; Michael H. Malim; et al. (Nat., 2017)

Nextstrain: real-time tracking of pathogen evolution. - James Hadfield; Colin Megill; Sidney M. Bell; John Huddleston; Barney Potter; Charlton Callender; Pavel Sagulenko; Trevor Bedford; Richard A. Neher (Bioinform., 2018)

dms-view: Interactive visualization tool for deep mutational scanning data. - Sarah Hilton; John Huddleston; Allison Black; Khrystyna North; Adam S. Dingens; Trevor Bedford; Jesse D. Bloom (J. Open Source Softw., 2020)

Early prediction of antigenic transitions for influenza A/H3N2. - Lauren Castro; Trevor Bedford; Lauren Ancel Meyers (PLoS Comput. Biol., 2020)

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. - John Huddleston; James Hadfield; Thomas R. Sibley; Jover Lee; Kairsten Fay; Misja Ilcisin; Elias Harkins; Trevor Bedford; Richard A. Neher; Emma B. Hodcroft (J. Open Source Softw., 2021)

Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition. - Jover Lee; James Hadfield; Allison Black; Thomas R. Sibley; Richard A. Neher; Trevor Bedford; John Huddleston (Frontiers Bioinform., 2023)

Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency. - Eslam Abousamra; Marlin Figgins; Trevor Bedford (PLoS Comput. Biol., 2024)