Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens.
(2026 Oct 2)
Bioinformatics 42(10):
Andrews KR, Chang J, Roemer C, Hadfield J, Lin V, Brito AF, Daodu RO, Joia IA, Kistler K, Li A, Moncla LH, Paredes MI, Kühnert D, Torres LM, Voitl L, Aksamentov I, Hodcroft EB, Huddleston J, McCrone JT, Anderson JSJ, Sibley TR, Lee J, Neher RA, Bedford T

Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection.
(2026)
Virus Evol 12(1): veag046
Kikawa C, Huddleston J, Turner SA, Loes AN, Liu J, Gang S, Griffiths T, Drapeau EM, Cowling BJ, Ho F, Leung NHL, Englund JA, Lacombe K, Watanabe S, Hasegawa H, Busch M, Lanteri M, Stone M, Spencer B, Neher RA, Smith DJ, Bedford T, Hensley SE, Bloom JD

Inferring variant-specific effective reproduction numbers from combined case and sequencing data.
(2026 Jul 9)
Elife 14():
Figgins MD, Bedford T

SARS-CoV-2 saltational events are recurrent and trace to persistent human infections.
(2026 Jun 19)
bioRxiv
Tran-Kiem C, Kistler K, Hisner R, Bedford T

Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines.
(2026 Jun 23)
J Virol 100(6): e0031726
Loes AN, Tarabi RAL, Li SH, Atkinson RK, Huddleston J, Kikawa C, Griffiths T, Drapeau EM, Wong S-S, Cheng SMS, Leung NHL, Cobey S, Cowling BJ, Bedford T, Hensley SE, Bloom JD