Nextstrain automates real-time phylodynamic analysis of open data for endemic and emerging pathogens.
(2026 Mar 26)
bioRxiv
Andrews KR, Chang J, Roemer C, Hadfield J, Lin V, Brito AF, Daodu R, Joia IA, Kistler K, Li AW, Moncla LH, Paredes MI, Kuhnert D, Torres LM, Voitl L, Aksamentov I, Hodcroft EB, Huddleston J, McCrone JT, Anderson JS, Sibley TR, Lee J, Neher RA, Bedford T

Characterizing the informativeness of pathogen genome sequence datasets about transmission between population groups.
(2026 Mar 18)
Proc Biol Sci 293(2067):
Tran-Kiem C, Perofsky AC, Lessler J, Bedford T

Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines.
(2026 Feb 23)
bioRxiv
Loes AN, Tarabi RA, Li SH, Atkinson RK, Huddleston J, Kikawa C, Griffths T, Drapeau EM, Wong SS, Cheng SM, Leung NH, Cobey S, Cowling BJ, Bedford T, Hensley SE, Bloom JD

Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection.
(2026 Feb 19)
bioRxiv
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

High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains.
(2026 Feb 23)
Elife 14():
Kikawa C, Loes AN, Huddleston J, Figgins MD, Steinberg P, Griffiths T, Drapeau EM, Peck H, Barr I, Englund JA, Hensley SE, Bedford T, Bloom JD