Publications by authors named "Trevor Bedford"

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SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse.
Frank Konings, Mark D Perkins, Jens H Kuhn, Mark J Pallen, Erik J Alm, Brett N Archer, Amal Barakat, Trevor Bedford, Jinal N Bhiman, Leon Caly

Nat Microbiol· July 2021

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HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations.
Nuno R Faria, Andrew Rambaut, Marc A Suchard, Guy Baele, Trevor Bedford, Melissa J Ward, Andrew J Tatem, João D Sousa, Nimalan Arinaminpathy, Jacques Pépin

October 2014

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High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains.
Caroline Kikawa, Andrea N Loes, John Huddleston, Marlin D Figgins, Philippa Steinberg, Trevor Bedford

bioRxiv· December 2025

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Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference.
Nicola F Müller, Ryan R Wick, Louise M Judd, Deborah A Williamson, Trevor Bedford

PLoS Pathog· December 2025

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Timely vaccine strain selection and genomic surveillance improve evolutionary forecast accuracy of seasonal influenza A/H3N2.
John Huddleston, Trevor Bedford

Elife· December 2025

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Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025.
Caroline Kikawa, John Huddleston, Andrea N Loes, Sam A Turner, Jover Lee, Trevor Bedford

Virus Evol· November 2025

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Hidden Markov Models Detect Recombination and Ancestry of SARS-CoV-2.
Nobuaki Masaki, Trevor Bedford

bioRxiv· November 2025

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Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025.
Caroline Kikawa, John Huddleston, Andrea N Loes, Sam A Turner, Jover Lee, Trevor Bedford

bioRxiv· October 2025

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Seasonal Influenza Viruses Show Distinct Adaptive Dynamics During Growth in Chicken Eggs.
Kathryn Kistler, Trevor Bedford

Mol Biol Evol· October 2025

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Frequency dynamics predict viral fitness, antigenic relationships and epidemic growth.
Marlin D Figgins, Trevor Bedford

medRxiv· September 2025

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MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions.
Nicola F Müller, Remco R Bouckaert, Chieh-Hsi Wu, Trevor Bedford

PLoS Comput Biol· September 2025

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Characterizing the informativeness of pathogen genome sequence datasets about transmission between population groups.
Cécile Tran-Kiem, Amanda C Perofsky, Justin Lessler, Trevor Bedford

medRxiv· August 2025

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Viral introductions and return to baseline sexual behaviors maintain low-level mpox incidence in Los Angeles County, USA, 2023-2024.
Miguel I Paredes, Citina Liang, Sze-Chuan Suen, Ian W Holloway, Jacob M Garrigues, Trevor Bedford

medRxiv· June 2025

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Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences.
Cécile Tran-Kiem, Miguel I Paredes, Amanda C Perofsky, Lauren A Frisbie, Hong Xie, Trevor Bedford

Nature· April 2025

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Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation.
Francesco Parino, Emanuele Gustani-Buss, Trevor Bedford, Marc A Suchard, Nídia S Trovão

PNAS Nexus· January 2025

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SARS-CoV-2 Diversity and Transmission on a University Campus across Two Academic Years during the Pandemic.
Amanda M Casto, Miguel I Paredes, Julia C Bennett, Kyle G Luiten, Peter D Han, Trevor Bedford

Clin Chem· January 2025

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Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences.
Cécile Tran-Kiem, Miguel I Paredes, Amanda C Perofsky, Lauren A Frisbie, Hong Xie, Trevor Bedford

medRxiv· November 2024

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Clinical and Genomic Epidemiology of Coxsackievirus A21 and Enterovirus D68 in Homeless Shelters, King County, Washington, USA, 2019-2021.
Sarah N Cox, Amanda M Casto, Nicholas M Franko, Eric J Chow, Peter D Han, Trevor Bedford

Emerg Infect Dis· November 2024

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Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.
Sravani Nanduri, Allison Black, Trevor Bedford, John Huddleston

Virus Evol· November 2024

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High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains.
Andrea N Loes, Rosario Araceli L Tarabi, John Huddleston, Lisa Touyon, Sook San Wong, Trevor Bedford

J Virol· October 2024

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Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency.
Eslam Abousamra, Marlin Figgins, Trevor Bedford

PLoS Comput Biol· September 2024

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Author Correction: Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution.
Cassia Wagner, Kathryn E Kistler, Garrett A Perchetti, Noah Baker, Lauren A Frisbie, Trevor Bedford

Nat Commun· September 2024

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Timely vaccine strain selection and genomic surveillance improves evolutionary forecast accuracy of seasonal influenza A/H3N2.
John Huddleston, Trevor Bedford

medRxiv· September 2024

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Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States.
Amanda C Perofsky, John Huddleston, Chelsea L Hansen, John R Barnes, Thomas Rowe, Trevor Bedford

Elife· September 2024

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Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin.
Frances C Welsh, Rachel T Eguia, Juhye M Lee, Hugh K Haddox, Jared Galloway, Trevor Bedford

Cell Host Microbe· August 2024

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Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.
Sravani Nanduri, Allison Black, Trevor Bedford, John Huddleston

bioRxiv· August 2024

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Spike deep mutational scanning helps predict success of SARS-CoV-2 clades.
Bernadeta Dadonaite, Jack Brown, Teagan E McMahon, Ariana G Farrell, Marlin D Figgins, Trevor Bedford

Nature· July 2024

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