Trevor Bedford

Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa

Also affiliated with Infectious Disease Research Institute, Howard Hughes Medical Institute, Fred Hutch Cancer Center, Cancer Research Center

MedicineMathematicsBiochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 67 papers. Top paper: “Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California”.

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

Science(2020)10.1126/science.abb9263

N/A

13.4DataRank · unranked

308 citations

Wei Gu, Scot Federman, Louis du Plessis, Oliver Pybus, Nuno R. Faria +45 more

Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State

eLife(2021)10.7554/elife.66448

N/A

0.950DataRank · unranked

25 citations

Allison Black, Chas DeBolt, Misty Lang, Nicholas R. Graff, Ailyn C. Pérez-Osorio +5 more

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

Nature Microbiology(2021)10.1038/s41564-021-00932-w

N/A

0.863DataRank · unranked

315 citations

Mark D. Perkins, Jens H. Kuhn, Mark J. Pallen, Erik Alm, Brett N. Archer +42 more

Evidence for Limited Early Spread of COVID-19 Within the United States, January–February 2020

MMWR Morbidity and Mortality Weekly Report(2020)10.15585/mmwr.mm6922e1

N/A

0.787DataRank · unranked

189 citations

Michelle A. Jorden, Sarah L. Rudman, Elsa Villarino, Stacey Hoferka, Megan T. Patel +32 more

Spike deep mutational scanning helps predict success of SARS-CoV-2 clades

Nature(2024)10.1038/s41586-024-07636-1

N/A

0.731DataRank · unranked

130 citations

Jack Brown, Teagan E. McMahon, Ariana Ghez Farrell, Marlin D Figgins, Daniel Asarnow +9 more

Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years

Nature Communications(2024)10.1038/s41467-024-48528-2

N/A

0.598DataRank · unranked

53 citations

C. Hansen, Roy Burstein, Shanda Boyle, Robin Prentice, Cooper Marshall +25 more

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

Cell Host & Microbe(2024)10.1016/j.chom.2024.06.015

N/A

0.557DataRank · unranked

40 citations

Rachel Eguia, Juhye Lee, Hugh K. Haddox, Jared Galloway, Nguyen Van Vinh Chau +14 more

High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains

Journal of Virology(2024)10.1128/jvi.00689-24

N/A

0.546DataRank · unranked

37 citations

Rosario Araceli L Tarabi, John Huddleston, Lisa Touyon, Sook‐San Wong, Samuel M. S. Cheng +7 more

SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing

Clinical Chemistry(2021)10.1093/clinchem/hvab132

N/A

0.529DataRank · unranked

33 citations

Sarah Heidl, Brian Pfau, Beth Martin, Peter D. Han, Weizhi Zhong +37 more

Remote Household Observation for Noninfluenza Respiratory Viral Illness

Clinical Infectious Diseases(2020)10.1093/cid/ciaa1719

N/A

0.477DataRank · unranked

23 citations

Jessica Heimonen, Jessica O’Hanlon, Ashley E. Kim, Naomi Wilcox, Denise J. McCulloch +16 more

Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data

medRxiv(2022)10.1101/2022.02.04.22270474

N/A

0.457DataRank · unranked

20 citations

Benjamin M. Althouse, Amanda Adler, Adam Akullian, Elizabeth Brandstetter, Shari Cho +30 more

Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county

PLoS Pathogens(2024)10.1371/journal.ppat.1012117

N/A

0.441DataRank · unranked

10 citations

Amanda C. Perofsky, Lauren Frisbie, Louise H. Moncla, Pavitra Roychoudhury, Hong Xie +26 more

Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States

eLife(2024)10.7554/elife.91849

N/A

0.416DataRank · unranked

15 citations

John Huddleston, C. Hansen, John Barnes, Thomas Rowe, Xiyan Xu +21 more

Remote surveillance and detection of SARS-CoV-2 transmission among household members in King County, Washington

BMC Infectious Diseases(2024)10.1186/s12879-024-09160-z

N/A

0.104DataRank · unranked

1 citations

Amanda M. Casto, Jessica Heimonen, Jessica O’Hanlon, Eric J. Chow, Constance Ogokeh +41 more

Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State

medRxiv(2020)10.1101/2020.10.19.20215442

N/A

0DataRank · unranked

1 citations

Allison Black, Chas DeBolt, Misty Lang, Nicholas R. Graff, Ailyn C. Pérez-Osorio +5 more

Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine

UNC Libraries(2020)10.17615/v71x-ac23

N/A

0DataRank · unranked

0 citations

Kristen M. Connolly, Clarissa Valim, Sélidji Todagbé Agnandji, Amanda Leach, John J. Aponte +27 more

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

The Journal of Open Source Software(2021)10.21105/joss.02906

N/A

0DataRank · unranked

273 citations

James Hadfield, Thomas R. Sibley, Jover Lee, Kairsten Fay, Misja Ilcisin +5 more

Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York

Nature(2021)10.1038/s41586-021-03908-2

N/A

0DataRank · unranked

140 citations

Hiroshi Mohri, Pengfei Wang, Manoj S. Nair, Jason Zucker, Zizhang Sheng +8 more

Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease

New England Journal of Medicine(2021)10.1056/nejmoa2024670

N/A

0DataRank · unranked

105 citations

Catherine Pratt, Mbusa Mutafali-Ruffin, Matthias Pauthner, Faustin N. Bile, Antoine Nkuba-Ndaye +45 more

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

Science Translational Medicine(2021)10.1126/scitranslmed.abf0202

N/A

0DataRank · unranked

80 citations

Cassia Wagner, Chris Frazar, Pavitra Roychoudhury, Jover Lee, Louise H. Moncla +38 more

Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo

Nature Medicine(2021)10.1038/s41591-021-01302-z

N/A

0DataRank · unranked

75 citations

Allison Black, Daniel Bamuleka Mukadi, James Hadfield, Placide Mbala‐Kingebeni, Catherine Pratt +24 more

Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses

Molecular Biology and Evolution(2021)10.1093/molbev/msab065

N/A

0DataRank · unranked

42 citations

John Huddleston, Trevor Bedford, Richard A. Neher, Pierre Barrat-Charlaix

Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York

medRxiv(2021)10.1101/2021.02.23.21252259

N/A

0DataRank · unranked

157 citations

Hiroshi Mohri, Pengfei Wang, Manoj S. Nair, Jason Zucker, Zizhang Sheng +8 more

Recombination patterns in coronaviruses

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.28.441806

N/A

0DataRank · unranked

21 citations

Kathryn E. Kistler, Trevor Bedford, Nicola F. Müller

Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.11.459844

N/A

0DataRank · unranked

21 citations

John Huddleston, Trevor Bedford, Kathryn E. Kistler

SARS-CoV-2 Epidemiology on a Public University Campus in Washington State

medRxiv(2021)10.1101/2021.03.15.21253227

N/A

0DataRank · unranked

6 citations

Sarah L Sohlberg, Jessica O’Hanlon, Amanda M. Casto, Anne Emanuels, Natalie Lo +31 more

A Remote Household-Based Approach to Influenza Self-Testing and Antiviral Treatment

medRxiv(2021)10.1101/2021.02.01.21250973

N/A

0DataRank · unranked

1 citations

Denise J. McCulloch, Jessica O’Hanlon, Ashley E. Kim, Anne Emanuels, Naomi Wilcox +14 more

Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

Cell Host & Microbe(2022)10.1016/j.chom.2022.03.018

N/A

0DataRank · unranked

112 citations

John Huddleston, Trevor Bedford, Kathryn E. Kistler

Associations Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants and Risk of Coronavirus Disease 2019 (COVID-19) Hospitalization Among Confirmed Cases in Washington State: A Retrospective Cohort Study

Clinical Infectious Diseases(2022)10.1093/cid/ciac279

N/A

0DataRank · unranked

80 citations

Stephanie M. Lunn, Michael Famulare, Lauren Frisbie, Ian Painter, Roy Burstein +40 more

A Bayesian approach to infer recombination patterns in coronaviruses

Nature Communications(2022)10.1038/s41467-022-31749-8

N/A

0DataRank · unranked

56 citations

Kathryn E. Kistler, Trevor Bedford, Nicola F. Müller

State-dependent evolutionary models reveal modes of solid tumor growth

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.05.502978

N/A

0DataRank · unranked

2 citations

Trevor Bedford, Nicola F. Müller, Alison F. Feder, Maya A. Lewinsohn

Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.27.514108

N/A

0DataRank · unranked

1 citations

Ryan R. Wick, Louise M. Judd, Deborah A. Williamson, Trevor Bedford, Benjamin P. Howden +3 more

State-dependent evolutionary models reveal modes of solid tumour growth

Nature Ecology & Evolution(2023)10.1038/s41559-023-02000-4

N/A

0DataRank · unranked

47 citations

Trevor Bedford, Nicola F. Müller, Alison F. Feder, Maya A. Lewinsohn

Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition

Frontiers in Bioinformatics(2023)10.3389/fbinf.2023.1069487

N/A

0DataRank · unranked

9 citations

James Hadfield, Allison Black, Thomas R. Sibley, Richard A. Neher, Trevor Bedford +2 more

Fitting stochastic epidemic models to gene genealogies using linear noise approximation

The Annals of Applied Statistics(2023)10.1214/21-aoas1583

N/A

0DataRank · unranked

7 citations

Gytis Dudas, Trevor Bedford, Vladimir N. Minin, Mingwei Tang

Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences

medRxiv(2023)10.1101/2023.04.05.23287263

N/A

0DataRank · unranked

4 citations

Trevor Bedford, Cécile Tran Kiem

Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States

medRxiv(2023)10.1101/2023.10.02.23296453

N/A

0DataRank · unranked

4 citations

John Huddleston, C. Hansen, John Barnes, Thomas Rowe, Xiyan Xu +21 more

Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution

medRxiv(2023)10.1101/2023.09.21.23295927

N/A

0DataRank · unranked

3 citations

Kathryn E. Kistler, Garrett A. Perchetti, Noah Baker, Lauren Frisbie, Laura Marcela Torres +9 more

Human mobility impacts the transmission of common respiratory viruses: A modeling study of the Seattle metropolitan area

medRxiv(2023)10.1101/2023.10.31.23297868

N/A

0DataRank · unranked

2 citations

C. Hansen, Roy Burstein, Shanda Boyle, Robin Prentice, Cooper Marshall +25 more

Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic

Cell(2024)10.1016/j.cell.2024.02.003

N/A

0DataRank · unranked

58 citations

Nashwa Ahmed, Marlin D Figgins, Vittoria Colizza, Philippe Lemey, John T. McCrone +4 more

Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency

PLoS Computational Biology(2024)10.1371/journal.pcbi.1012443

N/A

0DataRank · unranked

30 citations

Marlin D Figgins, Trevor Bedford, Eslam Abousamra

Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2305299121

N/A

0DataRank · unranked

27 citations

Trevor Bedford, Cécile Tran Kiem

Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution

Nature Communications(2024)10.1038/s41467-024-47599-5

N/A

0DataRank · unranked

27 citations

Kathryn E. Kistler, Garrett A. Perchetti, Noah Baker, Lauren Frisbie, Laura Marcela Torres +9 more

Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States

eLife(2024)10.7554/elife.91849.3

N/A

0DataRank · unranked

24 citations

John Huddleston, C. Hansen, John Barnes, Thomas Rowe, Xiyan Xu +21 more

Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation

PNAS Nexus(2024)10.1093/pnasnexus/pgae561

N/A

0DataRank · unranked

4 citations

Emanuele Gustani‐Buss, Trevor Bedford, Marc A. Suchard, Nídia S. Trovão, Andrew Rambaut +4 more

Clinical and Genomic Epidemiology of Coxsackievirus A21 and Enterovirus D68 in Homeless Shelters, King County, Washington, USA, 2019–2021

Emerging infectious diseases(2024)10.3201/eid3011.240687

N/A

0DataRank · unranked

1 citations

Amanda M. Casto, Nicholas Franko, Eric J. Chow, Peter D. Han, Luis Fernando Gamboa +18 more

High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.08.584176

N/A

0DataRank · unranked

12 citations

Rosario Araceli L Tarabi, John Huddleston, Lisa Touyon, Sook‐San Wong, Samuel M. S. Cheng +7 more

MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.06.583734

N/A

0DataRank · unranked

2 citations

Remco Bouckaert, Chieh‐Hsi Wu, Trevor Bedford, Nicola F. Müller

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.07.579374

N/A

0DataRank · unranked

1 citations

Allison Black, Trevor Bedford, John Huddleston, Sravani Nanduri

Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences

Nature(2025)10.1038/s41586-025-08637-4

N/A

0DataRank · unranked

12 citations

Miguel I. Paredes, Amanda C. Perofsky, Lauren Frisbie, Hong Xie, Kevin Kong +21 more

Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025

Virus Evolution(2025)10.1093/ve/veaf086

N/A

0DataRank · unranked

5 citations

John Huddleston, Andrea N. Loes, S. Richard Turner, Jover Lee, Ian Barr +15 more

High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains

eLife(2025)10.7554/elife.106811.2

N/A

0DataRank · unranked

1 citations

Andrea N. Loes, John Huddleston, Marlin D Figgins, Philippa Steinberg, Tachianna Griffiths +8 more

Hidden Markov models detect recombination and ancestry of SARS-CoV-2

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.08.687354

N/A

0DataRank · unranked

0 citations

Trevor Bedford, Nobuaki Masaki

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.12.571235

N/A

0DataRank · unranked

13 citations

Rachel Eguia, Juhye Lee, Hugh K. Haddox, Jared Galloway, Nguyễn Văn Vĩnh Châu +14 more

Cryptic transmission of SARS-CoV-2 in Washington state

Science(2020)10.1126/science.abc0523

N/A

0DataRank · unranked

329 citations

Alexander L. Greninger, Pavitra Roychoudhury, Lea M. Starita, Michael Famulare, Meei‐Li Huang +62 more

Ten recommendations for supporting open pathogen genomic analysis in public health

Nature Medicine(2020)10.1038/s41591-020-0935-z

N/A

0DataRank · unranked

122 citations

Duncan MacCannell, Thomas R. Sibley, Trevor Bedford, Allison Black

dms-view: Interactive visualization tool for deep mutational scanning data

The Journal of Open Source Software(2020)10.21105/joss.02353

N/A

0DataRank · unranked

42 citations

John Huddleston, Allison Black, Khrystyna North, Adam S. Dingens, Trevor Bedford +2 more

Early prediction of antigenic transitions for influenza A/H3N2

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007683

N/A

0DataRank · unranked

24 citations

Trevor Bedford, Lauren Ancel Meyers, Lauren Castro

CpG-creating mutations are costly in many human viruses

Evolutionary Ecology(2020)10.1007/s10682-020-10039-z

N/A

0DataRank · unranked

16 citations

Sarina Qin, Ryan Winstead, Jasmeen Kaur, Kaho H. Tisthammer, E. Geo Pineda +51 more

Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

PLoS Pathogens(2020)10.1371/journal.ppat.1008191

N/A

0DataRank · unranked

35 citations

Trevor Bedford, Philippe Dussart, Srey Viseth Horm, Sareth Rith, Philippe Buchy +8 more

Cryptic transmission of SARS-CoV-2 in Washington State

medRxiv(2020)10.1101/2020.04.02.20051417

N/A

0DataRank · unranked

86 citations

Alexander L. Greninger, Pavitra Roychoudhury, Lea M. Starita, Michael Famulare, Meei‐Li Huang +52 more

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

medRxiv(2020)10.1101/2020.03.27.20044925

N/A

0DataRank · unranked

36 citations

Wei Gu, Scot Federman, Louis du Plessis, Oliver Pybus, Nuno R. Faria +43 more

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.12.145151

N/A

0DataRank · unranked

6 citations

John Barnes, Thomas Rowe, Xiyan Xu, Rebecca Kondor, David E. Wentworth +14 more

dms-view : Interactive visualization tool for deep mutational scanning data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.14.096842

N/A

0DataRank · unranked

5 citations

John Huddleston, Allison Black, Khrystyna North, Adam S. Dingens, Trevor Bedford +2 more

Operationalizing genomic epidemiology during the Nord-Kivu Ebola outbreak, Democratic Republic of the Congo

medRxiv(2020)10.1101/2020.06.08.20125567

N/A

0DataRank · unranked

4 citations

Allison Black, Daniel Mukadi‐Bamuleka, James Hadfield, Placide Mbala‐Kingebeni, Catherine Pratt +22 more

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.30.352914

N/A

0DataRank · unranked

4 citations

Trevor Bedford, Kathryn E. Kistler

Ten Recommendations for Supporting Open Pathogen Genomic Analysis in Public Health Settings

Preprints.org(2020)10.20944/preprints202001.0107.v1

N/A

0DataRank · unranked

4 citations

Duncan MacCannell, Thomas R. Sibley, Trevor Bedford, Allison Black