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John Huddleston

Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa · ZA
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Area of research
Epidemiology · Molecular Biology
Research interest
Research interests include Influenza Virus Research Studies, Genomics and Phylogenetic Studies, Genomic variations and chromosomal abnormalities, and Chromosomal and Genetic Variations.
h-index
42
citations
39,700
works
130
NIH funding
primary concept
email

Recent publications

Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection
bioRxiv (Cold Spring Harbor Laboratory) 2026cited by 1position: middledoi
Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025
Virus Evolution 2025cited by 4position: middledoi
High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains
eLife 2025cited by 4position: middledoi
High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains
eLife 2025cited by 2position: middledoi
Timely vaccine strain selection and genomic surveillance improves evolutionary forecast accuracy of seasonal influenza A/H3N2
eLife 2025cited by 2position: firstdoi
Timely vaccine strain selection and genomic surveillance improve evolutionary forecast accuracy of seasonal influenza A/H3N2
eLife 2025cited by 1position: firstdoi
High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains
eLife 2025cited by 1position: middledoi
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin
Cell Host & Microbe 2024cited by 38position: middledoi
High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains
Journal of Virology 2024cited by 35position: middledoi
Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States
eLife 2024cited by 22position: middledoi
Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States
eLife 2024cited by 15position: middledoi
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
Virus Evolution 2024cited by 5position: lastdoi
Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States
eLife 2024cited by 1position: middledoi
Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition
Frontiers in Bioinformatics 2023cited by 9position: lastdoi
Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2
Cell Host & Microbe 2022cited by 109position: middledoi
Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition
Cell Host & Microbe 2020cited by 1,143position: middledoi
Cryptic transmission of SARS-CoV-2 in Washington state
Science 2020cited by 323position: middledoi
A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo
Nature Genetics 2020cited by 146position: middledoi
An evolutionary driver of interspersed segmental duplications in primates
Genome biology 2020cited by 53position: middledoi
dms-view: Interactive visualization tool for deep mutational scanning data
The Journal of Open Source Software 2020cited by 42position: middledoi
An evolutionary driver of interspersed segmental duplications in primates
Figshare 2020cited by 0position: middledoi
Nextstrain: real-time tracking of pathogen evolution
Bioinformatics 2018cited by 3,408position: middledoi
Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H ( <i>CFH</i> ) gene family
Proceedings of the National Academy of Sciences 2018cited by 70position: middledoi
The evolution and population diversity of human-specific segmental duplications
Nature Ecology & Evolution 2017cited by 182position: middledoi
The birth of a human-specific neural gene by incomplete duplication and gene fusion
Genome biology 2017cited by 59position: middledoi
Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana
Molecular Biology and Evolution 2017cited by 56position: middledoi
Epigenetic origin of evolutionary novel centromeres
Scientific Reports 2017cited by 43position: middledoi
A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)
GigaScience 2017cited by 24position: middledoi
Long-read sequence assembly of the gorilla genome
Science 2016cited by 395position: middledoi
Long-read sequencing and de novo assembly of a Chinese genome
Nature Communications 2016cited by 304position: middledoi

Grants

An Algorithm For the Nonlinear Dynamic Stability of Struts
NSF7513319$73,2001976–1979PIRePORTER

Frequent collaborators

Evan E. Eichler · Howard Hughes Medical Institute18 papers (2013–2020)Trevor Bedford · Fred Hutch Cancer Center16 papers (2018–2025)Maika Malig · ID Genomics (United States)11 papers (2013–2020)Andrea N. Loes · Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa8 papers (2020–2026)Jesse D. Bloom · Fred Hutch Cancer Center8 papers (2020–2025)Carl Baker · Seattle University8 papers (2013–2020)Ian Barr · Icahn School of Medicine at Mount Sinai7 papers (2024–2025)Janet A. Englund · Seattle Pacific University5 papers (2024–2025) · 5 papers (2013–2017)Hideki Hasegawa · Institut de Recherche Vaccinale5 papers (2024–2026)Richard K. Wilson · Nationwide Children's Hospital5 papers (2013–2018)Claudia Rita Catacchio · University of Edinburgh4 papers (2013–2020)Megan Y. Dennis · New York Psychoanalytic Society and Institute4 papers (2014–2017)Katherine M. Munson · University of Washington4 papers (2016–2020)Bradley J. Nelson · Saint Xavier University4 papers (2015–2018)Shinji Watanabe · National Institute of Infectious Diseases4 papers (2024–2026)Archana N. Raja · Stanford Medicine4 papers (2014–2017) · 4 papers (2025–2025)Ruth Harvey · The Francis Crick Institute4 papers (2024–2025)Heidi Peck · The Wallace H. Coulter Department of Biomedical Engineering4 papers (2025–2025)
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