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Publications

A highly virulent variant of HIV-1 circulating in the Netherlands.

Wymant C. et al, (2022), Science (New York, N.Y.), 375, 540 - 545

OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing.

Hinch R. et al, (2021), PLoS computational biology, 17

The epidemiological impact of the NHS COVID-19 app.

Wymant C. et al, (2021), Nature, 594, 408 - 412

Time to evaluate COVID-19 contact-tracing apps.

Colizza V. et al, (2021), Nat Med, 27, 361 - 362

Epidemiological changes on the Isle of Wight after the launch of the NHS Test and Trace programme: a preliminary analysis.

Kendall M. et al, (2020), The Lancet. Digital health, 2, e658 - e666

A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings.

Bonsall D. et al, (2020), Journal of clinical microbiology, 58

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing.

Ferretti L. et al, (2020), Science (New York, N.Y.)

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.

Ratmann O. et al, (2020), The lancet. HIV, 7, e173 - e183

Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052.

Zhang Y. et al, (2020), Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing

Ferretti L. et al, (2020)

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.

Ratmann O. et al, (2019), Nature communications, 10

Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission.

Thompson RN. et al, (2019), Virus evolution, 5

Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission

Thompson R. et al, (2018)

The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012.

van der Kuyl AC. et al, (2018), Virus research, 250, 51 - 64

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

Wymant C. et al, (2018), Virus evolution, 4

Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes.

Cornelissen M. et al, (2018), 1746, 55 - 61

PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.

Wymant C. et al, (2017), Molecular biology and evolution

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.

Ratmann O. et al, (2017), AIDS research and human retroviruses, 33, 1083 - 1098

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.

Blanquart F. et al, (2017), PLoS biology, 15

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict.

Croucher NJ. et al, (2016), PLoS biology, 14

Include forthcoming?