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Publications

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae

Azarian T. et al, (2020), PLOS Biology, 18, e3000878 - e3000878

ISARIC Clinical Data Report 4 October 2020

Pritchard M. et al, (2020)

COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme

Kendall M. et al, (2020)

Ethics of instantaneous contact tracing using mobile phone apps in the control of the COVID-19 pandemic.

Parker MJ. et al, (2020), Journal of medical ethics, 46, 427 - 431

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

Ferretti L. et al, (2020), Science, 368, eabb6936 - eabb6936

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

Lehtinen S. et al, (2020), Science Advances, 6, eaaz6137 - eaaz6137

Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda

Bbosa N. et al, (2020), Viruses, 12, 331 - 331

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

Ferretti L. et al, (2020)

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

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

Improved characterisation of MRSA transmission using within-host bacterial sequence diversity

Hall MD. et al, (2019), eLife, 8

Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae

Kwun MJ. et al, (2019), Genes, 10, 707 - 707

Determining the Origins of Human Immunodeficiency Virus Type 1 Drug-resistant Minority Variants in People Who Are Recently Infected Using Phylogenetic Reconstruction.

Mbisa JL. et al, (2019), Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 69, 1136 - 1143

HIV-1 Transmission Patterns in Men Who Have Sex with Men: Insights from Genetic Source Attribution Analysis.

Le Vu S. et al, (2019), AIDS research and human retroviruses, 35, 805 - 813

Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort.

Rose R. et al, (2019), The Journal of infectious diseases, 220, 1406 - 1413

Effect of Universal Testing and Treatment on HIV Incidence — HPTN 071 (PopART)

Hayes RJ. et al, (2019), New England Journal of Medicine, 381, 207 - 218

Quantifying the contribution of different aged men and women to onwards transmission of HIV-1 in generalised epidemics in sub-Saharan Africa: A modelling and phylogenetics approach from the HPTN071 (PopART) trial

Probert W. et al, (2019), JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 22, 107 - 107

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

Lehtinen S. et al, (2019)

On the evolutionary ecology of multidrug resistance in bacteria

Lehtinen S. et al, (2019), PLOS Pathogens, 15, e1007763 - e1007763

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