Christophe Fraser's Group
@christophraser.bsky.social
Posts from the research group of Christophe Fraser, Professor and Head of Data, Epidemiology and Analytics at the Pandemic Science Institute, University of Oxford. Infectious disease epidemiology & evolution: HIV, COVID, outbreaks, AMR.
Credit to lead Caitlin Pley and coauthors @chriswymant.bsky.social @kategrabowski.bsky.social @francescodilauro.bsky.social @jameshay.bsky.social @mlipsitch.bsky.social + others not on Bluesky
August 26, 2025 at 4:50 PM
Credit to lead Caitlin Pley and coauthors @chriswymant.bsky.social @kategrabowski.bsky.social @francescodilauro.bsky.social @jameshay.bsky.social @mlipsitch.bsky.social + others not on Bluesky
Credit to lead Tanya Golubchik, coauthors @chriswymant.bsky.social @astridgagall.bsky.social @helenzambart.bsky.social @kategrabowski.bsky.social + many more not on Bluesky
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August 26, 2025 at 4:32 PM
Credit to lead Tanya Golubchik, coauthors @chriswymant.bsky.social @astridgagall.bsky.social @helenzambart.bsky.social @kategrabowski.bsky.social + many more not on Bluesky
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HIV-phyloTSI is a random forest machine learning algorithm, combining measures of within-host diversity and divergence. We trained on data from 480 individuals with known approximate TSI, from four cohorts in Africa in Europe.
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August 26, 2025 at 4:32 PM
HIV-phyloTSI is a random forest machine learning algorithm, combining measures of within-host diversity and divergence. We trained on data from 480 individuals with known approximate TSI, from four cohorts in Africa in Europe.
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We're excited about to more to come in 2025!
December 16, 2024 at 8:57 AM
We're excited about to more to come in 2025!
Ferretti et al, preprint: we demonstrated why the discrete gamma substitution model, widely used for estimating phylogenetic trees, should no longer be used doi.org/10.1101/2024...
Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity
A standard procedure in phylogenetic reconstruction to represent variation in substitution rates between sites in the genome is the discrete Gamma model (DGM). Relative rates are assumed to be distrib...
doi.org
December 16, 2024 at 8:57 AM
Ferretti et al, preprint: we demonstrated why the discrete gamma substitution model, widely used for estimating phylogenetic trees, should no longer be used doi.org/10.1101/2024...
Igiraneza et al, PLoS Comp Bio: we showed how multi-task machine learning improves prediction of resistance to broadly neutralizing Abs from HIV viral genetic sequences, mitigating subtype biases in data and co-learning for combinations of bnAbs journals.plos.org/ploscompbiol...
Learning patterns of HIV-1 resistance to broadly neutralizing antibodies with reduced subtype bias using multi-task learning
Author summary Broadly neutralizing antibodies (bnAbs) have shown potential in treating and preventing HIV-1 infections. An important step before administering bnAbs is to determine which ones are lik...
journals.plos.org
December 16, 2024 at 8:57 AM
Igiraneza et al, PLoS Comp Bio: we showed how multi-task machine learning improves prediction of resistance to broadly neutralizing Abs from HIV viral genetic sequences, mitigating subtype biases in data and co-learning for combinations of bnAbs journals.plos.org/ploscompbiol...
Hall et al, Lancet Microbe: we characterised the demographics of sources of HIV-1 transmission in Zambia, identifying 300 probable transmission pairs + their direction using our molecular epi method phyloscanner www.sciencedirect.com/science/arti...
December 16, 2024 at 8:57 AM
Hall et al, Lancet Microbe: we characterised the demographics of sources of HIV-1 transmission in Zambia, identifying 300 probable transmission pairs + their direction using our molecular epi method phyloscanner www.sciencedirect.com/science/arti...
Hinch & Panovska‑Griffiths et al, Nature Sci Rep: we quantified how variable mpox case ascertainment delays over time in the UK distorted the relationship between growing case counts and the true epidemic growth
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Quantification of the time-varying epidemic growth rate and of the delays between symptom onset and presenting to healthcare for the mpox epidemic in the UK in 2022 - Scientific Reports
Scientific Reports - Quantification of the time-varying epidemic growth rate and of the delays between symptom onset and presenting to healthcare for the mpox epidemic in the UK in 2022
www.nature.com
December 16, 2024 at 8:57 AM
Hinch & Panovska‑Griffiths et al, Nature Sci Rep: we quantified how variable mpox case ascertainment delays over time in the UK distorted the relationship between growing case counts and the true epidemic growth
www.nature.com/articles/s41...
www.nature.com/articles/s41...
(Michelle Kendall, previously in our group, has handily summarised our work on app-based/digital contact tracing over the last five years here
bsky.app/profile/mish... )
bsky.app/profile/mish... )
December 16, 2024 at 8:57 AM
(Michelle Kendall, previously in our group, has handily summarised our work on app-based/digital contact tracing over the last five years here
bsky.app/profile/mish... )
bsky.app/profile/mish... )
Kendall & Ferretti et al, Science: we showed anonymised data from app-based contact tracing enables analytics for epidemic monitoring that is virtually real-time, high-resolution & national scale. Nice Science mag front cover 👀 (Remember outdoors safer than indoors!)
045.medsci.ox.ac.uk/monitoring
045.medsci.ox.ac.uk/monitoring
December 16, 2024 at 8:57 AM
Kendall & Ferretti et al, Science: we showed anonymised data from app-based contact tracing enables analytics for epidemic monitoring that is virtually real-time, high-resolution & national scale. Nice Science mag front cover 👀 (Remember outdoors safer than indoors!)
045.medsci.ox.ac.uk/monitoring
045.medsci.ox.ac.uk/monitoring