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

New paper: we argue that a promising approach for studying mpox vaccine effectiveness in Central Africa to incorporate mpox vaccination + testing data into existing cohort studies, especially those for HIV/STIs.
www.thelancet.com/journals/ebi...

Credit to lead Tanya Golubchik, coauthors @chriswymant.bsky.social ‪@astridgagall.bsky.social‬ ‪@helenzambart.bsky.social‬ @kategrabowski.bsky.social‬ + many more not on Bluesky
3/3

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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New paper: our method HIV-phyloTSI estimates time-since-infection for HIV using deep viral sequence data.
Estimating continuous TSI, not just recent / not-recent, gives incidence over time, allowing evaluation of the impact of interventions.
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bmcbioinformatics.biomedcentral.com/articles/10....

New postdoc positions with a number of exciting epidemic modelling projects opening in our Unit at @pasteur.fr in beautiful Paris. Deadline for applications: 26th June.
research.pasteur.fr/en/job/postd...

If less than 76.6% of your exploratory ideas fail, you’re not exploring enough…

How about a bit of good news? 8 patients were dismissed from the hospital in Uganda after recovering from Ebola. Many still in the quarantine period so outbreak still officially ongoing, but it's impressive that out of the 9 identified infections, there has only been one death (the index patient).

it helps

Please spread the word - a funded (home fees) DPhil (PhD) studentship available in @oxfordstatistics.bsky.social

Social optimisation of public-facing digital tools for health protection and trial frameworks for non-pharmaceutical interventions
www.stats.ox.ac.uk/research-stu...

🐔 On 21 Jan 2025, highly pathogenic avian influenza (HPAI) H5N1 was confirmed in commercial poultry at premises near Easingwold, Hambleton, North Yorkshire. #IDSky #IDEpi

🗺️ APHA Interactive Avian Influenza Disease Map: www.arcgis.com/apps/webappv...

🔗 Avian influenza: latest situation in England 👇

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...

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...

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...

(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... )

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

👋 Hello World! Some of our papers this year ICYMI
Ferretti & Wymant et al, Nature: using 7 million digitally recorded COVID exposures, we found app-based contact tracing successfully measured the actual risk of transmission and we decomposed contributors to risk 045.medsci.ox.ac.uk/risk_measure...

Trying something new:
A 🧵 on a topic I find many students struggle with: "why do their 📊 look more professional than my 📊?"

It's *lots* of tiny decisions that aren't the defaults in many libraries, so let's break down 1 simple graph by @jburnmurdoch.bsky.social

🔗 www.ft.com/content/73a1...

We have a new opportunity to work with the Department!

Come & apply for the role of #postdoc research assistant. You will join the Digital Pandemic Preparedness project at the @oxmartinschool.bsky.social, and led by Prof. Christl Donnelly and Moritz Kraemer.

App Deadline: 12pm, 07.01.25

Humanity’s history is a battle against infectious diseases. And for most of our history we were losing very decisively.

From my article about vaccines:
ourworldindata.org/microbes-bat...