Chris Wymant

PANGEA Webinars - YouTube

Not the best answer but an answer: some virus genomics / molecular epi videos live in the "PANGEA Webinars" playlist here www.youtube.com/playlist?lis... Christophe's how to interpret a viral phylogeny is good

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Job: Senior Group Leader in Community-based Control of Infectious Diseases, at the Pandemic Sciences Institute, University of Oxford.
"leading a research programme focused on the design and field evaluation of community-based infectious disease control interventions."
my.corehr.com/pls/uoxrecru...

Top three recommendations, at the paper level, the paragraph level, and the sentence level.

I gave a talk on writing academic scientific papers, and writing more generally
github.com/ChrisHIV/tea...

Confused writing is usually a symptom of confused thinking. As we struggle to clarify writing, we clarify our thoughts. AI writing aids rob us of that struggle, leaving clean-looking text and thoughts still confused for lack of inspection. Writing is not just a product; it is a diagnostic tool.

Clade I mpox vaccination: strategies for deployment and evaluation Clade I mpox continues to spread in Central Africa with no sign of abating,1 however very few doses of vaccine have been deployed. Mpox vaccination strategies using either of the licenced vaccines, MV...

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...

HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data - BMC Bioinformatics Background Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining TSI give a binary classification...

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.
1/3
bmcbioinformatics.biomedcentral.com/articles/10....

What is the relationship between viral prospecting in animals and medical countermeasure development? | mBio Sampling in animal populations to detect novel viruses before they infect humans has been a major activity justified by several considerations, notably by the idea that finding such viruses will stimu...

Very pleased to share this newly published work with Aishani Aatresh, part of her exceptional Harvard undergrad thesis. journals.asm.org/doi/10.1128/... .

We're hiring a modelling postdoc at PSI Oxford for two exciting projects: 1) modelling the early immune responses to Nipah vaccination, and 2) joining the PRESTO team working on immunobridging in vaccine evaluation studies.

tinyurl.com/5abbxrjh

Get in touch for more info! Deadline 4th August.

Please circulate to anyone interested: Senior Statistician role at UK Health Security Agency national Real-time Syndromic Surveillance Team. This would be a great job for any modellers or statisticians with an interest in surveillance.

www.healthjobsuk.com/job/UK/Londo...

Infectious Disease Modelling starter pack update! Many more modellers have joined Bluesky recently so this update is overdue. Pls keep on sending suggestions! (bio should contain experience relevant for this pack)
IDModelling pack 1: go.bsky.app/86Ao1a5
IDModelling pack 2 : go.bsky.app/2oBB7KX

John Drake shaking hands

Congrats to @jdrakephd.bsky.social on the important achievement of winning our* infectious disease pub quiz. Honorable mentions to Corin Yeats, Luca Ferretti, @christophraser.bsky.social and @aliciagill.bsky.social
* the Pandemic Sciences Institute; Data, Epidemiology and Analytics section

Testing samtools’ base alignment quality for HIV Testing the appropriateness of samtools’ base alignment quality (BAQ) calculation for HIV Recap: BAQ calculates a per-base probability of being misaligned, converts that to a quality score, then repl...

Virus genomics peeps: if you use samtools pileup to get base counts from files of mapped reads, you might want to switch off its calculation & use of 'base alignment quality'. I decided this was best for HIV, documented here (in 2019, better late than never) docs.google.com/document/d/1...

It's official: the #PandemicAccord is officially adopted by the World Health Assembly!

My warmest congratulations to @who.int Member States for their commitment to keeping their people and the world safer.

What a moment in global health history. Together!

First publication 10. How to be polite and show respect * In the old days of feudal Japan, a samurai warrior would shout You are trying to view Flash content, but you have no Flash plugin installed.

I had no idea samurai in feudal Japan were that dedicated to troubleshooting Flash

Come work with us! We're looking of postdoc(s) with experience in bacterial genomics and interest in mathematical modelling to work on bacterial ecology and evolution in the context of public health. tinyurl.com/n34vzszu

An astronomy professor colleague of mine once relayed trying to explain to his students why it was important that they actually write their class reports themselves. “The point is not to teach ME about neutron stars,” he said.

Academic paper/talk titles since time immemorial:
SUCCESSFUL PREDICTION OF THINGS THAT HAVE ALREADY HAPPENED

How should the advancement of large language models affect the practice of science? | PNAS Large language models (LLMs) are being increasingly incorporated into scientific workflows. However, we have yet to fully grasp the implications of...

An LLM "creates textual claims, and then predicts the citations that might be associated with similar text. Obviously, this practice violates all norms of scholarly citation.

At best, LLMs gesticulate toward the shoulders of giants."

Bender, West, and I contributed to this pro/con piece in PNAS.

Two postdoc positions to work on virus epi & evolution in response to vaccination, with both theoretical models + data analysis. Paris/Montpellier. With Sylvain Gandon, Sébastien Lion, François Blanquart, Katrina Lythgoe, & Troy Day
emploi.cnrs.fr/Offres/CDD/U...
emploi.cnrs.fr/Offres/CDD/U...

Does your team deposit and access pathogen genomic data via data-sharing platforms for public health use? Participate in WHO's online consultation on the critical features of pathogen genomic data-sharing platforms to meet public health needs.

All info here: www.who.int/news-room/ar...

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...

Unpacking sources of transmission in HIV prevention trials with deep-sequence pathogen data – BCPP/ Ya Tsie study To develop effective HIV prevention strategies that can guide public health policy it is important to identify the main sources of infection in HIV prevention studies. Accordingly, we devised a statis...

Thrilled that this work by Lerato Magosi with many colleagues is now out as a preprint www.medrxiv.org/content/10.1....
It suggests results from treatment-as-prevention HIV cluster-randomized trials are lower than many expected due to significant "spillover" of infections from untreated communities

Excited to share two new preprints from our team this week, both focusing on the shifting #HIV epidemic among adolescents and young adults (AYA) in #Uganda. Good news is the shift is happening in the right direction, as a result of both shifting behaviors and increasing coverage of interventions.

Viral and immune dynamics of genital human papillomavirus infections in young women with high temporal resolution Human papillomavirus (HPV) infections drive one in twenty new cancer cases, with a particular burden on women. This analysis of longitudinal clinical data using kinetics models reveals that HPV infect...

New Alizon-lab HPV paper in @plosbiology.org: 2 years of follow-up of young women in France, 76 infected with HPV. Viral load increases rapidly on infection (<2 months) then plateaus for 13-20 months in those clearing. Dynamics of immune cells, cytokines & Abs too
journals.plos.org/plosbiology/...

Top panels: graphs showing increases in spillover events, extinction rates, and temperature anomalies over the last few centuries. Bottom panel: a map of 10 pandemics since the year 1900. Four were linked to agriculture, two to wildlife use, and one to climate change.

🚨😷🧪 NEW: A growing body of evidence shows that pandemics, biodiversity loss, and climate change are part of a broader polycrisis - but there are no simple solutions. A sweeping overview of "Pathogens and planetary change" for the first issue of @natrevbiodiv.bsky.social, out now 🔓 rdcu.be/d6lHl

Google search for "caffeine per day" AI Overview gives potentially deadly advice, suggesting that 10 energy drinks per day is 400mg caffeine. It's actually around 2000. "The recommended daily caffeine intake for healthy adults is up to 400 milligrams (mg). This is equivalent to about four cups of brewed coffee or 10 cans of energy drinks. However, individual caffeine tolerance varies, and some people may experience negative effects at lower doses. It is important to listen to your body and adjust your caffeine intake accordingly. Pregnant women, children, and people with certain medical conditions may need to limit their caffeine intake further. Consult with a healthcare professional for personalized advice."

How is this production technology?

Here's Google Gemini potentially getting someone killed. Ten energy drinks is typically 1600-3000 mg of caffeine.

As with most epi forecasts, ranges often come from differences in model structure/data not sampling.

The same is true for elections, climate change, and many other domains.

We need more focus in our intro stats classes on these epistemic sources of noise, so people can better consume forecasts.

Job Opportunity at LSHTM: Professor (and Head of Department) The London School of Hygiene & Tropical Medicine (LSHTM) is one of the world’s leading public health universities. Our mission is to improve health and health equity in the UK and worldwide; working i...

Job opening for full professor and head of dept in infectious disease epidemiology and dynamics at @lshtm.bsky.social. Deadline 31st Jan: jobs.lshtm.ac.uk/vacancy.aspx...

(Redraw if all(TRUE) || all(!TRUE). Bluesky not the best place for while loops 8-)