Chris Wymant

Scene from OFFICE SPACE with Michael Bolton replying to Samir Nagheenanajar: “No way. Why should I change? He's the one who sucks.”

when someone tells me not to use em dashes because AI uses em dashes

bsky.app/profile/chri...

H3N2 preprint: there are concerns of a severe incoming influenza season due to the drifted H3N2 K clade. We at @psioxford.bsky.social analysed epi data and ran scenario models to see what we could discern about K clade transmission dynamics: zenodo.org/records/1770....

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The COVID inquiry conclusion that lockdown could have been avoided – and subsequent headlines – seems to have been based on a single opinion…

JOB: Postdoctoral Research Associate to work on the transmission dynamics of SARS-CoV-2 using a very large dataset of more than 120,000 viral genomes generated as part of the ONS Covid Survey in Prof Katrina Lythgoe's Ecology and Evolution of Viruses Research Group.

my.corehr.com/pls/uoxrecru...

Scientists themselves determine what is valued within science. Yet we act as if beholden to external managers, bean-counters who confuse the production of papers with scientific progress.

We don't have to find better ways to navigate the prison of metrics-driven scientific assessment.

If you use normally distributed random effects to distinguish between groups you might find this helpful: showing how, in stan, you can constrain them to sum to zero to remove a redundant degree of freedom
htmlpreview.github.io?https://gith...

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

😅

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...

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