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Chris Wymant

@chriswymant.bsky.social

670 followers 120 following 42 posts

Infectious disease epidemiology w stat/math modelling, genomics. Senior researcher at the Pandemic Sciences Institute, Oxford. Likes global & one health, sustainability; animals count too. Vegan, flyingless. Views own. https://github.com/ChrisHIV/teaching

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Chris Wymant @chriswymant.bsky.social · Dec 3

The hello post: I do virus epi, so far genomics and contact tracing using apps, henceforth vaccine trials. Main tips: ask the right question, do statistics with a model you understand that's tested on simulated data, prioritise clarity when communicating. I explain things→ github.com/ChrisHIV/tea...

GitHub - ChrisHIV/teaching

Contribute to ChrisHIV/teaching development by creating an account on GitHub.

github.com

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Nick Brown @steamtraen.eu · 1d

😅

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Chris Wymant @chriswymant.bsky.social · 1d

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...

Job Details

my.corehr.com

Chris Wymant @chriswymant.bsky.social · 23d

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

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

Reposted by Chris Wymant

Wayne Maddison @waynemaddison.bsky.social · Sep 5

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.

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Christophe Fraser's Group @christophraser.bsky.social · Aug 26

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...

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...

www.thelancet.com

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Christophe Fraser's Group @christophraser.bsky.social · Aug 26

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....

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...

bmcbioinformatics.biomedcentral.com

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Marc Lipsitch @mlipsitch.bsky.social · Aug 25

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

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...

journals.asm.org

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James Hay @jameshay.bsky.social · Jul 11

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.

Job Details

tinyurl.com

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Thomas House @tah-sci.com · Jul 7

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...

Job vacancy: Senior Statistician, UK Health Security Agency, Birmingham | trac.jobs

www.healthjobsuk.com

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Simon Cauchemez @scauchemez.bsky.social · Jul 1

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

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Chris Wymant @chriswymant.bsky.social · Jun 25

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

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Chris Wymant @chriswymant.bsky.social · May 21

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...

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...

docs.google.com

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Tedros Adhanom Ghebreyesus @drtedros.who.int · May 20

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!

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Faine Greenwood @faineg.bsky.social · May 14

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

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.

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Sonja Lehtinen @sonjalehtinen.bsky.social · Apr 28

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

Opportunités de carrière : Postdoctoral researcher in bacterial genomics (22209)

tinyurl.com

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Katie Mack @astrokatie.com · Apr 15

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.

Sam Halpert @samhalpert.bsky.social · Apr 15

Even accepting the premise that AI produces useful writing (which no one should), using AI in education is like using a forklift at the gym. The weights do not actually need to be moved from place to place. That is not the work. The work is what happens within you.

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Chris Wymant @chriswymant.bsky.social · Mar 10

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

Reposted by Chris Wymant

Carl T. Bergstrom @carlbergstrom.com · Jan 28

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.

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...

www.pnas.org

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Chris Wymant @chriswymant.bsky.social · Jan 30

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...

Portail Emploi CNRS - Offre d'emploi - Chercheur.e postdoctoral H/F en épidémiologie évolutive

emploi.cnrs.fr

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silargi.bsky.social @silargi.bsky.social · Jan 17

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...

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christldonnelly.bsky.social @christldonnelly.bsky.social · Jan 28

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...

Research Studentships | statistics

www.stats.ox.ac.uk

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Marc Lipsitch @mlipsitch.bsky.social · Jan 24

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

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...

www.medrxiv.org

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Kate Grabowski @kategrabowski.bsky.social · Jan 23

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.

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Chris Wymant @chriswymant.bsky.social · Jan 22

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/...

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...

journals.plos.org

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Colin Carlson @colincarlson.bsky.social · Jan 15

🚨😷🧪 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

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.

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