Chris Wymant
@chriswymant.bsky.social
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
Pinned
Chris Wymant
@chriswymant.bsky.social
· Dec 3
GitHub - ChrisHIV/teaching
Contribute to ChrisHIV/teaching development by creating an account on GitHub.
github.com
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...
Reposted by Chris Wymant
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...
my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
October 28, 2025 at 3:34 PM
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...
my.corehr.com/pls/uoxrecru...
Reposted by Chris Wymant
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.
We don't have to find better ways to navigate the prison of metrics-driven scientific assessment.
October 25, 2025 at 9:35 PM
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.
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...
htmlpreview.github.io?https://gith...
GitHub & BitBucket HTML Preview
htmlpreview.github.io
October 23, 2025 at 3:48 PM
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...
htmlpreview.github.io?https://gith...
Reposted by Chris Wymant
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...
"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
October 7, 2025 at 11:47 AM
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...
"leading a research programme focused on the design and field evaluation of community-based infectious disease control interventions."
my.corehr.com/pls/uoxrecru...
I gave a talk on writing academic scientific papers, and writing more generally
github.com/ChrisHIV/tea...
github.com/ChrisHIV/tea...
September 15, 2025 at 3:43 PM
I gave a talk on writing academic scientific papers, and writing more generally
github.com/ChrisHIV/tea...
github.com/ChrisHIV/tea...
Reposted by Chris Wymant
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.
September 5, 2025 at 3:20 PM
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.
Reposted by Chris Wymant
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...
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
August 26, 2025 at 4:50 PM
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...
www.thelancet.com/journals/ebi...
Reposted by Chris Wymant
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....
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....
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
August 26, 2025 at 4:32 PM
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....
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....
Reposted by Chris Wymant
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
August 25, 2025 at 7:43 PM
Very pleased to share this newly published work with Aishani Aatresh, part of her exceptional Harvard undergrad thesis. journals.asm.org/doi/10.1128/... .
Reposted by Chris Wymant
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.
tinyurl.com/5abbxrjh
Get in touch for more info! Deadline 4th August.
Job Details
tinyurl.com
July 11, 2025 at 11:32 AM
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.
tinyurl.com/5abbxrjh
Get in touch for more info! Deadline 4th August.
Reposted by Chris Wymant
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...
www.healthjobsuk.com/job/UK/Londo...
Job vacancy: Senior Statistician, UK Health Security Agency, Birmingham | trac.jobs
www.healthjobsuk.com
July 7, 2025 at 3:04 PM
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...
www.healthjobsuk.com/job/UK/Londo...
Reposted by Chris Wymant
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
IDModelling pack 1: go.bsky.app/86Ao1a5
IDModelling pack 2 : go.bsky.app/2oBB7KX
July 1, 2025 at 8:56 AM
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
IDModelling pack 1: go.bsky.app/86Ao1a5
IDModelling pack 2 : go.bsky.app/2oBB7KX
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
* the Pandemic Sciences Institute; Data, Epidemiology and Analytics section
June 25, 2025 at 9:35 PM
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
* the Pandemic Sciences Institute; Data, Epidemiology and Analytics section
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
May 21, 2025 at 4:00 PM
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...
Reposted by Chris Wymant
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!
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!
May 20, 2025 at 8:19 AM
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!
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!
Reposted by Chris Wymant
I had no idea samurai in feudal Japan were that dedicated to troubleshooting Flash
May 14, 2025 at 12:54 AM
I had no idea samurai in feudal Japan were that dedicated to troubleshooting Flash
Reposted by Chris Wymant
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
April 28, 2025 at 5:54 PM
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
Reposted by Chris Wymant
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.
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.
April 15, 2025 at 12:18 PM
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
SUCCESSFUL PREDICTION OF THINGS THAT HAVE ALREADY HAPPENED
March 10, 2025 at 3:41 PM
Academic paper/talk titles since time immemorial:
SUCCESSFUL PREDICTION OF THINGS THAT HAVE ALREADY HAPPENED
SUCCESSFUL PREDICTION OF THINGS THAT HAVE ALREADY HAPPENED
Reposted by Chris Wymant
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.
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
January 28, 2025 at 1:13 AM
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.
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...
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
January 30, 2025 at 10:11 AM
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...
emploi.cnrs.fr/Offres/CDD/U...
emploi.cnrs.fr/Offres/CDD/U...
Reposted by Chris Wymant
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...
All info here: www.who.int/news-room/ar...
January 17, 2025 at 9:46 AM
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...
All info here: www.who.int/news-room/ar...
Reposted by Chris Wymant
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...
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
January 28, 2025 at 7:55 PM
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...
Social optimisation of public-facing digital tools for health protection and trial frameworks for non-pharmaceutical interventions
www.stats.ox.ac.uk/research-stu...
Reposted by Chris Wymant
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
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
January 24, 2025 at 2:30 PM
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
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