The soundtrack from your favourite video game may be good background music for working: it's backgroundy by design, familiar, and you've already trained your mind to ignore it while you concentrate on problem solving. YouTube has extended recordings.

Are you a computational immunologist or bioinformatician interested in impactful vaccine research? We're hiring a postdoc to join @psioxford.bsky.social work in vaccine immunology and evaluation, working on the ChAdOx1 Nipah vaccine. Please get in touch! my.corehr.com/pls/uoxrecru...

The Prime Minister Pedro Sánchez Pérez-Castejón rightly so stressed that history will judge us: "And it will say whether we were capable of protecting life when we knew how to do so". We are one humanity. We share the same DNA. We must work together, for #HealthForAll. #WHA79

After 15 years of reporting on infectious disease outbreaks, what continues to fascinate me about them is the challenge of making high-stakes decisions under uncertainty. The hantavirus outbreak on the MV Hondius is a perfect example My story in @science.org is here (and a thread to come): 🧪 #IDsky

What to do with the passengers on the cruise ship hit by hantavirus?

Past studies of Andes virus offer scant evidence on transmission risks, and have sparked debate

science.org

COVID infected 17% of the Diamond Princess in a month. Hantavirus: 5% of the Hondius in five weeks. The biology explains why this outbreak won't scale. www.forbes.com/sites/johndr...

Why Hantavirus Will Not Be The Next Pandemic

An ecologist explains why the hantavirus cruise ship outbreak, while serious, will not become the next pandemic. The biology of Andes virus limits large-scale spread.

forbes.com

I wrote about how I am thinking about the hantavirus outbreak, and what I am watching for as the situation develops. (now with gift link) www.nytimes.com/2026/05/07/o...

Opinion | Here’s How Freaked Out You Should Be About the Hantavirus Cruise Ship

nytimes.com

Early career faculty (Coventry, United Kingdom) 6 Assistant Professor positions are available in the School of Life Sciences with research areas including infectious disease at University of Warwick More details: http://iddjobs.org/jobs/2524

Great take. We looked at the data a few weeks ago and concluded that other than starting early, this year's dynamics are comparable to previous bad seasons. Our scenario models suggest a peak in infections (not hospitalisations which lag 1/2 weeks) in early/mid December. zenodo.org/records/1770...

Prof Christina Pagel@chrischirp.bsky.social · 8mo ago

🧵 Is it a super flu year? Who knows, but I think the current reporting is stupid. A pissed off thread using data. Firstly - here are today's headlines and some from the last 3 years... spot the difference. 1/10

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

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.... (1/18)

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...

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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...

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.

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...

thelancet.com

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....

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

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

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

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

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

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!

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