iiinova — where your digital self keeps evolving

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Saloni @scientificdiscovery.dev · 05/09/2026

This is interesting. You get assigned to being born at a random place and time in history, to see what a typical person's life might have been like then. Unfortunately I was born in 1403 in the valley of Mexico and died at age 4 from dysentery.

anyhumanever.com

Any Human Ever

One life, drawn at random from all who have ever lived.

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Chris Wymant @chriswymant.bsky.social · 29/06/2026

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.

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James Hay @jameshay.bsky.social · 22/06/2026

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...

my.corehr.com

Job Details

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Tedros Adhanom Ghebreyesus @drtedros.who.int · 20/05/2026

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

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Kai Kupferschmidt @kakape.bsky.social · 08/05/2026

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

science.org

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

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John M. Drake @jdrakephd.bsky.social · 07/05/2026

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...

forbes.com

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.

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Caitlin Rivers @cmyeaton.bsky.social · 08/05/2026

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...

nytimes.com

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

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IDDjobs @iddjobs.org · 21/04/2026

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: iddjobs.org/jobs/2524

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James Hay @jameshay.bsky.social · 11/12/2025

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...

zenodo.org

Evaluation of the epidemiological outlook of the influenza A/H3N2 clade K in England during the 2025-26 season

Key findings England is currently experiencing a high growth rate of infections caused by the influenza A/H3N2 K clade. Antigenic change from the previously dominant clade, a rapid selective sweep evi...

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Abe Goldfarb @abegoldfarb.bsky.social · 30/11/2025

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

Scene from OFFICE SPACE with Michael Bolton replying to Samir Nagheenanajar:

“No way. Why should I change?
He's the one who sucks.”

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James Hay @jameshay.bsky.social · 25/11/2025

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)

zenodo.org

Evaluation of the epidemiological outlook of the influenza A/H3N2 clade K in England during the 2025-26 season

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Adam Kucharski @adamjkucharski.bsky.social · 22/11/2025

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

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Thomas House @tah-sci.com · 28/10/2025

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

Job Details

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Carl T. Bergstrom @carlbergstrom.com · 25/10/2025

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.

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Chris Wymant @chriswymant.bsky.social · 23/10/2025

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

GitHub & BitBucket HTML Preview

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Nick Brown @steamtraen.eu · 08/10/2025

😅

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Chris Wymant @chriswymant.bsky.social · 07/10/2025

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...

my.corehr.com

Job Details

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Chris Wymant @chriswymant.bsky.social · 15/09/2025

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.

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Wayne Maddison @waynemaddison.bsky.social · 05/09/2025

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 · 26/08/2025

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...

thelancet.com

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...

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Christophe Fraser's Group @christophraser.bsky.social · 26/08/2025

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....

bmcbioinformatics.biomedcentral.com

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...

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James Hay @jameshay.bsky.social · 11/07/2025

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

Job Details

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Thomas House @tah-sci.com · 07/07/2025

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...

healthjobsuk.com

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

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Simon Cauchemez @scauchemez.bsky.social · 01/07/2025

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 · 25/06/2025

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 · 21/05/2025

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...

docs.google.com

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...

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Tedros Adhanom Ghebreyesus @drtedros.who.int · 20/05/2025

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.com · 14/05/2025

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 · 28/04/2025

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

tinyurl.com

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

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Katie Mack @astrokatie.com · 15/04/2025

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.

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Chris Wymant @chriswymant.bsky.social · 10/03/2025

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

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Carl T. Bergstrom @carlbergstrom.com · 28/01/2025

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.

pnas.org

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...

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Chris Wymant @chriswymant.bsky.social · 30/01/2025

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

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

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silargi.bsky.social @silargi.bsky.social · 17/01/2025

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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Marc Lipsitch @mlipsitch.bsky.social · 24/01/2025

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

medrxiv.org

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...

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Kate Grabowski @kategrabowski.bsky.social · 23/01/2025

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 · 22/01/2025

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/...

journals.plos.org

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...

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Colin Carlson @colincarlson.bsky.social · 15/01/2025

🚨😷🧪 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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Carl T. Bergstrom @carlbergstrom.com · 11/01/2025

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

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."

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Sam Scarpino @scarpino.bsky.social · 06/01/2025

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.

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Chris Wymant @chriswymant.bsky.social · 25/12/2024

Festive family and friends fun that nerds can help administer: randomly partition a (WhatsApp) group in two, and the challenge is to think up a criterion that would result in this partition library(tidyverse) tibble(person = c("Joe", ...)) %>% mutate(group = rbernoulli(nrow(.))) %>% arrange(group)

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Aude Bernheim @audeber.bsky.social · 16/12/2024

The Institut Pasteur is recruiting group leaders! Pasteur is an absolute incredible environment to start your lab. Surrounded by so many great scientists, in the beautiful city of Paris. Come eat 🥐 and conduct awesome science. Contact me if you want info ! research.pasteur.fr/en/call/call...

research.pasteur.fr

Call for applications 2025 – Creation of new research groups at the Institut Pasteur | Research - Institut Pasteur

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Justin Sandefur @justsand.bsky.social · 16/12/2024

New @cgdev.org policy paper: *MALARIA VACCINES* are a huge scientific breakthrough. But the world is dragging its feet on rolling them out. We examine why, and how to go faster. 🧵

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Christophe Fraser's Group @christophraser.bsky.social · 16/12/2024

👋 Hello World! Some of our papers this year ICYMI Ferretti & Wymant et al, Nature: using 7 million digitally recorded COVID exposures, we found app-based contact tracing successfully measured the actual risk of transmission and we decomposed contributors to risk 045.medsci.ox.ac.uk/risk_measure...

Image shows how the probability of reported infection with SARS-CoV-2 among people notified by the NHS COVID-19 App increases with the risk score calculated by the app.

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Carl T. Bergstrom @carlbergstrom.com · 09/12/2024

I try not to be fussy about not being cited but making the exact same point *with the exact same title* fifteen months later in a sister venue? That feels like some—what’s the right word?—it’s on the tip of my tongue… undark.org/2023/04/06/c... www.scientificamerican.com/article/chat...

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Chris Wymant @chriswymant.bsky.social · 05/12/2024

When giving a talk, never say "as you all know". Introductory remarks are often familiar to many, there's no need to point this out. And you don't know the full background of every individual in the audience, so don't risk making anyone feel dumb. ("As we all heard in the previous talk" is OK.)

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