🚀 New tool: Reversible Jump MCMC running in your browser! Built an interactive widget for fitting mixture distributions when you don't know how many components you need. Check it out: dchodge.github.io/rjmc-widget-...

🔬 New to serological data? You’re not alone When I first saw spreadsheets full of columns labelled ELISA_OD, PRNT50, HI_titre, and PVNT_ID50, I had no idea what they really meant. That confusion inspired me to write a new blog post, “A Dummy’s Guide to Serological Assays” 👉 tinyurl.com/586dsy77

🚨 New paper out in PLOS Computational Biology! 🚨 We're excited to share our new paper, serojump, a new probabilistic framework and R package for inferring infections and antibody kinetics from longitudinal serological data. 📄 Full paper: tinyurl.com/re7du3t2 R package: seroanalytics.org/serojump

Just launched an interactive Bayesian epidemic modelling platform that runs entirely in your browser! No downloads, no installations, no expensive software licenses. Just open the link and start modelling disease dynamics with real-time parameter estimation. >> widget-bayesian-sir.davidhodgson.me

What does it really mean to be “infected”? PCR? Symptoms? Antibodies? Being able to pass it on? I’ve written a blog digging into why infection isn’t a simple on/off switch, and why the definition you choose matters for modelling, vaccines, & public health. davidhodgson.me/post/sm1_wha...

🚨 New vignette: reversible-jump MCMC for epidemic change-points Used RJMCMC to infer piecewise attack rates in an SEIR model — the sampler figures out how many change-points there are and where they happen. Code + walkthrough 👉 dchodge.github.io/rjmc/article... #R #Bayesian #Epidemiology #RJMCMC

We've got a new pre-print (spearheaded by @dchodge.bsky.social) on how to reconstruct unobserved antibody kinetics and infections - and use these to estimate correlates of protection: www.medrxiv.org/content/10.1... And here's the accompanying {serojump} R package: seroanalytics.org/serojump/

Why did neutralising antibody responses vary between the Oxford-AZ and Pfizer-BioNTech SARS-CoV-2 vaccines? And how did changing the duration between first and second dose affect the underlying biological processes? Our new paper, spearheaded by @dchodge.bsky.social had a look.... 1/

@dchodge.bsky.social and I developed an app using WebR and React, to see how this stack compares to RShiny. Looks quite promising I think! The app wraps the SeroSim R package by @jameshay.bsky.social for simulating serosurvey data: serosim.seroanalytics.org

Researcher: "We let the data speak for itself." Earlier that day:

Excited to move to the US and incorporate Popeye (but not his affinity with spinach) into all my modelling frameworks www.npr.org/2024/12/26/n...

🎅🌟 CHRISTMAS PRESENT 🌟🎅 Got a flexible reversible jump mcmc R packaged up for those who are keen to explore trans-dimensional spaces when fitting; cmmid.github.io/rjmc, with application to a mixture model here; cmmid.github.io/rjmc/article.... More theory and vignettes in 2025!!

Academic writing is getting harder to read - the humanities most of all https://www.economist.com/science-and-technology/2024/12/18/academic-writing-is-getting-harder-to-read-the-humanities-most-of-all

Seated podcast, vs treadmill podcast, vs book learning. Also they slapped an EEG on the subjects. #MedEd pmc.ncbi.nlm.nih.gov/articles/PMC...

Many, many thanks to colleagues, collaborators, students, friends and family for being with me on this awesome journey to Professor @lshtm.bsky.social! It has involved lots of hard but fun work as well as the usual dose of luck. Onwards and upwards to trying to tackle more challenges in #AMR!

Scientists: *develop a once-every-two-months HIV antiviral injection* Scientists: Hold my beer. *develop a once-every-six-months antiviral* Scientists: Hold my beer.

🚨 Exciting PhD Opportunity with me and @adamjkucharski.bsky.social at LSHTM (MRC LID)! 🚨 Dive into cutting-edge in-host immunological modeling: ✨ Explore immune responses to SARS-CoV-2 & Influenza. ✨ Develop Bayesian models to analyse immune dynamics. more info: mrc-lid.lshtm.ac.uk/2025-26-proj...

Have enjoyed early version of seroviz.seroanalytics.org to explore and discuss data - great work by @alexlizhill.com @dchodge.bsky.social And if you're interested in immunological kinetics for SARS-CoV-2 and influenza, we're currently advertising a PhD project: mrc-lid.lshtm.ac.uk/2025-26-proj...

For those wondering why we seem to be so behind when it comes to effective mucosal vaccines against respiratory viruses, this really excellent overview from leaders in the field offers a great summary: www.nature.com/articles/s41... few additional points for those who want a bit more detail🧵:

Two stages of writing: 1) This shouldn't take too long 2) Oh no

1/ 🎉 Thrilled to share our new study: Quantifying the impact of pre-vaccination titre and vaccination history on influenza vaccine immunogenicity 🦠💉 Published in Vaccine! link: authors.elsevier.com/a/1kD7x,60n7... with @adamjkucharski.bsky.social

My fan phylogeny from my thesis now ready for the club

Air Quality Stripes have long-term trends of air pollution in many cities across the world. Here is London. Nice work @jimmcquaid.bsky.social & @kirstypringle.bsky.social. airqualitystripes.info/stripes/?con... h/t @edhawkins.org

Very happy to share our new study out today in the New England Journal of Medicine, showing fewer PCV doses are non-inferior to standard schedules in maintaining control of vaccine-type carriage in Vietnam. This could make vacc programmes much more affordable for LMICs. www.nejm.org/doi/full/10....

Jay Bhattacharya might just be Donald Trump’s most extreme pick. If you don’t know about him, you need to.

1/ Academia can feel like a pressure cooker — tight deadlines, teaching, writing papers and grants, and all these things feel they need done “perfectly” to compete with others. What’s helped me deal with this is the concept of samskara, an ancient concept from Hindu and Buddhist philosophy. 👇

Look who's here @pnas.org ✔️ @science.org ✔️ @naturecellbiology.bsky.social ✔️ @natrevgenet.bsky.social ✔️ @naturebiotech.bsky.social ✔️ @naturemicrobiol.bsky.social ✔️ @naturechemistry.bsky.social ✔️ @genesdev.bsky.social ✔️ @cellchembiol.bsky.social ✔️ @genomeresearch.bsky.social ✔️ @jcellbiol.bsky.social ✔️

Conversations around men’s health shouldn't only be during #Movember Abhjit Nadkasrmi & Petra Gronholm highlight the impacts of social stigma on discussions around men's #MentalHealth. #PublicHealth www.lshtm.ac.uk/newsevents/n...

Ever wanted to sample over a discrete space using MCMC in R? I made a package for that years ago (dchodge.github.io/ptmc), and I just added a vignette to show how it works for a latent discrete variable (it involves negronis 🍹 and sunny days ☀️, dchodge.github.io/ptmc/article...)

Come do a PhD with us at @lshtm.bsky.social! We're advertising two projects: Understanding and predicting vector-borne epidemics (with Rachel Lowe): mrc-lid.lshtm.ac.uk/2025-26-proj... Kinetics of immunity to influenza and SARS-CoV-2 (with @dchodge.bsky.social): mrc-lid.lshtm.ac.uk/2025-26-proj...

Love it when it's one degree outside. Just one, on its own, doing the most, trying to keep me warm 🥹

just a reminder of how horrible the syntax of R metaprogramming is 🫥

Great study highlighting epidemiological and clinical features of #mpox clade Ib in #DRC - Mostly adult heterosexual transmission; typically have genital lesions and mild disease - 0.5% mortality - 15% of children infected in households, more severe disease www.medrxiv.org/content/10.1...

I’ll be giving a talk on epidemic dynamics at @lshtm.bsky.social next Monday at 5.30pm, from dengue and Zika to pandemic influenza and COVID. Free and open to all: www.lshtm.ac.uk/newsevents/e...

Pathogens clinging to #microplastics can weather water treatment, pose health risk www.cidrap.umn.edu/foodborne-di...

At last, there's a searchable directory of Bluesky starter packs, courtesy of @mubashariqbal.com! Just one more way third-party developers are helping to make this place better. Search starter packs by keyword, and sort by "Uses" to see which ones people are finding the most helpful

Love you melatonin "A randomized clinical trial of the impact of melatonin on influenza vaccine: Outcomes from the melatonin and vaccine response immunity and chronobiology study" www.tandfonline.com/doi/pdf/10.1...

Looking forward, I'll be performing all simulation recovery using this crucially important dataset github.com/cran/dragracer

My article on the coloniality of academic freedom and the Palestine exception still has free access. Check it out when you get a chance. www.tandfonline.com/doi/full/10....