🌟 Excited to share my first PhD publication! 🌟 Our paper in Epidemics uses a mathematical model + Scottish surveillance data to understand what COVID-19 pandemic disruptions revealed about RSV disease in young children.

We have our first epinowcast seminar of 2026 today at 3 pm UK time/4 pm in Central Europe. Excited to hear from @dchodge.bsky.social who will discuss tools for serological inference! www.epinowcast.org/seminars/202...

New pre-print with @dchodge.bsky.social @thushan-desilva.bsky.social and others looks at SARS-CoV-2 antibody kinetics and correlates of protection in The Gambia. What can different biomarkers tell us about protection in population where >80% infections asymptomatic? www.medrxiv.org/content/10.6...

Great to see the seroanalytics.org collection expanding with @dchodge.bsky.social 's work on seroCOP (R package for analysing correlates of protection using Bayesian methods)

I built an MCMC painter! I'm excited to share this project I've been working on for a long time, which sits at the intersection of computational statistics and generative art; mcmcPainter! Link here: mcmcpainter.davidhodgson.me

Getting started on Substack, just some rambling on Yoga Philosophy and a academia. Give me a follow if interested and share yours too! Open to reading anything 😊 open.substack.com/pub/themindf...

Three Paths to Freedom (And Why Academia Needs All of Them)

On Trimārga, the three yoga paths from the Bhagavad Gita, and what they mean for researchers

open.substack.com

Want to understand serological data better? We've compiled a suite of tools which can help you out 🔗 seroanalytics.org These tools are free, open source, peer reviewed and have comprehensive documentation. Big thanks to @alexlizhill.com, @jameshay.bsky.social and others for their contributions!

New blog post on Correlates of Protection! I try and give an overview of this very confusing concept: davidhodgson.me/post/sm3_cop1/ I think it's good ID modellers try and get a solid understanding of this as it's going become increasingly important for vaccine development over the next few years.

CORRELATES OF PROTECTION: FUMBLING THROUGH THE TERMINOLOGY | David Hodgson

Long ago, Edward Jenner made medical history by inoculating a young boy with cowpox and demonstrating protection against smallpox. Jenner had no idea why it worked, he just rolled with it, and thus in...

davidhodgson.me

🚀 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...

WHAT DOES IT MEAN TO BE INFECTED? | David Hodgson

Defining infection is like reading tarot cards - the interpretation depends on who’s asking and what they’re looking for. You wake up with a sore throat. You take a lateral flow...

davidhodgson.me

🚨 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...

Popeye, Tintin and more will enter the public domain in the new year

The copyrights of thousands of 20th-century films, books, compositions and sound recordings expire on Jan. 1, making them free for anyone to share and adapt. Here are some of the highlights.

npr.org

🎅🌟 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...

A Multimodal Evaluation of Podcast Learning, Retention, and Electroencephalographically Measured Attention in Medical Trainees

Introduction: Podcasts have become popular among medical trainees. However, it is unclear how well learners retain information from podcasts compared to traditional educational modalities, and whether...

pmc.ncbi.nlm.nih.gov

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.

Gilead to test once-a-year HIV prevention shot

Gilead is going to start testing a drug it believes could prevent HIV infection with just a single shot every year.

statnews.com

🚨 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🧵:

Challenges for developing broad-based mucosal vaccines for respiratory viruses - Nature Biotechnology

Nature Biotechnology - Challenges for developing broad-based mucosal vaccines for respiratory viruses

nature.com

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