Sign in

David Hodgson

@dchodge.bsky.social
777 followers 961 following 55 posts

Researcher at Charité. Interested in mathematically modelling immunity. 🧘🍰🎧🖥️🏃🧪🏳️‍🌈 seroanalytics.org davidhodgson.me

PostsRepliesMedia
Reposted by David Hodgson
Clara Brigitta @clarabrigitta.bsky.social · 06/03/2026
🌟 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.
143
Reposted by David Hodgson
Kelly Charniga @kcharniga.bsky.social · 14/01/2026
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...
epinowcast.org
David Hodgson – Epinowcast
Epinowcast community site
011
Reposted by David Hodgson
Adam Kucharski @adamjkucharski.bsky.social · 05/01/2026
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...
1113
Reposted by David Hodgson
Adam Kucharski @adamjkucharski.bsky.social · 10/12/2025
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)
072
David Hodgson @dchodge.bsky.social · 26/10/2025
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
192
David Hodgson @dchodge.bsky.social · 12/10/2025
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...
open.substack.com
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
010
David Hodgson @dchodge.bsky.social · 09/10/2025
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!
seroanalytics.org
Seroanalytics
041
David Hodgson @dchodge.bsky.social · 05/10/2025
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.
davidhodgson.me
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...
040
David Hodgson @dchodge.bsky.social · 30/09/2025
🚀 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-...
dchodge.github.io
Dynamic Mixture Model Analysis
295
David Hodgson @dchodge.bsky.social · 27/09/2025
🔬 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
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
021
David Hodgson @dchodge.bsky.social · 23/09/2025
🚨 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
seroanalytics.org
A serological inference package using reversible jump mcmc
The `serojump` package provides tools for fitting serological models to antibody kinetics data using reversible-jump Markov Chain Monte Carlo (RJ-MCMC). It enables researchers to model the dynamics of...
2195
David Hodgson @dchodge.bsky.social · 19/09/2025
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
widget-bayesian-sir.davidhodgson.me
Interactive Bayesian Epidemic Modelling
2226
David Hodgson @dchodge.bsky.social · 17/09/2025
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...
davidhodgson.me
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...
272
David Hodgson @dchodge.bsky.social · 15/09/2025
🚨 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
dchodge.github.io
Example 2: SEIR change-point attack rate
060
Reposted by David Hodgson
Adam Kucharski @adamjkucharski.bsky.social · 09/04/2025
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/
0234
Reposted by David Hodgson
Adam Kucharski @adamjkucharski.bsky.social · 31/03/2025
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/
13010
Reposted by David Hodgson
Alex Hill @alexlizhill.com · 06/03/2025
@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
serosim.seroanalytics.org
SeroSim
Web interface for serosurvey data simulation
062
Reposted by David Hodgson
Khoa @khoavuumn.bsky.social · 02/01/2025
Researcher: "We let the data speak for itself." Earlier that day:
9679171003
David Hodgson @dchodge.bsky.social · 26/12/2024
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...
npr.org
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.
010
David Hodgson @dchodge.bsky.social · 22/12/2024
🎅🌟 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!!
cmmid.github.io
A general-purpose package to run reversible-jump mcmc
What the package does (one paragraph).
020
Reposted by David Hodgson
Marcel Salathé @marcelsalathe.bsky.social · 19/12/2024
Academic writing is getting harder to read - the humanities most of all www.economist.com/science-and-techn…
2143
Reposted by David Hodgson
Mike @empiricgame.bsky.social · 15/12/2024
Seated podcast, vs treadmill podcast, vs book learning. Also they slapped an EEG on the subjects. #MedEd pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov
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...
4154
Reposted by David Hodgson
Gwen Knight @gmknght.bsky.social · 11/12/2024
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!
Prof Gwen Knight and some members of her group outside LSHTM
12535
Reposted by David Hodgson
Saloni @scientificdiscovery.dev · 11/12/2024
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.
statnews.com
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.
1935163
David Hodgson @dchodge.bsky.social · 12/12/2024
🚨 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...
mrc-lid.lshtm.ac.uk
2025-26 Project (Hodgson & Kucharski) - MRC London Intercollegiate Doctoral Training Partnership Studentships
Modelling the kinetics of immunity to influenza and SARS-CoV-2 in different populations SUPERVISORY TEAM Supervisor...
175
Reposted by David Hodgson
Adam Kucharski @adamjkucharski.bsky.social · 09/12/2024
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...
1193
Reposted by David Hodgson
Edward Nirenberg @enirenberg.bsky.social · 07/12/2024
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🧵:
nature.com
Challenges for developing broad-based mucosal vaccines for respiratory viruses - Nature Biotechnology
Nature Biotechnology - Challenges for developing broad-based mucosal vaccines for respiratory viruses
1927882
Reposted by David Hodgson
Neil Renic @ncrenic.bsky.social · 04/12/2024
Two stages of writing: 1) This shouldn't take too long 2) Oh no
561370947005
David Hodgson @dchodge.bsky.social · 05/12/2024
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
authors.elsevier.com
2207
Reposted by David Hodgson
Zooplank, MS² @zooplank.bsky.social · 28/11/2024
My fan phylogeny from my thesis now ready for the club
620127
Reposted by David Hodgson
Hannah Ritchie @hannahritchie.bsky.social · 29/11/2024
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
1327974
Reposted by David Hodgson
Billy Quilty @bquilty.bsky.social · 28/11/2024
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....
nejm.org
Effect of a Reduced PCV10 Dose Schedule on Pneumococcal Carriage in Vietnam | NEJM
After pneumococcal disease and colonization have been controlled through vaccination campaigns, a reduced pneumococcal conjugate vaccine (PCV) schedule may be sufficient to sustain that control at ...
14717
Reposted by David Hodgson
Walker Bragman @walkerbragman.bsky.social · 27/11/2024
Jay Bhattacharya might just be Donald Trump’s most extreme pick. If you don’t know about him, you need to.
913557
David Hodgson @dchodge.bsky.social · 26/11/2024
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. 👇
2204
Reposted by David Hodgson
Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 25/11/2024
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 ✔️
34503237
Reposted by David Hodgson
London School of Hygiene & Tropical Medicine @lshtm.bsky.social · 25/11/2024
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...
097
David Hodgson @dchodge.bsky.social · 21/11/2024
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...)
dchodge.github.io
A general-purpose package to run parallel tempering mcmc with continuou discrete data
The `ptmc` package provides tools for fitting parallel tempering mcmc.
162
Reposted by David Hodgson
Adam Kucharski @adamjkucharski.bsky.social · 21/11/2024
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...
Photos of research group meetings and data collectionPrevious papers published by MRC LID PhD students - you can also search Kucharski/Lowe/Hodgson on Google Scholar
15937
David Hodgson @dchodge.bsky.social · 21/11/2024
Love it when it's one degree outside. Just one, on its own, doing the most, trying to keep me warm 🥹
040
David Hodgson @dchodge.bsky.social · 20/11/2024
just a reminder of how horrible the syntax of R metaprogramming is 🫥
030
Reposted by David Hodgson
Krutika Kuppalli, MD FIDSA @krutikakuppalli.bsky.social · 20/11/2024
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...
medrxiv.org
Epidemiological and Clinical Features of Mpox during the Clade Ib outbreak in South-Kivu, Democratic Republic of the Congo: a prospective cohort study
BACKGROUND Clade Ib, a new strain of the Clade I monkeypox virus, emerged in Eastern Democratic Republic of the Congo, sparking an international outbreak. Comprehensive studies are needed to assess it...
03114
Reposted by David Hodgson
Adam Kucharski @adamjkucharski.bsky.social · 18/11/2024
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...
lshtm.ac.uk
The perils of prediction: how untangling transmission drivers can improve epidemic response | LSHTM
Exploring research untangling the different factors driving epidemic transmission, from behaviour to immunity
814043
Reposted by David Hodgson
Judy Stone @drjudystone.bsky.social · 18/11/2024
Pathogens clinging to #microplastics can weather water treatment, pose health risk www.cidrap.umn.edu/foodborne-di...
cidrap.umn.edu
Report: Pathogens clinging to microplastics can weather water treatment, pose health risk
13414
Reposted by David Hodgson
Joshua J. Friedman @joshuajfriedman.com · 08/11/2024
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
blueskydirectory.com
All - Bluesky Directory
A curated collection of all things relating to the Blue Sky social media platform.
87556123018
David Hodgson @dchodge.bsky.social · 17/11/2024
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...
tandfonline.com
000
David Hodgson @dchodge.bsky.social · 17/11/2024
Looking forward, I'll be performing all simulation recovery using this crucially important dataset github.com/cran/dragracer
github.com
GitHub - cran/dragracer: :exclamation: This is a read-only mirror of the CRAN R package repository. dragracer — Data Sets for RuPaul's Drag Race
:exclamation: This is a read-only mirror of the CRAN R package repository. dragracer — Data Sets for RuPaul's Drag Race - GitHub - cran/dragracer: :exclamation: This is a read-only mirror of...
020
Reposted by David Hodgson
Jairo I. Fúnez-Flores @insurgentthought.bsky.social · 16/11/2024
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....
tandfonline.com
The Coloniality of Academic Freedom and the Palestine Exception
This article reflects on my experience of being suspended and reinstated. It demonstrates how administrators, including those at my institution, knowingly violate academic freedom and free speech. ...
22459179