David Hodgson
@dchodge.bsky.social
Researcher at Charité. Interested in mathematically modelling immunity.
🧘🍰🎧🖥️🏃🧪🏳️🌈
seroanalytics.org
davidhodgson.me
🧘🍰🎧🖥️🏃🧪🏳️🌈
seroanalytics.org
davidhodgson.me
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
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
October 26, 2025 at 6:52 PM
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
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
October 12, 2025 at 2:44 PM
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...
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
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
seroanalytics.org
October 9, 2025 at 7:34 AM
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
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.
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
October 5, 2025 at 7:25 PM
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.
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.
🚀 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-...
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-...
Dynamic Mixture Model Analysis
dchodge.github.io
September 30, 2025 at 12:35 PM
🚀 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-...
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
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
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
September 27, 2025 at 6:18 PM
🔬 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
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
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
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...
seroanalytics.org
September 23, 2025 at 12:36 PM
🚨 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
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
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
Interactive Bayesian Epidemic Modelling
widget-bayesian-sir.davidhodgson.me
September 19, 2025 at 4:53 PM
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
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...
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
September 17, 2025 at 8:37 AM
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...
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
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
Example 2: SEIR change-point attack rate
dchodge.github.io
September 15, 2025 at 2:45 PM
🚨 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
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
Reposted by David Hodgson
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/
And here's the accompanying {serojump} R package: seroanalytics.org/serojump/
April 9, 2025 at 8:30 AM
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/
And here's the accompanying {serojump} R package: seroanalytics.org/serojump/
Reposted by David Hodgson
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/
Our new paper, spearheaded by @dchodge.bsky.social had a look.... 1/
March 31, 2025 at 2:05 PM
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/
Our new paper, spearheaded by @dchodge.bsky.social had a look.... 1/
Reposted by David Hodgson
@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
The app wraps the SeroSim R package by @jameshay.bsky.social for simulating serosurvey data:
serosim.seroanalytics.org
SeroSim
Web interface for serosurvey data simulation
serosim.seroanalytics.org
March 6, 2025 at 10:39 AM
@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
The app wraps the SeroSim R package by @jameshay.bsky.social for simulating serosurvey data:
serosim.seroanalytics.org
Reposted by David Hodgson
Researcher: "We let the data speak for itself."
Earlier that day:
Earlier that day:
January 2, 2025 at 3:31 PM
Researcher: "We let the data speak for itself."
Earlier that day:
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.
www.npr.org
December 26, 2024 at 6:19 PM
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!!
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!!
A general-purpose package to run reversible-jump mcmc
What the package does (one paragraph).
cmmid.github.io
December 22, 2024 at 9:44 PM
🎅🌟 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!!
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!!
Reposted by David Hodgson
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
https://www.economist.com/science-and-technology/2024/12/18/academic-writing-is-getting-harder-to-read-the-humanities-most-of-all
December 19, 2024 at 6:10 AM
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
https://www.economist.com/science-and-technology/2024/12/18/academic-writing-is-getting-harder-to-read-the-humanities-most-of-all
Reposted by David Hodgson
Seated podcast, vs treadmill podcast, vs book learning. Also they slapped an EEG on the subjects.
#MedEd
pmc.ncbi.nlm.nih.gov/articles/PMC...
#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
December 15, 2024 at 3:55 AM
Seated podcast, vs treadmill podcast, vs book learning. Also they slapped an EEG on the subjects.
#MedEd
pmc.ncbi.nlm.nih.gov/articles/PMC...
#MedEd
pmc.ncbi.nlm.nih.gov/articles/PMC...
Reposted by David Hodgson
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!
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!
December 11, 2024 at 3:03 PM
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!
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!
Reposted by David Hodgson
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.
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.
www.statnews.com
December 11, 2024 at 11:53 PM
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.
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...
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...
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...
mrc-lid.lshtm.ac.uk
December 12, 2024 at 8:11 AM
🚨 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...
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...
Reposted by David Hodgson
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...
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...
December 9, 2024 at 8:00 AM
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...
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...
Reposted by David Hodgson
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🧵:
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
www.nature.com
December 7, 2024 at 2:41 PM
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🧵:
www.nature.com/articles/s41...
few additional points for those who want a bit more detail🧵:
Reposted by David Hodgson
Two stages of writing:
1) This shouldn't take too long
2) Oh no
1) This shouldn't take too long
2) Oh no
December 4, 2024 at 7:36 PM
Two stages of writing:
1) This shouldn't take too long
2) Oh no
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
authors.elsevier.com
December 5, 2024 at 7:59 AM
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