Sebastian Funk

Great talk on composable infectious disease modelling. Making real-time outbreak modelling more principled and flexible has been a long-standing challenge, and Sam has been leading the charge on solving it. With a growing group of people keen on this it feels like we're finally getting somewhere.

PhD position (London, UK)
Real-time modelling of infectious disease outbreaks.
with @sbfnk.bsky.social @anne-cori.bsky.social @seabbs.bsky.social
at @epiforecasts.io @cmmid-lshtm.bsky.social
More details: http://iddjobs.org/jobs/2440

and Chris Overton (UKHSA).

Joint supervision between @cmmid-lshtm.bsky.social (w/ @seabbs.bsky.social), @imperialcollegeldn.bsky.social dn.bsky.social (w/ @anne-cori.bsky.social), and @ukhsa.bsky.social (Edwin van Leeuwen).

Looking for people excited about infectious disease epidemiology who enjoy programming and want to develop their statistical modelling skills. DMs open if you have questions.

Two more fully funded PhDs in real-time infectious disease modelling & forecasting — developing methods for operational use by @ukhsa.bsky.social and others in outbreak response. UK home students, starting April or September 2026.

www.lshtm.ac.uk/study/fees-a...

💉 Our annual lecture will be given by Prof Caroline Trotter, who will explore work estimating the #PublicHealth impact of vaccination of Gavi & discuss its implications for #vaccine policy

🗓️ Thursday 27 November, 17:30 GMT
📍 LSHTM | Online

Details ⬇️
www.lshtm.ac.uk/newsevents/e...

👋Don't miss LSHTM research funding opportunities!

We have 2 new PhD #studentships for home fee students as part of @nihr.bsky.social Health Protection Research Units for #Vaccines & Immunisation, & #InfectiousDisease modelling.

Find out more & apply 👇
www.lshtm.ac.uk/study/fees-a...

These should be pretty great I think!

Want some more background on the kind of fun methods these will build off? Open source course here: nfidd.github.io/sismid/

2 PhD positions (London, UK)
In real-time infectious disease modelling
with @‪@sbfnk.bsky.social‬ @‪@anne-cori.bsky.social‬ @‪@seabbs.bsky.social‬
at @‪@lshtm.bsky.social‬ @‪@imperialcollegeldn.bsky.social‬ @‪@ukhsa.bsky.social‬
More details: http://iddjobs.org/jobs/2336

Exciting HPRU PhD opportunities (home fees only) at LSHTM with co-supervision at Imperial and UKHSA: www.lshtm.ac.uk/study/fees-a...

So disappointing to still see papers in big publisher journals with data/code links that don't work (e.g. private github repos). If editors and reviewers can't even be bothered to do a minimal check that the linked resource exists, what does that imply for the integrity of the whole review process?

All I said is that they have health benefits. But I completely agree that there other routes to achieving these (education on safe knife use / assembly from reusable components that could be used for other things) which are preferable. doi.org/10.1016/j.aj...

Really enjoyed giving a talk at the @rki.de Colloquium in Berlin today. Slides are at epiforecasts.io/slides/rki_2...

Collaborative forecasting of influenza-like illness in Italy: The Influcast experience Collaborative hubs that integrate multiple teams to generate ensemble projections and forecasts for shared targets are now regarded as state-of-the-ar…

Latest out in Epidemics: "Collaborative forecasting of influenza-like illness in Italy: The Influcast experience"

www.sciencedirect.com/science/arti...

👇

The new epidist release just dropped which includes support for the marginal model as well as lots of other goodies

epidist.epinowcast.org/news/index.h...

TLDRP: its 20-lots faster depending on number of stratifications in the data and not approximate.

I was speaking about the epinowcast package, ecosystem, and community with a little bit of a pitch for modelling in Julia at the end.

If any of this work takes your interest this PhD on delay estimation may interest you.

bsky.app/profile/iddj...

PhD position (London, UK)
Machine Learning for infectious disease forecasting during epidemics and pandemics
with @sbfnk.bsky.social Daniela de Angelis
at @cmmid-lshtm.bsky.social @lshtm.bsky.social @epiforecasts.io
More details: http://iddjobs.org/jobs/2264

PhD position (London, UK)
Improving Estimation of Reproduction Numbers in Dynamic Outbreak Contexts
with @anne-cori.bsky.social @sbfnk.bsky.social Edwin van Leeuwen
at @imperial-jameel.bsky.social
More details: http://iddjobs.org/jobs/2263

PhD position (London, UK)
Improving Estimation and Analysis of Epidemiological Delays for Infectious Disease Outbreaks
with @sbfnk.bsky.social @anne-cori.bsky.social @seabbs.bsky.social
at @cmmid-lshtm.bsky.social @lshtm.bsky.social...
More details: http://iddjobs.org/jobs/2261

PhD position (London, UK)
Improving Infectious Disease Forecasts and Forecast Evaluation
with @sbfnk.bsky.social @anne-cori.bsky.social Edwin van Leeuwen
at @cmmid-lshtm.bsky.social @lshtm.bsky.social @epiforecasts.io
More details: http://iddjobs.org/jobs/2262

Quantecol - Marginalisation

New blog post! I show how to marginalise discrete variables from Bayesian ecological models in Stan and how to recover their posterior distributions after estimation. I cover occupancy and N-mixture models using multiple parameterisations and model types. quantecol.com.au/blog/margina...

To apply go to www.lshtm.ac.uk/study/fees-a... and in the meantime get in touch with any questions.

If generally interested in a PhD in this area have a look at all projects - they're great selection of topics to be taken on by a cohort of students interested in improving pandemic preparedness. The full list is at www.lshtm.ac.uk/media/87071

These are all in collaboration with Imperial @anne-cori.bsky.social and UKHSA so give lots of opportunities for collaboration and applications to case studies of immediate public health relevance.

Improving Estimation of Reproduction Numbers in Dynamic Outbreak Contexts

The final project is to improve real-time estimation of reproduction numbers through better understanding of transmission processes and the drivers that shape them. These estimates can directly inform required control efforts but also be used to monitor changes in transmission.

Improving Infectious Disease Forecasts and Forecast Evaluation

Another project aims to improve real-time forecasts of infectious disease outbreaks, involving ensemble methods and a variety of models and testing different data sets that can inform them. Crucially, we need to validate predictions to improve them so evaluation is a big part of this project.

Improving Estimation and Analysis of Epidemiological Delays for Infectious Disease Outbreaks

On project is to improve our ability to characterise things like reporting delays, incubation periods, generation times etc. in real time, i.e. during ongoing outbreaks. These can inform control options such as contact tracing but this requires fully understanding the variation in observed delays.

It's rare to have so many PhD studentships open at the same time that are fully funded at the project level - do apply if any of these strike your interest (unfortunately, UK home fee eligible candidates only). I'll describe the 3 projects that involve me / @epiforecasts.io in a bit more detail.

Peer review is an essential, uneven, and flawed process at the heart of scientific publishing practices. Whether a study has been published in a journal with reputable peer review practices is often one of the first questions other scientists, journalists, or policy makers have when discussing a new study. However, a few minutes of online searching will turn up countless items on shortcomings in the process, with examples of quackery and outrageous, humorous, fraudulent, or just unreliable research articles that passed review and got published in the scientific literature.

quite.

h/t @hertzpodcast.bsky.social
source doi.org/10.1093/etoj...