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Sebastian Funk

@sbfnk.bsky.social
1.5K followers 991 following 27 posts

Professor of Infectious Disease Dynamics at @lshtm.bsky.social. Developing methods for making sense of outbreak data. Outside of work trying to make sense of the rest of the world.

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Reposted by Sebastian Funk
Sam Abbott @seabbs.bsky.social · 28/09/2026
A few years ago we (Kelly Charniga @sangwoopark.bsky.social et al.) did some thinking on how we should estimate and report epidemiological delay distributions (i.e incubation periods etc. etc.). journals.plos.org/ploscompbiol...
journals.plos.org
Best practices for estimating and reporting epidemiological delay distributions of infectious diseases
Epidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strat...
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Eloise Newman @eloisenewman.bsky.social · 21/09/2026
Fantastic to have attended “Modelling Epidemics with Julia” at the LSHTM run by Simon Frost, Sandra Montes and @seabbs.bsky.social My first formal foray into #julia and gosh! How powerful it is for modelling. Exciting to see the toolkit available for modelling outbreaks! Will be using in the PhD!
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Michael Marks @drmichaelmarks.bsky.social · 03/09/2026
Post-doc modelling post @lshtm.bsky.social Working on UK STI modelling & collab with @ukhsa.bsky.social Deadline 17th Sept. @tah-sci.com @sbfnk.bsky.social @yhgrad.bsky.social @anne-cori.bsky.social @lizfearon.bsky.social @petedodd24.bsky.social @drlouisedyson.bsky.social @ollycm.bsky.social
jobs.lshtm.ac.uk
Job Opportunity at LSHTM: Research Fellow
The London School of Hygiene & Tropical Medicine (LSHTM) is one of the world’s leading public health universities. Our mission is to improve health and health equity in the UK and worldwide; working i...
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Reposted by Sebastian Funk
Sam Abbott @seabbs.bsky.social · 22/05/2026
Estimating the current size of the 2026 DRC Bundibugyo virus outbreak: a joint Bayesian re-analysis of the McCabe et al. report w/ @kathsherratt.bsky.social Sam Brand and @sbfnk.bsky.social
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Sebastian Funk @sbfnk.bsky.social · 17/04/2026
🎓 One last PhD studentship on offer on health analytics and modelling, jointly between @hpruham.bsky.social and @hprurespinf.bsky.social. Real-time use of data from household studies to inform pandemic and epidemic preparedness, with Anne Cori, @seabbs.bsky.social and Chris Overton. Link ↓
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Sebastian Funk @sbfnk.bsky.social · 27/03/2026
Every week ~2,000 new preprints appear on medRxiv and bioRxiv. Here's a tool that matches them to journals: given a journal, it shows which recent preprints fit its scope. Given a preprint, it predicts where it'll end up. Feedback welcome! preprints.epiforecasts.io
preprints.epiforecasts.io
Preprint Match
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Sebastian Funk @sbfnk.bsky.social · 26/03/2026
Really enjoyed this thought-provoking workshop this week at @cmmid-lshtm.bsky.social @lshtm.bsky.social on evaluation & responsibility in infectious disease modelling. Brilliantly organised and led by @kathsherratt.bsky.social, with Erica Thompson. Great discussions on both practice and training.
Word cloud from the workshop introduction. Positive qualities like transparent, open, reproducible, honest in blue and green at the top; negative ones like biased, overconfident, closed, opaque in orange and red at the bottom.
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Sebastian Funk @sbfnk.bsky.social · 24/03/2026
Really great day and exciting to see the range of research happening across @hpruham.bsky.social. Thanks to @ukhsa.bsky.social for hosting and everyone who presented!
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Sebastian Funk @sbfnk.bsky.social · 19/02/2026
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.
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IDDjobs @iddjobs.org · 02/01/2026
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: iddjobs.org/jobs/2440
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Sebastian Funk @sbfnk.bsky.social · 17/12/2025
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...
lshtm.ac.uk
PhD Studentships in Health Analytics and Modelling | LSHTM
The London School of Hygiene & Tropical Medicine (LSHTM), Imperial College London and the UK Health Security Agency (UKHSA) are pleased to invite applications for two PhD studentships in real-time
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CMMID @cmmid-lshtm.bsky.social · 04/11/2025
💉 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...
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London School of Hygiene & Tropical Medicine @lshtm.bsky.social · 23/07/2025
👋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...
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Sam Abbott @seabbs.bsky.social · 15/07/2025
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/
nfidd.github.io
Nowcasting and forecasting infectious disease dynamics - SISMID – NFIDD SISMID
Nowcasting and forecasting infectious disease dynamics - SISMID
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IDDjobs @iddjobs.org · 15/07/2025
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: iddjobs.org/jobs/2336
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Anne Cori @anne-cori.bsky.social · 08/07/2025
Exciting HPRU PhD opportunities (home fees only) at LSHTM with co-supervision at Imperial and UKHSA: www.lshtm.ac.uk/study/fees-a...
lshtm.ac.uk
PhD studentships in real-time infectious disease modelling | LSHTM
The London School of Hygiene & Tropical Medicine (LSHTM), Imperial College London and the UK Health Security Agency (UKHSA) are pleased to invite applications for two PhD studentships in real-time
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Sebastian Funk @sbfnk.bsky.social · 11/07/2025
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?
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Sebastian Funk @sbfnk.bsky.social · 19/05/2025
Really enjoyed giving a talk at the @rki.de Colloquium in Berlin today. Slides are at epiforecasts.io/slides/rki_2...
epiforecasts.io
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Nicolò Gozzi @ngozzi.bsky.social · 20/02/2025
Latest out in Epidemics: "Collaborative forecasting of influenza-like illness in Italy: The Influcast experience" www.sciencedirect.com/science/arti... 👇
sciencedirect.com
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…
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Sam Abbott @seabbs.bsky.social · 12/02/2025
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.
epidist.epinowcast.org
Changelog
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Sam Abbott @seabbs.bsky.social · 14/02/2025
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...
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Reposted by Sebastian Funk
IDDjobs @iddjobs.org · 14/02/2025
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: iddjobs.org/jobs/2264
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IDDjobs @iddjobs.org · 14/02/2025
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: iddjobs.org/jobs/2263
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IDDjobs @iddjobs.org · 14/02/2025
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: iddjobs.org/jobs/2261
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IDDjobs @iddjobs.org · 14/02/2025
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: iddjobs.org/jobs/2262
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Matthijs Hollanders @matthollanders.bsky.social · 04/02/2025
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...
quantecol.com.au
Quantecol - Marginalisation
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Sebastian Funk @sbfnk.bsky.social · 03/02/2025
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.
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Sebastian Funk @sbfnk.bsky.social · 30/01/2025
quite. h/t @hertzpodcast.bsky.social source doi.org/10.1093/etoj...
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.
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Reposted by Sebastian Funk
Anne Cori @anne-cori.bsky.social · 29/01/2025
Amazing opportunity: a few PhD positions in Health Analytics, Epidemic Modelling and Health Economics available with myself and colleagues from @mrc-outbreak.bsky.social, @ccmid.bsky.social and @ukhsa.bsky.social. Please apply/circulate widely!
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Dr Roz Eggo @rozeggo.bsky.social · 29/01/2025
Senior post at LSHTM closes in 2 days (31st Jan). Do apply if you want to lead/join a department focussed on infectious disease epi and dynamics. Unrelated: the UK doesn’t have executive orders.
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Sebastian Funk @sbfnk.bsky.social · 29/01/2025
This is a great post, and every point in there applies to the assessment of infectious disease forecasts.
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Sebastian Funk @sbfnk.bsky.social · 13/01/2025
🚀 We're hiring! Professor / Head of Department position at @lshtm.bsky.social
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Dr Roz Eggo @rozeggo.bsky.social · 07/01/2025
Open Recruitment of a Full Professor and Head of the Department of Infectious Disease Epidemiology & Dynamics: jobs.lshtm.ac.uk/vacancy.aspx... Good research culture, friendly colleagues, inspiring public health leaders, great connections across epi & PH, & very dedicated students. Join!
jobs.lshtm.ac.uk
Job Opportunity at LSHTM: Professor (and Head of Department)
The London School of Hygiene & Tropical Medicine (LSHTM) is one of the world’s leading public health universities. Our mission is to improve health and health equity in the UK and worldwide; working i...
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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
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Will Lowe @conjugateprior.org · 06/12/2024
Just a side point really, but I think it's time for this concept of "output (in the traditional academic sense)" to crawl back into the publisher's boardroom where it was born and expire.
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Sam Abbott @seabbs.bsky.social · 06/12/2024
Struck today looking at the {EpiNow2} contributors page how much work it takes to maintain a package over the long term. Below link is filtered to just the maintenance period in which there has been no "output" (in the traditional academic sense). github.com/epiforecasts...
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Anne Rimoin @annerimoin.bsky.social · 06/12/2024
My perspective on the unknown pathogen currently causing a severe respiratory outbreak in #DRCongo in this @NBCNews article: A lot we don’t yet know. Good news is that there are experienced local teams on the ground investigating. Lab analyses are critical next step. www.nbcnews.com/health/healt...
nbcnews.com
Mysterious illness in Congo has killed dozens of people, health authorities report
An unidentified disease has killed 79 people and sickened 376, according to the Democratic Republic of Congo's Ministry of Public Health, Hygiene and Social Security.
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Joshua Weitz @joshuasweitz.bsky.social · 27/11/2024
This framing misses the bigger point. As I describe in my book (bit.ly/asymptomatic...) Bhattacharya co-led a flawed April 2020 study that wrongly concluded (wrong at the time) that COVID-19 was far less a threat given a misestimation of evidence of prior infections. www.bbc.com/news/article...
bbc.com
Jay Bhattacharya: Trump picks Covid lockdown sceptic to lead top health agency
The physician and economist was the face of the Great Barrington Declaration, which opposed widespread lockdowns.
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Dr Roz Eggo @rozeggo.bsky.social · 26/11/2024
Position with @mert0248.bsky.social and me in modelling the potential impact of next generation flu vaccines: iddjobs.org/jobs/modelli...
iddjobs.org
IDDjobs — Modelling the potential impact and value of developing a new generation of influenza vaccines, and their potential utility during a pandemic. — LSHTM
Find infectious disease dynamics modelling jobs, studentships, and fellowships.
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Sebastian Funk @sbfnk.bsky.social · 22/11/2024
If there are any users of the socialmixr R package for estimating contact matrices here: we're planning some substantial changes to the user interface and would love to hear your thoughts/views. Please feel free to comment at github.com/epiforecasts...
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Jonathan Bartlett @jonathan-bartlett.bsky.social · 21/11/2024
10th Dec - join us in person or online for a talk by Sofia Villar from MRC BSU on 'Response-adaptive randomization in clinical trials: myth vs reality', organised by LSHTM's Data and Statistical Science for Health Centre. More details here: www.lshtm.ac.uk/newsevents/e...
lshtm.ac.uk
Response-adaptive randomization in clinical trials: myth vs reality | LSHTM
Exploring the academic debates around recent developments within response-adaptive randomization (RAR) including its increased use in machine learning.
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Sebastian Funk @sbfnk.bsky.social · 19/11/2024
I need a starter pack of starter packs.
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