Sebastian Funk
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sbfnk.bsky.social
Sebastian Funk
@sbfnk.bsky.social
1.4K followers 990 following 17 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
lshtm.bsky.social
👋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...
July 23, 2025 at 1:43 PM
Reposted by Sebastian Funk
seabbs.bsky.social
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/
July 15, 2025 at 10:39 AM
Reposted by Sebastian Funk
iddjobs.org
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
July 15, 2025 at 6:31 AM
Reposted by Sebastian Funk
anne-cori.bsky.social
Exciting HPRU PhD opportunities (home fees only) at LSHTM with co-supervision at Imperial and UKHSA: www.lshtm.ac.uk/study/fees-a...
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
www.lshtm.ac.uk
July 8, 2025 at 8:28 AM
sbfnk.bsky.social
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?
July 11, 2025 at 10:34 AM
sbfnk.bsky.social
Really enjoyed giving a talk at the @rki.de Colloquium in Berlin today. Slides are at epiforecasts.io/slides/rki_2...
epiforecasts.io
May 19, 2025 at 4:38 PM
Reposted by Sebastian Funk
ngozzi.bsky.social
Latest out in Epidemics: "Collaborative forecasting of influenza-like illness in Italy: The Influcast experience"

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

👇
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…
www.sciencedirect.com
February 20, 2025 at 9:51 PM
Reposted by Sebastian Funk
seabbs.bsky.social
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.
February 12, 2025 at 2:45 PM
Reposted by Sebastian Funk
seabbs.bsky.social
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...
iddjobs.org IDDjobs @iddjobs.org · Feb 14
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
February 14, 2025 at 10:12 AM
Reposted by Sebastian Funk
iddjobs.org
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
February 14, 2025 at 6:19 AM
Reposted by Sebastian Funk
iddjobs.org
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
February 14, 2025 at 6:14 AM
Reposted by Sebastian Funk
iddjobs.org
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
February 14, 2025 at 6:10 AM
Reposted by Sebastian Funk
iddjobs.org
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
February 14, 2025 at 6:08 AM
Reposted by Sebastian Funk
matthollanders.bsky.social
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 - Marginalisation
quantecol.com.au
February 4, 2025 at 2:53 AM
sbfnk.bsky.social
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.
adamjkucharski.bsky.social Adam Kucharski @adamjkucharski.bsky.social · Jan 29
11 PhD studentships now available in Health Analytics, Epidemic Modelling and Health Economics, jointly between LSHTM, Imperial and UKHSA, to start autumn 2025. Deadline 7 March: www.lshtm.ac.uk/study/fees-a...
PhD Studentships in Health Analytics and Modelling | LSHTM
www.lshtm.ac.uk
February 3, 2025 at 1:00 PM
sbfnk.bsky.social
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.
January 30, 2025 at 3:10 PM
Reposted by Sebastian Funk
anne-cori.bsky.social
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!
January 29, 2025 at 1:39 PM
Reposted by Sebastian Funk
rozeggo.bsky.social
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.
rozeggo.bsky.social Dr Roz Eggo @rozeggo.bsky.social · Jan 7
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!
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...
jobs.lshtm.ac.uk
January 29, 2025 at 1:45 PM
sbfnk.bsky.social
This is a great post, and every point in there applies to the assessment of infectious disease forecasts.
magnusar.bsky.social Magnus Ross @magnusar.bsky.social · Dec 3
I wrote a slightly controversially titled blog post about benchmarking for time series models. Often the benchmarks don't align with real world problems, which I think is slowing progress!

magnusross.github.io/posts/tsf_benchmarks/
Time series benchmarks are broken | Magnus Ross
magnusross.github.io
January 29, 2025 at 12:29 PM
sbfnk.bsky.social
🚀 We're hiring! Professor / Head of Department position at @lshtm.bsky.social
rozeggo.bsky.social Dr Roz Eggo @rozeggo.bsky.social · Jan 7
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!
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...
jobs.lshtm.ac.uk
January 13, 2025 at 3:58 PM
Reposted by Sebastian Funk
rozeggo.bsky.social
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!
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...
jobs.lshtm.ac.uk
January 7, 2025 at 4:53 PM
Reposted by Sebastian Funk
gmknght.bsky.social
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
December 11, 2024 at 3:03 PM
Reposted by Sebastian Funk
conjugateprior.org
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.
seabbs.bsky.social Sam Abbott @seabbs.bsky.social · Dec 6
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...
December 6, 2024 at 12:19 PM
Reposted by Sebastian Funk
seabbs.bsky.social
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...
December 6, 2024 at 11:08 AM
Reposted by Sebastian Funk
annerimoin.bsky.social
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...
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.
www.nbcnews.com
December 6, 2024 at 4:13 AM