Brendan J. Kelly

Modelling Like an Experimentalist Dahlin et al. (2024) apply experimental thinking to a model of mosquito-borne disease transmissions.

"Validate With Simulated Truth: A first habit is to test whether an analytical pipeline can recover known conditions."

Very good advice below. So much COVID nonsense (e.g. 'immunological dark matter') basically came down to a non-identifiable model that hadn't been properly tested.

Pseudomonas aeruginosa has big slug energy. #IDsky #MicroSky

Effectiveness of Nirmatrelvir/Ritonavir or Molnupiravir Use in Immunocompromised Patients on B-Cell–Depleting Therapy With COVID-19: A Target Trial Emulation Study This target trial emulation study assessed nirmatrelvir/ritonavir and molnupiravir effectiveness in COVID-19 patients receiving B-cell–depleting therapy. N

A study of COVID therapeutics in immunocompromised individuals on B-cell depleting therapy!!!

Nirmatrelvir/ritonavir significantly more effective than no rx (HR 0.56) molnupiravir w non significant trend to improved outcomes (HR also 0.56)… #IDSky #covid

academic.oup.com/cid/advance-...

On an Arctic archipelago, frozen soil may preserve a hidden history of viruses Scientists are hunting for ancient RNA in Svalbard’s permafrost, hoping to shed light on the evolution of viral diseases

I am fascinated by how viruses evolve - and not just since #SARSCoV2 has shown us at the global stage how consequential virus evolution can be for us.
In my new story in @science.org I got to explore how researchers are probing deeper into the past with old RNA virus genome.
So a 🧪 thread…

💻Join online! 🎧
Süßmilch Lecture at the Max Planck Institute for Demographic Research (MPIDR)
Putting Science Before #Statistics
🗣️Richard McElreath 🐈‍⬛ MPI-EVA Leipzig
📅Oct 21, 2025
🕒3 pm CEST
✏️Sign up now:
https://ow.ly/uxfc50Xb5Yx

Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈

What could possibly go wrong? #IDSky

ELLIS PhD Program: Call for Applications 2025 The ELLIS mission is to create a diverse European network that promotes research excellence and advances breakthroughs in AI, as well as a pan-European PhD program to educate the next generation of AI...

I'm looking for a doctoral student with Bayesian background to work on Bayesian workflow and cross-validation (see my publication list users.aalto.fi/~ave/publica... for my recent work) at Aalto University.

Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...

Fantastic discussion of the BALANCE trial -- and randomized trial preparation / design in general. Also, great to hear Communicable and Breakpoints teaming up! #IDSky

"It turns out boredom is the Cadillac of feelings."

library(tidyverse) mtcars |> head(8) |> rownames_to_column("name") |> ggplot(aes(x = drat, y = name, fill = name)) + geom_col() + theme(panel.widths = unit(50, "mm"), panel.heights = unit(50, "mm"))

The new ggplot2 4.0.0 now supports absolute plot dimensions 🤩

#rstats #dataviz #phd

#IDsky

Happy International Microorganism Day! 🎉

Today, we are celebrating the tiny powerhouses that have a massive impact on our world. From the bacteria in our gut to the fungi that give us antibiotics, these incredible organisms are essential to life.

Let's make some noise for the microscopic!

Typhus, a disease once nearly eradicated in the U.S., is on the rise in Texas Texas is seeing an explosion of cases of typhus, a disease that – if untreated – can be fatal. Typhus was almost eradicated from the United States, but now it's making a comeback.

Typhus, a disease once nearly eradicated in the U.S., is on the rise in Texas

"76-year-old Clark contracted #typhus from clearing weeds from her garden"
🦠

flip.it/Zzrht7

Learning ecosystem-scale dynamics from microbiome data with MDSINE2 - Nature Microbiology This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice.

#Newresearch

This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice.

#MicroSky

www.nature.com/articles/s41...

David Rose memorial poster

Remembering David Rose today. www.bbc.com/news/article...

Image showing the table of content of issue 36 in 2025: Rapid communication Detection and characterisation of Xpert CT/NG assay Neisseria gonorrhoeae diagnostic escape mutants, England, June 2025 An interseasonal outbreak of influenza A(H1N1)pdm09 related to a music festival, Denmark, August 2025 Research Progress towards HIV transmission elimination targets: model-based estimation of incidence and the extent of undiagnosed infection, Scotland, 1981 to 2022 Repeated cross-sectional surveys show a decreasing trend in Borrelia burgdorferi sensu lato seroprevalence over a 50-year period, Finland, 1966 to 2017

This week's rapid communications describe

➡️A strain of Neisseria gonorrhoeae producing false negative results on Xpert CT/NG assay in England

🔎An atypical sixfold rise in #influenza A(H1N1)pdm09 cases in Denmark during summer

Full issue here 👉 bit.ly/eus2036

#EpiSky #IDSky #MedSky #STISky 🛟🦠🧫⚕️

ASM Young Ambassadors at ASM Microbe 2025

Attention early-career scientists! Apply for ASM’s Young Ambassador Program to gain leadership experience, build your network and inspire the next generation of microbiologists. Applications are due Nov. 1. asm.social/2Ah

output from a GAM in the linked essay

Simon Wood, the GOAT of generalized additive models & creator of the mgcv #rstats package, has an Annual Review of Statistics essay on GAMs, available open access #statssky #mlsky

www.annualreviews.org/content/jour...

Outbreak of Neisseria meningitidis Conjunctivitis ... This report describes 41 cases of Neisseria meningitidis conjunctivitis among military trainees living in a communal setting in Texas.

More on the outbreak of Neisseria meningitidis conjunctivitis among military trainees, from the MMWR… #IDSky

www.cdc.gov/mmwr/volumes...

Interesting that an unencapsulated meningococcal strain was responsible. Outbreaks of pneumococcal conjunctivitis have also involved unencapsulated strains (Baumgartner. N Engl J Med, 2003; Crum. Clin Infect Dis, 2004).

As national medical, scientific, public health and patient organizations, we call for the resignation of HHS Secretary Robert F. Kennedy Jr. to ensure the health of the American people.

Our statement: https://bit.ly/45LeJHi

Full or Associate Professor in Infectious Disease Modeling APPLICATION INSTRUCTIONS: CURRENT PENN STATE EMPLOYEE (faculty, staff, technical service, or student), please login to Workday to complete the internal application process. Please do not apply here, a...

The Center for Infectious Disease Dynamics (CIDD) at Penn State is hiring for a senior-level position in Infectious Disease Modeling. Come join our dynamic group of disease researchers!

Feel free to message me for details

psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...

In my dept today we discussed deriving estimators from causal models. This can be opaque, but as a simple e.g. instrumental variable Z for estimating X on Y.

Z –a–> X –b–> Y, and X <– U –> Y, where U is unmeasured, a and b are path coefs. We want to know b. U prevents direct approach. >>

I had a blast at #useR2025.

Here are my slides on `tinyplot`. grantmcdermott.com/tinyplot/vig...

(Rendering of the title slide is a bit off on mobile. I'll fix when when I get sec.)

Two major points on influenza-associated acute necrotizing encephalopathy

- High mortality (27%)
- Most affected children were unvaccinated & did not have major comorbid conditions

#PedSky #IDSky

Across 42 countries, the proportion of CD4<200 at ART initiation (among those with measurement) still >= 30%.

So much to do still to diagnose and intervene early, made more difficult in limited funding climate…

#IDSky

A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)

Quantifying the varying harvest of fermentation products from the human gut microbiota Fermentation products are the most abundant gut microbial metabolites absorbed by the host, with important dose-dependent consequences for health. In this study, we present a systems-level analysis in...

Brilliant piece of work from Markus Arnoldini and Jonas Cremer into how much your gut bacteria really do for you!

www.cell.com/cell/fulltex...

A brilliant article by @rmcelreath.bsky.social . I had not heard of ‘bread scientists’ before but see them everywhere. Related to the strong case for teaching reliable, rigorous methods, I see as a major problem the selection of “optimistic” stat methods. #StatsSky #EpiSky