Brendan J. Kelly
@bjklab.bsky.social
š¤ 2523
š„ 1372
š 28
infectious diseases / epidemiology / microbial ecology
https://motionlab.site
Philadelphia, PA, USA
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Brendan J. Kelly
MC Stan
4 days ago
Three weeks time to submit contributed talk abstract to StanCon 2026! You can also submit a poster abstract early, if you need to make early travel plans. There will be travel and accommodation support for students, too! More information about submitting at
www.stancon2026.org/abstracts/
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Brendan J. Kelly
The New York Review of Books
10 days ago
Fintan OāToole
@fotoole.bsky.social
on the murders of RenƩe Good and Alex Pretti
https://go.nybooks.com/4bmNB4F
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The Crime of Witness | Fintan OāToole
RenĆ©e Good and Alex Pretti were murdered for daring to interfere with the Trump administrationās efforts to normalize abductions and state violence.
https://go.nybooks.com/4bmNB4F
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Watched
#Saboteur
last night --
#Hitchcock
captured the internal battle between democracy and fascism in 1942. A reminder that American fascists were fighting against democracy even during WW2:
youtu.be/-rtlkILRmEQ
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Alfred Hitchcock's 1942 Saboteur (Scene)
YouTube video by Molarkie
https://youtu.be/-rtlkILRmEQ?si=FFjy6mgAfk-x_I87
13 days ago
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Brendan J. Kelly
Leah Litman
15 days ago
from what I can see, the video shows a beating followed by an execution.
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Brendan J. Kelly
MƄns Magnusson
18 days ago
StanCon 2026 tutorial and workshop deadlines in one week:
discourse.mc-stan.org/t/stancon-20...
@mc-stan.org
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StanCon 2026 Deadline for tutorial and workshop in one week
Hi everyone, The submission deadline for contributing tutorials and workshops is one week from now, on the 28th of January. Tutorial Tutorials provide hands-on learning experiences to help attendee...
https://discourse.mc-stan.org/t/stancon-2026-deadline-for-tutorial-and-workshop-in-one-week/40855
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Brendan J. Kelly
Internet Archive
29 days ago
When works become public domain, anyone can reimagine and reuse them. š The Little Engine That Could can be freely reinterpretedālike this video marrying pages of the 1930 book to a Librivox audio recording. š+š¤ Learn more ⤵ļø
blog.archive.org/2026/01/01/w...
#PublicDomainDay
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Brendan J. Kelly
Richard McElreath šāā¬
about 1 month ago
And we're live, Lecture A1 is online. Introduction to Bayesian workflow, generative models, estimands, estimators, estimates, error checking, beginnings of probability theory and Bayesian updating.
www.youtube.com/watch?v=ztbY...
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Brendan J. Kelly
UW Infectious Disease Fellowship Program
about 1 month ago
Great overview of current knowledge. Many patient factors impact the management of people w/ presumed infectious diarrhea. Therefore, multispecialty engagement optimizes access, linkage to care, and judicious use of diagnostics and therapeuticsā¦
academic.oup.com/cid/article/...
#IDSky
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State-of-the-Art Review: Infectious Diarrhea
This State of the Art Review describes a multidisciplinary approach to the care of people with diarrhea, considering both infectious and non-infectious eti
https://academic.oup.com/cid/article/81/5/e250/8403850
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Brendan J. Kelly
Richard McElreath šāā¬
about 1 month ago
Including the old black cat adoptions survival analysis example as a case study in the forthcoming Bayesian Workflow book. This is presented as a whole incremental workflow with simulation, validation, and model comparison. Just now went through code and extra-commented and cleaned. Getting close!
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Brendan J. Kelly
Aki Vehtari
about 2 months ago
We're doing the final sprint, and I think we're able to send the PDF of the forthcoming Bayesian Workflow book to the publisher in the next two weeks (500+ pages), which would mean it would be published some time next year
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Brendan J. Kelly
Carl Zimmer
about 2 months ago
American food safety could be headed for a breakdown. Story by
@sarah-todd.bsky.social
www.statnews.com/2025/12/22/a...
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American food safety could be headed for a breakdown
More Americans will be exposed to foodborne illnessĀ as a result of this year's funding cuts, food safety experts predict
https://www.statnews.com/2025/12/22/american-food-safety-funding-cuts-foodnet/
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Brendan J. Kelly
Andrew Heiss
about 2 months ago
Grading and googling hallucinated citations, as one does nowadays, and now that LLMs have been around for a while, I've discovered new horrors: hallucinated journals are now appearing in Google Scholar with dozens of citations bc so many people are citing these fake things
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Richard McElreath šāā¬
2 months ago
I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students. I will record lectures & all will be found at this link:
github.com/rmcelreath/s...
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Brendan J. Kelly
NEJM.org
2 months ago
Twelve former commissioners of the FDA express concern that the agencyās recent moves will undermine a regulatory model designed to ensure vaccine safety, effectiveness, and availability. Read the full Perspective:
nej.md/48Ova76
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Brendan J. Kelly
Adam Kucharski
3 months ago
"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.
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Modelling Like an Experimentalist
Dahlin etĀ al. (2024) apply experimental thinking to a model of mosquito-borne disease transmissions.
https://onlinelibrary.wiley.com/doi/10.1111/ele.70251
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Pseudomonas aeruginosa has big slug energy.
#IDsky
#MicroSky
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3 months ago
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Brendan J. Kelly
UW Infectious Disease Fellowship Program
4 months ago
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)ā¦
#IDSky
#covid
academic.oup.com/cid/advance-...
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Effectiveness of Nirmatrelvir/Ritonavir or Molnupiravir Use in Immunocompromised Patients on B-CellāDepleting 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-cellādepleting therapy. N
https://academic.oup.com/cid/advance-article-abstract/doi/10.1093/cid/ciaf521/8300646
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Brendan J. Kelly
Kai Kupferschmidt
4 months ago
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 š§Ŗ threadā¦
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On an Arctic archipelago, frozen soil may preserve a hidden history of viruses
Scientists are hunting for ancient RNA in Svalbardās permafrost, hoping to shed light on the evolution of viral diseases
https://www.science.org/content/article/arctic-archipelago-frozen-soil-may-preserve-hidden-history-viruses
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Brendan J. Kelly
Max Planck Institute for Demographic Research (MPIDR)
4 months ago
š»Join online! š§ SüĆmilch Lecture at the Max Planck Institute for Demographic Research (MPIDR) Putting Science Before #Statistics š£ļø
Richard McElreath šāā¬
MPI-EVA Leipzig
š Oct 21, 2025 š3 pm CEST āļøSign up now:
https://ow.ly/uxfc50Xb5Yx
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Brendan J. Kelly
Rachel M. Wheatley
4 months ago
Is a healthy microbiome one that is rich in phages? š¦ 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 š
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What could possibly go wrong?
#IDSky
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4 months ago
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Brendan J. Kelly
Aki Vehtari
4 months ago
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...
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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...
https://ellis.eu/news/ellis-phd-program-call-for-applications-2025
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Fantastic discussion of the BALANCE trial -- and randomized trial preparation / design in general. Also, great to hear Communicable and Breakpoints teaming up!
#IDSky
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4 months ago
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"It turns out boredom is the Cadillac of feelings."
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4 months ago
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Brendan J. Kelly
Jan Broder Engler
5 months ago
The new ggplot2 4.0.0 now supports absolute plot dimensions š¤©
#rstats
#dataviz
#phd
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#IDsky
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5 months ago
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Brendan J. Kelly
FEMS
5 months ago
Happy International Microorganism Day! š 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!
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Brendan J. Kelly
CƩsar SƔnchez
5 months ago
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" š¦
flip.it/Zzrht7
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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 ā if untreated ā can be fatal. Typhus was almost eradicated from the United States, but now it's making a comeback.
https://flip.it/Zzrht7
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Brendan J. Kelly
Nature Microbiology
5 months ago
#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...
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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.
https://www.nature.com/articles/s41564-025-02112-6?utm_source=bluesky&utm_medium=social&utm_campaign=nmicrobiol
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Remembering David Rose today.
www.bbc.com/news/article...
5 months ago
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Brendan J. Kelly
Eurosurveillance journal
5 months ago
This week's rapid communications describe ā”ļøA strain of Neisseria gonorrhoeae producing false negative results on Xpert CT/NG assay in England šAn atypical sixfold rise in
#influenza
A(H1N1)pdm09 cases in Denmark during summer Full issue here š
bit.ly/eus2036
#EpiSky
#IDSky
#MedSky
#STISky
šš¦ š§«āļø
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Brendan J. Kelly
ASM
5 months ago
Attention early-career scientists! Apply for ASMās 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
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Brendan J. Kelly
Adam L
5 months ago
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...
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Brendan J. Kelly
UW Infectious Disease Fellowship Program
5 months ago
More on the outbreak of Neisseria meningitidis conjunctivitis among military trainees, from the MMWRā¦
#IDSky
www.cdc.gov/mmwr/volumes...
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Outbreak of Neisseria meningitidis Conjunctivitis ...
This report describes 41 cases of Neisseria meningitidis conjunctivitis among military trainees living in a communal setting in Texas.
https://www.cdc.gov/mmwr/volumes/74/wr/mm7433a1.htm
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Brendan J. Kelly
Ferric Fang, MD
5 months ago
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).
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Brendan J. Kelly
IDSA
5 months ago
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
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Brendan J. Kelly
Jason Rasgon
6 months ago
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...
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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...
https://psu.wd1.myworkdayjobs.com/en-US/PSU_Academic/job/Full-or-Associate-Professor-in-Infectious-Disease-Modeling_REQ_0000070169-1
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Brendan J. Kelly
Richard McElreath šāā¬
6 months ago
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 āaā> X ābā> Y, and X <ā U ā> Y, where U is unmeasured, a and b are path coefs. We want to know b. U prevents direct approach. >>
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Brendan J. Kelly
Grant McDermott
6 months ago
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.)
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tinyplot ā
https://grantmcdermott.com/tinyplot/vignettes/useR2025/useR2025.html
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Brendan J. Kelly
Samir S. Shah
6 months ago
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
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Brendan J. Kelly
UW Infectious Disease Fellowship Program
6 months ago
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 climateā¦
#IDSky
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Brendan J. Kelly
Sten Linnarsson
8 months ago
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!)
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Brendan J. Kelly
Emma Slack
6 months ago
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...
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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...
https://www.cell.com/cell/fulltext/S0092-8674(25)00794-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867425007949%3Fshowall%3Dtrue
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Brendan J. Kelly
Frank Harrell
7 months ago
A brilliant article by
@rmcelreath.bsky.social
. I had not heard of ābread scientistsā before but see them everywhere. Related to the strong case for teaching reliable, rigorous methods, I see as a major problem the selection of āoptimisticā stat methods.
#StatsSky
#EpiSky
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Brendan J. Kelly
Nature Reviews Genetics
7 months ago
New online! Viromics approaches for the study of viral diversity and ecology in microbiomes
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Viromics approaches for the study of viral diversity and ecology in microbiomes
Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00871-wIn this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing on uncultivated viruses of microorganisms.
https://www.nature.com/articles/s41576-025-00871-w?utm_source=dlvr.it&utm_medium=bluesky
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@rmcelreath.bsky.social
with a radical proposal for science: "Research should be intelligible. Access is not sufficient."
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7 months ago
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Brendan J. Kelly
Infectious Diseases Fellowship at Indiana University
7 months ago
#idboardreview
50 M recently returned after visiting family in Cost Rica x2wks, stayed in urban area, on return F, HA, retrobulbar pain, petechial rash on arm/trunk, leukopenia, normal diff, plt 120. CXR normal. vector?
#medEd
#idmedEd
#idsky
#idfellows
#idfellowship
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Brendan J. Kelly
Moritz Kraemer
7 months ago
BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference
www.nature.com/articles/s41...
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BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference - Nature Methods
BEAST X advances Bayesian phylogenetic, phylogeographic and phylodynamic analysis by incorporating a broad range of complex models and leveraging advanced algorithms and techniques to boost statistica...
https://www.nature.com/articles/s41592-025-02751-x
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Brendan J. Kelly
Andrew Heiss
7 months ago
apparently the trick to long life is to eat fewer than 365 hot dogs per year
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Brendan J. Kelly
Adam Kucharski
7 months ago
"The assumption of perfect smoothness is demonstrably flawed, just as the assumption of an abrupt change is flawed; the reality likely lies somewhere between these extremes." Useful discussion on challenges of reconstructing infection peak from delayed outcomes:
academic.oup.com/jrsssa/advan...
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