Brendan J. Kelly
@bjklab.bsky.social
Reposted by Brendan J. Kelly
"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.
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.
Modelling Like an Experimentalist
Dahlin et al. (2024) apply experimental thinking to a model of mosquito-borne disease transmissions.
onlinelibrary.wiley.com
November 9, 2025 at 9:18 PM
"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.
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.
Cool 🦠
William Schmidt
Gerard Wong Lab @UCLA
Nature Microbiology
Pseudomonas aeruginosa lays down Psl exopolysaccharide as it crawls
Other cells detect and follow these trails using type IV pili pulling against adhesins like CdrA triggering c-di-GMP & cAMP surges to shift into early biofilm mode
William Schmidt
Gerard Wong Lab @UCLA
Nature Microbiology
Pseudomonas aeruginosa lays down Psl exopolysaccharide as it crawls
Other cells detect and follow these trails using type IV pili pulling against adhesins like CdrA triggering c-di-GMP & cAMP surges to shift into early biofilm mode
Pseudomonas aeruginosa senses exopolysaccharide trails using type IV pili and adhesins during biofilm formation - Nature Microbiology
Opposing forces generated by exopolysaccharide trail binding versus type IV pilus retraction generate a high cyclic diGMP–high cyclic AMP state in Pseudomonas aeruginosa that promotes social motility.
www.nature.com
October 29, 2025 at 7:59 PM
Reposted by Brendan J. Kelly
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-...
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-...
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
academic.oup.com
October 25, 2025 at 1:53 PM
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-...
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-...
Reposted by Brendan J. Kelly
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…
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…
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
www.science.org
October 18, 2025 at 10:02 AM
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…
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…
Reposted by Brendan J. Kelly
💻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
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
October 15, 2025 at 8:00 AM
💻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
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
Reposted by Brendan J. Kelly
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 📈
New research article
Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA
Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA
October 10, 2025 at 1:12 PM
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
“Roughly 70 Epidemic Intelligence Service officers — the so-called “disease detectives” who respond to outbreaks around the globe — received layoff notices, according to a person familiar with them. The service was spared during an earlier round of layoffs in February.”
Trump Administration Lays Off Dozens of C.D.C. Officials
www.nytimes.com
October 11, 2025 at 12:33 PM
What could possibly go wrong? #IDSky
Reposted by Brendan J. Kelly
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...
Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...
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...
ellis.eu
October 6, 2025 at 9:28 AM
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...
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
The 2nd #Communicable & #Breakpoints collaboration drops on 19 Sept! Hosts @angelahuttner.bsky.social & @erinmccreary.bsky.social invite BALANCE trial leads Nick Daneman & Robert Fowler to discuss everything from the trial's humble start to its meteoric impact in clinical practice.
#IDSky #clinmicro
#IDSky #clinmicro
October 1, 2025 at 8:20 PM
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."
This final post from Kaleb Horton is very beautiful and hits hard. This is just so sad. RIP.
2025, So Far
I wish I had a time machine so I could go back in time and talk to my dad in 1988, just before I was born, and tell him what it’s like to live in the future. I’d tell him all the amazing things that a...
kalebhorton.ghost.io
September 27, 2025 at 7:41 PM
"It turns out boredom is the Cadillac of feelings."
Reposted by Brendan J. Kelly
September 18, 2025 at 6:28 PM
Reposted by Brendan J. Kelly
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!
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!
September 17, 2025 at 7:01 AM
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!
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!
Reposted by Brendan J. Kelly
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
"76-year-old Clark contracted #typhus from clearing weeds from her garden"
🦠
flip.it/Zzrht7
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.
flip.it
September 14, 2025 at 12:23 PM
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
"76-year-old Clark contracted #typhus from clearing weeds from her garden"
🦠
flip.it/Zzrht7
Reposted by Brendan J. Kelly
#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...
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...
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.
www.nature.com
September 12, 2025 at 3:51 PM
#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...
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...
Remembering David Rose today. www.bbc.com/news/article...
September 12, 2025 at 12:54 PM
Remembering David Rose today. www.bbc.com/news/article...
Reposted by Brendan J. Kelly
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 🛟🦠🧫⚕️
➡️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 🛟🦠🧫⚕️
September 11, 2025 at 8:41 PM
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 🛟🦠🧫⚕️
➡️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 🛟🦠🧫⚕️
Reposted by Brendan J. Kelly
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
September 10, 2025 at 1:32 PM
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
Reposted by Brendan J. Kelly
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...
www.annualreviews.org/content/jour...
September 10, 2025 at 2:15 AM
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...
www.annualreviews.org/content/jour...
Reposted by Brendan J. Kelly
More on the outbreak of Neisseria meningitidis conjunctivitis among military trainees, from the MMWR… #IDSky
www.cdc.gov/mmwr/volumes...
www.cdc.gov/mmwr/volumes...
Outbreak of Neisseria meningitidis Conjunctivitis ...
This report describes 41 cases of Neisseria meningitidis conjunctivitis among military trainees living in a communal setting in Texas.
www.cdc.gov
September 5, 2025 at 12:29 PM
More on the outbreak of Neisseria meningitidis conjunctivitis among military trainees, from the MMWR… #IDSky
www.cdc.gov/mmwr/volumes...
www.cdc.gov/mmwr/volumes...
Reposted by Brendan J. Kelly
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).
September 5, 2025 at 12:04 AM
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).
Reposted by Brendan J. Kelly
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
Our statement: https://bit.ly/45LeJHi
September 3, 2025 at 10:30 PM
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
Our statement: https://bit.ly/45LeJHi
Reposted by Brendan J. Kelly
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...
Feel free to message me for details
psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...
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...
psu.wd1.myworkdayjobs.com
August 26, 2025 at 11:35 PM
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...
Feel free to message me for details
psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...
Reposted by Brendan J. Kelly
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. >>
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. >>
August 21, 2025 at 10:57 AM
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. >>
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. >>
Reposted by Brendan J. Kelly
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.)
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.)
tinyplot –
grantmcdermott.com
August 10, 2025 at 5:39 PM
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.)
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.)