Casey Middleton, PhD
@caseymiddleton.bsky.social
Infectious disease modeling
Views are my own
Views are my own
Dear authors,
If you submit a manuscript without line numbers, I can only assume you are actively trying to destroy my life.
Hatefully,
Reviewer #3 😭
If you submit a manuscript without line numbers, I can only assume you are actively trying to destroy my life.
Hatefully,
Reviewer #3 😭
October 1, 2026 at 3:30 PM
Dear authors,
If you submit a manuscript without line numbers, I can only assume you are actively trying to destroy my life.
Hatefully,
Reviewer #3 😭
If you submit a manuscript without line numbers, I can only assume you are actively trying to destroy my life.
Hatefully,
Reviewer #3 😭
Interested in creating community and finding collaboration opportunities in infectious disease dynamics?
Join the GSIDD Connect Series!
📆 Friday, Sept. 11
🕐 1pm ET
🔗 www.gsidd.org/events
Join the GSIDD Connect Series!
📆 Friday, Sept. 11
🕐 1pm ET
🔗 www.gsidd.org/events
Events | GSIDD
www.gsidd.org
September 10, 2026 at 2:35 PM
Interested in creating community and finding collaboration opportunities in infectious disease dynamics?
Join the GSIDD Connect Series!
📆 Friday, Sept. 11
🕐 1pm ET
🔗 www.gsidd.org/events
Join the GSIDD Connect Series!
📆 Friday, Sept. 11
🕐 1pm ET
🔗 www.gsidd.org/events
Ten years ago, Beans was put up for adoption because a family member was abusing him. If you ask me, she should’ve divorced the man and kept the dog.
Happy National Dog Day, Beanbo Doggins. You’re the coolest little dude I ever met!
Happy National Dog Day, Beanbo Doggins. You’re the coolest little dude I ever met!
August 26, 2026 at 11:17 PM
Ten years ago, Beans was put up for adoption because a family member was abusing him. If you ask me, she should’ve divorced the man and kept the dog.
Happy National Dog Day, Beanbo Doggins. You’re the coolest little dude I ever met!
Happy National Dog Day, Beanbo Doggins. You’re the coolest little dude I ever met!
Reposted by Casey Middleton, PhD
Literally this. They’re acting like people didn’t die. Like we all didn’t live through it and see it with our own eyes, and Trump wasn’t President at the time.
It’s wild to watch.
It’s wild to watch.
July 29, 2026 at 4:29 PM
Literally this. They’re acting like people didn’t die. Like we all didn’t live through it and see it with our own eyes, and Trump wasn’t President at the time.
It’s wild to watch.
It’s wild to watch.
Reposted by Casey Middleton, PhD
I'm excited to share a preprint that's been years in the making: the idea took shape during the COVID pandemic. Anecdotally, people would sometimes spread COVID at work but not at home, and vice versa. Why? One explanation would be if infectiousness is fleeting...
How bursty infectiousness shapes epidemic dynamics
An epidemic’s expected course is determined by the magnitude and timing of a typical person’s infectiousness — captured, in turn, by the basic reproduction number and the generation-time distribution....
www.medrxiv.org
July 29, 2026 at 3:14 PM
I'm excited to share a preprint that's been years in the making: the idea took shape during the COVID pandemic. Anecdotally, people would sometimes spread COVID at work but not at home, and vice versa. Why? One explanation would be if infectiousness is fleeting...
Reposted by Casey Middleton, PhD
If you’re watching Fauci’s testimony remember that science isn’t an ideology. It doesn’t lie. It evolves. COVID-19 was a once-in-a-century pandemic caused by a brand-new virus, recommendations changed because the evidence changed. That’s not deception. That’s how it works.
July 29, 2026 at 1:34 PM
If you’re watching Fauci’s testimony remember that science isn’t an ideology. It doesn’t lie. It evolves. COVID-19 was a once-in-a-century pandemic caused by a brand-new virus, recommendations changed because the evidence changed. That’s not deception. That’s how it works.
Throughout your scientific career, you will read hundreds of dense manuscripts.
📚 As the literature stack piles up, remembering exactly where you saw a specific methodology or finding can be tough.
Here is how I use a relational database to keep track of it all (and et al.). 👇
📚 As the literature stack piles up, remembering exactly where you saw a specific methodology or finding can be tough.
Here is how I use a relational database to keep track of it all (and et al.). 👇
July 9, 2026 at 7:03 PM
Throughout your scientific career, you will read hundreds of dense manuscripts.
📚 As the literature stack piles up, remembering exactly where you saw a specific methodology or finding can be tough.
Here is how I use a relational database to keep track of it all (and et al.). 👇
📚 As the literature stack piles up, remembering exactly where you saw a specific methodology or finding can be tough.
Here is how I use a relational database to keep track of it all (and et al.). 👇
Reposted by Casey Middleton, PhD
1. A bit of evolutionary biology.
I'm really intrigued by a new perspective piece from Steve Frank that explores connections between how natural selection creates systems that generalize and recent work in machine learning about the surprising capabilities of massively overparameterized systems.
I'm really intrigued by a new perspective piece from Steve Frank that explores connections between how natural selection creates systems that generalize and recent work in machine learning about the surprising capabilities of massively overparameterized systems.
Generalization as the great leap in evolvability: insights from machine learning
Abstract. Natural selection encodes learned information in the genome. Learned solutions may be tuned specifically to past challenges, failing in altered e
academic.oup.com
July 4, 2026 at 6:51 AM
1. A bit of evolutionary biology.
I'm really intrigued by a new perspective piece from Steve Frank that explores connections between how natural selection creates systems that generalize and recent work in machine learning about the surprising capabilities of massively overparameterized systems.
I'm really intrigued by a new perspective piece from Steve Frank that explores connections between how natural selection creates systems that generalize and recent work in machine learning about the surprising capabilities of massively overparameterized systems.
Reposted by Casey Middleton, PhD
PhD position (Melbourne, Australia)
Mechanistic modelling of the epidemic dynamics of vector-borne zoonotic diseases in Australia
with Oliver Eales, Freya Shearer, Marya Potorek
at University of Melbourne
More details: http://iddjobs.org/jobs/2561
Mechanistic modelling of the epidemic dynamics of vector-borne zoonotic diseases in Australia
with Oliver Eales, Freya Shearer, Marya Potorek
at University of Melbourne
More details: http://iddjobs.org/jobs/2561
July 3, 2026 at 7:03 PM
PhD position (Melbourne, Australia)
Mechanistic modelling of the epidemic dynamics of vector-borne zoonotic diseases in Australia
with Oliver Eales, Freya Shearer, Marya Potorek
at University of Melbourne
More details: http://iddjobs.org/jobs/2561
Mechanistic modelling of the epidemic dynamics of vector-borne zoonotic diseases in Australia
with Oliver Eales, Freya Shearer, Marya Potorek
at University of Melbourne
More details: http://iddjobs.org/jobs/2561
Reposted by Casey Middleton, PhD
Calculations on the containment of Bundibugyo ebolavirus with @caseymiddleton.bsky.social:
www.medrxiv.org/content/10.6...
We estimate:
1. Symptom screening misses 68%–86% of infected travelers.
2. A 7d post-travel quarantine misses 26% of infections.
→ 18%–23% missed by combined measures. 1/
www.medrxiv.org/content/10.6...
We estimate:
1. Symptom screening misses 68%–86% of infected travelers.
2. A 7d post-travel quarantine misses 26% of infections.
→ 18%–23% missed by combined measures. 1/
June 8, 2026 at 9:20 PM
Calculations on the containment of Bundibugyo ebolavirus with @caseymiddleton.bsky.social:
www.medrxiv.org/content/10.6...
We estimate:
1. Symptom screening misses 68%–86% of infected travelers.
2. A 7d post-travel quarantine misses 26% of infections.
→ 18%–23% missed by combined measures. 1/
www.medrxiv.org/content/10.6...
We estimate:
1. Symptom screening misses 68%–86% of infected travelers.
2. A 7d post-travel quarantine misses 26% of infections.
→ 18%–23% missed by combined measures. 1/
Today's academic birthday gifts:
✨ Opinion piece rejected.
🏅 Tiny change required for resubmission of preprint.
🏆 Mandatory Disclosure of External Professional Activities due.
Another day in paradise 🌴😎
✨ Opinion piece rejected.
🏅 Tiny change required for resubmission of preprint.
🏆 Mandatory Disclosure of External Professional Activities due.
Another day in paradise 🌴😎
June 4, 2026 at 8:56 PM
Today's academic birthday gifts:
✨ Opinion piece rejected.
🏅 Tiny change required for resubmission of preprint.
🏆 Mandatory Disclosure of External Professional Activities due.
Another day in paradise 🌴😎
✨ Opinion piece rejected.
🏅 Tiny change required for resubmission of preprint.
🏆 Mandatory Disclosure of External Professional Activities due.
Another day in paradise 🌴😎
Reposted by Casey Middleton, PhD
6/ We eliminated measles 26 years ago. We eradicated New World Screwworm 60 years ago. Keeping diseases at bay requires sustained investment, trained people, and ongoing engagement.
June 4, 2026 at 8:31 PM
6/ We eliminated measles 26 years ago. We eradicated New World Screwworm 60 years ago. Keeping diseases at bay requires sustained investment, trained people, and ongoing engagement.
Last night, we celebrated two birthdays:
Cecil Earnest Middleton, born May 23, 1941
Casey Elaine Middleton, born June 4, 1996
Highly recommend celebrating your birthday with your granddad ✨
Cecil Earnest Middleton, born May 23, 1941
Casey Elaine Middleton, born June 4, 1996
Highly recommend celebrating your birthday with your granddad ✨
June 1, 2026 at 1:26 PM
Last night, we celebrated two birthdays:
Cecil Earnest Middleton, born May 23, 1941
Casey Elaine Middleton, born June 4, 1996
Highly recommend celebrating your birthday with your granddad ✨
Cecil Earnest Middleton, born May 23, 1941
Casey Elaine Middleton, born June 4, 1996
Highly recommend celebrating your birthday with your granddad ✨
Reposted by Casey Middleton, PhD
This is such a moving piece. If your interested in #Ebola — the damage it causes, the trauma families and communities and responders face during and after an outbreak — please read it. www.statnews.com/2026/05/20/e...
I saw Ebola as both doctor and patient. I wish people cared more about the Africans I worked alongside
“As another Ebola outbreak unfolds, we cannot repeat the mistakes of the past,” writes Krutika Kuppalli.
www.statnews.com
May 20, 2026 at 7:00 PM
This is such a moving piece. If your interested in #Ebola — the damage it causes, the trauma families and communities and responders face during and after an outbreak — please read it. www.statnews.com/2026/05/20/e...
🚨 Disease modelers: Do you use empirical VE estimates interchangeably to inform vaccine effect parameters?
Me too, and it’s distorting our predictions.
VE estimates often do not align with model parameters. We discuss these pitfalls & solutions in our new preprint:
arxiv.org/abs/2605.18571 🧵👇
Me too, and it’s distorting our predictions.
VE estimates often do not align with model parameters. We discuss these pitfalls & solutions in our new preprint:
arxiv.org/abs/2605.18571 🧵👇
Incorporating vaccine effects into epidemiological models: common pitfalls and solutions
Incorporating vaccination into mathematical models appears deceptively simple: models integrate vaccine-derived protections, such as reduced susceptibility to infection, using parameters informed by e...
arxiv.org
May 19, 2026 at 6:58 PM
🚨 Disease modelers: Do you use empirical VE estimates interchangeably to inform vaccine effect parameters?
Me too, and it’s distorting our predictions.
VE estimates often do not align with model parameters. We discuss these pitfalls & solutions in our new preprint:
arxiv.org/abs/2605.18571 🧵👇
Me too, and it’s distorting our predictions.
VE estimates often do not align with model parameters. We discuss these pitfalls & solutions in our new preprint:
arxiv.org/abs/2605.18571 🧵👇
Reposted by Casey Middleton, PhD
My four year old: I do number maths. Adults do maths with letters they don’t know.
Me: Actually, yes, they do!
Him: Why don’t they know all the letters yet? I do.
Me: Actually, yes, they do!
Him: Why don’t they know all the letters yet? I do.
May 5, 2026 at 8:33 PM
My four year old: I do number maths. Adults do maths with letters they don’t know.
Me: Actually, yes, they do!
Him: Why don’t they know all the letters yet? I do.
Me: Actually, yes, they do!
Him: Why don’t they know all the letters yet? I do.
Today's micro-feminist win: changed my email signature from
Thanks so much,
to
Thanks,
Please hold your applause 🏅
Thanks so much,
to
Thanks,
Please hold your applause 🏅
April 29, 2026 at 4:54 PM
Today's micro-feminist win: changed my email signature from
Thanks so much,
to
Thanks,
Please hold your applause 🏅
Thanks so much,
to
Thanks,
Please hold your applause 🏅
Reposted by Casey Middleton, PhD
Claude has started refusing to give citations.
Yes, this technically means fewer hallucinations.
But it doesn’t mean that AI is now hallucination-free in the way a careful researcher is.
Yes, this technically means fewer hallucinations.
But it doesn’t mean that AI is now hallucination-free in the way a careful researcher is.
April 24, 2026 at 3:12 PM
Claude has started refusing to give citations.
Yes, this technically means fewer hallucinations.
But it doesn’t mean that AI is now hallucination-free in the way a careful researcher is.
Yes, this technically means fewer hallucinations.
But it doesn’t mean that AI is now hallucination-free in the way a careful researcher is.
Reposted by Casey Middleton, PhD
For years, Jay Bhattacharya has been upset at the MMWR for publishing findings that run contrary to his predetermined conclusions (e.g., on immunity after covid vaccination) and his political agenda. Now he's in a position to prevent those findings from being published.
April 9, 2026 at 2:54 PM
For years, Jay Bhattacharya has been upset at the MMWR for publishing findings that run contrary to his predetermined conclusions (e.g., on immunity after covid vaccination) and his political agenda. Now he's in a position to prevent those findings from being published.
Reposted by Casey Middleton, PhD
"This is not reversing the damage. It is spending more than we spent on WHO to create an institution that’s unlikely to survive and will certainly accomplish only a fraction of what we did by working together with the entire world.”
- Atul Gawande, @agawande.bsky.social
🎁
wapo.st/4tKRwyM
- Atul Gawande, @agawande.bsky.social
🎁
wapo.st/4tKRwyM
After leaving WHO, Trump officials propose more expensive replacement to duplicate it
HHS proposes spending $2 billion a year to re-create systems the U.S. accessed through the WHO at a fraction of the cost, according to officials briefed on the matter.
wapo.st
February 19, 2026 at 4:26 PM
"This is not reversing the damage. It is spending more than we spent on WHO to create an institution that’s unlikely to survive and will certainly accomplish only a fraction of what we did by working together with the entire world.”
- Atul Gawande, @agawande.bsky.social
🎁
wapo.st/4tKRwyM
- Atul Gawande, @agawande.bsky.social
🎁
wapo.st/4tKRwyM
Reposted by Casey Middleton, PhD
In a new preprint, we combine modeling with school-level vaccine data to contextualize the risk of 'breakthrough infections' and impacts on the ongoing US measles outbreak. #idsky #episky
www.medrxiv.org/content/10.6...
www.medrxiv.org/content/10.6...
Interpreting Breakthrough Infections Given Assortative Mixing of Partially Vaccinated Populations
Declining vaccine coverage across the United States has increased the risk of outbreaks of vaccine-preventable diseases. Even when vaccines have low primary failure rates, conventional epidemic theory...
www.medrxiv.org
January 27, 2026 at 2:34 PM
In a new preprint, we combine modeling with school-level vaccine data to contextualize the risk of 'breakthrough infections' and impacts on the ongoing US measles outbreak. #idsky #episky
www.medrxiv.org/content/10.6...
www.medrxiv.org/content/10.6...
Models can be powerful tools to study associations in data. But do they reliably reveal the truth?
🚨 In our new study, @danlarremore.bsky.social and I show that the model used to estimate VE from test-negative designs (TNDs) may not translate to other correlates of risk.
doi.org/10.1093/aje/...
🚨 In our new study, @danlarremore.bsky.social and I show that the model used to estimate VE from test-negative designs (TNDs) may not translate to other correlates of risk.
doi.org/10.1093/aje/...
Statistical methods for estimating the protective effects of immune markers using test-negative designs
Abstract. While widely used to study vaccine effectiveness, test-negative designs (TNDs) also provide a platform for identifying and quantifying immunologi
doi.org
January 26, 2026 at 5:32 PM
Models can be powerful tools to study associations in data. But do they reliably reveal the truth?
🚨 In our new study, @danlarremore.bsky.social and I show that the model used to estimate VE from test-negative designs (TNDs) may not translate to other correlates of risk.
doi.org/10.1093/aje/...
🚨 In our new study, @danlarremore.bsky.social and I show that the model used to estimate VE from test-negative designs (TNDs) may not translate to other correlates of risk.
doi.org/10.1093/aje/...
If you live outside of Minneapolis but want to support the community, Lisa and her husband are doing boots on the ground work to protect families! Donate to their work via Venmo @lisa-szabo-1
January 25, 2026 at 4:25 AM
If you live outside of Minneapolis but want to support the community, Lisa and her husband are doing boots on the ground work to protect families! Donate to their work via Venmo @lisa-szabo-1
Sometimes it feels really heavy to pretend everything is okay in our country and just keep doing research.
It seems like the best thing I can do for my career is the worst thing I can do as a human being.
It seems like the best thing I can do for my career is the worst thing I can do as a human being.
January 20, 2026 at 7:52 PM
Sometimes it feels really heavy to pretend everything is okay in our country and just keep doing research.
It seems like the best thing I can do for my career is the worst thing I can do as a human being.
It seems like the best thing I can do for my career is the worst thing I can do as a human being.
It really says something about the state of our country that I no longer believe banning LED headlights should be a top federal government policy priority…
But I still hate them, to be clear 😑
But I still hate them, to be clear 😑
January 14, 2026 at 9:25 PM
It really says something about the state of our country that I no longer believe banning LED headlights should be a top federal government policy priority…
But I still hate them, to be clear 😑
But I still hate them, to be clear 😑