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Sarah Cobey

@cobey.bsky.social

3.9K followers 700 following 79 posts

Professor at U. Chicago. Computational epidemiology, evolution, influenza, SARS-CoV-2, vaccines, and B cells. Infectious disease dynamics across scales.

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Sarah Cobey @cobey.bsky.social · 2d

It was surreal to be quizzed on “freedom of inquiry” and other values in my mandated U. Chicago/NIH/NSF research security training tonight given the restrictions to our research over the past eight months. Jeremy describes the experience perfectly below. (His piece is outstanding.)

Jeremy Berg @jeremymberg.bsky.social · 2d

6/14

In communicating with some of the scientists affected by grant terminations, it was striking (but not surprising) that many felt abandoned by their institutions and the scientific establishment at large. This was fueled, in part, by the contrast between this acquiescence and the rapid institutional responses, including lawsuits, after the administration had proposed a cap on the rate of reimbursement for so-called indirect costs of research. The scientific establishment had the capacity to push back vigorously when some of their values (financial viability) were threatened but could not seem to muster much energy when other principles were under assault.

Reposted by Sarah Cobey

Erin Green @erinrgreen.bsky.social · 4d

Job alert ‼️ UChicago Micro is hiring! Open to tenured/tenure track faculty at all levels in any area of microbiology. Come join our amazing and growing department. apply.interfolio.com/174404

Reposted by Sarah Cobey

Michael Baym @baym.lol · 18d

Immigrants, particularly on H1Bs, are the lifeblood of American innovation. If you wanted to hurt US competitiveness in the next century, I can think of few more effective ways than a move like this

Even when found illegal, the mere intent will have irreparably harmed our future

Sarah Cobey @cobey.bsky.social · Aug 30

This doesn’t affect your main point, but I think the imprinting/“original antigenic sin” hypothesis, in which differences in mortality arise from differences in early influenza exposures by birth cohort, has much more support.

Reposted by Sarah Cobey

Will Ratcliff @wcratcliff.bsky.social · Aug 12

But it does not *want* to do that. It has the personality and confidence of a 10x coder, and *absolutely lies to your face* to maintain the illusion.

It races to establish huge frameworks, call up parallel agents, and build you something that gives an output.

Reposted by Sarah Cobey

J. Emory Parker 🏳️‍🌈 @jaspar.bsky.social · Jul 1

NEW: I just observed two interesting data deletions from the CDC's website. Both having to do with vaccine surveillance in children. There's nothing about these datasets that would have tripped any "gender" flags.

You can still download them from our site: www.statnews.com/2025/02/14/t...

Removed datasets: "Percent Positivity of Viral Detections Among Enrolled Children in the New Vaccine Surveillance Network (NVSN), Acute Respiratory Illnesses (ARI), 2017–Present" and "Pathogen Detections Among Enrolled Children in the New Vaccine Surveillance Network (NVSN), Acute Respiratory Illnesses (ARI), 12 Month Rolling Period"

Chart showing the deletion of data from the CDC's website over time, it starts with 1,488 items last year and currently stands at 1,398 items.

Reposted by Sarah Cobey

Simon Cauchemez @scauchemez.bsky.social · Jun 23

Just few days left to apply to one of these postdoc positions in my infectious disease modelling Unit at @pasteur.fr in Paris!

Simon Cauchemez @scauchemez.bsky.social · Jun 5

New postdoc positions with a number of exciting epidemic modelling projects opening in our Unit at @pasteur.fr in beautiful Paris. Deadline for applications: 26th June.
research.pasteur.fr/en/job/postd...

Postdoctoral positions in epidemic mathematical/statistical modelling - Research

Job description We are recruiting postdocs to contribute to research projects in the Mathematical Modelling of Infectious Diseases Unit, at Institut Pasteur in Paris. The candidates will be expected t...

research.pasteur.fr

Sarah Cobey @cobey.bsky.social · Jun 23

Coauthors are Bjarke Nielsen, Emily Howerton, and Bryan Grenfell. This work was mostly funded by the Life Sciences Research Foundation and NIH. Daniel is no longer on social media but is happy to answer any questions. [8/8]

Sarah Cobey @cobey.bsky.social · Jun 23

Overall, quantifying pathogen resilience offers a new perspective on understanding how pathogens respond to both large and small perturbations. These insights have important implications for pathogen persistence, prediction, and model validation. [7/8]

Sarah Cobey @cobey.bsky.social · Jun 23

We've focused on resilience in the context of large perturbations. We also showed that resilience determines how sensitive a system is to smaller stochastic perturbations, with less resilient systems exhibiting greater deviations from deterministic trajectories under demographic stochasticity. [6/8]

Sarah Cobey @cobey.bsky.social · Jun 23

What determines how resilient a pathogen is? It depends on the per-capita rate of replenishment of the susceptible population. Faster replenishment = more resilient dynamics, where the rate of replenishment depends on the duration of immunity and basic reproduction number (R0). [5/8]

Sarah Cobey @cobey.bsky.social · Jun 23

We estimated that common respiratory pathogens are much more resilient than vaccine-preventable infections, such as measles. Our predictions about pathogen return also closely match the observed deviations (or lack thereof) from the pre-COVID dynamics of respiratory pathogens. [4/8]

Sarah Cobey @cobey.bsky.social · Jun 23

We analyzed relevant time series data from Hong Kong, Canada, Korea, and the US. By quantifying the resilience of common respiratory pathogens, we could predict when each pathogen would eventually return to its pre-pandemic dynamics. [3/8]

Sarah Cobey @cobey.bsky.social · Jun 23

COVID-19 interventions disrupted the circulation of many pathogens. To understand if and when they might return to pre-pandemic patterns, we developed a framework for quantifying the rate of return to pre-pandemic patterns—a measure of pathogen resilience in a given host population. [2/8]

Sarah Cobey @cobey.bsky.social · Jun 23

Sang Woo (Daniel) Park and I are excited to share a new preprint, "Susceptible host dynamics explain pathogen resilience to perturbations" [1/8]

www.biorxiv.org/content/10.1...

Reposted by Sarah Cobey

Nigel Goldenfeld @nigelgoldenfeld.bsky.social · Jun 9

🧪 You can sign a supporting letter in solidarity with the NIH scientists here:

www.standupforscience.net/bethesda-dec...

Reposted by Sarah Cobey

Sam Wang @samwang.bsky.social · Jun 7

More of this, please: a class action lawsuit by UC Berkeley researchers to restore illegally cut federal grants. www.nbcnews.com/news/us-news...

UC Berkeley researchers team up for first-of-its-kind lawsuit over Trump funding cuts

University of California staff members hope to use a class action lawsuit to restore their research funding.

www.nbcnews.com

Reposted by Sarah Cobey

Joshua Weitz @joshuasweitz.bsky.social · May 31

How bad will it be? Catastrophic.

Proposed cuts to #NSF, #NIH, and #NASA will set the US R&D landscape back 25 yrs+, cause economic and job loss now, and undermine innovations to come.

But, this is the WH's *proposed* budget.

Speak up now before it is too late.

(inflation adjusted $-s below)

NSF, NASA and NIH budgets per year, inflation adjusted from 2000-2025 along with the proposed cuts. NSF includes research component only. Massive cuts across all sectors, well below support spanning 25 years.

Reposted by Sarah Cobey

Tulio de Oliveira @tuliodna.bsky.social · May 23

A not very happy Friday. CERI had 6 NIH grants canceled, which will impact operations, surveillance and response to epidemics. We are working to try to minimize disturbance but not easy with 6 grants terminated at the same moment. A crisis is unfolding in SA www.news24.com/southafrica/...

SA universities face funding crisis as US federal agencies freeze research grants | News24

An investigation into the impact of the US aid freeze on research funding to South African universities has found that 44 programmes worth R2.5 billion were affected.

Reposted by Sarah Cobey

Claus Wilke @clauswilke.com · May 20

I was working on a proposal in response to one of these calls. Submission deadline next week. The proposal was 95% done, and I only learned about the cancellation from this post. 🤷‍♂️

Gabi Serrato Marks @gserratomarks.bsky.social · May 20

NIH moved up the expiration date for some funding opportunities, effectively *canceling* the next application date without removing it from the standard table. I can't even imagine how many people are still prepping these grants.

👀 List of impacted opportunities:
grants.nih.gov/grants/guide...

Screenshot of NIMH BRAINS funding opportunity. The expiration date is now before the next application due date.

Sarah Cobey @cobey.bsky.social · May 19

Tbh I'm reading a review right now that completely misses some of our important contributions to a topic. Meanwhile it incorporates unnecessary jargon from some splashy articles in glam journals. In a dark reflective mood.

Sarah Cobey @cobey.bsky.social · May 19

Unfortunately there's a risk people might not even notice your discovery unless it's in such a journal. Good work should speak for itself but it obviously doesn't fully. Sometimes I see publishing in 'higher impact' journals as a shortcut to having to give so many talks/wait for discovery.

Sarah Cobey @cobey.bsky.social · May 15

This is such an important point. The timescales for lawsuits are much too slow to prevent the tremendous damage already occurring.

Reposted by Sarah Cobey

Michael Baym @baym.lol · May 15

Yes, that’s exactly what they are doing. They are trying to hurt Harvard by destroying my research

Sarah Cobey @cobey.bsky.social · May 10

PO