SeppeKuehnLab

A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...

The Abreu lab at NYU is hiring another postdoc! We study microbial ecology and evolution, using yeast/bacteria microcosms, DNA barcoding for evolutionary lineage tracking, and simple mathematical modeling. Apply here: apply.interfolio.com/179949

Screenshot from GRC portal confirming microbial population biology meeting June 27, 2027 in Andover, New Hampshire.

It’s officially happening folks! The Microbial Population Biology Gordon Research Conference is back in Andover, New Hampshire starting June 27th of 2027!
See you there!!

@wcratcliff.bsky.social @ksbakes.bsky.social @surtlab.bsky.social

#microsky #mevosky

Poster for my January 21 talk

Hello, Chicago! I'll be giving a public talk on Wednesday about reporting on science in these rocky times. events.uchicago.edu/event/259056...

Just quit Quitting projects in science is hard, but we should be doing a lot more of it.

Blog post: Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.

open.substack.com/pub/arjunraj...

Predicting drug inactivation by changes in bacterial growth dynamics - npj Antimicrobials and Resistance npj Antimicrobials and Resistance - Predicting drug inactivation by changes in bacterial growth dynamics

Our recent paper in npj Antimicrobials and Resistance is a great example of scientific serendipity: after staring at thousands of bacterial growth curves over many studies, we started wondering whether the curve shapes themselves carry mechanistic information 1/9 🦠🧪
www.nature.com/articles/s44...

Have a research group you’d love to bring to NITMB?

Apply for an NITMB Focused Research Group Award, welcoming small groups of participants from multiple institutions to gather at NITMB to focus intently on independent, ambitions joint research projects

www.nitmb.org/research/foc...

We're hiring faculty at the interface of climate systems engineering and ecology -- climateengineering.uchicago.edu/opportunitie...

Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!

NO KINGS in Chicago · No Kings **In America, we don’t put up with would-be kings.** Here in Chicago we know how to rise up, fight back, and support each other. It is more important than ever that we do that together on October 18t...

I'm attending No Kings's event, “NO KINGS in Chicago” - sign up here www.mobilize.us/nokings/even...

Schmidt AI + Science. Amazing fellowship opportunity at UChicago! apply.interfolio.com/173322

Great new paper from Kyle Crocker -- a talented postdoc in the group who is ** on the job market now ** !! @kylecrocker.bsky.social bsky.app/profile/kyle...

Center for Living Systems -- seeking strong post docs at the interface of physics and biology. Consider applying by Oct. 13! docs.google.com/forms/d/e/1F...

Super well written and informative.

Just cursor or copilot

For me, it speeds up coding by 10x easily. But it requires that you already know what you're doing with your data -- why, and how... and then requires validation. Clearly not a PhD in the pocket.

Wait, this is news? Gulp.

RevTex is far and away the best IMO.

Challenges in interpreting functional redundancy and quantifying functional selection in microbial communities Microbiomes often show similar functional profiles despite highly variable taxonomic compositions, a phenomenon attributed to “functional redundancy” …

This important contribution sharpens the ill-defined concept of functional redundancy in microbial communities. It's a term we use a lot, but the exact meaning is elusive, and this paper is the first to sharpen it via proper null models. @ po-yi ho and KC Huang. www.sciencedirect.com/science/arti...

Mathematical Frameworks for Stability, Evolution, and Control in Microbial Communities

Explore new NITMB-Supported Research from @ssm57.bsky.social (Professor, University of Illinois Urbana-Champaign) and @seppekuehnlab.bsky.social (Associate Professor, University of Chicago)!

tinyurl.com/378ua7ws

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

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

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

The “infer phenotypic traits” claim seems a bit of an overshoot given the training data does not include phenotypes. What we get is genomic patterns….and that itself can be super interesting, but the connect to phenotypes? How?

Scientific bedlam at the world’s weirdest and wildest research conference Woodstock Bio2 + Night Science aimed to encourage collaborations through creativity. The walk-on music for presentations was fun, too.

🥂This was the highlight of my year. The "instigators", led by local master of the ceremony @svobodalab.bsky.social will never forget the privilege of organizing it and i think every participant will treasure the experience forever ❤️ @nature.com @josiegz.bsky.social www.nature.com/articles/d41...

Great thread! The sickle cell- malaria example blew me away and was news to me!

A universal trade-off between growth and lag in fluctuating environments - PubMed The rate of cell growth is crucial for bacterial fitness and drives the allocation of bacterial resources, affecting, for example, the expression levels of proteins dedicated to metabolism and biosynt...

Few are as convincing as this one pubmed.ncbi.nlm.nih.gov/32669712/

📢 We're seeking a postdoc to work on a project funded by HFSP @hfspo.bsky.social at the intersection of bacterial physiology, ecology and evolution. You can find more details about the project, the position, and how to apply here www.dalbellolab.com/hfsp-project! #bacteria #ecosky #MevoSky #microSky

Excited to report that Joy Bergelson (bergelsonlab.org) and I will be running a brand new GRC conference on the Function of Evolving Systems in the summer of 2026. The 2028 one will be chaired by Mikhail Tikhonov (physics.wustl.edu/people/mikha...) and @asanchezlab.bsky.social! Stay tuned!

Evolutionary Games: Mathematical Theory and Biological Insights

I am really happy to share that there will be a @nitmb.bsky.social workshop next year on mathematical and biological features of evolutionary game theory.

It was really fun to co-organize this workshop with Olivia Chu, Alex McAvoy, and @jplotkin.bsky.social.

www.nitmb.org/evolutionary...

Simple rules govern soil microbiome responses to environmental change Research from UChicago shows how environmental changes lead to predictable responses in soil microbiome metabolism.

Story from UChicago press office - biologicalsciences.uchicago.edu/news/soil-mi...

Junior, Assistant, or Associate Specialist – Xue Lab University of California, Irvine is hiring. Apply now!

The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601