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SeppeKuehnLab

@seppekuehnlab.bsky.social
1.7K followers 1.3K following 229 posts

Physics and biology of microbial communities. Structure, function, evolution. Center for the Physics of Evolving Systems. Dept. of Ecology and Evolution. UChicago. @NITMB, @CLS. kuehnlab.org

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Dmitri Petrov @petrovadmitri.bsky.social · 17/09/2026
We are searching for an Assistant Professor in Evolutionary Biology! Looking for colleagues asking fundamental questions relating to evolutionary processes and drivers of evolutionary patterns. If you think it is you, please do apply! And please repost. facultypositions.stanford.edu/jobs/assista...
facultypositions.stanford.edu
Assistant Professor in Evolutionary Biology - Stanford University, California, United States
The Department of Biology at Stanford University seeks applicants for a tenure-track Assistant Professor in Evolutionary Biology. A successful candidate will conduct research that asks fundamental que...
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Rogier Braakman @rogierbraakman.bsky.social · 03/09/2026
Job alert! Please RT! Looking for bioinformatics technician to help in projects using metagenomes to study microbial degradation of organic carbon in the ocean and in the human gut. Opportunity to gain research experience before graduate school. careers.peopleclick.com/careerscp/cl...
careers.peopleclick.com
Research Support Associate 1, Bioinformatics
MIT - Research Support Associate 1, Bioinformatics - Cambridge MA 02139
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SeppeKuehnLab @seppekuehnlab.bsky.social · 07/08/2026
New preprint! A monumental four year effort by Vaibhhav Sinha: when a bacterium eats organic carbon, how much becomes biomass and how much comes back out as CO₂? The answer is structured hierarchically by substrate and taxonomy. 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Hierarchical control of bacterial growth efficiency by substrate and taxonomy
Heterotrophic bacteria utilize organic carbon as a source of energy and material for growth. The balanced allocation of carbon between these two processes, termed growth efficiency, is a key physiolog...
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Dmitri Petrov @petrovadmitri.bsky.social · 15/07/2026
Cannot be more excited about the lineup for the inaugural Function of Evolving Systems GRC conference I am co-organizing with the amazing Joy Bergelson. Less than a month away: August 9 - 14, 2026. Still a few spots left! And do check out the amazing list of speakers: www.grc.org/function-of-...
grc.org
2026 Function of Evolving Systems Conference GRC
The 2026 Gordon Research Conference on Function of Evolving Systems will be held in Waterville Valley, New Hampshire. Apply today to reserve your spot.
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SeppeKuehnLab @seppekuehnlab.bsky.social · 29/06/2026
New paper out today in Nature Microbiology: "Epistatic interactions inform rational design of synthetic microbial communities for bioremediation." 🧵https://www.nature.com/articles/s41564-026-02386-4 @kiseokmicro.bsky.social @nitmb.bsky.social
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SeppeKuehnLab @seppekuehnlab.bsky.social · 15/06/2026
New preprint w/Milena Chakraverti-Wuerthwein with Alissa Domenig. “Everything is everywhere; the environment selects.” But which traits does the environment select on? Is there a relationship between evolutionary conservation of traits and variation in community composition? doi.org/10.64898/202...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 18/05/2026
New preprint! www.biorxiv.org/content/10.6... A theory to explain global epistasis in microbial communities
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SeppeKuehnLab @seppekuehnlab.bsky.social · 05/03/2026
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...
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Clare Abreu @clabreu.bsky.social · 20/01/2026
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
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Heather Hendrickson @drhhnz.bsky.social · 10/12/2025
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
Screenshot from GRC portal confirming microbial population biology meeting June 27, 2027 in Andover, New Hampshire.
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Carl Zimmer @carlzimmer.com · 19/01/2026
Hello, Chicago! I'll be giving a public talk on Wednesday about reporting on science in these rocky times. events.uchicago.edu/event/259056...
Poster for my January 21 talk
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Arjun Raj @arjunraj.bsky.social · 30/12/2025
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...
open.substack.com
Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.
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Amir Mitchell @amitchell.bsky.social · 22/12/2025
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...
nature.com
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
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NSF-Simons NITMB @nitmb.bsky.social · 28/11/2025
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...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 12/11/2025
We're hiring faculty at the interface of climate systems engineering and ecology -- climateengineering.uchicago.edu/opportunitie...
climateengineering.uchicago.edu
Assistant Professors - Ecological Consequences of Climate Engineering
Salary Range: $140,000 – $180,000 a year The University of Chicago’s Department of Ecology & Evolution in the Biological Sciences Division and the Climate Systems Engineering Initiative (CSEi) are sea...
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Ben Good @benjaminhgood.bsky.social · 12/11/2025
Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!
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SeppeKuehnLab @seppekuehnlab.bsky.social · 18/10/2025
I'm attending No Kings's event, “NO KINGS in Chicago” - sign up here www.mobilize.us/nokings/even...
mobilize.us
NO KINGS in Chicago · No Kings
**In America, we don’t put up with would-be kings.** Here in Chicago we know how to rise up, fight back, and support each other. It is more important than ever that we do that together on October 18t...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 26/09/2025
Schmidt AI + Science. Amazing fellowship opportunity at UChicago! apply.interfolio.com/173322
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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SeppeKuehnLab @seppekuehnlab.bsky.social · 16/09/2025
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...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 04/09/2025
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...
docs.google.com
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SeppeKuehnLab @seppekuehnlab.bsky.social · 10/08/2025
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...
sciencedirect.com
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” …
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NSF-Simons NITMB @nitmb.bsky.social · 06/08/2025
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
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 04/08/2025
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! 🧵
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.
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Oded Rechavi @odedrechavi.bsky.social · 31/07/2025
🥂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...
nature.com
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.
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Martina Dal Bello @martinadalbello.bsky.social · 23/07/2025
📢 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
dalbellolab.com
HFSP project — dal bello lab
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Dmitri Petrov @petrovadmitri.bsky.social · 30/12/2024
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!
physics.wustl.edu
Faculty
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Daniel Cooney @danielcooney1.bsky.social · 18/07/2025
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...
nitmb.org
Evolutionary Games: Mathematical Theory and Biological Insights
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SeppeKuehnLab @seppekuehnlab.bsky.social · 18/07/2025
Story from UChicago press office - biologicalsciences.uchicago.edu/news/soil-mi...
biologicalsciences.uchicago.edu
Simple rules govern soil microbiome responses to environmental change
Research from UChicago shows how environmental changes lead to predictable responses in soil microbiome metabolism.
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Katherine Xue @ksxue.bsky.social · 17/07/2025
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
recruit.ap.uci.edu
Junior, Assistant, or Associate Specialist – Xue Lab
University of California, Irvine is hiring. Apply now!
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Nature @nature.com · 17/07/2025
Nature research paper: Functional regimes define soil microbiome response to environmental change go.nature.com/3IqdJzd
go.nature.com
Functional regimes define soil microbiome response to environmental change - Nature
Experimental perturbation of soil pH leads to a generalizable model of the soil microcosm comprising three functional regimes with distinct mechanisms linking environmental change to metabolite dynamics.
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SeppeKuehnLab @seppekuehnlab.bsky.social · 17/07/2025
This work was supported by @nitmb.bsky.social, National Science Foundation, NIH, @cziscience.bsky.social , Simons Foundation, UChicago. bsky.app/profile/sepp...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 17/07/2025
New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 10/07/2025
First paper we've found that validates auxotrophy predictions from genomes. in non-host associated communities (e.g. soils) auxotrophy is rare. I believe the assumption of prevalent auxotrophies emerging out of pervasive cross-feeding needs to be reconsidered.. www.nature.com/articles/s41...
nature.com
Taxonomic and environmental distribution of bacterial amino acid auxotrophies - Nature Communications
Many microorganisms are auxotrophic, that is, unable to synthesize the compounds they require for growth. Here, Ramoneda et al. predict amino acid biosynthetic capabilities of over 26,000 bacterial ge...
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NSF-Simons NITMB @nitmb.bsky.social · 30/06/2025
The Regular Registration deadline for the NITMB MathBio Converge Conference is Monday, July 14th Register today to secure your spot at the conference! www.nitmb.org/nitmb-mathbi...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 28/06/2025
Being rich doesn’t make you smart or ethical. When will science contend with these fools? www.nytimes.com/2025/06/28/t...
nytimes.com
The Narrowing of Mark Zuckerberg and Priscilla Chan’s Philanthropy
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Johannes Hohlbein @hohlbeinlab.bsky.social · 19/06/2025
Very much enjoyed yesterday's Physics of Life community event in Utrecht! @seppekuehnlab.bsky.social: microbial communities, #PhilippSavakis: yeast glycolysis, @janniharju.bsky.social: DNA organization in bacteria, #ArthurHernandez: axis formation in hydra, and #LouiseJawerth: protein condensates
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Glen Dsouza @nonresidentdesi.bsky.social · 13/06/2025
Thrilled to share our new paper in @science.org describing our discovery that bacteria can switch from competitors to bonafide predators when resources run dry—arming nanoscale “spears” (T6SS) to stab & consume neighbours. www.science.org/doi/10.1126/... #MicroSKy #Microbiology
science.org
Antagonism as a foraging strategy in microbial communities
In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependen...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 10/06/2025
I can't say I agree with everything here, especially as I think it overstates how much evolutionary theory can explain about what we observe in Nature. However, I very much appreciate the perspective and a bit of muckraking. www.pnas.org/doi/10.1073/...
pnas.org
Complexity myths and the misappropriation of evolutionary theory | PNAS
Recent papers by physicists, chemists, and geologists lay claim to the discovery of new principles of evolution that have somehow eluded over a cen...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 02/06/2025
PhD students interested in ecology and evolution -- consider applying. Reach out to me if you are interested in discussing. www.simonsfoundation.org/grant/simons...
simonsfoundation.org
Simons Graduate Fellowships in Ecology and Evolution
The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...
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NSF-Simons NITMB @nitmb.bsky.social · 27/05/2025
Are you interested in the math-bio interface? Secure your place at the NITMB MathBio Convergence Conference! www.nitmb.org/nitmb-mathbi...
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Jeremy Berg @jeremymberg.bsky.social · 23/04/2025
ACTION ITEM-----ACTION ITEM Implementation of Schedule F This is what a lot of us have been worried about. This allows for many civil service positions to replaced with political appointees. This could include NIH institute directors and even POs. BUT THERE IS A COMMENT PERIOD... 1/n
media.tenor.com
the word alert is in a purple circle
ALT: the word alert is in a purple circle
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Cathy Gao-Howard MD MS @catgaohow.bsky.social · 18/05/2025
Northwestern has not received any NIH funds since March. No written communication about why or what can be done. Thank you Ben Singer for raising awareness at #ATS2025
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SeppeKuehnLab @seppekuehnlab.bsky.social · 17/05/2025
youtu.be/6ZHWIYHlXOs?...
youtu.be
Land of Hope and Dreams
YouTube video by Bruce Springsteen
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SeppeKuehnLab @seppekuehnlab.bsky.social · 12/05/2025
www.science.org/content/arti...
science.org
Exclusive: NSF faces radical shake-up as officials abolish its 37 divisions
Changes seen as a response to presidential directives on what research to fund
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SeppeKuehnLab @seppekuehnlab.bsky.social · 12/05/2025
This is the best tool I've seen for rapidly writing your reps. DO IT! www.aps.org/initiatives/...
aps.org
Write Your Own Letter to Congress
The American Physical Society is a nonprofit membership organization working to advance physics by fostering a vibrant, inclusive, and global community dedicated to science and society.
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gulliver-lab.bsky.social @gulliver-lab.bsky.social · 05/05/2025
It is a great pleasure to listen to @seppekuehnlab.bsky.social His talk is about ´Learning microbiome design principles from natural variation ´. Below, the #liveSketch painting during the seminar and given at the end! #ArtAndScience #MediationScientifique
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Leslie Rissler @ljrissler.bsky.social · 03/05/2025
SaveNSF is a coalition of concerned scientists and allies who are working to save funding for scientific grants through the NSF. The mission is to support and advocate for the continuation of vital research and innovation. Join: www.savensf.com
savensf.com
Home | Savensf
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SeppeKuehnLab @seppekuehnlab.bsky.social · 31/03/2025
Third preprint! – We use community-function landscapes to rationally design communities for bioremediation in soils! Spoiler - it works! Led by Mahmoud Yousef, with @kiseokmicro.bsky.social, J. Tang, V. Charisopoulos, B Willett. @nitmb.bsky.social, NSF, MSTP UChicago. www.biorxiv.org/content/10.1...
biorxiv.org
Collective Microbial Effects Drive Toxin Bioremediation and Enable Rational Design
The metabolic activity of microbial communities is essential for host and environmental health, influencing processes from immune regulation to bioremediation. Given this importance, the rational desi...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 26/03/2025
Another preprint! Microbiomes are often structured in guilds, or groups of taxa that use similar resources - wastewater, fermentation, human gut. How do these guilds respond to environmental fluctuations? Can we learn these guilds from time series in the wild?
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SeppeKuehnLab @seppekuehnlab.bsky.social · 24/03/2025
It’s increasingly clear that the language of microbial communities is one of resources. Conserved metabolism leads to regular, reliable resource flows across ecosystems—from the gut to wastewater. In complex communities, one serious challenge is: who is eating what?
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