Theoretical physicist thinking about ecology and evolution. Of microbes, and spheres in vacuum.
Joined February 2017
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Officially out - very excited to share! “Emergent simplicity” in microbial ecosystems has long been an appealing idea—but meant different things to different people. As a result, the field hasn't agreed: is it real? surprising? useful? 1/3 doi.org/10.1126/science.adr1…
We define emergent predictability—a rigorous way to ask whether simple models make better predictions in more diverse communities, *beyond* simple averaging. Across two experiments, coarse descriptions indeed become more predictive at higher richness. 2/3
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Inspired by the earlier perspective with @joybergelson, Martin Kreitman, @PetrovADmitri, @asanchez_lab
elifesciences.org/articles/6…
—really excited to keep developing these ideas. 3/3
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Excited to share the fruit of a collaboration with the
@SeppeKuehnLab
and Madhav Mani, just out in Nature. Driven by the powerhouse duo of
@kiseokmicro
and Siqi Liu. Predictable functional regimes in minimally processed soil + a simple model recapitulates functional dynamics!
Published in Nature today! Here, we sought to systematically ask how natural community's metabolism changes with the environment. A simple consumer-resource model can predict N cycle metabolism and, more importantly, the mechanism behind its change.
nature.com/articles/s41586-0…
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Now out in MBE! Fitness assays often involve barcoding, but barcode-dependent amplification bias can cause fitness misestimates. We present a method to detect/remove such bias with no changes to the exp. protocol. doi.org/10.1093/molbev/msae1… @RS_McGee @GrantKinsler @PetrovADmitri 1/2
Very excited about this work. "Emergent simplicity" in microbial systems is an old hope, but the term means different things to different people. As a result, the field never quite agreed: is it real? If it’s real, is it surprising? @MoranJacobT arxiv.org/abs/2403.19372 1/3
And if it’s surprising, is it useful for making *predictions*? We present a framework to rigorously define emergent simplicity of prediction, and show it in data. Two experiments, 4 of 5 properties: simple models become more predictive at high diversity. The magic is real! 2/3
As a throwback to this perspective with @joybergelson, Martin Kreitman, @PetrovADmitri, @asanchez_lab elifesciences.org/articles/6… -- this is our group's first step trying to practice what we preach! 3/3
Preprint! If you had a soil sample from Mars, what would you look for as evidence of life? Many proposals focus on specific compounds, but extraterrestrial life need not resemble ours. And no known signature comes from self-replication alone.1/2 @eltanin4 arxiv.org/abs/2403.18614
Excited to share the fruit of a collaboration with the fantastic @SeppeKuehnLab and Madhav Mani, driven by the powerhouse duo of @kiseokmicro and Siqi Liu. Predictable functional phases in minimally processed soil + a simple model recapitulates functional dynamics!
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Our new preprint: How can methods as simple as the @oxcordero group's EQO (based on a linear regression) work for identifying relevant microbial groups? Reason: finding the right *variables* is different from finding the right model! 1/2 doi.org/10.1101/2024.01.21.5…
Just put out a fun new paper with @RS_McGee! In bulk assays where strains/mutants are identified by barcodes, those barcodes are not strictly inert - can differ by e.g. susceptibility to amplification bias. Imagine you wanted to be SUPER careful & correct for that.
One way could be to label every mutant with 10 barcodes… But you don't have to! At least in one popular context (bulk fitness measurement) you can correct for biases with no changes to protocol, even retroactively. Thanks to awesome collaborators @PetrovADmitri @GrantKinsler 2/2
A fantastic collaboration and what a pleasure to be spending my sabbatical with @SeppeKuehnLab at @UChicago. Now we just need to understand *why* this works!
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Excited to share that our coarse-graining paper is out in Physical Review X! Highlights in the thread below. go.aps.org/3MiFCWM
1/4 Excited to share our new work! Coarse-grained descriptions of ecology clearly work (@asanchez_lab), but the strains they group together can behave very differently indeed (@oxcordero). How do we reconcile the paradox? biorxiv.org/content/10.1101/…
Mikhail Tikhonov retweeted
We developed an experiment to increase the scale of QTL mapping so that we may observe how 'low effect' variants play a role in determining phenotypes. 1/4
Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast biorxiv.org/cgi/content/shor… #biorxiv_genetic