I will be talking about some recent work on using niche theory to model host associated microbiomes in a couple of hours!

📣Tomorrow! 📣Purushottam Dixit (Yale Engineering) will present: 'Niche dimensionality drives microbial community structure'

How do cells know which way to move in a chemical gradient? 🧭 New work by graduate student Andrew Goetz proposes that receptors can compute direction. This new mechanism for directional sensing was published in PNAS late last year: www.pnas.org/doi/10.1073/...

What if aging isn’t just cellular damage, but a lossy transmission of information? We used single-cell data and physics-based models to show that as cells age, the flow of transcriptional information collapses. Here’s what that means. 👇

Just out: new preprint (with @ralitsamadsen.bsky.social) is now #Reviewed at @eLife! "Non-equilibrium strategies for ligand specificity in signaling networks". We show how cells use non-equilibrium strategies to discriminate between ligands in surprising ways 🔗 elifesciences.org/reviewed-pre...

We have a funding for postdoctoral fellowship that needs to be filled very soon. We are exploring new directions (1) at the interface of non-equilibrium computations and physical learning and (2) in building ecologically motivated machine learning models for microbiomes. Please spread the word!

Just learnt that our collaborative grant proposal on identifying master regulators of T cell metabolism in Lupus will not be reviewed as the study section was indefinitely postponed, along with many other grants that are vital to biomedical research.

Has anybody looked at approximate Bayesian computation (ABC) using stat mech? The formulation used in rejection ABC: rho(S(D),S(D')) < eps (rho is discrepancy function, S is a summary stat, D is data, D' is simulated data) looks an awful lot like the microcanonical ensemble with an energy = S(D).

Our work on computational design of microbiomes with desired host properties using mechanistic models is now out in mSystems: journals.asm.org/doi/10.1128/...

Happy to present our second paper on understanding ligand sensing using non-equilibrium reaction networks. Here, we look at some counterintuitive results on how eukaryotic cells sense extracellular spatial gradients in ligands (e.g. growth factors): www.biorxiv.org/content/10.1...

As my first post here, I am really excited to share a new manuscript with @ralitsamadsen.bsky.social on this platform. We looked how non-equilibrium thermodynamics helps ligand discrimination in signaling networks: t.co/ZA6NteUmaS