Pradyumna Harlapur
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Pradyumna Harlapur
@pradyumnavh.bsky.social
140 followers 1.1K following 0 posts
PhD Student in BioEngg @ IISc | Studying biological networks, gene regulation, and cellular decision-making through computational models.
moltenecdysone09.github.io
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Reposted by Pradyumna Harlapur
saezlab.bsky.social
We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta
GRETA graphical abstract
December 23, 2024 at 8:43 AM
Reposted by Pradyumna Harlapur
adamlmaclean.bsky.social
Transition paths across the EMT landscape are dictated by network logic.

A 🧵 on the perils of ignoring logic in ODE models of gene regulatory networks (GRNs)

🌟 also read on if you like: EMT, bifurcations, multistability, or Waddington-esque landscapes

www.biorxiv.org/content/10.1...
A figure with six panels (Fig 1B from: doi:10.1101/2024.12.03.626660). Each panel shows the transition path represented by a bifurcation plot of the response B with respect to input signal S. There are four different tristable transition paths indicated by whether or not the intermediate state is accessible, and two bistable transition paths.
December 13, 2024 at 9:57 PM
Reposted by Pradyumna Harlapur
fabiantheis.bsky.social
1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇
biorxiv.org/content/10.1101/2024.12.11.627935v1
December 12, 2024 at 2:48 PM