S. Choubey

Role of protein-protein interactions on model chromatin organization

This study uses a polymer-based model to show how protein-protein interactions and DNA sequence influence chromatin organization and compartmentalization.

Decoding the role of DNA sequence on protein-DNA co-condensation

This paper develops a polymer-based model to study how DNA sequence affects protein-DNA co-condensation, showing that sequence heterogeneity leads to multiple condensates.

Governing principles of transcriptional logic out of equilibrium

This study investigates transcriptional logic out of equilibrium and finds that non-equilibrium binding of transcription factors enables new logic operations not accessible in equilibrium.

Efficacy of information transmission in cellular communication

The paper studies how diffusion and advection affect information transmission in cell signaling using a one-dimensional model and finds that mutual information increases with advection when the Peclet number exceeds one.

Surface condensation of a pioneer transcription factor on DNA

This study uses optical tweezers to observe Klf4 condensation on DNA, showing surface-mediated microphases that reconcile phase separation with nuclear organization.

Probing mechanisms of transcription elongation through cell-to-cell variability of RNA polymerase

The paper uses stochastic simulations to analyze cell-to-cell variability in RNA polymerase numbers and distances to infer transcriptional regulation mechanisms in yeast ribosomal genes.