Shubham Tripathi

PROFET Predicts Continuous Gene Expression Dynamics from scRNA-seq Data to Elucidate Heterogeneity of Cancer Treatment Responses

A multi-level formalism to model hybrid phenotypes in Epithelial-Mesenchymal Plasticity

The paper introduces a multilevel Boolean model to capture hybrid epithelial-mesenchymal phenotypes, revealing more stable and biologically relevant hybrid states than traditional binary models.

Constraints and tunability of antigen-agnostic memory durability

This study develops mathematical models and simulations to show that antigen-agnostic memory durability is constrained by immune cell turnover, cytokine dependence, and epigenetic state transmission, and can be tuned via cytokine-mediated feedback.

Reconstruction of single cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition

This study uses optimal transport analysis on scRNA-seq data to reconstruct EMT trajectories in MCF10A cells, identifying three distinct fates and novel genes associated with different EMT states.

Minimal frustration underlies the usefulness of incomplete and inexact regulatory network models in biology

The paper shows that minimal frustration in biological networks allows simple, low-dimensional behavior despite their complexity, explaining the effectiveness of incomplete regulatory network models.