Marta Biondo

The intrinsic dimension of gene expression during cell differentiation

This study applies intrinsic dimension analysis to single-cell transcriptomic data to capture expression trajectories and define a cell potency score across species and differentiation processes.

Intrinsic dimensionality of single-cell transcriptomic data reveals potency landscapes during cell reprogramming

The paper introduces IDEAS, a tool for computing intrinsic dimensionality from scRNA-seq data to assess cell potency without clustering, and applies it to reprogramming datasets to study potency changes and trajectories.

Out-of-equilibrium gene expression fluctuations in presence of extrinsic noise

The paper analyzes how extrinsic noise affects protein concentration variability during gene activation or inactivation using a stochastic model and simulations.