Ashok Prasad

Morphological parameters can capture emergent properties of dynamic disordered cytoskeletal networks

The paper uses morphological descriptors to classify dynamic disordered cytoskeletal networks and finds that no single descriptor can fully capture differences in simulated trajectories.

Impact of variability in cell generation times on cell-to-cell variability of protein concentrations

The paper analyzes how variability in cell division times affects protein concentration variability in cell lineages and populations, showing age-dependent differences in variance and skewness.

Quantitative modeling reveals sources of variability in transcriptional activation assays

The paper develops a workflow to identify and minimize biological variability in transcriptional activation assays using mathematical modeling and sensitivity analysis.

Matrix Stiffness Dictates Doxorubicin-Induced Apoptosis by Modulating Cell-Cycle State in HeLa Cells

This study shows that substrate stiffness affects doxorubicin-induced apoptosis in HeLa cells by altering cell-cycle state, not cytoskeletal mechanics.

Cyclo-stationary distributions of mRNA and Protein counts for random cell division times

The paper develops an analytical method to compute mRNA and protein count distributions under random cell division times and analyzes noise contributions from intrinsic and extrinsic sources.

A Genetic Toggle Switch in Plants

The paper develops a toggle switch genetic circuit in plants using computationally selected components and in silico models, demonstrating predictable function in stably engineered plants.

Exact distributions of threshold crossing times of proteins under post-transcriptional regulation by small RNAs

The paper calculates exact distributions of protein threshold crossing times under post-transcriptional regulation by small RNAs, showing non-monotonic noise behavior and parameter-dependent fluctuations.

Cell Morphology accurately predicts the nuclear shape of adherent cells

The paper trains a model to predict nuclear shape from cell shape and shows that actomyosin contractility influences nuclear morphology.

Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets

This paper introduces DeCOr-MDS, a robust MDS method that detects and corrects orthogonal outliers to improve embedding quality in biological datasets.

Amphibian segmentation clock models suggest mechanisms of slowed development across increasing genome size and nuclear volume

The paper uses a mathematical model of the somitogenesis clock to investigate how increased genome and nuclear size slow developmental tempo in amphibians.