David M. Umulis

The paper develops a stochastic model of BMP receptor interactions to show the heterodimer-heterotetramer complex functions as a low-pass filter in zebrafish dorsoventral axis formation.

The paper develops an agent-based model of zebrafish epiboly to study force generation and tissue deformation during early development.

CalciumInsights provides a user-friendly tool for analyzing calcium signals across multiple organisms and tissues without requiring programming expertise.

This study shows ROS inhibit myosin phosphorylation to counteract wound contraction, delay closure, and impair regrowth, while chronic ROS depletion alters tissue stiffness and impairs healing.

The paper quantifies Ca2+ wave propagation in Arabidopsis cells in response to MAMPs and wounding, showing distinct mechanisms for each.

The paper develops a core mathematical model of BMP signaling that can replicate gradient dynamics in both Drosophila and zebrafish with minimal parameter changes.

The paper examines how the BMP-Smad pathway balances trade-offs among response speed, noise amplification, and sensitivity to receptor input by tuning non-conserved parameters.

This study shows that a linear BMP signaling gradient establishes radial patterning in the mouse cochlea, with SOX2 refining precision in specific regions.

The paper quantifies BMP signaling gradients in zebrafish embryos and shows how noise and Sizzled maintain the gradient during DV patterning.

WaveletSEG provides a robust, automatic 3D nuclei segmentation method for multicellular embryo analysis without preprocessing, achieving high accuracy in noisy data.

The paper develops a 3D PDE model to simulate BMP signaling during zebrafish blastula development and evaluates its sensitivity to biophysical parameters.

This study quantifies BMP signaling gradient scaling in zebrafish embryos of varying sizes and finds scale invariance up to 30% reduction in cross-sectional perimeter.