Ronald R. Coifman

GeneTrajectory infers gene trajectories instead of cell trajectories to uncover progressive gene dynamics in biological processes.

This study uses calcium imaging in awake mice to show that rapid changes in cortical functional connectivity encode spontaneous behaviors and reveal subnetworks not captured by traditional parcellation.

The paper introduces PHATE, a visualization method that captures nonlinear structure in biological data, showing it preserves patterns better than existing tools and reveals novel insights in scRNA-seq data.

The paper introduces a method for extracting cellular structures and denoising temporal signals in calcium imaging data using graph-based clustering and nonlinear mapping.