The role of intracellular interactions in the collective polarization of tissues and its interplay with cellular geometry. - Shahriar Shadkhoo; Madhav Mani (PLoS Comput. Biol., 2019)

EMBEDR: Distinguishing signal from noise in single-cell omics data. - Eric M. Johnson; William L. Kath; Madhav Mani (Patterns, 2022)

A Waddington landscape for prototype learning in generalized Hopfield networks. - Nacer Eddine Boukacem; Allen Leary; Robin Thériault; Felix Gottlieb; Madhav Mani; Paul François (CoRR, 2023)

Bayesian inference of relative fitness on high-throughput pooled competition assays. - Manuel Razo-Mejia; Madhav Mani; Dmitri Petrov (PLoS Comput. Biol., 2024)