Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries. - Thomas R. Sokolowski; Thorsten Erdmann; Pieter Rein ten Wolde (PLoS Comput. Biol., 2012)

A Tight Upper Bound on Mutual Information. - Michal Hledík; Thomas R. Sokolowski; Gasper Tkacik (ITW, 2019)

Stable developmental patterns of gene expression without morphogen gradients. - Maciej Majka; Nils B. Becker; Pieter Rein ten Wolde; Marcin Zagórski; Thomas R. Sokolowski (PLoS Comput. Biol., 2024)

AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis. - Michael Alexander Ramirez Sierra; Thomas R. Sokolowski (PLoS Comput. Biol., 2024)

Comparing AI versus optimization workflows for simulation-based inference of spatial-stochastic systems. - Michael Alexander Ramirez Sierra; Thomas R. Sokolowski (Mach. Learn. Sci. Technol., 2025)

Unifying Physics- and Data-Driven Modeling via Novel Causal Spatiotemporal Graph Neural Network for Interpretable Epidemic Forecasting. - Shuai Han; Lukas Stelz; Thomas R. Sokolowski; Kai Zhou; Horst Stöcker (CoRR, 2025)