Approximating the solution of the chemical master equation by combining finite state projection and stochastic simulation. - Aron Hjartarson; Jakob Ruess; John Lygeros (CDC, 2013)

Identifying stochastic biochemical networks from single-cell population experiments: A comparison of approaches based on the Fisher information. - Jakob Ruess; John Lygeros (CDC, 2013)

On the Use of the Moment Equations for Parameter Inference, Control and Experimental Design in Stochastic Biochemical Reaction Networks. - Jakob Ruess; John Lygeros (CMSB, 2013)

Grey-box techniques for the identification of a controlled gene expression model. - Francesca Parise; Jakob Ruess; John Lygeros (ECC, 2014)

Moment-based methods for the analysis and identi cation of stochastic models of biochemical reaction networks. - Jakob Ruess (2014)

Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks. - Jakob Ruess; John Lygeros (ACM Trans. Model. Comput. Simul., 2015)

Adaptive moment closure for parameter inference of biochemical reaction networks. - Christian Schilling 001; Sergiy Bogomolov; Thomas A. Henzinger; Andreas Podelski; Jakob Ruess (Biosyst., 2016)

Can optimal experimental design serve as a tool to characterize highly non-linear synthetic circuits? - Maxim Kryukov; Arthur Carcano; Grégory Batt; Jakob Ruess (ECC, 2019)

Optimal control of an artificial microbial differentiation system for protein bioproduction. - Élise Weill; Virgile Andréani; Chetan Aditya; Pierre Martinon; Jakob Ruess; Grégory Batt; J. Frédéric Bonnans (ECC, 2019)

Estimating information in time-varying signals. - Sarah Anhala Cepeda-Humerez; Jakob Ruess; Gasper Tkacik (PLoS Comput. Biol., 2019)

Molecular noise of innate immunity shapes bacteria-phage ecologies. - Jakob Ruess; Maros Pleska; Calin C. Guet; Gasper Tkacik (PLoS Comput. Biol., 2019)

Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes. - Davin Lunz; Grégory Batt; Jakob Ruess; J. Frédéric Bonnans (PLoS Comput. Biol., 2021)

Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level. - Andela Davidovic; Remy Chait; Grégory Batt; Jakob Ruess (PLoS Comput. Biol., 2022)