Implementing GliderAgent - an agent-based decision support system for glider pilots. - Jan J. Domanski; Radoslaw Dziadkiewicz; Maria Ganzha; Andrzej Gab; Mariusz Marek Mesjasz; Marcin Paprzycki (Software Agents, Agent Systems and Their Applications, 2012)

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. - Richard J. Gowers; Max Linke; Jonathan Barnoud; Tyler J. E. Reddy; Manuel N. Melo; Sean L. Seyler; Jan J. Domanski; David L. Dotson; Sébastien Buchoux; Ian M. Kenney; Oliver Beckstein (SciPy, 2016)

Ligandbook: an online repository for small and drug-like molecule force field parameters. - Jan J. Domanski; Oliver Beckstein; Bogdan I. Iorga (Bioinform., 2017)

Atomistic mechanism of transmembrane helix association. - Jan J. Domanski; Mark S. P. Sansom; Phillip J. Stansfeld; Robert B. Best (PLoS Comput. Biol., 2020)