Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. - Michele Seeber; Angelo Felline; Francesco Raimondi 001; Stefanie Muff; Ran Friedman; Francesco Rao; Amedeo Caflisch; Francesca Fanelli (J. Comput. Chem., 2011)

Computer simulations of the signalling network in FLT3 +-acute myeloid leukaemia - indications for an optimal dosage of inhibitors against FLT3 and CDK6. - Antoine Buetti-Dinh; Ran Friedman (BMC Bioinform., 2018)

Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations. - Antoine Buetti-Dinh; Malte Herold; Stephan Christel; Mohamed El Hajjami; Francesco Delogu; Olga Ilie; Sören Bellenberg; Paul Wilmes; Ansgar Poetsch; Wolfgang Sand; Mario Vera; Igor V. Pivkin; et al. (BMC Bioinform., 2020)

Inferring time-dependent population growth rates in cell cultures undergoing adaptation. - H. Jonathan G. Lindström; Ran Friedman (BMC Bioinform., 2020)

Pattern and Dynamics of FLT3 Duplications. - Guido Todde; Ran Friedman (J. Chem. Inf. Model., 2020)

Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH···Nucleophile in Transition State Stabilization in Arabidopsis thaliana Cell-Wall Invertase 1. - Wijitra Meelua; Tanchanok Wanjai; Natechanok Thinkumrob; Ran Friedman; Jitrayut Jitonnom (J. Chem. Inf. Model., 2023)

Beyond IC50 - A computational dynamic model of drug resistance in enzyme inhibition treatment. - J. Roadnight Sheehan; Astrid S. de Wijn; Thales Souza Freire; Ran Friedman (PLoS Comput. Biol., 2024)

Interplay of mutations, alternate mechanisms, and treatment breaks in leukaemia: Understanding and implications studied with stochastic models. - H. Jonathan G. Lindström; Astrid S. de Wijn; Ran Friedman (Comput. Biol. Medicine, 2024)

Synergy and antagonism between azacitidine and FLT3 inhibitors. - Jingmei Yang; Ran Friedman (Comput. Biol. Medicine, 2024)

Estimation of Absolute Binding Free Energies for Drugs That Bind Multiple Proteins. - Erik Lindahl; Ran Friedman (J. Chem. Inf. Model., 2025)