Maximizing predictability of a bottom-up complex multi-scale model through systematic validation and multi-objective multi-level optimization. - Jean-Marie C. Bouteiller; Zhuobo Feng; Alexander Onopa; Mike Huang; Eric Y. Hu; Endre T. Somogyi; Michel Baudry; Serge Bischoff; Theodore W. Berger (NER, 2015)

libRoadRunner: a high performance SBML simulation and analysis library. - Endre T. Somogyi; Jean-Marie Bouteiller; James A. Glazier; Matthias König 003; J. Kyle Medley; Maciej H. Swat; Herbert M. Sauro (Bioinform., 2015)

Formalizing knowledge in multi-scale agent-based simulations. - Endre T. Somogyi; James P. Sluka; James A. Glazier (MoDELS, 2016)

Towards a multi-scale agent-based programming language methodology. - Endre T. Somogyi; Amit Hagar; James A. Glazier (WSC, 2016)

ProtoMD: A prototyping toolkit for multiscale molecular dynamics. - Endre T. Somogyi; Andrew Abi Mansour; Peter J. Ortoleva (Comput. Phys. Commun., 2016)

A modeling and simulation language for biological cells with coupled mechanical and chemical processes. - Endre T. Somogyi; James A. Glazier (SpringSim (TMS), 2017)

A Dynamic Non-Manifold Mesh Data Structure to Represent Biological Materials. - Endre T. Somogyi (J. WSCG, 2018)

Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. - Geoffrey C. Fox; James A. Glazier; J. C. S. Kadupitiya; Vikram Jadhao; Minje Kim; Judy Qiu; James P. Sluka; Endre T. Somogyi; Madhav V. Marathe; Abhijin Adiga; Jiangzhuo Chen; Oliver Beckstein; et al. (IPDPS Workshops, 2019)