Concurrency in Biological Modeling: Behavior, Execution and Visualization. - David Harel; Yaki Setty; Sol Efroni; Naamah Swerdlin; Irun R. Cohen (FBTC@CONCUR, 2007)

Generic Reactive Animation: Realistic Modeling of Complex Natural Systems. - David Harel; Yaki Setty (FMSB, 2008)

Crafting game-models using reactive system design. - David Harel; Itai Segall; Hillel Kugler; Yaki Setty (Future Play, 2008)

On Using Divide and Conquer in Modeling Natural Systems. - Yaki Setty; Irun R. Cohen; Avi E. Mayo; David Harel (Algorithmic Bioprocesses, 2009)

Modeling Biology using Generic Reactive Animation. - Yaki Setty; Irun R. Cohen; David Harel (Fundam. Informaticae, 2010)

How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex. - Yaki Setty; Chih-Chun Chen; Maria Secrier; Nikita Skoblov; Dimitrios Kalamatianos; Stephen Emmott (BMC Syst. Biol., 2011)

Multi-scale computational modeling of developmental biology. - Yaki Setty (Bioinform., 2012)

Executable Modeling of Morphogenesis: A Turing-Inspired Approach. - Yaki Setty; Irun R. Cohen; David Harel (Fundam. Informaticae, 2012)

A methodological, task-based approach to Procedure-Specific Simulations training. - Yaki Setty; Oren Salzman (Int. J. Comput. Assist. Radiol. Surg., 2016)