The Immune System as a Reactive System: Modeling T Cell Activation With Statecharts. - Na'aman Kam; Irun R. Cohen; David Harel (HCC, 2001)

Modeling biological reactivity: statecharts vs. Boolean logic. - Na'aman Kam; Irun R. Cohen; David Harel (AVI, 2002)

Reactive Animation. - David Harel; Sol Efroni; Irun R. Cohen (FMCO, 2002)

Reactive Animation: Realistic Modeling of Complex Dynamic Systems. - Sol Efroni; David Harel; Irun R. Cohen (Computer, 2005)

Immune System Computation and the Immunological Homunculus. - Irun R. Cohen (MoDELS, 2006)

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

Emergent Dynamics of Thymocyte Development and Lineage Determination. - Sol Efroni; David Harel; Irun R. Cohen (PLoS Comput. Biol., 2007)

The Lymph Node B Cell Immune Response: Dynamic Analysis In-Silico. - Naamah Swerdlin; Irun R. Cohen; David Harel (Proc. IEEE, 2008)

GemCell: A generic platform for modeling multi-cellular biological systems. - Hila Amir-Kroll; Avital Sadot; Irun R. Cohen; David Harel (Theor. Comput. Sci., 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)

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

Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans. - Miri Gordin; Hagit Philip; Alona Zilberberg; Moriah Gidoni; Raanan Margalit; Christopher Clouser; Kristofor Adams; Francois Vigneault; Irun R. Cohen; Gur Yaari; Sol Efroni (PLoS Comput. Biol., 2021)

The biosphere computes evolution by autoencoding interacting organisms into species and decoding species into ecosystems. - Irun R. Cohen; Assaf Marron (CoRR, 2022)

Challenges in Modeling and Unmodeling Emergence, Rule Composition, and Networked Interactions in Complex Reactive Systems. - Assaf Marron; Irun R. Cohen; Guy Frankel; David Harel; Smadar Szekely (MODELSWARD, 2023)

Challenges in Modeling and Unmodeling Complex Reactive Systems: Interaction Networks, Reaction to Emergent Effects, Reactive Rule Composition, and Multiple Time Scales. - Assaf Marron; Irun R. Cohen; Guy Frankel; David Harel; Smadar Szekely (MODELSWARD (Revised Selected Papers), 2023)

Meta-autoencoders: An approach to discovery and representation of relationships between dynamically evolving classes. - Assaf Marron; Smadar Szekely; Irun R. Cohen; David Harel (CoRR, 2025)