Facile: a command-line network compiler for systems biology. - Fernando Siso-Nadal; Julien F. Ollivier; Peter S. Swain (BMC Syst. Biol., 2007)

Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks. - Julien F. Ollivier; Vahid Shahrezaei; Peter S. Swain (PLoS Comput. Biol., 2010)

Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks. - Song Feng; Julien F. Ollivier; Orkun S. Soyer (PLoS Comput. Biol., 2016)