Using Evolutionary Methods to Study G-Protein Coupled Receptors. - Orkun S. Soyer; Matthew W. Dimmic; Richard R. Neubig; Richard A. Goldstein (Pacific Symposium on Biocomputing, 2002)

A Formal and Integrated Framework to Simulate Evolution of Biological Pathways. - Lorenzo Dematté; Corrado Priami; Alessandro Romanel; Orkun S. Soyer (CMSB, 2007)

In silico evolution of chemotaxis. - Richard A. Goldstein; Orkun S. Soyer (ALIFE, 2008)

Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics. - Richard A. Goldstein; Orkun S. Soyer (PLoS Comput. Biol., 2008)

Evolving BlenX programs to simulate the evolution of biological networks. - Lorenzo Dematté; Corrado Priami; Alessandro Romanel; Orkun S. Soyer (Theor. Comput. Sci., 2008)

Evolution under Fluctuating Environments Explains Observed Robustness in Metabolic Networks. - Orkun S. Soyer; Thomas Pfeiffer 003 (PLoS Comput. Biol., 2010)

On the role of ultrasensitivity in biomolecular control systems. - Francesco Montefusco; Arno Steinacher; Ozgur E. Akman; Declan G. Bates; Orkun S. Soyer (CDC, 2012)

Split Histidine Kinases Enable Ultrasensitivity and Bistability in Two-Component Signaling Networks. - Munia Amin; Steven L. Porter; Orkun S. Soyer (PLoS Comput. Biol., 2013)

Phosphorelays Provide Tunable Signal Processing Capabilities for the Cell. - Varun B. Kothamachu; Elisenda Feliu; Carsten Wiuf; Luca Cardelli; Orkun S. Soyer (PLoS Comput. Biol., 2013)

Phosphate Sink Containing Two-Component Signaling Systems as Tunable Threshold Devices. - Munia Amin; Varun B. Kothamachu; Elisenda Feliu; Birgit E. Scharf; Steven L. Porter; Orkun S. Soyer (PLoS Comput. Biol., 2014)

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)

MetQy - an R package to query metabolic functions of genes and genomes. - Andrea S. Martinez-Vernon; Frederick Farrell; Orkun S. Soyer (Bioinform., 2018)