Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. - Ali R. Zomorrodi; Costas D. Maranas (BMC Syst. Biol., 2010)

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities. - Ali R. Zomorrodi; Costas D. Maranas (PLoS Comput. Biol., 2012)

Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits. - Ali R. Zomorrodi; Costas D. Maranas (Eur. J. Oper. Res., 2014)

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design. - Anupam Chowdhury; Ali R. Zomorrodi; Costas D. Maranas (PLoS Comput. Biol., 2014)

Bilevel optimization techniques in computational strain design. - Anupam Chowdhury; Ali R. Zomorrodi; Costas D. Maranas (Comput. Chem. Eng., 2015)

Precision game engineering through reshaping strategic payoffs. - Elie Eshoa; Ali R. Zomorrodi (CoRR, 2024)