A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks. - Madhukar S. Dasika; Anshuman Gupta; Costas D. Maranas; Jeffrey D. Varner (Pacific Symposium on Biocomputing, 2004)

Optimization based automated curation of metabolic reconstructions. - Vinay Satish Kumar; Madhukar S. Dasika; Costas D. Maranas (BMC Bioinform., 2007)

OptCircuit: An optimization based method for computational design of genetic circuits. - Madhukar S. Dasika; Costas D. Maranas (BMC Syst. Biol., 2008)

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189. - Patrick F. Suthers; Madhukar S. Dasika; Vinay Satish Kumar; Gennady Denisov; John I. Glass; Costas D. Maranas (PLoS Comput. Biol., 2009)

Rewriting yeast central carbon metabolism for industrial isoprenoid production. - Adam L. Meadows; Kristy M. Hawkins; Yoseph Tsegaye; Eugene Antipov; Youngnyun Kim; Lauren Raetz; Robert H. Dahl; Anna Tai; Tina Mahatdejkul-Meadows; Lan Xu; Lishan Zhao; Madhukar S. Dasika; et al. (Nat., 2016)