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)

Large-scale inference of the transcriptional regulation of Bacillus subtilis. - Anshuman Gupta; Jeffrey D. Varner; Costas D. Maranas (Comput. Chem. Eng., 2005)

Computationally Derived Points of Fragility of a Human Cascade Are Consistent with Current Therapeutic Strategies. - Deyan Luan; Michael Zai; Jeffrey D. Varner (PLoS Comput. Biol., 2007)

Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation. - Joshua Lequieu; Anirikh Chakrabarti; Satyaprakash Nayak; Jeffrey D. Varner (PLoS Comput. Biol., 2011)

Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1. - Russell Gould; David M. Bassen; Anirikh Chakrabarti; Jeffrey D. Varner; Jonathan T. Butcher (PLoS Comput. Biol., 2016)

JuPOETs: a constrained multiobjective optimization approach to estimate biochemical model ensembles in the Julia programming language. - David M. Bassen; Michael Vilkhovoy; Mason Minot; Jonathan T. Butcher; Jeffrey D. Varner (BMC Syst. Biol., 2017)

Dynamic Optimization with Particle Swarms (DOPS): a meta-heuristic for parameter estimation in biochemical models. - Adithya Sagar; Rachel LeCover; Christine Ann Shoemaker; Jeffrey D. Varner (BMC Syst. Biol., 2018)

Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors. - Mengrou Shan; David Dai; Arunodai Vudem; Jeffrey D. Varner; Abraham Duncan Stroock (PLoS Comput. Biol., 2018)