A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases. - Dipak Barua; James R. Faeder; Jason M. Haugh (PLoS Comput. Biol., 2009)

An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models. - Dipak Barua; Joonhoon Kim; Jennifer L. Reed (PLoS Comput. Biol., 2010)

Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells. - Dipak Barua; William S. Hlavacek (PLoS Comput. Biol., 2013)

BioNetGen 2.2: advances in rule-based modeling. - Leonard A. Harris; Justin S. Hogg; José Juan Tapia; John A. P. Sekar; Sanjana Gupta; Ilya Korsunsky; Arshi Arora; Dipak Barua; Robert P. Sheehan; James R. Faeder (Bioinform., 2016)

A Multiscale Algorithm for Spatiotemporal Modeling of Multivalent Protein-Protein Interaction. - MD Shahinuzzaman; Dipak Barua (J. Comput. Biol., 2017)

A Scalable Parallel Framework for Multicellular Communication in Bacterial Quorum Sensing. - Satyaki Roy; Mohammad Aminul Islam; Dipak Barua; Sajal K. Das 001 (BICT, 2019)

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. - Keesha E. Erickson; Oleksii S. Rukhlenko; MD Shahinuzzaman; Kalina P. Slavkova; Yen Ting Lin; Ryan Suderman; Edward C. Stites; Marian Anghel; Richard G. Posner; Dipak Barua; Boris N. Kholodenko; William S. Hlavacek (PLoS Comput. Biol., 2019)