Peer Reviewed Publications


  • Candiello, J., Richardson, T., Padgaonkar, K., Task, K., Kumta, P., Banerjee, I. (2016) Alginate encapsulation of chitosan nanoparticles: A viable alternative to soluble chemical signaling in definitive endoderm induction of human embryonic stem cells. J.Mater.Chem.B.
  • Zhang, L., Parker, R., Swigon, D., Banerjee, I., Bahrami, S., Redl, H., Clermont, G. (2016) A one-nearest-neighbor approach to identify the original time of infection using censored baboon sepsis data. Critical Care Medicine. 
  • Richardson, T., Barner, S., Candiello, J., Kumta, P., Banerjee, I. (2016) Capsule stiffness regulates the efficiency of pancreatic differentiation of human embryonic stem cells. Acta Biomater.


  • Fan, Y., Tajima, A., Goh, SK, Geng, X, Gualtierotti, G., Grupillo, M., Coppola, A., Bertera, S., Rudert, WA, Banerjee, I., Bottino, R., Trucco, M. (2015) Bioengineering Thymus Organoids to Restore Thymic Function and Induce Donor-Specific Immune Tolerance to Allografts. Mol Ther, 23(7), 1262-77
  • Mathew, S., Sundararaj, S. and Banerjee, I. (2015) Network analysis identifies crosstalk interactions governing TGF-β signaling dynamics during endoderm differentiation of human embryonic stem cells. MDPI Processes, 3(2), 286-308


  • Mathew, S. and Banerjee, I. (2014) Quantitative analysis of robustness of dynamic response and signal transfer in insulin mediated PI3K/AKT pathway. Computers and Chemical Engineering, 71: 715-27
  • Jaramillo, M., Mathew, S., Mamiya, H., Goh, S.K. and Banerjee, I. (2014) Endothelial Cells Mediate Islet-specific Maturation of Human Embryonic Stem Cell Derived Pancreatic Progenitor Cells. Tissue Engineering Part A, 21(1-2):14-25
  • Singh, S., Roy, A., Lee, B.E., Ohodnicki, J., Loghmanian, A., Banerjee, I. and Kumta, P.N. (2014) A study of strontium doped calcium phosphate coatings on AZ31 Mater Sci Eng C Mater Biol Appl, Jul 1;40:357-65. doi: 10.1016/j.msec.2014.03.062
  • Singh, S., Roy, A., Lee, B.E., Banerjee, I. and Kumta, P.N. (2014) MC3T3-E1 Proliferation and Differentiation on Biphasic Mixtures of Mg Substituted β-Tricalcium Phosphate and Amorphous Calcium Phosphate. Mater Sci Eng C Mater Biol Appl, 45:589-98 
  • Richardson, T., Kumta, P., Banerjee, I., (2014) Alginate Encapsulation of Human Embryonic Stem Cells to Enhance Directed Differentiation to Pancreatic Islet-like cells. Tissue Engineering Part A, 20 (23-24)
  • Mathew, S., Bartels, J., Banerjee, I., and Vodovotz, Y. (2014) Global sensitivity analysis of a mathematical model of acute inflammation identifies nonlinear dependence of global tissue damage on host interleukin-6 responses. J. Theo. Biol. 358:132-148.
  • Mathew, S., Sundararaj, S., Mamiya, H. and Banerjee, I. (2014) Regulatory interactions maintaining self-renewal of human embryonic stem cells as revealed through systems analysis of PI3K/AKT pathway. Bioinformatics 30 (16): 2334-42
  • Jaramillo, M., Mathew, S., Task, K., Barner, S. and Banerjee, I. (2014) Potential for pancreatic maturation of differentiating human embryonic stem cells is sensitive to the specific pathway of definitive endoderm commitment. PLoS ONE 9(4), e94307
  • Task, K., D'Amore, A., Singh, S., Candiello, J., Jaramillo, M., Wagner, W., Kumta, P. and Banerjee, I. (2014) Systems level approach reveals the correlation of endoderm differentiation of mouse embryonic stem cells with specific microstructural cues of fibrin gels. J. R. Soc. Interface 11: 95


  • Candiello J, Singh SS,Task K, Kumta PN, Banerjee I (2013) Early differentiation patterning of mouse embryonic stem cells in response to variations in alginate substrate stiffness. J Biol Eng 7: 9 
  • Goh S-K, Bertera S, Olsen P, Candiello JE, Halfter W, Uechi G, Balasubramani M, Johnson SA, Sicari BM, Kollar E, Badylak SF, Banerjee I (2013) Perfusion-decellularized pancreas as a natural 3D scaffold for pancreatic tissue and whole organ engineering. Biomaterials 34(28):6760-72 
  • Goh S-K, Olsen P, Banerjee I (2013) Extracellular Matrix Aggregates from Differentiating Embryoid Bodies as a Scaffold to Support ESC Proliferation and Differentiation. PLoS ONE 8: e61856 


  • Chemmangattuvalappil N, Task K, Banerjee I (2012) An integer optimization algorithm for robust identification of non-linear gene regulatory networks. BMC Syst Biol, 6: 119
  • Jaramillo M, Singh SS, Velankar S, Kumta PN, Banerjee I (2012) Inducing endoderm differentiation by modulating mechanical properties of soft substrates. J Tissue Eng Regen Med, doi: 10.1002/term.1602
  • Maria J, Banerjee I (2012) Endothelial cell co-culture mediates maturation of human embryonic stem cell to pancreatic insulin producing cells in a directed differentiation approach. J Vis Exp, 61, pii: 3759, doi:10.3791/3759.
  • Mathew S, Jaramillo M, Zhang X, Zhang LA, Soto-Gutierrez A, Banerjee I (2012) Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences. BMC Syst Biol 6: 154 
  • Task K, Jaramillo M, Banerjee I (2012) Population based model of human embryonic stem cell (hESC) differentiation during endoderm induction. PLoS ONE 7: e32975 
  • Zhang X, Jaramillo M, Singh S, Kumta P and Banerjee I (2012) Analysis of regulatory network involved in mechanical induction of embryonic stem cell differentiation. PLoS ONE, 7: e35700 
  • Banerjee I, Task K, Maiti S. A Genetic Network Identification Algorithm Combining Experiment and Computation. In Computational Biology of Embryonic Stem Cells. Ed. M. Zhan. Bentham Science Publishers, 2012.


  • Banerjee I, Sharma N,Yarmush M (2011) Impact of co-culture on pancreatic differentiation of embryonic stem cells. J Tissue Eng Regen Med, 5: 313-323 
  • Candiello JE, Jaramillo M, Goh SK, Banerjee I (2011) Role of substrates in diabetes therapy: stem cell differentiation and islet transplantation. Crit Rev Biomed Eng, 39: 535-555


  • Banerjee I, Maiti S, Parashurama N, Yarmush M (2010) An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells. Bioinformatics 26: 1332-1339 
  • Barua S, Linton RS, Gamboa J, Banerjee I, Yarmush ML, Rege K (2010) Lytic peptide-mediated sensitization of TRAIL-resistant prostate cancer cells to death receptor agonists. Cancer Lett 293: 240-253 
  • Banerjee, I., Pal, S. and Maiti, S. (2010) Computationally efficient black-box modeling for feasibility analysis. Computers and Chemical Engineering, 34:1515-1521

Before 2010 

  • Banerjee, I., and M.G. Ierapetritou. (2006) An Adaptive Reduction Scheme to Model Reactive Flow. Combust. & Flame., 144(3), 619–633
  • Banerjee, I., and M.G. Ierapetritou. (2005) Feasibility Evaluation of Nonconvex Systems using Shape Reconstruction Techniques. Ind Eng Chem Res, 44, 3638.
  • Banerjee, I., and M.G. Ierapetritou. (2004) Model Independent Parametric Decision Making. Ann Oper Res, 132, 135.
  • Banerjee, I., and M.G. Ierapetritou. (2003) Development of an Adaptive Chemistry Model Considering Micromixing Effects. Chem Eng Sci, 8, 4537.
  • Banerjee, I., and M.G. Ierapetritou. (2003) Process Synthesis under Parameter Variability. Comput Chem Eng, 27, 1499.
  • Balakrishnan, S., P. Georgopoulos, Banerjee I and M.G. Ierapetritou. (2002) Uncertainty Considerations in the Complex Kinetic Mechanisms Reduction. AIChE J, 48, 2875.
  • Banerjee, I. and M.G. Ierapetritou. Design Optimization under Parameter Uncertainty for General Black Box Models Ind & Eng Chem Res, 41, 6687.
  • Banerjee, I., J.M. Modak, K. Bandopadhyay. Mathematical Model for Evaluation of Mass Transfer Limitations in Phenol Biodegradation by Immobilized Pseudomonas Putida, J Biotech, 87, 211.

Refereed Conference Proceedings

  • Banerjee, I., and M.G. Ierapetritou. A Novel Feasibility Analysis Approach Based on Dimensionality Reduction and Shape Reconstruction. CM-017, page 85, ESCAPE 15, Barcelona, Spain, May 2005.
  • Banerjee, I., and M.G. Ierapetritou. An Adaptive Reduction Scheme to Develop Flexible Reduced Chemistry Models for Reactive Flow Simulations. MS-036, page 247, ESCAPE 15, Barcelona, Spain, May 2005.
  • Banerjee, I., and M.G. Ierapetritou. An Adaptive Chemistry Scheme to Develop Flexible Reduced Chemistry Models for Reactive Flow Simulations. 17th ONR Propulsion Meeting, Los Angeles, MA, 2004.
  • Banerjee, I., and M.G. Ierapetritou. Adaptive Chemistry Model Development for Combustion. 16th ONR Propulsion Meeting, Los Angeles, CA, 2003