Staff information

Biography

Dr. Harish Shankaran is a biomedical engineer with expertise in the computational modeling of biological systems. His research involves the application of tools and techniques from the engineering sciences" specifically from the areas of nonlinear dynamics, control systems theory, biochemical systems theory, optimization, parametric sensitivity analysis and image processing" to gain a systems level understanding of cell function. In addition to predictive modeling of biomolecular network dynamics, Dr. Shankaran is interested in the development of methods to deduce network structure using data from high throughput experiments. He is the author of several publications in the areas of biophysics and computational biology.

Research Interests

• Cell Biology
• Mathematical Modeling
• Nonlinear Dynamics
• Control Systems Theory
• Optimization

Education and Credentials

• Ph.D., Chemical & Biological Engineering, State University of New York at Buffalo
• B.Tech (Honors), Chemical Engineering, Indian Institute of Technology, Kharagpur, India

PNNL Publications

2012

• Shankaran H, TJ Weber, CH Freiin von Neubeck, and MB Sowa. 2012. "Using Imaging Methods to Interrogate Radiation-Induced Cell Signaling." Radiation Research 177(4 ):496-507.  doi:10.1667/RR2669.1
• Freiin von Neubeck CH, H Shankaran, NJ Karin, PM Kauer, WB Chrisler, X Wang, RJ Robinson, KM Waters, SC Tilton, and MB Sowa. 2012. "Cell Type-dependent Gene Transcription Profile in Three Dimensional Human Skin Tissue Model Exposed to Low Doses of Ionizing Radiation: Implications for Medical Exposures." Environmental and Molecular Mutagenesis 53(4):247-259.  doi:10.1002/em.21682
• McDermott JE, KD Jarman, RC Taylor, MJ Lancaster, H Shankaran, KB Vartanian, SL Stevens, M Stenzel-Poore, and AP Sanfilippo. 2012. "Modeling Dynamic Regulatory Processes in Stroke." PLoS Computational Biology 8(10):e1002722.  doi:10.1371/journal.pcbi.1002722
• Shankaran H, Y Zhang, WB Chrisler, JA Ewald, HS Wiley, and H Resat. 2012. "Integrated Experimental and Model-based Analysis Reveals the Spatial Aspects of EGFR Activation Dynamics." Molecular Biosystems 8(11):2868-2882.  doi:10.1039/C2MB25190F

2011

• Resat H, MN Costa, and H Shankaran. 2011. "Spatial Aspects in Biological System Simulations." Chapter 17 in Methods in Enzymology: Computer Methods, Part C, vol. 487, ed. M Johnson and L Brand, pp. 485-511.  Elsevier, Amsterdam, Netherlands. 
• McDermott JE, H Shankaran, AJ Eisfeld, S Belisle, G Neumann, C Li, SK Mcweeney, CL Sabourin, Y Kawaoka, MG Katze, and KM Waters. 2011. "Conserved Host Response to Highly Pathogenic Avian Influenza Virus Infection in Human Cell Culture, Mouse and Macaque Model Systems." BMC Systems Biology 5:Article No. 190.  doi:10.1186/1752-0509-5-190

2010

• Shankaran H, and HS Wiley. 2010. "Oscillatory Dynamics of the Extracellular Signal-regulated Kinase Pathway." Current Opinion in Genetics & Development 20(6):650-655.  doi:10.1016/j.gde.2010.08.002
• Shankaran H, WB Chrisler, RL Sontag, and TJ Weber. 2010. "Inhibition of ERK Oscillations by Ionizing Radiation and Reactive Oxygen Species." Molecular Carcinogenesis 50(6):424-432.  doi:10.1002/mc.20724
• Joslin EJ, H Shankaran, LK Opresko, N Bollinger, DA Lauffenburger, and HS Wiley. 2010. "Structure of the EGF receptor transactivation circuit integrates multiple signals with cell context." Molecular Systems Biology 6(7):1293-1306.  doi:10.1039/c003921g
• Weber TJ, H Shankaran, HS Wiley, LK Opresko, WB Chrisler, and RD Quesenberry. 2010. "Basic Fibroblast Growth Factor Regulates Persistent ERK Osciliations in Premaligant but not Malignant JB6 Cells." Journal of Investigative Dermatology 130(5):144-156. 

2009

• Shankaran H, DL Ippolito, WB Chrisler, H Resat, N Bollinger, LK Opresko, and HS Wiley. 2009. "Rapid and Sustained Nuclear-Cytoplasmic ERK Oscillations Induced by Epidermal Growth Factor." Molecular Systems Biology 5:Article Number: 332.  doi:10.1038/msb.2009.90
• Zhang Y, LK Opresko, H Shankaran, WB Chrisler, HS Wiley, and H Resat. 2009. "HER/ErbB Receptor Interactions and Signaling Patterns in Human Mammary Epithelial Cells." BMC Cell Biology 10 :Article No. 78.  doi:10.1186/1471-2121-10-78

2008

• Shankaran H, Y Zhang, L Opresko, and H Resat. 2008. "Quantifying the effects of co-expressing EGFR and HER2 on HER activation and trafficking." Biochemical and Biophysical Research Communications 371(2):220-224.  doi:10.1016/j.bbrc.2008.04.043
• Wiley HS, and H Shankaran. 2008. "Smad Signaling Dynamics: Insights from a Parsimonious Model." Science Signaling 1(36):pe41. 
• Zhang Y, H Shankaran, L Opresko, and H Resat. 2008. "System theoretical investigation of human epidermal growth factor receptor-mediated signalling." IET Systems Biology 2(5):273-284.  doi:10.1049/iet-syb:20080116

2007

• Shankaran H, H Resat, and HS Wiley. 2007. "Cell surface receptors for signal transduction and ligand transport - a design principles study." PLoS Computational Biology 3(6):e101.  doi:10.1371/journal.pcbi.0030101
• Shankaran H, HS Wiley, and H Resat. 2007. "Receptor downregulation and desensitization enhance the information processing ability of signaling receptors." BMC Systems Biology 1:Art. No. 48. 

2006

• Shankaran H, HS Wiley, and H Resat. 2006. "Modeling the effects of HER/ErbB1-3 co-expression on receptor dimerization and biological response." Biophysical Journal 90(11):3993-4009. 
• Shankaran H, HS Wiley, and H Resat. 2006. "Modeling the Effects of HER/ErbB1-3 Coexpression on Receptor Dimerization and Biological Response ." Biophysical Journal 90(11):3993-4009.  doi:10.1529/biophysj.105.080580
• Singh I, H Shankaran, ME Beauharnois, Z Xiao, P Alexandridis, and S Neelamegham. 2006. "Solution structure of human von Willebrand factor studied using small angle nuetron scattering." Journal of Biological Chemistry 281(50):38266-38275. 
• Xiao Z, HL Goldsmith, FA MacIntosh, H Shankaran, and S Neelamegham. 2006. "Biomechanics of P-selectin PSGL-1 bonds: Shear threshold and integrin-independent cell adhesion." Biophysical Journal 90(6):2221-2234.  doi:10.1529/biophysj.105.065789