Avijit Ghosh

Background

Welcome to my Departmental Web Page. My main interest is in Biophysics particularly Computational Biophysics. I try to use some of the mathematical tools of physics : Classical Mechanics, Statistical Mechanics, Kinetics to model and understand the behavior and properties of large macromolecules and their interactions among one another.

Gene Network/Proteomic Interaction Prediction

Currently, I am studying the cascade of interactions involved in signaling pathways by modeling both the hydrodynamic transport of inactive and activated members of the signal cascade in combination with the reaction kinetics of activation and dephosphorylation/inactivation events using Systems Biology approaches and optimized spatio-temporal integrators.

For a more detailed look at our work please take a look at our Current Research page as well as our recently developed systems Biology Page.

Education

• NSF Postdoctoral Fellow - Cornell University

• Ph.D. Columbia University
• M.Phil. Columbia University
• M.A. Columbia University

• B.S.,B.S. University of Houston

Recent (and upcoming) Invited Talks

• March 12, 2007, University of Pennsylvania, Special Topics on Electrical and Systems Engineering, Systems Biology
• February 2007, Drexel University, School of Biomedical Engineering , Systems Biology ICSB-2006
• October 9-13 2006, Yokohama, Japan, The 7th International Conference on Systems Biology ICSB-2006
• June 9th 2006, Forschungszentrum Julich, Germany CBSB, From Simulation to Therapy: A Systems Biology Approach to Oncogene Detection and Drug Design
• April 25th 2006 Georgetown University, Department of Physics, A Systems Biology Approach to Cancer Therapy and Early Detection
• September 8th 2005 University of Cincinnati, Medical Center Computational Studies on Proteins

• April 8th 2005 Biomedical Engineering Systems Biology Series, Drexel University Systems Biology Approaches to Cancer Therapy and Early Detection PDF Link

• December 3rd 2004 NYU Courant Institute

• November 11th 2004 Department of Physics, Drexel University

• November 5th 2004 Department of Chemical Engineering, Drexel University
• October 13th 2004 - BMES Conference BioNetworks Workshop

• October 5th 2004 - A Systems Biology Approach to Oncogene Detection PDF link

  This talk is part of the Computational Orchestra series sponsored by Greater Philadelphia Bioinformatics Alliance

• September 2004 - Drexel University Departmental Introduction

• May 2004 - Drexel University Department of Mathematics Seminar series

Physics Colloquium Talks

I have been organizing the Physics Colloquium series within the department. A calendar of events may be found here. Alternatively, if your calendaring software supports "ics" format calendars, you may subscribe to our colloquium series here

Recent Publications

• Ghosh, A., Kumar, A., Zou, R., Miller, D. "A Systems Biology Approach for Lead Drug Target Prediction with Applications to the MAPK Signal Transduction Pathway". (Prep)

• Miller, D., Ghosh, A. "A Fully Adaptive Second-Order Reaction-Diffusion Operator Splitting Integration Scheme with Applications to System Biology" J. Comp. Phys.)
• Ghosh, A., Pant, D., Kumar, A., Zou, R., Miller D. "From Simulation to Therapy: A Systems Biology Approach to Oncogene Detection" (In Press) Book Chapter, CBSB Conference
• Zou, R. Ghosh, A. "Automated Sensitivity Analysis of Stiff Biochemical Systems using a 4th Order Adaptive Step Size Rosenbrock Method", IEE Proc. Systems Biology (2006) IEE Proc. Sys. Biol. 153(2):79-90 Article Link

• Pant, D., Ghosh, "A Systems Biology Approach for the Study of Cumulative Oncogenes, with Applications to the MAPK Signal Transduction Pathway" Biophys. Chem. (2006) Biophys. Chem. 119(1):49-60 Article Link

• Aravindhan, K., Webb, C.L., Jaye, M., Ghosh, A., Willette, R.N., DiNardo, N.J., Jucker, B.M., (2006) "Assessing the effects of LXR agonists on cellular cholesterol, handling: a stable isotope tracer study", J. Lipid Press 47(6):1250-60.

• Ghosh, A., Miller, D., Zou, R., Sokhansanj, B., Kriete A., (2006) "Spatio-Temporal Systems Biology" Book Chapter in Computational Systems Biology Elsevier Press

• Ghosh, A., Miller, D., Zou, R., Pais, H., Sokhansanj, B., Kriete, A. "Integrated Spatio-temporal Model of Cell Signaling" FOSBE 2005 Article Link

• Scheraga, H.A., A.Liwo, S.Oldziej, C.Czaplewski, J. Pillardy, J. Lee, D.R. Ripoll, J.A. Vila, R. Kazmierkiewicz, J.A. Saunders, Y.A. Arnautova, K.D. Gibson, A. Jagielska, M. Khalili, M. Chinchio, M. Nanias, Y.K. Kang, H. Schafroth, A. Ghosh, R. Elber, M. Makowski., (2005) "The Protein Folding Problem" Book Chapter in New Algorithms for Macromolecular Simulation Springer-Verlag 49, 89-97.

• Pant, D. and A. Ghosh (2005) "Automated oncogene detection in complex protein networks, with applications to the MAPK signal transduction pathway." Biophys. Chem. 113(3):275-88. Article Link

• Vila, J.A., Baldoni, H.A. Baldoni, D.R. Ripoll, A. Ghosh, H.A. Scheraga (2004) "Polyproline II helix conformation in a proline-rich environment: a theoretical study." Biophys. J. 86(2):731-742 Article Link

• Elber, R., A. Ghosh et.al (2003) "Bridging the Gap between Reaction Pathways, Long Time Dynamics and Calculation of Rates. Advances in Chemical Physics126:93-129

• Elber, R. A. Ghosh et.al. (2002) "Long time dynamics of complex systems." Accounts of Chemical Research35(6):396-403 Article Link

• Elber, R. A. Ghosh .et.al. (2002) "The Stochastic Difference Equation as a Tool to Compute Long Time Dynamics" Bridging The Time Scale Gap Berlin, Springer Verlag

• Ghosh, A., R. Elber, et.al. (2002) "An atomically detailed study of the folding pathways of protein A with the stochastic difference equation." Proceedings of the National Academy of Sciences of the United States of America 99(16): 10394-10398 Article Link

• Zhou, R.H., Friesner, R.A., Ghosh, A., Rizzo, R.C., Jorgenson, W.L., Levy, R.M., (2001) "New linear interaction method for binding affinity calculations using a continuum solvent model," Journal of Physical Chemistry B105 (42):10388-10397.Article Link

• Ghosh, A., Rapp, C.S., Friesner, R.A., (1998) "Generalized Born Model Based on a Surface Integral Formulation," Journal of Physical Chemistry 102 (52):10983-10990. Article Link