[View Image] [View Image] [View Image] [View Image]

Research

Our research interests are broadly in the areas of modeling and simulation of complex networks with a focus on biological networks and distributed computing.

Research Summary

 

1) Stochastic Modeling, Analysis and Simulation of complex Biological Systems – currently working on the development of a discrete event simulation tool (iSimBioSys 2.0) for a quantitative understanding of complex processes in life sciences. Sub-projects include:

                 (a)            Influenza Viral Life-cycle simulation (in collaboration with U.T. Southwestern Medical Center in Dallas)

                 (b)            RNAi Pathway Simulation (in collaboration with Pfizer-Global Research Labs, Groton).

                 (c)             Aβ aggregation pathway simulation in Alzheimer’s Disease (in collaboration with    Univ of Southern Mississippi).

2) Reverse Engineering algorithms for Gene regulatory networks (GRN), their analysis and visualization techniques. Sub-projects include:

                 (a)            Staphylococcus aureus network analysis and visualization toolset (in collaboration with Univ of Southern Mississippi)

                 (b)            Time-lagged information theoretic algorithms to reverse engineer GRNs (in collaboration with US Army Corps of Engineers: ERDC-Vicksburg).

3)  Designing robust wireless sensor networks using the concept of attractor sites from gene regulatory networks (in collaboration with the US Army Corps of Engineers: ERDC-Vicksburg).

4)  Cyber-Infrastructure development for data preprocessing and reverse-engineering tools in gene regulatory networks (in collaboration with IIOAB, India).

5) Economic theory based pricing, resource management and job scheduling issues in distributed systems with an emphasis on mobile grid computing (in collaboration with U.T. Arlington).

6) Architecture design, time-slot scheduling and performance analysis of optical burst switched (OBS) core transport network and wireless sensor networks.

 

Research Grants                

 

External awards:

1) NSF-EPSCOR RII: subcontract of the "Modeling and Simulation of Complex Systems" grant, $1,090,000, 2009 - 2014, Role: senior personnel.

2) U.S. Army ERDC, "Bayesian Learning and Optimization Approaches to Microarray Data Analysis and Gene Regulatory Network Reconstruction," $439,608, 2008-2010, Role: Co-PI.

3) NSF CCF, "Molecular-level stochastic simulations to predict the dynamics of protein misfolding and aggregation", $125,000, 2010-2013, Role: PI.

4) NSF CNS, "Improving the Efficiency of Wireless Sensor Networks using Principles of Genomic Robustness", $218,409, 2010-2013, Role: PI.

5) US Army ERDC, Context-specific systems level inference and visualization of gene regulatory networks in Ecotoxicology, $90,000, 2010-2013, Role: Co-PI.

6) NIH-PAR-08-150 Seed grant (PI): “Molecular-level simulations to predict the on-pathway dynamics of Aβ aggregation”, $20,000, 2010-2011.

7) US Army ERDC, "Reverse Engineering the Robustness of Biological Signaling Networks", $881,300, 2012-2015, Role: Co-PI.

 

Internal Awards:

8) $1900, VCU Global Education Office to support summer research for an undergraduate student.

9) Virginia Commonwealth University, $50,000 (2011-14), Role: PI.

10) University of Southern Mississippi, $40,000 (2008-11), Role: PI.

 

Presentations

·      Systems Biology: Computational means towards drug discovery. Department of Information Technology, Rajabazar Science College, West Bengal University of Science & Technology, Kolkata, India, August 2011.

·      Systems Biology: Computational means towards drug discovery. Department of Computer Science, Indian Statistical Institute, Kolkata, India, August 2011

·      Systems Biology: Computational means towards drug discovery. IAB Meeting at the Department of Computer Science, VCU, February 2012

·      Can biological network topologies benefit engineered systems? NSF Sponsored Workshop on “Biologically Inspired Networking”, NSF, Washington DC, July 2011

·      “Modeling, Simulation and Algorithms to comprehend Bio-Complexity: a Systems approach towards Drug Discovery”, Seminar at US Army Labs, March 2011.

·      “Modeling, Simulation and Algorithms to comprehend Bio-Complexity: a Systems approach towards Drug Discovery”, Seminar at Computer Science department at Virginia Commonwealth University, Feb 2011.

·      “Modeling, Simulation and Algorithms to comprehend Bio-Complexity: a Systems approach towards Drug Discovery”, Seminar at Computer Science department at Louisiana State University, Aug 2010.

·      “Molecular Simulations to understand the dynamics of Protein Aggregation Systems”, Biomedical Research Symposium at USM, Sep 2010.

·      "Stochastic Simulation of Biological Networks", seminar talk at US Army: Engineer Research & Development Center (ERDC), Vicksburg, Feb 2009.

·      "A Stochastic Model to study the Influenza Molecular Infection Machinery", paper presented at MCBIOS 2009, Starkville, Feb 2009.

·      “How does Network Uncertainty map to Complex Biological Systems”, NSF, 2010.

·      “Simulating the RNAi pathway”, Department of Biological Sciences, USM, 2009.

·      “Systems Biology: Computational means toward drug discovery” School of Computing Summer Camp, USM, 2009.

·      “Mobile Grid Computing: From Theory to Practice”, NASA Stennis Space Research Center, 2009.

·      "A Discrete Event based Stochastic Simulation Approach for studying the dynamics of Complex Biological Systems", seminar talk at University of Southern Mississippi, April 2008.

·      "Parametric and Stochastic models for Discrete Event based biological system simulations", seminar talk at Pfizer Inc., PGRD-Groton, CT, June 2007.

·      "Applications of Systems Biology in the Pharmaceutical Industry: Some studies on the RNA Interference technology and Pocket Mining Activities", seminar talk at Pfizer Inc., PGRD-Groton, CT, August 2007.

·      "A Diffusion Model to Estimate the Inter-arrival Time of Charged Molecules in Stochastic Event based Modeling of Complex Biological Networks", paper presented at CSB 2005, Stanford, CA, August 2005.

·      "Modeling the Diffusion process in Stochastic Event based Simulation of the PhoPQ system", paper presented at ISBB 2006, Bhubaneshwar, India, Dec 2006.

·      "Parametric and Stochastic Modeling of Molecular Reactions in the Cell", paper presented at DABC 2005, U.T. Southwestern Medical Centre, USA, August 2006.

·      "A Game Theory based Pricing Strategy for Job allocation in Mobile Grids", paper presented at IPDPS 2004, Santa Fe, USA, April 2004.

·      "Cost-Optimal Job Allocation Schemes for Bandwidth-Constrained Distributed Computing Systems", paper presented at HiPC 2005, Goa, India, Dec 2005.

·      "A Photonic Container Switched Transport Network to Support Long-Haul Traffic at the Core", paper presented at BROADNETS 2005, Boston, USA, Oct 2005.

·      "A Cross-Layer Design to Improve Quality of Service in Online Multiplayer Wireless Gaming Networks", paper presented at BROADNETS 2005, Boston, USA, Oct 2005.

 

 

[View Image]
View graphic versionView graphic versionView graphic version