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Research

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My goal is to develop close collaborations with strong experimental and theoretical components. By blending cross and inter-disciplinary expertise we hope to expand scientific inquiry in new and exciting directions.

General reports on our research:

Current Research Support

  • NSF PHY 1205840, Damage mitigation in signal transduction networks (PI)
  • NSF MCB 1715826, Systems Biology of Heterotrimeric G-protein Signaling in Overlapping Stomatal Closure Pathways (co-PI)
  • NSF IIS 1814405, Collaborative Research: Network Analysis and Anomaly Detection via Global Curvatures (PI)

Research Group

  • Dr. Jorge G. T. Zanudo
  • Dr. David Wooten
  • Xiao Gan
  • Parul Maheshwari
  • Jordan Rozum
  • Fatemeh Sadat Fatemi

Group Alumni

Ph.D. Graduates (2003-2018)

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  1. Dr. Gang Yang
  2. Dr. Steven Steinway, MD, PhD
  3. Dr. Zhongyao Sun
  4. Dr. Assieh Saadatpour
  5. Dr. Ranran Zhang
  6. Dr. Usha Nandini Raghavan
  7. Dr. Hari Thadakamalla
  8. Dr. Claire Christensen
  9. Dr. Song Li

Postdoctoral Associates (2003-2018)

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  1. Dr. Jorge G. T. Zanudo
  2. Dr. Colin Campbell
  3. Dr. Anshuman Gupta
  4. Dr. Jaewook Joo
  5. Dr. Juilee Thakar
  6. Dr. Suann Yang
  7. Dr. Rui-Sheng Wang

Research Areas

Modeling epithelial to mesenchymal transition in liver cancer

Epithelial-to-mesenchymal transition (EMT) is a developmental process hijacked by cancer cells to leave the primary tumor site, invade surrounding tissue, and establish distant metastases. We have constructed an EMT network of 70 nodes and 135 edges by integrating the signaling pathways involved in developmental EMT and known dysregulations in invasive liver cancer. We then used discrete dynamic modeling to understand the dynamics of the EMT network driven by TGFβ. We used the model to identify combinatorial interventions for the suppression of EMT, and validated them by siRNA experiments. We also found that many apparently successful single interventions may lead to steady states that are in-between epithelial and mesenchymal states.

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Collaborators:

  • Thomas P. Loughran, M.D., University of Virginia School of Medicine

Modeling ecological communities

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Relationships such as those between predators and prey, or symbiotic interactions like those of plants and insect pollinators, link the species of an ecological community into a complex network of interdependence. This means that the demise of one species can have knock-on effects that are hard to predict and may occasionally be catastrophic.

Collaborators:

  • Prof. Katriona Shea, Professor of Biology, Penn State

Signal transduction in plant guard cells

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Plants have developed sophisticated signal transduction mechanisms to be able to respond to changing environmental conditions. One such mechanism is the opening of stomata (pores) to light and closing them in response to drought conditions. We have synthesized experimental information on light and drought signaling to reconstruct and model the signal transduction network of guard cells. Our work has identified knowledge gaps and has generated new predictions and hypotheses.

Collaborators:

  • Prof. Sarah Assmann, Waller Professor of Biology, Department of Biology, Penn State