Projects

• Large-Scale Emergency Response (LaSER)
• Mapping and Sequencing
• Bioinformatics (Language, Environments & Algorithms)
• Functional Genomics
• Cell Informatics (BioSpice, Simpathica)
• Databases (NYUMAD)

Large-Scale Emergency Response (LaSER) Project

• Computational Modeling of Large Magnitude Casualty
  Department of Homeland Security (DHS): 2005-2006.
  • Development of mathematical models to improve preparedness and response capabilities in urban areas.
• PLAN C: Agent-Based model Simulation tool for Planning responses to Catastrophes

Cell Informatics (Modeling and Reasoning)

• Algorithmic Tools and Computational Frameworks for Cell Informatics (BioSpice, Simpathica)
  DARPA : 2001-2005.
  
  • Tools for modeling cellular, inter-cellular and genomic processes with specific applications to understanding signal transduction among cancer cells.
  Collaborator: Mike Wigler, CSHL.
• Cell Signaling and Single Molecule Models for BioComputation
  Air Force (Rome): 2001-2004.
• Selected Publications

Functional Genomics

• N2010: Nitrogen Networks in Plants
  National Science Foundation: 2001-2005.
  
  • Modeling and determining cellular processes involved in the Nitrogen network for Arabidopsis.
  Collaborators: Dan Bush, Nigel Crawford and Gloria Coruzzi, UIUC, UCSD & NYU.

Mapping & Sequencing

• High-Density Gene Copy Number Microarrays
  National Institutes of Health (Joint with CSHL) : 2000-2003.
  
  • Design of a microarray-based statistical analysis system to compare related genomes to find fluctuation in copy numbers of various genomic elements. Primary application of this approach is to compare healthy genomic DNA against DNA from cancer tumor tissues to determine the locations of oncogenes and tumor suppressor genes.
  Collaborator: Mike Wigler, CSHL.

Bioinformatics
(Language, Environments & Algorithms)

• BioInformatics Prototyping Language for Mapping, Sequence Assembly and Data Analysis
  Department of Energy :2000-2003. (Project Summary)
  • Development of Valis Bioinformatics language and environment for very large-scale genome-wide statistical analysis.
• Faculty Development Program for Bioinformatics and Genomics
  New York State Office of Science, Technology, & Academic Research (NYSTAR) : 2001-2004.
  
  • Development of a computational infrastructure and algorithms for computational biology.

Databases

• NYU Microarray Database (NYU MAD)
  
  • The MicroArray Database at NYU's Bioinformatics department is a tool under development whose goal is to assist bioinformatics programs around the world collaborate on research and lower barriers to cooperation by providing a standard interface to the large data sets inherent in such research.