DEEPAK BANDYOPADHYAY
Address: Department of Computer Science 
         CB #3175, Sitterson Hall 
         University of North Carolina 
         Chapel Hill, NC 27599-3175
Phone  : (919) 969-7826  (h), (919) 962-1894 (w) 
Email  : debug @ cs.unc.edu 
Web    : http://www.cs.unc.edu/~debug


OBJECTIVE: A challenging research and development position in bioinformatics 
in a technology-driven company or research institution.


INTERESTS: Biogeometry (Computational Geometry in Molecular Biology), Structural Bioinformatics, Computational Geometry, Data Mining, Algorithm Design for Proteomics, Computer Graphics


EDUCATION:

University of North Carolina at Chapel Hill, NC, USA
	   Ph.D. in Computer Science, expected July 2005
	   M.S. in Computer Science, May 2002
Indian Institute of Technology, Delhi, India
	   B.Tech. in Computer Science and Engineering, Aug 1999, GPA=3.56/4.0


SKILLS:

Languages: C, C++(CGAL/STL/OpenGL), Java, MATLAB, scripting(Unix, Perl), HTML.
Tools: Molecular modeling (Sybyl, Accelrys, Deepview, VMD, Kinemage, Pymol); standard bioinformatics sequence and structure methods and web services  
Platforms: Windows, Linux and other Unix flavors


EXPERIENCE:

Research Assistant, University of North Carolina at Chapel Hill, 6/01-present 

Ph.D. Thesis: Developed a geometric framework for robust nearest neighbor analysis in imprecise points, such as coordinates 
from protein structures (Almost-Delaunay simplices, C++/CGAL implementation available). Developed applications in analysis of protein structure: scoring functions for protein packing; secondary structure assignment from C-alphas; subgraph mining to find family-specific spatial motifs for functional annotation of structural genomics targets; and analysis of hinges and conformational change. (advisor: Dr. Jack Snoeyink). 

Instructor, University of North Carolina at Chapel Hill, 6/03-7/03

Designed and taught an introductory undergraduate course on computer programming with Java

Summer Intern, BIWI (Computer Vision Lab), ETH Zurich, Switzerland. 6/02-8/02

Implemented the framework for a simultaneous multi-projector and multi-camera structured light system which was used for real-time capture of the human body.

Research Assistant, University of North Carolina at Chapel Hill, 8/00-6/01

Developed Dynamic Shader Lamps, an interactive Augmented Reality system for painting on moving real objects using projectors.

Summer Intern, HRL Labs, Malibu, CA. 6/00-8/00

Wrote applications for synchronized recording of video and sensor data streams for use with a simulation testbed for visualizing occlusions in an outdoor Augmented Reality system.

Research Assistant, University of North Carolina at Chapel Hill, 8/99-5/00

Worked on occlusion resolving methods for the use of Augmented Reality in ultrasound-guided needle biopsy.

Summer Intern, Kent Ridge Digital Labs, Singapore. 6/98-7/98

Built GUI application for visual feature extraction and feature-based query on a video database, using Java, which was integrated into Video Indexing software being developed at KRDL.  

Academic Projects - Graduate: Kinemage visualization for almost-Delaunay tetrahedra; Structured light based 3D object localization; Distance functions for geometric simplification; Stained-glass shader; 3D painting for spatially augmented reality; Parallel N-body simulations; Robust Internet audio codec

Undergraduate: Distributed Virtual Environment for multi-user control of an articulated figure (thesis project); Face recognition; Simulation of network congestion control schemes; Distributed matrix multiplication and exponentiation; Slot machine simulation on FPGAs.


PUBLICATIONS:

Computational Geometry and Structural Bioinformatics: 

Bandyopadhyay, Deepak and Jack Snoeyink. Almost-Delaunay Simplices : Nearest Neighbor Relations for Imprecise Points. ACM-SIAM Symposium on Discrete Algorithms (SODA), Jan 11-13, 2004, pp. 403-412.

Bandyopadhyay, Deepak and Jack Snoeyink. Almost-Delaunay Simplices : Robust Neighbor Relations for Imprecise 3D Points Using CGAL. 2nd CGAL User Workshop, June 12, 2004. 

Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins and Alexander Tropsha. Mining Protein Family-Specific Residue Packing Patterns from Protein Structure Graphs. Eighth International Conference on Research in Computational Molecular Biology (RECOMB) 2004, pp. 308-315. 

Jun Huan, Deepak Bandyopadhyay, Wei Wang, Jack Snoeyink, Jan Prins and Alexander Tropsha. Comparing Graph Representations of Protein Structure for Mining Protein Family-Specific Residue Packing Motifs. Journal of Computational Biology, 2005, in press.

Bandyopadhyay, Deepak, Alexander Tropsha and Jack Snoeyink. A Robust Score for Protein Packing using Almost-Delaunay Tetrahedra. 2004, in submission. 

Bandyopadhyay, Deepak, Jun Huan, Jinze Liu, Jack Snoeyink, Wei Wang and Jan Prins. Protein Functional Family Identification by Fast Subgraph Isomorphism Using Structure-Based Fingerprints Mined from SCOP and EC families. 2004, in submission.

Bandyopadhyay, Deepak, Alexander Tropsha and Jack Snoeyink. Analyzing Protein Structure using Almost-Delaunay Tetrahedra. UNC-CS Technical Report TR03-043, 2003.

Graphics:

Bandyopadhyay, Deepak, Ramesh Raskar and Henry Fuchs. Dynamic Shader Lamps: Painting on Real Objects. International Symposium on Augmented Reality (ISAR), Oct 29-30, 2001.

Raskar, Ramesh, Greg Welch, Kok-Lim Low and Deepak Bandyopadhyay. Shader Lamps: Animating Real Objects With Image-Based Illumination. Eurographics Workshop on Rendering, EGWR 2001, June 25-27, 2001.


RELEVANT  COURSES:

Graduate: Data Mining, Biomolecular Informatics, Applied Optimization in Computational Biology, Structure of Biological Macromolecules, Computational Geometry, Game Engine Design, Advanced Image Synthesis, Geometric and Solid Modeling, Virtual Worlds, Scientific and Geometric Computing, Parallel and Distributed Computing, Multimedia Networking, Software Design, Computer Architecture

Undergraduate: Computer Graphics, Computer Vision, Digital Image Processing, Computer Networks, Artificial Intelligence, Programming Languages, Algorithms, Digital Electronics, Linear Algebra, Optimization Methods, Probability and Stochastics, Modern Physics, Physical Chemistry, Technical Communication.



AWARDS:

* Secured the 49th rank among over 100,000 applicants in the Joint Entrance Exam for the IITs (Highest scores were in Chemistry; long standing aptitude and interest). 
* Qualified for the Singapore Airlines (SIA-NOL) scholarship, 1995.
* Secured a rank amongst the top 1% (all India) in National Physics Olympiad 1994-95. 
* Selected (one of 750 all India) for National Talent Search Examination (NTSE) scholarship, 1993.
* Received merit prize (top 25 from class of 375) for two semesters at IITD, 1995-97.

REFERENCES:
Furnished upon request