DEEPAK BANDYOPADHYAY
Department of Computer Science
CB #3175, Sitterson Hall
University of North Carolina
Chapel Hill, NC 27599-3175		 (919) 968-1253  (h)
(919) 962-1894 (w)
debug @ cs.unc.edu
http://www.cs.unc.edu/~debug

OBJECTIVE:

 A challenging research and development position in the areas of structural bioinformatics, computational geometry or computer graphics.

INTERESTS:

 Structural Bioinformatics, Computational Geometry, Computer Graphics, Augmented Reality.

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

EXPERIENCE:

 Research Assistant, Computational Geometry group, UNC Chapel Hill, 6/01-present
Ph.D. Thesis: Developed a geometric framework for robust nearest neighbor analysis in imprecise points (Almost-Delaunay simplices, C++/CGAL implementation available from http://www.cs.unc.edu/~debug/software), and some of its applications in the analysis of protein structure: robust scoring functions for protein packing; secondary structure assignment in noisy data; subgraph mining to find family-specific spatial motifs for functional annotation of structural genomics proteins; 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 undergraduate course on Introduction to Computer Programming with Java.

Summer Intern at 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, STC Office of the Future group, UNC Chapel Hill, 8/00-6/01
Developed Dynamic Shader Lamps, an interactive Augmented Reality system for painting on moving real objects using projectors; demonstrated it at the ISAR 2001 conference in New York city.

Summer Intern at 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, Ultrasound research group, UNC-Chapel Hill, 8/99-5/00
Explored occlusion resolving methods for Augmented Reality in ultrasound-guided needle biopsy.

Summer Intern at Kent Ridge Digital Labs, Singapore. 6/98-7/98
Built complete 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:

Academic Projects - 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/exponentiation; Slot machine simulation on FPGAs.

SKILLS:

 Technologies:
Expert: C, C++ (STL/generic, OpenGL), MATLAB, Java, HTML, UNIX scripting
Familiar: 3D graphics (DirectX Media SDK, procedural shading/Renderman, GPU basics), parallel programming (MPI, OpenMP), Perl, Python, COM, VRML2.0, TCP/IP, multimedia networking.
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.

SELECTED 

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) 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, 2004, pp. 403-412.

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. Longer version appeared in Analyzing Protein Structure using Almost-Delaunay Tetrahedra, UNC-CS Technical Report TR03-043.

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 preparation.

Graphics:

Bandyopadhyay, Deepak, Ramesh Raskar and Henry Fuchs. Dynamic Shader Lamps : Painting on Real Objects. International Symposium on Augmented Reality (ISAR 2001), New York, 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, London.

  (See academic CV or research page for full list including tech reports.)

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, Microprocessors, Digital Hardware Design, Digital Electronics, Technical Communication.

AWARDS:
  • Secured the 49th rank among over 100,000 applicants in the Joint Entrance Exam for the IITs.
  • Received merit prize (among top 25 students in class of 375) for two semesters at IIT Delhi.
  • Secured a rank amongst the top 1% (all India) at the National Physics Olympiad 1994-95.
  • National Talent Search Examination (NTSE) scholarship, 1993.

AFFILIATIONS:

 ISCB (International Society for Computational Biology) student member.

REFERENCES:

 Furnished on request