Current research projects:

Almost-Delaunay tetrahedra	Modelling protein packing (SNAPP, image courtesy Stephen Cammer).	Assigning secondary structure (α-helix shown)

• Computational Geometry - Since Fall 2001 I have been working with Prof. Jack Snoeyink in Computational Geometry. My thesis project is on finding robust neighbor relations for imprecise points, such as protein coordinates, by computing the Almost-Delaunay Simplices (simplices that are within an ε-perturbation of being Delaunay) and estimating their probability of being Delaunay, given random Gaussian perturbations. The code, implemented using CGAL, has been released and is available from my Software Page. I maintain a project web page, with an implementation for almost-Delaunay edges, triangles and tetrahedra in 3D, and applications to the analysis of protein packing, determining protein secondary structure in noisy data, subgraph mining to find family-specific packing patterns applied to function inference for structural genomics, and analysis of conformational change.

Subgraph mining using AD edges yields protein family fingerprints for classification and annotation (joint work with Luke Huan)	Subgraphs and AD tetrahedra may also be used for sequence family annotation (joint work with Ruchir Shah)	Comparing AD tetrahedra in conformations of a flexible protein identifies hinges of the conformational change

Other recent work (graphics):

• STC Dynamic Shader Lamps (2000-2001) - Shader lamps refers to a technique for image-based illumination of real objects using projectors, first proposed by Ramesh Raskar. My work extends shader lamps to paint on a moving, tracked object. Details of my system are in a tech report published in Feb 2001, as well as a paper in ISAR 2001 ( go to web page). Some pictures of my system running are here and below.





• STC Structured Light Tracking (2000) - I worked on techniques to localize and track moving objects in a room using active vision (structured light). Here is a description of my prototype implementation.
• Ultrasound AR (1999-2000) - My project in the Ultrasound research group was to write a simulator for methods to accurately resolve occlusions between the real world and virtual objects.

Publications:

Computational Geometry and Analysis of Protein Structure:

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



• Deepak Bandyopadhyay and Jack Snoeyink. Almost-Delaunay Simplices : Robust Neighbor Relations for Imprecise 3D Points Using CGAL. 2nd CGAL User Workshop, New York, 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.
  • Invited to Journal of Computational Biology


• 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 preparation.



• Jun Huan, Deepak Bandyopadhyay, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang and Alexander Tropsha. Detection of Structural Similarities between Remote Protein Families. submitted.



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



Graphics:

• Deepak Bandyopadhyay, Ramesh Raskar and Henry Fuchs. "Dynamic Shader Lamps : Painting on real Objects". Proceedings of the International Symposium on Augmented Reality (ISAR 2001), New York City, October 29-30, 2001.



• Ramesh Raskar, Greg Welch, Kok-Lim Low and Deepak Bandyopadhyay. "Shader Lamps : Illuminating Real Objects with Image-Based Illumination". Proceedings of the Eurographics Rendering Workshop (EGRW 2001), London, June 25-27, 2001.



• Deepak Bandyopadhyay, Ramesh Raskar, Andrei State and Henry Fuchs. "Dynamic Spatially Augmented 3D Painting". UNC-CS Technical Report TR01-006, Feb 2001.

Talks (other than conference talks):

• In July 2004 I spoke at EBI (European Bioinformatics Institute) on methods and applications for nearest neighbor analysis of protein structures, mentioning my research and that of my UNC collaborators. Here are my PowerPoint slides.
• In August 2004 at the ISMB/ECCB 2004 conference, I gave a laptop presentation on graph representations and algorithms for protein structure classification and functional annotation (PowerPoint slides). Ruchir Shah also gave another presentation on some joint work on protein sequence-structure motifs.
• I've given two talks at the Duke Algorithms Seminar, on almost-Delaunay simplices and subgraph mining (with Luke Huan).
• HTML slides of a presentation I gave in IIT Delhi on Jan 5, 2000 on the work done by my group and others at UNC.