DEEPAK BANDYOPADHYAY CURRENT ADDRESS: CONTACT INFORMATION: Johnson & Johnson Pharmaceutical R&D 665 Stockton Drive, Exton, PA 19341 Home:(610) 363-7531 dbandyop@prdus.jnj.com Work: (610) 458-5264 x6621 http://www.cs.unc.edu/~debug SUMMARY Currently postdoctoral research fellow at Johnson & Johnson Pharmaceutical R&D, developing advanced cheminformatics and computational chemistry algorithms for molecular modeling, conformational analysis, virtual screening and 3D database search applied to drug discovery. Recent Computer Science Ph.D. graduate from UNC Chapel Hill, with broad experience and expertise in the application of computational geometry and data mining techniques to structural bioinformatics. Key research contributions are a geometric technique that makes nearest neighbor analysis of protein structures more robust, and development of many new applications including robust packing scores, graph mining to find family-specific structural motifs, function inference for structural genomics, and analysis of conformational change. Background in graphics, strong visualization skills. Strong software development abilities in C++ and Java, prototyping and numerical analysis in MATLAB and scripting in Unix/Perl, with industry experience. Detailed knowledge of protein structure and function from courses, independent study, and collaboration with domain experts. EDUCATION University of North Carolina at Chapel Hill Ph.D. in Computer Science, September 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 Subjects: Computational Chemistry and Cheminformatics; Biogeometry (Computational Geometry in Molecular Biology); Computational Biology and Bioinformatics (especially Structural Bioinformatics); Computational Geometry; Data Mining; Algorithm Design; Statistical Methods; Computer Graphics and Visualization; Virtual and Augmented Reality Languages: C, C++, Java, MATLAB, scripting(Unix, Perl), HTML. Software released (in C++): Almost-Delaunay Simplices in CGAL, June 2004; gzstream library (with Lutz Kettner), Sep. 2001; Dynamic Shader Lamps (with Ramesh Raskar), Aug. 2001 Technologies and APIs: Computational Geometry (CGAL, LEDA); Databases and Data Mining (ODBC/JDBC, FFSM subgraph mining, SVM); Graphics and Multimedia (OpenGL, Renderman, Java3D, Swing, VRML, DirectMedia SDK); Vision and Image Processing (OpenCV, Matrox Imaging Library); Generic programming (STL, Boost); Parallel programming (MPI, OpenMP) Bioinformatics and Cheminformatics Tools: Molecular modeling (Schrödinger, Sybyl, Accelrys, DeepView, VMD, Kinemage, Pymol, Spock); Data Warehousing (ABCD/3DX/DirectedDiversity); Standard bioinformatics sequence and structure methods and web services (particularly: BLAST, PSI-BLAST, ClustalW, PROSITE, InterPro, PFam, DSSP/DSSPcont, PROMOTIF, SCOP, CATH, VAST, DALI, PDB, PDBSum, EC, GO, MolMovDB, SFLD, PINTS, SNAPP) Development Tools and Platforms: Windows (Visual C++ .NET, Intel Compiler, JBuilder, Eclipse), Linux and Unix variants (variety of compilers, editors, debuggers, and other tools) Other Software Packages: Geometric modeling (3D studio MAX, Rhino3D, Maya), Image manipulation (Paint Shop Pro, Photoshop, GIMP), Video editing (Adobe Premiere) EXPERIENCE * Postdoc, Johnson & Johnson Pharmaceutical Research & Development, 10/2005-present Developing computational chemistry algorithms with the Molecular Design and Informatics group (now part of Research and Early Development Information Management / Informatics). Special emphasis on the development of 3D geometric algorithms for molecular modeling, conformational analysis, 3D database searching and virtual screening, and on their deployment within ABCD, an in-house data warehousing software for cheminformatics and bioinformatics used by Johnson & Johnson's drug discovery scientists worldwide. (supervisor: Dr. Dimitris K. Agrafiotis). * Research Assistant, University of North Carolina at Chapel Hill, 6/2001-9/2005 Ph.D. Thesis: Developed a geometric framework for robust nearest neighbor analysis in imprecise points (Almost-Delaunay simplices), and some of its applications in analysis of protein structure: scoring functions for protein packing; secondary structure determination; subgraph mining to find family-specific spatial motifs for functional annotation of structural genomics targets; and analysis of conformational change. (advisor: Dr. Jack Snoeyink). * Instructor, University of North Carolina at Chapel Hill, 6/2003-7/2003 Designed and taught an undergraduate course on introductory programming with Java * Summer Intern, BIWI (Computer Vision Lab), ETH Zurich, Switzerland. 6/2002-8/2002 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, 8/2000-6/2001 Developed Dynamic Shader Lamps, an interactive Augmented Reality system for painting on moving real objects using projectors; demonstrated at ISAR'01 conference in New York. * Summer Intern, HRL Labs, Malibu, CA. 6/2000-8/2000 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, 8/1999-5/2000 Explored occlusion resolving methods for Augmented Reality in ultrasound-guided biopsy. * Summer Intern, Kent Ridge Digital Labs, Singapore. 6/1998-7/1998 Built GUI application for visual feature extraction and feature-based query on a video database, using Java, which was integrated into KRDL's video indexing software. ACADEMIC PROJECTS Graduate: * Kinemage visualization of almost-Delaunay tetrahedra: Developed MATLAB code to generate kinemage files for visualization of AD tetrahedra, packing, secondary structures, spatial motifs and hinges. Course project, Structure of Biological Macromolecules. * Structured light for 3D object localization: Projector-camera system for real-time tracking of a moving object, such as the user's hand. Course project, Advanced Image Synthesis. * Distance functions for geometric simplification: Studied effects of choosing a non-Euclidean distance function on a geometric simplification method based on edge collapsing with a quadric error metric (with M. Gopi). Course project, Geometric and Solid Modeling. * Stained-glass mosaic shader: Designed a Renderman shader and designed ray-traced scenes with stained-glass mosaic effects and translucency. Project, Advanced Image Synthesis. * Parallel N-body simulations: Implemented work-efficient parallel simulations using MPI and OpenMP on a 64-processor machine. Course Project, Parallel and Distributed Computing. * Robust Internet audio codec: Implemented system for low bitrate transmission of real-time audio in the presence of simulated load and noise. Course Project, Multimedia Networking. 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. PUBLICATIONS Refereed journal papers Computational Geometry, Structural Bioinformatics and Cheminformatics: Deepak Bandyopadhyay and Dimitris K Agrafiotis. A New Self-Organizing Algorithm for Molecular Alignment and Pharmacophore Development. submitted. Dimitris K Agrafiotis, Deepak Bandyopadhyay, Giorgio Carta, Andrew J S Knox and David G Lloyd. On the Effects of Permuted Input on Conformational Sampling: An Evaluation of Stochastic Proximity Embedding (SPE). submitted. Dimitris K Agrafiotis, Deepak Bandyopadhyay, Joerg K Wegner and Herman van Vlijmen. Recent Advances in Chemoinformatics. Journal of Chemical Information and Modeling, 2007, to appear. Dimitris K Agrafiotis, Deepak Bandyopadhyay and Michael Farnum. Radial Clustergrams: Visualizing the Aggregate Properties of Hierarchical Clusters. Journal of Chemical Information and Modeling, 2007, vol. 47, pp. 69-75. Bandyopadhyay, Deepak and Jack Snoeyink. Almost-Delaunay Simplices : Robust Neighbor Relations for Imprecise 3D Points Using CGAL. Journal of Computational Geometry Theory and Applications (CGTA), 2007, doi:10.1016/j.comgeo.2006.11.003 Bandyopadhyay, Deepak, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang, and Alexander Tropsha. Structure-Based Function Inference Using Family-Specific Fingerprints. Protein Science, vol. 15, June 2006, pp. 1537-1543. 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 (JCB), Vol. 12, No. 6, July 2005, pp. 657-671. Jun Huan, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, Alexander Tropsha and Wei Wang. Distance-based Identification of Spatial Motifs in Proteins Using Constrained Frequent Subgraph Mining. Journal of Bioinformatics and Computational Biology (JBCB), 2007, invited and under review. Refereed conference and workshop papers Computational Geometry and Structural Bioinformatics: Jun Huan, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, Alexander Tropsha and Wei Wang. Distance-based Identification of Spatial Motifs in Proteins Using Constrained Frequent Subgraph Mining. Proceedings of the IEEE Life Sciences Society Computational Systems Bioinformatics (CSB) conference, Aug. 14-18, 2006. Bandyopadhyay, Deepak, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang, and Alexander Tropsha. Structure-Based Function Inference Using Family-Specific Subgraph Fingerprints Mined from Protein Families. Proceedings of the first ISMB Special Interest Group meeting on Automated Function Prediction (AFPSIG), 2005. Bandyopadhyay, Deepak and Jack Snoeyink. Almost-Delaunay Simplices: Nearest Neighbor Relations for Imprecise Points. ACM-SIAM Symposium on Discrete Algorithms (SODA), Jan. 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 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. International Conference on Research in Computational Molecular Biology (RECOMB), March 2004, pp. 308-315. Graphics: Bandyopadhyay, Deepak, Ramesh Raskar and Henry Fuchs. Dynamic Shader Lamps: Painting on Real Objects. International Symposium on Augmented Reality (ISAR), Oct. 2001. Raskar, Ramesh, Greg Welch, Kok-Lim Low and Deepak Bandyopadhyay. Shader Lamps: Animating Real Objects with Image-Based Illumination. Eurographics workshop(EGWR), 2001 Non-refereed publications (technical reports and posters) Bandyopadhyay, Deepak. New Self-Organizing Algorithm for Molecular Alignment and Pharmacophore Development. Talk at eCheminfo 2006, Oct. 2006, Bryn Mawr, PA. Bandyopadhyay, Deepak, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink and Wei Wang. Function Inference Using Family-Specific Subgraph Fingerprints Mined From Protein Families. Poster presented at Intelligent Systems for Molecular Biology (ISMB) 2005, June 2006, Detroit, MI. Bandyopadhyay, Deepak, Jack Snoeyink, Alexander Tropsha and Charlie Carter. Analysis of Protein Conformational Change Using Almost-Delaunay Tetrahedra. Poster presented at Pacific Symposium on Biocomputing (PSB), Jan. 2005, Big Island of Hawaii. Bandyopadhyay, Deepak, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink and Wei Wang. Using Fast Subgraph Isomorphism for Protein Function Annotation Using SCOP and Gene Ontology. UNC-CS Technical Report TR04-031, 2004. Bandyopadhyay, Deepak, Jun Huan, Wei Wang and Jack Snoeyink. A Fast Subgraph Search Scheme Using a Local Index for Functional Annotation of Protein Structures. Poster presented at Intelligent Systems for Molecular Biology (ISMB-ECCB'04), Aug. 2004, Glasgow, UK. Bandyopadhyay, Deepak. Graph Representations and Algorithms for Protein Family Classification and Functional Annotation. Laptop Presentation at the Special Interest Group meeting in Structural Bioinformatics (3DSIG), ISMB-ECCB'04, July 2004, Glasgow, UK Bandyopadhyay, Deepak, Alexander Tropsha and Jack Snoeyink. Analyzing Protein Structure using Almost-Delaunay Tetrahedra. UNC-CS Technical Report TR03-043, 2003. Poster presented at RECOMB 2004, March 2004, San Diego, CA. Bandyopadhyay, Deepak, Ramesh Raskar, Andrei State and Henry Fuchs. Dynamic Spatially Augmented 3D Painting. UNC-CS Technical Report TR01-006, 2001. INVITED TALKS (other than conference presentations) * National Center for Biotechnology Information, Bethesda, MD, Feb. 2005 A geometric framework for robust neighbor analysis of protein structure and function * European Bioinformatics Institute, Cambridge, UK, July 2004 Methods and applications for nearest neighbor analysis of protein structures * Duke Algorithms Seminar, Duke University, Durham, NC o Almost-Delaunay tetrahedra for analyzing protein structure, March 2003 o Mining family-specific residue packing patterns from protein structure graphs (with Luke Huan), Nov. 2004 * Biogeometry PI meetings o Computing Almost-Delaunay triangles and edges, Stanford University, Oct. 2001 o Structure-based function inference using family-specific subgraph fingerprints mined from protein families, Big Island of Hawaii, Jan. 2005 * Indian Institute of Technology, Delhi, India, Jan. 2000 Graphics research at UNC Chapel Hill PROFESSIONAL ACTIVITIES AND AFFILIATIONS Reviewer for ISMAR (augmented reality), CIKM and KDD (databases and data mining), Computational Geometry: Theory and Applications, and Bioinformatics. ISCB (International Society for Computational Biology) member since 2004 ACS (American Chemical Society) member since 2006 AWARDS * Secured the 49th rank among over 100,000 applicants in Joint Entrance Exam for the IITs. * Qualified for the Singapore Airlines (SIA-NOL) scholarship, 1995. * Received merit prize (among top 25 students in class of 375) for 2 semesters at IIT Delhi. * Secured a rank amongst the top 1% (all India) in National Physics Olympiad 1994-95. * National Talent Search Examination (NTSE) scholarship, 1993. OTHER INTERESTS Travel, creative writing, trivia and word games, crossword creation, digital photography Language skills: English, Hindi (native speaker); French, Bengali (conversational) REFERENCES Furnished upon request