Dynamic Shader Lamps: Painting on Movable Objects. - Deepak Bandyopadhyay; Ramesh Raskar; Henry Fuchs (ISAR, 2001)

Shader Lamps: Animating Real Objects With Image-Based Illumination. - Ramesh Raskar; Greg Welch; Kok-Lim Low; Deepak Bandyopadhyay (Rendering Techniques, 2001)

Mining protein family specific residue packing patterns from protein structure graphs. - Jun Huan; Wei Wang 010; Deepak Bandyopadhyay; Jack Snoeyink; Jan F. Prins; Alexander Tropsha (RECOMB, 2004)

Almost-Delaunay simplices: nearest neighbor relations for imprecise points. - Deepak Bandyopadhyay; Jack Snoeyink (SODA, 2004)

Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs. - Jun Huan; Deepak Bandyopadhyay; Wei Wang 010; Jack Snoeyink; Jan F. Prins; Alexander Tropsha (J. Comput. Biol., 2005)

Almost-Delaunay simplices: Robust neighbor relations for imprecise 3D points using CGAL. - Deepak Bandyopadhyay; Jack Snoeyink (Comput. Geom., 2007)

Radial Clustergrams: Visualizing the Aggregate Properties of Hierarchical Clusters. - Dimitris K. Agrafiotis; Deepak Bandyopadhyay; Michael Farnum (J. Chem. Inf. Model., 2007)

Functional Neighbors: Inferring Relationships between Non-Homologous Protein Families Using Family-Specific Packing Motifs. - Deepak Bandyopadhyay; Jun Huan; Jinze Liu; Jan F. Prins; Jack Snoeyink; Wei Wang 010; Alexander Tropsha (BIBM, 2008)

A self-organizing algorithm for molecular alignment and pharmacophore development. - Deepak Bandyopadhyay; Dimitris K. Agrafiotis (J. Comput. Chem., 2008)

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development. - Deepak Bandyopadhyay; Jun Huan; Jan F. Prins; Jack Snoeyink; Wei Wang 010; Alexander Tropsha (J. Comput. Aided Mol. Des., 2009)

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications. - Deepak Bandyopadhyay; Jun Huan; Jan F. Prins; Jack Snoeyink; Wei Wang 010; Alexander Tropsha (J. Comput. Aided Mol. Des., 2009)

Functional neighbors: inferring relationships between nonhomologous protein families using family-specific packing motifs. - Deepak Bandyopadhyay; Jun Huan; Jinze Liu; Jan F. Prins; Jack Snoeyink; Wei Wang 010; Alexander Tropsha (IEEE Trans. Inf. Technol. Biomed., 2010)

Stochastic Proximity Embedding: A Simple, Fast and Scalable Algorithm for Solving the Distance Geometry Problem. - Dimitris K. Agrafiotis; Deepak Bandyopadhyay; Eric Yang (Distance Geometry, 2013)

Scaffold-Based Analytics: Enabling Hit-to-Lead Decisions by Visualizing Chemical Series Linked across Large Datasets. - Deepak Bandyopadhyay; Constantine Kreatsoulas; Pat G. Brady; Joseph Boyer; Zangdong He; Genaro Scavello; Tyler Peryea; Ajit Jadhav; Dac-Trung Nguyen; Rajarshi Guha (J. Chem. Inf. Model., 2019)