| 2007 | SAC | BWT-based efficient shape matching. | Donald A. Adjeroh, Uma Kandaswamy, Nan Zhang, Amar Mukherjee, M. T. Brown, Tim Bell |
| 2006 | ISMB | Constructing Near-Perfect Phylogenies with multiple homoplasy events. | Ravi Vijaya Satya, Amar Mukherjee, Gabriela Alexe, Laxmi Parida, Gyan Bhanot |
| 2006 | SIGGRAPH | Inside just-in-time radiance transfer. | Weifeng Sun, Amar Mukherjee |
| 2005 | DCC | Multiple-Pattern Matching In LZW Compressed Files Using Aho-Corasick Algorithm. | Tao Tao, Amar Mukherjee |
| 2005 | DCC | A Flexible Compressed Text Retrieval System Using a Modified LZW Algorithm. | Nan Zhang, Tao Tao, Ravi Vijaya Satya, Amar Mukherjee |
| 2005 | ICCS | Constructibility of Signal-Crossing Solutions in von Neumann 29-State Cellular Automata. | William R. Buckley, Amar Mukherjee |
| 2004 | DCC | LZW Based Compressed Pattern Matching. | Tao Tao, Amar Mukherjee |
| 2004 | SPIRE | New Algorithms for Finding Monad Patterns in DNA Sequences. | Ravi Vijaya Satya, Amar Mukherjee |
| 2003 | DCC | A Dictionary-Based Multi-Corpora Text Compression System. | Weifeng Sun, Nan Zhang, Amar Mukherjee |
| 2003 | DCC | Approximate Pattern Matching Using the Burrows-Wheeler Transform. | Nan Zhang, Amar Mukherjee, Donald A. Adjeroh, Tim Bell |
| 2002 | DCC | Pattern Matching in BWT-Transformed Text. | Donald A. Adjeroh, Tim Bell, Matt Powell, Nan Zhang, Amar Mukherjee |
| 2002 | DCC | Searching BWT Compressed Text with the Boyer-Moore Algorithm and Binary Search. | Tim Bell, Matt Powell, Amar Mukherjee, Donald A. Adjeroh |
| 2001 | DCC | LIPT: A Reversible Lossless Text Transform to Improve Compression Performance. | Fauzia S. Awan, Nan Zhang, Nitin Motgi, Raja Tanveer Iqbal, Amar Mukherjee |
| 2001 | RSP | Prototyping of Efficient Hardware Algorithms for Data Compression in Future Communication Systems. | Amar Mukherjee, Nitin Motgi, Jrgen Becker, A. Friebe, C. Habermann, Manfred Glesner |
| 2000 | DCC | A Spatially Coherent Discrete Wavelet Transform - Accessing the Localization Property for Data Compression. | Kunal Mukherjee, Amar Mukherjee |
| 2000 | DCC | Distributed Internet-Adaptive Image Compression. | Kunal Mukherjee, Amar Mukherjee, Tinku Acharya |
| 2000 | FPGA | Novel hardware-software architecture for the recursive merge filtering algorithm (poster abstract). | Piyush Jamkhandi, Amar Mukherjee, Kunal Mukherjee, Robert Franceschini |
| 1999 | DCC | Improving Text Compression Ratios with the Burrows-Wheeler Transform. | Holger Kruse, Amar Mukherjee |
| 1999 | DCC | Joint Optical Flow Motion Compensation and Video Compression Using Hybrid Vector Quantization. | Kunal Mukherjee, Amar Mukherjee |
| 1999 | DCC | "Bit Rate on Demand" Using Pruned Tree-Structured Hierarchical Lookup Vector Quantization. | Kunal Mukherjee, Amar Mukherjee, Tinku Acharya |
| 1999 | ICASSP | Embedded optical flow motion compensation and finite state hierarchical vector quantization. | Kunal Mukherjee, Amar Mukherjee |
| 1998 | DCC | Preprocessing Text to Improve Compression Ratios. | Holger Kruse, Amar Mukherjee |
| 1996 | DCC | Data Compression Using Encrypted Text. | Robert Franceschini, Amar Mukherjee |
| 1996 | ICPR | An efficient algorithm for detection of road-like structures in satellite images. | Amar Mukherjee, Swapan K. Parui, Debasis Chaudhuri, B. B. Chaudhuri, R. Krishnan |
| 1994 | ICPR | Detection of linear features in satellite imagery using robust estimation. | Amar Mukherjee, Swapan K. Parui, B. B. Chaudhuri, R. Krishnan, K. K. Rao |
| 1992 | ICCD | MARVLE: A VLSI Chip for Variable Length Encoding and Decoding. | Amar Mukherjee, Jeffrey W. Flieder, N. Ranganathan |
| 1991 | DCC | Multibit Decoding/Encoding of Binary Codes Using Memory Based Architectures. | Amar Mukherjee, H. Bheda, Mostafa A. Bassiouni, Tinku Acharya |
| 1991 | ICPP | Mapping Task Trees onto a Linear Array. | Dipak Ghosal, Amar Mukherjee, Ramakrishna Thurimella, Yaacov Yesha |
| 1989 | ICCD | Adaptive and pipelined VLSI designs for tree-based codes. | Amar Mukherjee, N. Ranganathan, Mostafa A. Bassiouni |
| 1989 | ICDE | On Software and Hardware Techniques of Data Engineering. | Mostafa A. Bassiouni, Amar Mukherjee, N. Ranganathan |
| 1988 | SC | A scheme for data compression in supercomputers. | Mostafa A. Bassiouni, N. Ranganathan, Amar Mukherjee |
| 1988 | SSDBM | Software and Hardware Enhancement of Arithmetic Coding. | Mostafa A. Bassiouni, N. Ranganathan, Amar Mukherjee |
| 1987 | SIGIR | A VLSI Chip for Efficient Transmission and Retrieval of Information. | Amar Mukherjee, Mostafa A. Bassiouni |