Peptide Identification Tools for Tandem Mass Spectrometry

• HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models
  X. Wu, C.-W. Tseng, and N. Edwards
  Journal of Computational Biology, 14(8):1025-1043, 2007.

• Peptide Identification via Tandem Mass Spectroscopy
  X. Wu, N. Edwards, and C.-W. Tseng
  in Computational Biology and Bioinformatics, Advances in Computers, Volume 68 (C.-W. Tseng, ed.), Elsevier, 2006.

• Searching Sequence Databases Using High Performance BLASTs
  X. Wu, and C.-W. Tseng
  Parallel Computing for Bioinformatics and Computational Biology (A. Zomaya, ed.), John Wiley & Sons, 2005.

• ESTmapper: Efficiently Aligning DNA Sequences to Genomes
  X. Wu, W.-J. Lee, and C.-W. Tseng
  4th IEEE International Workshop on High Performance Computational Biology (HiCOMB'05), Denver, CO, April 2005.

• Towards a First Vertical Prototyping of an Extremely Fine-grained Parallel Programming Approach
  D. Naishlos, J. Nuzman, C.-W. Tseng, and U. Vishkin
  13th ACM Symposium on Parallel Algorithms and Architectures (SPAA'01), Crete, Greece, July 2001.

• Evaluating Multi-threading in the Prototype XMT Environment
  D. Naishlos, J. Nuzman, C.-W. Tseng, and U. Vishkin
  4th ACM Workshop on Multi-threaded Execution, Architecture, and Compilation (MTEAC-4), Monterey, CA, December 2000.
  (Best paper award)

• Evaluating the Impact of Memory System Performance on Software Prefetching and Locality Optimizations
  A.-H. Badawy, A. Aggarwal, D. Yeung, and C.-W. Tseng.
  2001 International Conference on Supercomputing (ICS'01), Sorrento, Italy, June 2001.

• Characterizing the Memory Behavior of Compiler-Parallelized Applications
  E. Torrie, M. Martonosi, C.-W. Tseng, and M. Hall.
  IEEE Transactions on Parallel and Distributed Systems, 7(12):1225-1238, December 1996.

• Exploiting Locality for Irregular Scientific Codes
  H. Han and C.-W. Tseng
  IEEE Transactions on Parallel and Distributed Systems, 17(7):606-618, July 2006.

• Improving Compiler and Run-Time Support for Adaptive Irregular Codes
  H. Han and C.-W. Tseng.
  International Conference on Parallel Architectures and Compilation Techniques (PACT'98), Paris, France, October 1998.

• Tiling Optimizations for 3D Scientific Computations
  G. Rivera and C.-W. Tseng.
  SC'00, Dallas, TX, November 2000.

• A Comparison of Compiler Tiling Algorithms
  G. Rivera and C.-W. Tseng.
  8th International Conference on Compiler Construction (CC'99), Amsterdam, The Netherlands, March 1999.

• Data Transformations for Eliminating Conflict Misses
  G. Rivera and C.-W. Tseng.
  1998 ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI'98), Montreal, Canada, June 1998.

• Compiler Optimizations for Improving Data Locality
  S. Carr, K. McKinley, and C.-W. Tseng.
  Sixth International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS-VI), San Jose, CA, October 1994.

• Compile-time Synchronization Optimizations for Software DSMs
  H. Han and C.-W. Tseng.
  12th International Parallel Processing Symposium (IPPS'98), Orlando, FL, April 1998.
  (Extended paper)

• Enhancing Software DSM for Compiler-Parallelized Applications
  P. Keleher and C.-W. Tseng.
  11th International Parallel Processing Symposium (IPPS'97), Geneva, Switzerland, April 1997.
  (Extended paper)

• Compiler Optimizations for Eliminating Barrier Synchronization
  C.-W. Tseng.
  5th ACM Symposium on Principles and Practice of Parallel Programming (PPOPP'95), Santa Barbara, CA, July 1995.

• Unified Compilation Techniques for Shared and Distributed Address Space Machines
  C.-W. Tseng, J. Anderson, S. Amarasinghe, and M. Lam,
  1995 International Conference on Supercomputing (ICS'95), Barcelona, Spain, July 1995.

• Performance of the Prototype Fortran D Compiler
  C.-W. Tseng.
  Software: Practice and Experience, 7(27):763-796, July 1997.

• Compiling Fortran D for MIMD Distributed-Memory Machines
  S. Hiranandani, K. Kennedy, and C.-W. Tseng.
  Communications of the ACM, 35(8):66-80, August 1992.
  (Invited paper from Supercomputing'91)

• The D Editor: A New Interactive Parallel Programming Tool
  S. Hiranandani, K. Kennedy, C.-W. Tseng, and S. Warren.
  Supercomputing '94 (SC'94), Washington, DC, November 1994.

• Analysis and Transformation in the ParaScope Editor
  K. Kennedy, K. McKinley, and C.-W. Tseng.
  1991 International Conference on Supercomputing (ICS'91), Cologne, Germany, June 1991.

• The Power Test for Data Dependence
  M. J. Wolfe and C.-W. Tseng.
  IEEE Transactions on Parallel and Distributed Systems, 3(5):591-601, September 1992.

• Practical Dependence Testing
  G. Goff, K. Kennedy, and C.-W. Tseng.
  ACM SIGPLAN '91 Conference on Programming Language Design and Implementation (PLDI'91), Toronto, Canada, June 1991.