Publications

2005
• Exact Algorithms for Motif Search
  Proc. of 3rd Asia-Pacific Bioinformatics Conference (APBC), Singapore. (to appear)
  (with S. Rajasekaran, S. Balla, V. Thapar, M. Gryk, M. Maciejewski and M. Schiller)
• Exact Algorithms for Planted Motif Challenge Problems
  Proc. of 3rd Asia-Pacific Bioinformatics Conference (APBC), Singapore. (to appear)
  (with S. Rajasekaran and S. Balla)

2004
• Toward a Distributed UMLS
  Proc. of 2nd Biological Language Conference (BLC), Carnegie-Mellon University, 77-78.
• Toward Cooperative Genomic Knowledge Inference
  Parallel Computing Journal, 30(9-10):1127-1135. (with C.-W. Lee)
• A Randomized Algorithm for Distance Matrix Calculations in Multiple Sequence
  Alignment, First Int'l Conference on Knowledge Exploration in Life Science
  Informatics (KELSI), LNAI 3303:33-45, Springer-Verlag, 2004.
  (with S. Rajasekaran, V. Thapar and H. Dave)
• High-Performance Parallel Bio-computing
  Parallel Computing Journal, 30(9-10):999-1000. (with S. Rajasekaran)
• Biomedical Computations on the Grid - Organizing Chairs' Note
  Proc. of the 4-th IEEE/ACM Symposium on Cluster Computing and the Grid (CCGrid)
  - Second BioGrid Workshop, published in CD-ROM. (with S. Rajasekaran)
• Finding Hamiltonian Paths in Tournaments on Clusters
  Journal of Cluster Computing, accepted. (with X. He and L. Yang and S. Rajasekaran)
• Distributed Path-Based Inference in Semantic Networks
  Proc. of 7th IEEE Int'l Symp. on Parallel Architectures, Algorithms and Networks (I-SPAN),
  232-237. (with C.-W. Lee, S. Rajasekaran, L. Yang and D. Frank Hsu)
• Distributed Path-Based Inference in Semantic Networks
  Journal of Supercomputing, 29(2):211-227. (with C.-W. Lee, L. Yang and S. Rajasekaran)

2003
• TROJAN: A Scalable Parallel Semantic Network System
  Proc. of 15th IEEE Int'l Conference on Tools with Artificial Intelligence (ICTAI),
  219-223. (with C.-W. Lee and S. Rajasekaran)
• Parallel Pattern Identification in Biological Sequences on Clusters
  IEEE Transactions on NanoBioscience, 2(1):29-34. (with S. Rajasekaran)

2002
• Average-Case Communication-Optimal Parallel Parenthesis Matching
  Proc. of the 13th Int'l Symp. on Algorithms and Computation (ISAAC),
  LNCS 2518:308-319, Springer-Verlag, 2002. (with X. He)


• Parallel Pattern Identification in Biological Sequences on Clusters
  Proc. of the 4th IEEE International Conference on Cluster Computing (IEEE Cluster),
  127-134, 2002.


• Finding Double Euler Trails of Planar Graphs in Linear Time
  SIAM Journal on Computing, 31(4):1255-1285. (with Z.Z. Chen and Xin He)


• Grid-Enabled Parallel Divide-And-Conquer -- Theory and Practice
  Proc. of the 17th ACM SIGAPP Symposium on Applied Computing (SAC), 865-869, 2002.

2001
• Communication-Efficient BSP Algorithm for All Nearest Smaller Values Problem
  Journal of Parallel and Distributed Computing, 61:1425-1438. (with Xin He)


• Finding Hamiltonian Paths in Tournaments on Clusters - A Communication-Efficient Approach
  Proc. of the 16th ACM SIGAPP Symposium on Applied Computing (SAC), 549-553.
  (with Xin He)


• Parallel Range Searching in Large Databases Based on General Parallel Prefix Computation
  Proc. of the 10th SIAM Conference on Parallel Processing for Scientific Computing,
  3 pages.(with Xin He)


• Communication-Efficient Bulk Synchronous Parallel Algorithm for Parentheses Matching
  Proc. of the 10th SIAM Conference on Parallel Processing for Scientific Computing,
  9 pages.(with Xin He)
  2000
• Scalable Coarse Grained Parallel Interval Graph Algorithms
  Proc. of the Int'l Conference on Parallel and Distributed Processing Techniques and Applications
  (PDPTA), 2000, 1369-1376, (with Xin He)
• Communication-Efficient Coarse-Grained Parallel Algorithm for All Nearest Smaller Values
  Problem and its Applications
  Proc. of the Int'l Conference on Parallel and Distributed Processing Techniques and Applications
  (PDPTA), 2000, 1377-1384, (with Xin He)

1999
• Finding Double Euler Trails of Planar Graphs in Linear Time
  Proc. of the 40th IEEE Symposium on Foundations of Computer Science (FOCS), 319-329.
  (with Z.Z. Chen and Xin He)