Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. Proceedings of the International Symposium on Bioinformatics Research and Applications, Atlanta, Georgia, May, 2007.

Mary Fletcher, Cheryl McCosh, Guohua Jin, and Ken Kennedy. Compiling Parallel Matlab for General Distributions Using Telescoping Languages. Proceedings of the 2007 International Conference on Acoustics, Speech, and Signal Processing, Honolulu, Hawaii, April, 2007.

Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study. Molecular Biology and Evolution, 24(1): 324-337, January, 2007.

Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Maximum Likelihood of Phylogenetic Networks. Bioinformatics, 22(21): 2604-2611, November, 2006. Supplementary material.

Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. Bioinformatics, 23(2):e123-e128, January, 2007. (Proceedings of the 5th European Conference on Computational Biology, Eilat, Israel, 2006.)

Guohua Jin and John Mellor-Crummey. Using Space-filling Curves for Computation Reordering. Proceedings of the Los Alamos Computer Science Institute Sixth Annual Symposium , Santa Fe, New Mexico, October, 2005.

Guohua Jin and John Mellor-Crummey. Improving Performance by Reducing the Memory Footprint of Scientific Applications. International Journal of High Performance Computing Applications, 19(4): 433-451, 2005.

Luay Nakhleh, Guohua Jin, Fengmei Zhao, and John Mellor-Crummey. Reconstructing Phylogenetic Networks Using Maximum Parsimony. Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference, Stanford, California, August 2005.

Guohua Jin and John Mellor-Crummey. Space-filling Curve Generation: A Table-based Approach. Proceedings of the 2005 International Conference on Algorithmic Mathematics and Computer Science, Las Vegas, Nevada, June 2005.

Daniel Chavarría-Miranda, Guohua Jin, and John Mellor-Crummey. COTS Clusters vs. the Earth Simulator: An Application Study Using IMPACT-3D. Proceedings of the 2005 International Parallel and Distributed Processing Symposium, Denver, Colorado, April 2005.

Guohua Jin and John Mellor-Crummey. SFCGen: A Framework for Efficient Generation of Multi-dimensional Space-filling Curves by Recursion. ACM Transactions on Mathematical Software, 31(1), March 2005.

Guohua Jin and John Mellor-Crummey. On Reducing Storage Requirement of Scientific Applications. Proceedings of the Los Alamos Computer Science Institute Fourth Annual Symposium , Santa Fe, New Mexico, October, 2003.

Apan Qasem, Guohua Jin, and John Mellor-Crummey. Improving Performance with Integrated Program Transformations. Technical Report TR03-419, Rice University, October, 2003.

John Mellor-Crummey, Vikram Adve, Bradley Broom, Daniel Chavarría-Miranda, Robert Fowler, Guohua Jin, Ken Kennedy, and Qing Yi. Advanced Optimization Strategies in the Rice dHPF Compiler. Concurrency: Practice and Experience, 14(8-9), 2002, pp. 741-767.

Guohua Jin and John Mellor-Crummey. Experiences Tuning SMG98 -- a Semicoarsening Multigrid Benchmark based on the hypre Library. Proceedings of 2002 International Conference on Supercomputing, New York, June 2002.

Robert Fowler, John Mellor-Crummey, Guohua Jin, and Apan Qasem. A Source-to-source Loop Transformation Tool. Extended poster abstract, Proceedings of the Los Alamos Computer Science Institute Third Annual Symposium , Santa Fe, New Mexico, October, 2002.

Guohua Jin, John Mellor-Crummey, and Robert Fowler. Increasing Temporal Locality with Skewing and Recursive Blocking. Proceedings of SC01: High-Performance Computing and Networking, Denver, Colorado, November 2001.

Guohua Jin, Zhiyuan Li, and Fujie Chen. A Theoretical Foundation for Program Transformations to Reduce Cache Thrashing due to True Data-sharing. Theoretical Computer Science, 255(1-2), March 2001, pp. 449--481.

Bradley Broom, Daniel Chavarría-Miranda, Rob Fowler, Guohua Jin, Ken Kennedy, and John Mellor-Crummey. Overpartitioning with the Rice dHPF Compiler. Proceedings of the 4th Annual HPF User Group meeting, Tokyo, Japan, October 2000.

Y. Charlie Hu, Guohua Jin, S. Lennart Johnsson, Dimitris Kehagias and Nadia Shalaby. HPFBench: A High Performance Fortran Benchmark Suite. ACM Transactions on Mathematical Software, 26(1), March 2000, pp. 99--149.

Guohua Jin and Y. Charlie Hu. An Evaluation of High Performance Fortran Compilers Using the HPFBench Benchmark Suite. Proceedings of Euro-Par'99, Toulouse, France, August 1999.

Vikram Adve, Guohua Jin, John Mellor-Crummey and Qing Yi. High Performance Fortran Compilation Techniques for Parallelizing Scientific Codes. Proceedings of SC98: High-Performance Computing and Networking, Orlando, Florida, November 1998.

Guohua Jin, Zhiyuan Li, and Fujie Chen. An Efficient Solution to the Cache Thrashing Problem. IEEE Transactions on Computers, 47(5), May 1998, pp. 527--543.

Zhiyuan Li, Jian Huang, and Guohua Jin. Page Mapping Techniques to Reduce Cache Conflicts on CC-NUMA Multiprocessors. Journal of Microprocessors and Microsytems, 22(3), August 1998, pp. 165--174.

Jian Huang, Guohua Jin, and Zhiyuan Li. Reducing Cache Misses for CC-NUMA by Careful Page Mapping. Proc. of the 3rd IEEE International Conference on Algorithms and Architectures for Parallel Processing, Melbourne, Australia. December 10-12, 1997, pp. 91 -- 104.

Guohua Jin and Fujie Chen. Theories and Techniques for Program Parallelization on MPP Systems. Science Press, China, January 1995.

Guohua Jin and Fujie Chen. Rearranging the Iteration Space to Eliminate the True Sharing Thrashing in Parallel Processing Systems. Proc. of the 7th SIAM Conference on Parallel Processing for Scientific computing, San Francisco, California, February, 1995.

Guohua Jin and Fujie Chen. Determining the True and False Sharing Thrashing in Parallel Processing Systems. Proc. of the 7th SIAM Conference on Parallel Processing for Scientific computing, San Francisco, California, February, 1995.

Guohua Jin and Fujie Chen. On the Problem of Optimizing Parallel Programs for Complex Memory Hierarchies. Journal of Computer Science and Technology, Vol.9, No.1, 1994.

Guohua Jin and Fujie Chen. Revisiting Loop Skewing. Acta Electronica Sinica (Chinese), Vol.22, No.5, May 1994.

Guohua Jin and Fujie Chen. Eliminating False Sharing Cache Line Thrashing for Simple Access Patterns. Journal of Computers (Chinese), Vol.17, No.6, 1994.

Guohua Jin and Fujie Chen. Eliminating False Sharing Cache Line Thrashing for Complex Access Patterns. Journal of Computers (Chinese), Vol.17, No.6, 1994.

Guohua Jin and Fujie Chen. A New Extensive Alias Analysis Algorithm. Journal of Software (Chinese), Vol.5, No.7, 1994.

Guohua Jin, Fengmei Zhao, Tao Wu, and Fujie Chen. Partitioning the Iteration Space to Reduce the Interprocessor Communications in MPP Systems. Proc. of the International Symposium of Young Investigators on Information, Computer, and Control , Beijing, February 1994.

Guohua Jin. Staggering and Blocking: a Technique to Optimize the Parallel Programs for Large Scale Parallel Processing Systems. Proc. of the IEEE TENCON94, , Singapore, August 1994.

Tao Wu, Wei Wu, Guohua Jin, and Xiejun Yang. The Model of Supercomputer-oriented Self-adapting Operating System. Proc. of the International Conference on Systems, Control, Information, Methodologies, and Applications, Wuhan, China, October 1994.

Guohua Jin and Fujie Chen. Advanced Compiler Techniques for the Cache Line Thrashing. Computers and Artificial Intelligence, Vol.12, No.4, 1993.

Guohua Jin, Xiejun Yang, and Fujie Chen. Loop Staggering, Loop Compacting: Restructuring Techniques for Thrashing Problem. Journal of Computer Science and Technology, Vol.8, No.1, 1993.

Guohua Jin and Fujie Chen. Optimizing Fortran Programs for Hierarchical Memory Parallel Processing Systems. Journal of Computer Science and Technology, Vol.8, No.3, 1993.

Guohua Jin and Fujie Chen. Loop Restructuring Techniques for Thrashing Problem. Proc. of the Parallel Architectures and Languages Europe, Lecture Notes in Computer Science, Vol.605, Springer, Paris, France, June 1992.

Guohua Jin and Fujie Chen. Compiler Strategies for Parallelizing Programs on Hierarchical Memory Multiprocessors. Proc. 1992 International Conference on Parallel and Distributed Systems, 1992.

Guohua Jin and Fujie Chen. Hybrid Loop Interchange: Optimization for Parallel Programs. Proc. of the 6th IEEE International Parallel Processing Symposium. Beverly Hills, California, March 1992.

Guohua Jin and Fujie Chen. Optimizing Fortran Loops for RISC-based Parallel Processing Systems. Proc. of the 5th International Conference on Parallel and Distributed Computing and Systems. Pittsburgh, Pennsylvania, October 1992.

Guohua Jin and Fujie Chen. Loop Staggering, Loop Staggering and Loop Compacting: Restructuring Techniques for Thrashing Problem. Proc. of the 20th International Conference on Parallel Processing, Chicago, Illinois, August 1991.

Guohua Jin and Fujie Chen. Design and Implementation of a Knowledge-based Parallelizing tool. Proc. of the 2nd IES Conference on Information Technology, Singapore, 1991.

Guohua Jin and Fujie Chen. A Loop Restructuring Technique to Exploit the Irregular Parallelism. Proc. of the 2nd International Conference for Young Computer Scientists, Beijing, July 1991.