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Publications

Journal Papers:

  1. Yaohang Li, “MOMCMC: An Efficient Monte Carlo Method for Multi-Objective Sampling over Real Parameter Space,” Computers and Mathematics with Applications, 64: 3542-3556, 2012. (Impact factor: 1.747)
     

  2. A. Yaseen, Yaohang Li, “Accelerating Knowledge-based Energy Evaluation in Protein Structure Modeling with Graphics Processing Units,” Journal of Parallel and Distributed Computing, 72(2): 297-307, 2012. (Impact factor: 1.078)
     

  3. Yaohang Li, I. Rata, E. Jakobsson, “Sampling Multiple Scoring Functions Can Improve Protein Loop Structure Prediction Accuracy,” Journal of Chemical Information and Modeling, 51(7): 1656-1666, 2011. (Impact factor: 3.882)
     

  4. W. Zhu, A. Yaseen, Yaohang Li, “DEMCMC-GPU: An Efficient Multi-Objective Optimization Method with GPU Acceleration on the Fermi Architecture,” New Generation Computing, 29(2): 163-184, 2011. (Impact factor: 0.416)
     

  5. Yaohang Li, I. Rata, S. Chiu, E. Jakobsson, “Improving Predicted Protein Loop Structure Ranking using a Pareto-Optimality Consensus Method,” BMC Structural Biology, 10: 22, 2010. (Impact factor: 2.790)
     

  6. I. Rata, Yaohang Li, E. Jakobsson, “Backbone Statistical Potential from Local Sequence-Structure Interactions in Protein Loops,” Journal of Physical Chemistry B, 114(5): 1859-1869, 2010. (Impact factor: 4.189)
     

  7. Yaohang Li, V. A. Protopopescu, N. Arnold, X. Zhang, A. Gorin, “Hybrid Parallel Tempering/Simulated Annealing Method,” Applied Mathematics and Computation, 212: 216-228, 2009. (Impact factor: 1.124)
     

  8. Yaohang Li, M. Mascagni, A. Gorin “A Decentralized Parallel Implementation for Parallel Tempering Algorithm,” Parallel Computing, 35(5): 269-283, 2009. (Impact factor: 1.471)
     

  9. Yaohang Li, C. E. M. Strauss, A. Gorin, “Hybrid Parallel Tempering and Simulated Annealing Method – an Efficient Sampling Method in ab initio Protein Folding,” International Journal of Computational Science, 2(5): 646-661, 2008.
     

  10. Yaohang Li, Y. D. Song, “An Adaptive and Trustworthy Software Testing Framework on the Grid,” Journal of Supercomputing, 46: 124-138, 2008. (Impact factor: 0.615)
     

  11. Yaohang Li, D. Chen, X. Yuan, “Trustworthy Remote Compiling Service for Grid-based Scientific Applications,” Journal of Supercomputing, 41(2):119-131, 2007. (Impact factor: 0.615)
     

  12. Yaohang Li, “A Bio-inspired Adaptive Job Scheduling Mechanism on the Grid,” International Journal of Computer Science and Network Security, 6(3B): 1-7, 2006.
     

  13. Yaohang Li, M. Mascagni, “Grid-based Quasi-Monte Carlo Applications,” Monte Carlo Methods and Applications, 11: 39-55, 2005.
     

  14. Yaohang Li, V. A. Protopopescu, A. Gorin, “Accelerated Simulated Tempering,” Physics Letters A, 328(4): 274-283, 2004. (Impact factor: 2.174)
     

  15. Yaohang Li, M. Mascagni, R. van Engelen, Q. Cai, “A Grid Workflow-Based Monte Carlo Simulation Environment,” Journal of Neural Parallel and Scientific Computations, 12:439-455, 2004.
     

  16. Yaohang Li, M. Mascagni, “Analysis of Large-scale Grid-based Monte Carlo Applications,” International Journal of High Performance Computing Applications (IJHPCA), 17(4): 369-382, 2003. (Impact factor: 1.824)
     

  17. Y. Zhang, Yaohang Li, M. H. Peters, “Nonequilibrium, Multiple-Time Scale Simulations of Ligand-Receptor Interactions in Structured Protein Systems,” Proteins: Structure, Function, and Genetics, 52(3): 339-348, 2003. (Impact factor: 4.684)
     

  18. M. Mascagni, A. Karaivanova, Yaohang Li, “Quasi-Monte Carlo method for elliptic boundary value problems”, Monte Carlo Methods and Applications, 7: 283-294, 2001.
     

Book Chapters:

  1. Yaohang Li, M. Mascagni, “An Overview of Grid-based Monte Carlo Computing,”  Grid Technologies, Emerging from Distributed Architectures to Virtual Organizations, WIT Press, ISBN: 978-1-84564-055-2, 2006.
     

  2. Y. D. Song, Yaohang Li, M. Bikdash, T. Dong, ”Cooperative Control of Multiple UAV’s in Close Formation Flight via Nonlinear Adaptive Approach,”  Theory and Algorithms for Cooperative Systems, World Scientific Publishing Company, ISBN: 978-9-81256-020-9, 2004.
     

Selected Papers in Conference Proceedings:

  1. A. Yaseen, Yaohang Li, "Enhancing Protein Disulfide Bonding Prediction Accuracy with Context-based Features," Proceedings of Biotechnology and Bioinformatics Symposium, (BIOT2012), Provo, 2012.
     

  2. H. Ji, Yaohang Li, "Reusing Random Walks in Monte Carlo Methods for Linear Systems," Proceedings of International Conference on Computational Science, (ICCS2012), Omaha, 2012.
     

  3. L. Tran, D. Banerjee, J. Wang, A. Kumar, F. McKenzie, Yaohang Li, J. Li, “A Large-Scale Manifold Learning Approach for Brain Tumor Progression Prediction,” Proceedings of 2nd International Workshop on Machine Learning in Medical Imaging, (MLMI2011), Toronto, 2011.
     

  4. W. Zhu, Yaohang Li, “GPU-Accelerated Differential Evolutionary Markov Chain Monte Carlo Method for Multi-Objective Optimization over Continuous Space,” Proceedings of 2nd Workshop on Bio-Inspired Algorithms for Distributed Systems, (BADS2010), Washington DC, 2010.
     

  5. Yaohang Li, W. Zhu, “GPU-Accelerated Multi-scoring Functions Protein Loop Structure Modeling,” Proceedings of 9th IEEE International Workshop on High Performance Computational Biology, (HiCOMB2010), Atlanta, 2010.
     

  6. Yaohang Li, I. Rata, E. Jakobsson, “Integrating Multiple Scoring Functions to Improve Protein Loop Structure Conformation Space Sampling,” Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, (CIBCB2010), Montreal, 2010.
     

  7. Yaohang Li, D. Wardell, “Study of Computing Consolidation Techniques in Computational Protein Loop Structure Modeling,” Proceedings of the 2nd International Conference on Bioinformatics and Computational Biology, (BICoB-2010), Honolulu, 2010.
     

  8. I. Waddell, N. Jones, C. Steed, X. Yuan, Yaohang Li, “Using the Workflow Technology in Secure Software Engineering Education,” Proceedings of 14th Colloquium for Information Systems Security Education, (CISSE2010), Baltimore, 2010.
     

  9. Yaohang Li, D. Wardell, V. Freeh, “A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications,” Proceedings of the 8th IEEE International Workshop on High Performance Computational Biology, (HiCOMB09), Rome, 2009.
     

  10. Yaohang Li, “A Population-based Approach for Diversified Protein Loop Structure Sampling,” Proceedings of the International Conference on Computational Science, (ICCS09), Baton Rouge, 2009.
     

  11. Yaohang Li, A. J. Bordner, Y. Tian, X. Tao, A. Gorin, “Extensive Exploration of the Conformational Space Improves Rosetta Results for Short Protein Domains,” 7th Annual International Conference on Computational Systems Bioinformatics (CSB08), Stanford, 2008.
     

  12. A. Frazier, S. Hudson, Yaohang Li, X. Yuan, “Developing Software System Security Modules,” Proceedings of 12th Colloquium for Information Systems Security Education (CISSE08), Dallas, 2008.
     

  13. Yaohang Li, M. Mascagni, A. Gorin, “Decentralized Replica Exchange Parallel Tempering: An Efficient Implementation of Parallel Tempering using MPI and SPRNG,” Proceedings of International Conference on Computational Science and Its Applications (ICCSA07), Kuala Lumpur, 2007.
     

  14. Yaohang Li, T. Dong, X. Zhang, Y. Song, X. Yuan, “Large-Scale Software Unit Testing on the Grid,” Proceedings of IEEE International Conference on Granular Computing (GrC06), Atlanta, 2006.
     

  15. X. Zhang, Yaohang Li, A. Myklebust, “Hybrid Optimization of Geometrically Trimmed NURBS Surfaces,” Proceedings of ASME International Mechanical Engineering Congress and Exposition (IMECE05), Orlando, 2005.
     

  16. Yaohang Li, M. Mascagni, “A Bio-inspired Job Scheduling Algorithm for Monte Carlo Applications on a Computational Grid,” proceedings of 17th IMACS World Congress, Scientific Computation, Applied Mathematics, and Simulation, Paris, 2005.
     

  17. Yaohang Li, C. E. M. Strauss, A. Gorin, “Parallel Tempering in Rosetta Practice,” Proceedings of International Conference on Bioinformatics and its Applications, (ICBA’04), Fort Lauderdale, 2004.
     

  18. Yaohang Li, M. Mascagni, “e-Science Workflow on the Grid,” Proceedings of the IADIS International Conference, e-Society 2004, Avila, 2004.
     

  19. Yaohang Li, M. Mascagni, M. H. Peters, “Grid-based Nonequilibrium Multiple-Time Scale Molecula Dynamics/Brownian Dynamics Simulations of Ligand-Receptor Interactions in Structured Protein Systems,” Proceedings of the First BioGrid Workshop at the 3rd IEEE/ACM Symposium Cluster Computing and the Grid, (BioGrid03), Tokyo, 2003.
     

  20. M. Mascagni, Yaohang Li, “Computational Infrastructure for Parallel, Distributed, and Grid-based Monte Carlo Computations,” Proceedings of the Fourth International Conference on Large-Scale Scientific Computations (LSSC'03), Sozopol, Bulgaria, Lecture Notes in Computer Sciences, 2907: 39-52, 2003.
     

  21. Yaohang Li, M. Mascagni, “Improving Performance via Computational Replication on a Large-Scale Computational Grid,” proceedings of the GP2PC at the IEEE/ACM International Symposium on Cluster Computing and the Grid, IEEE/ACM (CCGRID03), Tokyo, 2003.
     

  22. Yaohang Li, M. Mascagni, “Grid-based Monte Carlo Applications,” Lecture Notes in Computer Science, 2536:13-24, Grid Computing Third International Workshop/Conference (GRID02), Baltimore, 2002.