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Publications

Journal Papers:

  1. M. Abdelrasoul, K. Ponniah, A. Mao, M. S. Warden, W. Elhefnawy, Yaohang Li, S. M. Pascal, "Conformational Clusters of Phosphorylated Tyrosine," Journal of the American Chemical Society, in press, 2017.

  2. M. Li, X. Meng, R. Zheng, F. Wu, Yaohang Li, Y. Pan, J. Wang, "Identification of protein complexes by using a spatial and temporal active protein interaction network," IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, 2017.

  3. M. LiR. ZhengYaohang LiF. WuJ. Wang"MGT-SM: A Method for Constructing Cellular Signal Transduction Networks," IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, 2017.

  4. Y. Liang, X. Xing, Yaohang Li, "A GPU-based Large-scale Monte Carlo Simulation Method for Systems with Long-range Interactions," Journal of Computational Physics, 338: 252-268, 2017.

  5. H. Ji, Yaohang Li, "Block Conjugate Gradient Algorithms for Least Squares Problems," Journal of Computational and Applied Mathematics, 317: 203-217, 2017.

  6. H. Ji, Yaohang Li, "A Breakdown-Free Block Conjugate Gradient Method," BIT Numerical Mathematics, 57(2): 379-403, 2017.

  7. H. Ji, Yaohang Li, S. Weinberg, "Calcium Ion Fluctuations Alter Channel Gating in a Stochastic Luminal Calcium Release Site Model," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14(3): 611-619, 2017.

  8. J. L. Hung, M. C. Wang, S. Wang, M. Abdelrasoul, Yaohang Li, W. He, "Identifying At-Risk Students for Early Interventions - A Time Series Clustering Approach," IEEE Transactions on Emerging Topics in Computing, 5(1): 45-55, 2017.

  9. J. López-Blanco, A. Canosa-Valls, Yaohang Li, P. Chacón, "RCD+: Fast loop modeling server," Nucleic Acids Research, 44(W1): W395-W400, 2016.

  10. A. Yaseen, M. Nijim, B. Williams, L. Qian, J. Wang, M. Li, Yaohang Li, "FLEXc: Protein Flexibility Prediction using Context-based Statistics, Predicted Structural Features, and Sequence Information," BMC Bioinformatics, 17(S8):281, 2016.

  11. A. Yaseen, H. Ji, Yaohang Li, "A Load-Balancing Workload Distribution Scheme for Three-Body Interaction Computation on Graphics Processing Units (GPU)," Journal of Parallel and Distributed Computing, 87: 91-101, 2016.

  12. Y. Liang, D. Wu, G. Liu, Yaohang Li, C. Gao, Z. Ma, W. Wu, "Big Data-enabled Multiscale Serviceability Analysis for Aging Bridges," Digital Communications and Networks, 2(3): 97-107, 2016.

  13. W. Lan, J. Wang, M. Li, J. Liu, Yaohang Li, F. Wu, Y. Pan, "Predicting drug–target interaction using positive-unlabeled learning," Neurocomputing, 206: 50-57, 2016.

  14. B. Zhao, J. Wang, M. Li, X. Li, Yaohang Li, F. Wu, Y. Pan, "A new method for predicting protein functions from dynamic weighted interactome networks," IEEE Transactions on NanoBioscience, 15(2): 131-139, 2016.

  15. W. Elhefnawy, L. Chen, Y. Han, Yaohang Li, ICOSA: A Distance-dependent, Orientation-specific Coarse-grain Contact Potential for Protein Structure Modeling, Journal of Molecular Biology, 427(15): 2562-2576, 2015.

  16. W. He, J. Shen, X. Tian, Yaohang Li, A. Akula, G. Yan, R. Tao, “Gaining Competitive Intelligence from Social Media Data: Evidence from Two Largest Retail Chains in the World,” Industrial Management & Data Systems, 115(9): 1622-1636, 2015.

  17. A. Yaseen, Yaohang Li, Context-based Features Enhance Protein Secondary Structure Prediction Accuracy, Journal of Chemical Information and Modeling, 54(3): 992-1002, 2014.

  18. A. Yaseen, Yaohang Li, “CASA: A Protein Solvent Accessibility Prediction Server using Context-based Features to Enhance Prediction Accuracy, BMC Bioinformatics, in press, 2014.

  19. W. He, A. Kshirsagar, A. Nwala, Yaohang Li, Teaching Information Security with Workflow Technology – A Case Study Approach, Journal of Information Systems Education, 25(3): 201-210, 2014.

  20. A. Yaseen, Yaohang Li, Template-based C8-SCORPION: a Protein 8-state Secondary Structure Prediction Method using Structural Information and Context-based Features, BMC Bioinformatics, 15(S8): S3, 2014.

  21. H. Ji, M. Mascagni, Yaohang Li, “Convergence Analysis of Markov Chain Monte Carlo Linear Solvers using Ulam-von Neumann Algorithm,” SIAM Journal on Numerical Analysis, 51(4): 2107-2122, 2013.

  22. A. Yaseen, Yaohang Li, Dinosolve: A Protein Disulfide Bonding Prediction Server using Context-based Features to Enhance Prediction Accuracy, BMC Bioinformatics, 14(S13): S9, 2013.

  23. L. Tran, D. Banerjee, J. Wang, A. Kumar, F. McKenzie, Yaohang Li, J. Li, High-Dimensional MRI Data Analysis using a Large-Scale Manifold Learning Approach, Machine Vision and Applications, 24(5): 995-1014, 2013.

  24. Yaohang Li, Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview, Computational and Structural Biotechnology Journal, 5(6): e201302003, 2013.

  25. Yaohang Li, H. Liu, I. Rata, E. Jakobsson, “Building a Knowledge-based Statistical Potential by Capturing High-Order Inter-Residue Interactions and its Applications in Protein Secondary Structure Assessment,” Journal of Chemical Information and Modeling, 53(2): 500-508, 2013.

  26. 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.

  27. 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.

  28. 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.

  29. 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.

  30. 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.

  31. 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.

  32. 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.

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

  34. 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.

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

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

  37. 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.

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

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

  40. 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.

  41. 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.

  42. 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.

  43. 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. Y. Liang, D. Wu, D. Huston, G. R. Liu, Yaohang Li, C. Gao, J. Ma, "Civil Infrastructure Serviceability Evaluation Based on Big Data," Guide to Big Data Application, Springer Publishing, 2017.

  2. H. Ji, Yaohang Li, Monte Carlo Methods and their Applications in Big Data Analysis, Mathematical Problems in Data Science - Theoretical and Practical Methods, Springer, ISBN: 978-3-319-25127-1, 2015.

  3. 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.

  4. 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. W. Yu, Y. Gu, J. Li, S. Liu, Yaohang Li, "Single-Pass PCA of Large High-Dimensional Data," Proceedings of the Twenty-Sixth International Joint Conference on Artificial Intelligence (IJCAI-17), Melbourne, 2017.

  2. Yaohang Li, R. Mukkamala, M. Mascagni, "Validating the Correctness of Outsourced Computational Tasks using Pseudorandom Number Generators," Proceedings of the 15th IEEE International Conference on Dependable, Autonomic and Secure Computing, (DASC 2017), Orlando, 2017.

  3. W. Elhenfnawy, Yaohang Li, "Construction of Protein Backbone Fragments Libraries on Large Protein Sets using a Randomized Spectral Clustering Algorithm," Proceedings of International Symposium on Bioinformatics Research and Applications (ISBRA2017), Hononulu, 2017.

  4. P. Ni, M. Li, P. Zhong, G. Duan, J. Wang, Yaohang Li, F. Wu, "Relating Diseases Based on Disease Module Theory," Proceedings of International Symposium on Bioinformatics Research and Applications (ISBRA2017), Hononulu, 2017.

  5. W. Elhenfnawy, J. Wright, K. Kallepalli, K. Racheal, A. Gupta, Yaohang Li, R. Parimi, P. Shah,  "What Differentiates News Articles with Short and Long Shelf Lives? A Case Study on News Articles at Bloomberg.com," Proceedings of 6th IEEE International Conference on Big Data and Cloud Computing (BDCloud 2016), Atlanta, 2016.

  6. M. Abdelrasoul, Yaohang Li, "Coarse-grained Contact Potential Helps Improve Fold Recognition Sensitivity in Template-based Protein Structure Modeling," Proceedings of Big Data And Cloud Computing in Bioinformatics (BDACCB2016) Workshop, Atlanta, 2016.

  7. H. Ji, S. H. Weinberg, M. Li, J. Wang, Yaohang Li, "An Apache Spark Implementation of Block Power Method for Computing Dominant Eigenvalues and Eigenvectors of Large-Scale Matrices," Proceedings of Applications of Big Data Science (ABDS16) Workshop, Atlanta, 2016.

  8. H. Ji, Yaohang Li, S. H. Weinberg, "Calcium ion fluctuations alter channel gating in a stochastic luminal calcium release site model," Proceedings of International Symposium on Bioinformatics Research and Applications (ISBRA2015), Norfolk, 2015.

  9. H. Ji, E. O'Saben, A. Boudion, Yaohang Li, "March Madness Prediction: A Matrix Completion Approach," Proceedings of Modeling, Simulation, and Visualization Student Capstone Conference, Sulfolk, 2015. (Best Paper Award)

  10. W. He, X. Tian, J. Shen, Yaohang Li, "Understanding Mobile Banking Applications’ Security risks through Blog Mining and the Workflow Technology," Proceedings of the International Conference on Information Systems, Fort Worth, 2015.

  11. H. Ji, M. Sosonkina, Yaohang Li, "An Implementation of Block Conjugate Gradient Algorithm on CPU-GPU Processors," Proceedings of 1st International Workshop on Hardware-Software Co-Design for High Performance Computing (Co-HPC2014), New Orleans, 2014.

  12. Q. Li, S. Pascal, Yaohang Li, "Intrinsically Disorder Protein Prediction using Undersampling Feedforward Neural Networks and Predicted Amino Acid Features," Proceedings of Modeling, Simulation, and Visualization Capstone Conference, Sulfolk, 2014.

  13. H. Ji, Yaohang Li, "GPU Accelerated Randomized Singular Value Decomposition and Its Application in Image Compression," Proceedings of Modeling, Simulation, and Visualization Capstone Conference, Sulfolk, 2014. (Best Paper Award)

  14. A. Yaseen, Yaohang Li, "Predicting Protein Solvent Accessibility with Sequence, Evolutionary Information and Context-based Features," Proceedings of Biotechnology and Bioinformatics Symposium, (BIOT2013), Provo, 2013.

  15. A. Yaseen, Yaohang Li, "Template-based Prediction of Protein 8-state Secondary Structures," Proceedings of 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences, (ICCABS2013), New Orleans, 2013.

  16. I. Rata, K. Wessells, Yaohang Li, "An Improved Statistics-based Backbone Torsion Potential Energy for Protein Loop Structure Modeling," Proceedings of 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences, (ICCABS2013), New Orleans, 2013.

  17. Yaohang Li, A. Yaseen, "Pareto-based Optimal Sampling Method and Its Applications in Protein Structural Conformation Sampling," Proceedings of AAAI Workshop on Artificial Intelligence and Robotics Methods in Computational Biology, Bellevue, 2013.

  18. Yaohang Li, "A Coarse-grained, Context-dependent Contact Potential for Protein Decoy Discrimination," Proceedings of the 5th International Conference on Bioinformatics and Computational Biology, (BICoB-2013), Honolulu, 2013.

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

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

  21. 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.

  22. 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.

  23. 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.

  24. 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.

  25. 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.

  26. 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.

  27. 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.

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

  29. X. Zhang, S. Watts, Yaohang Li, D. Tortorelli, "Minkowski Functionals Study of Random Number Sequences," Proceedings of the International Conference on Computational Science, (ICCS09), Baton Rouge, 2009.

  30. 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.

  31. 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.

  32. 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.

  33. 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.

  34. 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.

  35. 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.

  36. 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.

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

  38. 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.

  39. 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.

  40. 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.

  41. 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.