Professor of Mathematics
Professor of Electrical & Computer Engineering
Adjunct Professor of Biochemistry & Molecular Biology
Center for Mathematical Molecular Biosciences
619 Red Cedar Road
Phone: 517 353 4689
Fax: 517 432 1562
o Topology based deep learning for drug design, The 3rd Annual Meeting of SIAM Central States Section, September 29 — October 1, 2017, Colorado State University
§ MIBPB: Online server for electrostatic analysis using the second-order accurate Poisson-Boltzmann solver
§ ESES: Open-source online server for the generation of Eulerian solvent excluded surface
§ FRI: Online server for the flexibility analysis of biomolecules based on flexibility and rigidity index
§ RI-Score: Online server for geometric graph theory or rigidity index (RI) based scoring function for protein ligand binding affinity prediction
§ TML-BP: Online server for topological learning for protein-ligand binding affinity prediction
§ TML-MP: Online server for topology based machine learning for the prediction of protein folding stability change upon mutation
§ TDL-BP: Online server for topological deep learning for protein-ligand binding affinity prediction
§ TDL-MP: Online server for topological deep learning for the prediction of protein folding stability change upon mutation
§ TopP-S: Online server for topological learning of partition coefficient (LogP) and aqueous solubility (LogS)
§ TopTox: Online server for computing element-specific topological descriptors (ESTDs) for toxicity endpoint predictions
o Founding Editor-in-Chief, Molecular Based Mathematical Biology
o Advisory Editor, Journal of Theoretical and Computational Chemistry
o Honorary Editor, International Journal of Engineering and Applied Sciences
o Associate Editor, Frontiers in Molecular Biosciences, Biomolecular Modeling and Simulation
o Member of Editorial Board, International Journal of Modern Nonlinear Theory and Application
o Member of Editorial Board, International Journal of Biomedical Imaging
o Member of Editorial Board, Journal of Modeling in Mechanics and Materials
o Editor-in-Chief, Journal of Theoretical and Computational Chemistry , 2012-2016
o Associate Editor, Frontiers in Molecular Biosciences, Mathematics of Biomolecules, 2014-2017
o Member of Editorial Board, International Journal for Numerical Methods in Biomedical Engineering, 2010-2013
o Member of Editorial Board, Modeling and Simulation in Engineering, 2012-2103
o Member of Editorial Board, Communications for Numerical Methods in Engineering, 2008-2010
Recent grant support:
· Fall 2017: MTH994-001, Machine learning for biological and biomedical data I: Basic algorithms, TueThu: 2:40-4:00pm, C517WH
· Spring 2018: MTH994-001, Machine learning for biological and biomedical data II: Applications, TueThu: 1:00-2:20pm, C517WH
· Spring 2018: MTH496, Machine learning.
Students, postdocs and visiting scholars:
Yin Cao, Progressive Insurance, (PhD 2017)
Zhixiong Zhao, Assistant Professor, Foshan University (Postdoc, 2014-2016)
Bao Wang, Postdoc, University of California, Los Angeles (PhD 2016).
Kristopher Opron, Senior analyst, University of Michigan Health System (PhD 2016).
Lin Mu, Oak Ridge National Laboratory (Postdoc, 2012-2015).
Jin Kyoung Park, Assistant Professor (Tenure-track), Ivy Tech Community College, Indiana (PhD 2014).
Langhua Hu, Analyst (first job), Discover Financial Services, Riverwoods, IL (PhD 2013).
Kelin Xia, Assistant Professor (tenure-track), Nanyang Technological University (PhD 2012 and postdoc 2013-2016).
Zhan Chen, Assistant Professor (tenure-track), Georgia Southern University (PhD 2011).
Duan Chen, Assistant Professor (tenure-track), University of North Carolina, Charlotte (PhD 2010).
Siyang Yang, Assistant Professor (tenure-track), City University of Hong Kong (Declined due to family reasons) (Visiting assistant professor, 2010-2012).
Weihua Geng, Assistant Professor (tenure-track), South Methodist University (PhD 2008).
Manfeng Hu, Professor, Jiangnan University (Visiting scholar, 2008-2009).
Yuhui Sun, Analyst (first job), Eli Lilly, Indianapolis, IN (PhD 2007).
Sining Yu, Structured transaction analyst (first job), International Power America (PhD 2007).
Yongcheng Zhou, Associate Professor, Colorado State University (PhD 2006).
Yibao Zhao, Senior Lecturer,
Shan Zhao, Professor,
Zujun Hou, Research Scientist, Singapore Bioimaging Consortium (PhD 2003).
Shuguang Guan, Professor, East China Normal University (PhD 2002).
Meng Zhan, Professor, Huazhong University of Science and Technology (Postdoc, 2001-2002).
Zhenhai Shao, Professor, University of Electronic Science Technology of China (Postdoc, 2000-2001).
Prasad Patnaik, Professor, Indian Institute of
Decheng Wan, Professor, Shanghai Jiao Tong University, China (Postdoc, 1999-2001).
o Mathematics of Drug Design/Discovery, The Fields Institute for Research in Mathematical Sciences, Toronto, Canada, June 4 - 8, 2018.
o Mathematical Biophysics and Molecular Biosciences, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 19-23, 2016.
o SIAM Conference on the Life Sciences (LS16), The Westin Boston Waterfront, Boston, Massachusetts, USA, July 11-14, 2016.
o MBI Emphasis Year on Mathematical Molecular Biosciences Fall 2015, MBI, Columbus, August 16-December 31, 2015.
o Mathematics of Biological Charge Transport: Molecular and Beyond, IMA, University of Minnesota, July 20-24, 2015.
o Workshop on Persistent Homology for Biosciences, East Lansing, October 18, 2014.
o International Conference on Mathematical Modeling and Computation, Wuhan, China, May 16-19, 2013,
o CTW: Mathematical Challenges in Biomolecular/Biomedical Imaging and Visualization, MBI, Columbus, Feb 18-22, 2013
2nd Midwest Conference on Mathematical Methods for Images and Surfaces, Lansing, August 27-28, 2011.
o , Mathematical Bioscience Institute, Columbus, April 25-29, 2011.
o Workshop on Nano-Bio Mathematics and Mechanics, East Lansing, August 5, 2010.
o Workshop on Nano-Bio Mathematics, East Lansing, August 4, 2009.
o Midwest Conference on Mathematical Methods for Images and Surfaces, Lansing, April 18-19, 2009
o MSU-UM Math-Biology Day, Dec. 1, 2007
Stage 2 of D3R Grand Challenge 2 world-wide competition in drug design, our
prediction of protein-drug binding free ranking (Kendall's Tau) was ranked 1st,
and our prediction of protein-ligand binding free energies was ranked 2nd for