MSU Foundation Professor
619 Red Cedar Road
Phone: 517 353 4689
Fax: 517 432 1562
Dedicated to those who lost their lives to the pandemic:
Review of the mechanisms of SARS-CoV-2 evolution and transmission, (2021).
Artificial intelligence design of mutation-proof COVID-19 antibody therapies, (2021).
Review of SARS-CoV-2 main protease inhibitors, Journal of Medicinal Chemistry (2021).
Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2, Chemical Reviews (2021).
Revealing the threat of emerging SARS-CoV-2 mutations to antibody therapies, Journal of Molecular Biology, 433, 167155 (2021).
UMAP-assisted K-means clustering of large-scale SARS-CoV-2 mutation datasets, Computers in Biology and Medicine, 131, 104264 (2021).
Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies, Chemical Science, 12, 6929 - 6948 (2021).
SARS-CoV-2 becoming more infectious as revealed by algebraic topology and deep learning, Communications in Information and Systems, 21(1), 31-36 (2021).
Host immune response driving SARS-CoV-2 evolution, Viruses, 12, 1095 (2020).
Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants, Communications Biology, 4, 228 (2021).
Decoding asymptomatic COVID-19 infection and transmission, The Journal of Physical Chemistry Letters, 11, 10007-10015 (2020).
Review of COVID-19 antibody therapies, Annual Review of Biophysics, 50, 1-30, (2021).
Mutations strengthened SARS-CoV-2 infectivity, Journal of Molecular Biology, 432, 5212-5226 (2020).
Mutations on COVID-19 diagnostic targets, Genomics, 112, 5204-5213 (2020).
Repositioning of 8565 existing drugs for COVID-19, The Journal of Physical Chemistry Letters, 11, 13, 5373–5382 (2020).
Unveiling the molecular mechanism of SARS-CoV-2 main protease inhibition from 92 crystal structures, Chemical Science, 11, 12036 - 12046 (2020).
Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine, Journal of Chemical Information and Modeling, 60, 5853-5865 (2020).
o How Math and AI are Revolutionizing Biosciences, Beyond TDA - Persistent topology and its applications in data sciences, August 28, 2021.
o Can AI discover the drugs of the future? The 8th International Congress of Chinese Mathematicians, Beijing, June 9 - 15, 2019.
o Ten lectures at NSF-CBMS Regional Research Conference: Mathematical Molecular Bioscience and Biophysics, The University of Alabama, May 13 - 17, 2019. [Lecture outlines]. [Lecture slides and videos].
o Is it time for a great chemistry between mathematics and biology? Harvard University, March 25, 2018.
o Topology based deep learning for drug design, The 3rd Annual Meeting of SIAM Central States Section, Colorado State University, September 29 - October 1, 2017.
§ 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.
§ PPD: Online server for Protein Pocket Detection.
§ 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.
§ DG-GL: Online server for differential geometry based geometric learning (DG-GL) of molecular datasets.
§ AGL-Score: Online server for algebraic graph theory-based protein-ligand binding scoring, ranking, docking and screening.
§ GGL-Tox: Online server for the geometric graph learning of Tox21 predictions.
§ HERMES: Open-source software package for simultaneous topological data analysis (persistent Betti numbers) and geometric data analysis (persistent eigenvalues).
o Associate Editor, Journal of Chemical Information and Modeling.
o Founding Editor-in-Chief, Computational and Mathematical Biophysics.
o Advisory Editor, Journal of Computational Biophysics and Chemistry.
o Advisory editor, Engineering Reports.
o Honorary Editor, International Journal of Engineering and Applied Sciences.
o Editorial Board, Chemical Physics Letters.
o Editorial Board, International Journal of Modern Nonlinear Theory and Application.
o Editorial Board, International Journal of Biomedical Imaging.
o Member of Editorial Board, Journal of Modeling in Mechanics and Materials.
o Associate Editor, Frontiers in Molecular Biosciences, Mathematics of Biomolecules, 2014-2017.
o Editorial Advisory Board, Journal of Chemical Information and Modeling, 2018-2020.
o Advisory Editor, Journal of Theoretical and Computational Chemistry 2016-2020.
o Editor-in-Chief, Journal of Theoretical and Computational Chemistry, 2012-2016.
o Editorial Board, International Journal for Numerical Methods in Biomedical Engineering, 2010-2013.
o Editorial Board, Modeling and Simulation in Engineering, 2012-2103.
o Editorial Board, Communications for Numerical Methods in Engineering, 2008-2010.
Recent grant support:
· Spring 2021: MTH994-001, Deep learning, TueThu: 6:00-7:30pm, Online
Students, postdocs and visiting scholars:
David Bramer, Instructor, Michigan State University (PhD, 2019).
Duc Nguyen, Assistant Professor (tenure-track), the University of Kentucky (Postdoc, 2015-2018).
Zixuan Cang, Assistant Professor (tenure-track), North Carolina State University (PhD 2018).
Kedi Wu, Principal Quantitative Analyst, Capital One Financial Corporation, Plano, Texas (PhD 2018).
Yin Cao, R&D Analyst, Progressive Insurance, Cleveland, (PhD 2017).
Zhixiong Zhao, Assistant Professor, Foshan University (Postdoc, 2014-2016)
Bao Wang, Assistant Professor (tenure-track), the University of Utah, (PhD 2016).
Kristopher Opron, Senior Bioinformatician and Computational Biologist, University of Michigan Health System (PhD 2016).
Lin Mu, Assistant Professor (tenure-track), University of Georgia, Athens (Postdoc, 2012-2015).
Jin Kyoung Park, Assistant Professor (Tenure-track), Ivy Tech Community College, Indiana (PhD 2014).
Langhua Hu, Analyst (first job), Discovery Financial Services, Riverwoods, IL (PhD 2013).
Kelin Xia, Assistant Professor (tenure-track), Nanyang Technological University (PhD 2012 and postdoc 2013-2016).
Zhan Chen, Associate Professor, Georgia Southern University (PhD 2011).
Duan Chen, Associate Professor, 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, Associate Professor, South Methodist University (PhD 2008).
Changjun Chen, Associate Professor, Huazhong University of Science and Technology (Postdoc, 2008-2009).
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, 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).
Baofeng Feng, Professor,
Prasad Patnaik, Professor, Indian Institute of
Decheng Wan, Professor, Shanghai Jiao Tong University, China (Postdoc, 1999-2001).
o The fourth conference on Computational and Mathematical Bioinformatics and Biophysics, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 13-17, 2021.
o Computational Topology and Application, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 13-17, 2021.
o The third conference on Computational and Mathematical Bioinformatics and Biophysics, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 21-25, 2020.
o Computational Topology and Application, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 7-11, 2020 (cancelled).
o Quantum Dynamics & Beyond, Symposium in honor of Donal J Kouri, ACS Philadelphia, March 24-25, 2020.
o The second conference on Computational and Mathematical Bioinformatics and Biophysics, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 9-13, 2019.
o TGDA@OSU TRIPODS workshop on Structure in the Micro-world, Ohio State University, May 28-31, 2019.
o Computational and Mathematical Approaches for Bioinformatics and Biophysics, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 10-14, 2018.
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