Welcome to Guo-Wei Wei's  Home Page

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Guowei  Wei, Ph.D.

MSU Foundation Professor 

Mathematics

Biochemistry  &  Molecular Biology

Electrical  &  Computer Engineering


Contact information:

Department  of  Mathematics
Michigan State University
D301 Wells Hall

619 Red Cedar Road
East Lansing, MI 48824, USA
Phone:  517 353 4689

Fax: 517 432 1562

Weigatmsu.edu  

 

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Dedicated to those who lost their lives to the pandemic:

*     SARS-CoV-2 Mutation Tracker

*     Third party YouTube about our work on SARS-CoV-2

 

Research Interests:

 

Publication (Google Scholar):

 

Selected lectures:

o   Persistent Topological Laplacians, Applied Algebraic Topology Research Network (AATRN), April 26, 2023.

o   Discovering the mechanisms of SARS-CoV-2 evolution and transmission, FDA's Office of Clinical Pharmacology - Innovative Data Analytics Seminar Series, July 12, 2022 (passcode: IDA2022!).

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.

o   Mathematics is the champion of biomolecular data challenges,  MBI, Ohio State University, September 16, 2016

o   Persistent Homology for biomolecular systems, SIAM Life Conference, August 2014 

o   PDE  transform: A unified paradigm for image analysis and multiscale modeling, Courant Institute, 2012

o   Variational multiscale  models for ion channel transport, University of  Oxford, September 6, 2011

 

Data library

§  2D data library for chemical, biophysical, and biological information

§  3D data library for chemical, biophysical, and biological information

 

Software packages:

§  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 persistence (harmonic spectra) and shape of data (non-harmonic spectra).

§  CCP: Correlated Clustering and Projection for dimensionality reduction.

 

Journal Editorship:

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   Associate Editor, Frontiers in Molecular Biosciences, Biomolecular Modeling and Simulation.

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   Editorial Board, Journal of Modeling in Mechanics and Materials.

o   Editorial Board, MDPI/Mathematical Biology. 

o   Editorial Board, Artificial Intelligence Chemistry.

o   Editorial Board, American Journal of Computational Mathematics.

o   Editorial Board, CMC - Computers, Materials & Continua.

o   Editor (Co-Editor-in-Chiefs), International Journal for Numerical Methods in Biomedical Engineering, 2013-2021.    

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:

 

Teaching:

o   Fall 2023: MTH994-001, Machine learning, TueThu: 10:20-11:40pm, A306WH.

o   Fall 2023: MTH133-024 Calculus II, MWF: 12:40-1:30pm, A304WH.

Office hours: Friday: 2:00-4:00pm and by appointment.

 

 

Students, postdocs and visiting scholars:

 

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Some recent group alumni:

*     Azzam Alfarraj, Assistant Professor, King Fahd University of Petroleum & Minerals (Ph.D. 2018-2023).

*     Jiahui Chen, Assistant Professor (tenure-track), University of Arkansas (Visiting assistant professor 2019-2023). 

*     Rui Wang, Simons Center Postdoctoral Fellow, New York University (PhD 2022, Visiting assistant professor 2022-2023).

*     Dong Chen (PhD 2022, Visiting assistant professor 2022-).

*     Kaifu Gao, Data scientist at BAKX Therapeutics (Research associate 2018-2022).

*     Timothy Szocinski, Data scientist at Auray (PhD 2021).

*     Menglun Wang, The United States Food and Drug Administration (PhD 2021).

*     David Bramer, Instructor, Michigan State University (PhD, 2019). 

*     Duc Nguyen, Assistant Professor (tenure-track), the University of Kentucky (Visiting assistant professor, 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 (Research Associate, 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, Associate Professor, University of Georgia, Athens (Visiting assistant professor, 2012-2015).

*     Kelin Xia, Associate Professor, Nanyang Technological University (PhD 2012 and postdoc 2013-2016).

*     Jin Kyoung Park, Associate Professor, Ivy Tech Community College, Indiana (PhD 2014).

*     Langhua Hu, Analyst (first job), Discovery Financial Services, RiverwoodsIL (PhD 2013).

*     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 (Research Associate, 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, Singapore Management University (PhD 2004).

*     Shan Zhao, Professor, University of Alabama (Ph.D. 2003 and Research Associate 2003-2006).

*     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 (Research Associate, 2001-2002).

*     Zhenhai Shao, Professor, University of Electronic Science Technology of China (Research Associate, 2000-2001).

*     Baofeng Feng, Professor, University of Texas –Pan American (Research Associate, 2000-2001).

*     Prasad Patnaik, Professor, Indian Institute of Technology, Madras (Research Associate, 1999-2001).

*     Decheng Wan, Professor, Shanghai Jiao Tong University, China (Research Associate, 1999-2001).

 

Positions available:

 

Mathematical Seminars

 

Conferences organized: 

o   TSIMF International workshop on Computational topology and application, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 18-22, 2023.

o   The fifth conference on Computational and Mathematical Bioinformatics and Biophysics, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 11-15, 2023.

o   The Mathematics of Soft Matter --- Structure and Dynamics, Institute for Mathematical and Statistical Innovation, February 28-March 4, 2022.

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   Beyond TDA--Persistent topology and its applications in data sciences, Online meeting, August 28-30, 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   Topology of the biomolecular world, America Institute of Mathematics,  San Jose, California. July 24-28, 2017.

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

o   2nd Midwest Conference on Mathematical Methods for Images and Surfaces, Lansing, August 27-28, 2011.

o   Modeling and computation of biomolecular structure and dynamics, 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

o   MSU-UM  Math-Biology  Day,  Ann Arbor, Dec.  2,  2006

o   Midwest  Quantitative  Biology  Conference,  Mackinac Island, Michigan, Sept 29-Oct. 1,  2006

o   Workshop on Advanced Algorithms for Science and Engineering, Singapore, March, 2000

Links:

Ø  Mathematics Genealogy Project 

Ø  Drug Design Data Resource Grand Challenge

 

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The Unreasonable Effectiveness of Mathematics in the Natural Sciences  ---  Eugene Wigner