Guowei Wei, Ph.D.
MSU Research Foundation Professor
Biochemistry & Molecular Biology
Electrical & Computer Engineering
Contact information:
Department
Michigan State University
D301 Wells Hall
619 Red Cedar Road
East Lansing,
Phone: 517 353 4689
Fax: 517 432 1562
Weigatmsu.edu
Dedicated to those
who lost their
lives to the
pandemic:
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
Persistent Homology
for biomolecular systems, SIAM Life Conference, August 2014
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 Editor-in-Chief, Journal of Computational Biophysics and 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 2024: MTH994-001, Machine learning, TueThu: 10:00-11:20am, A306WH.
Office hours: Thursday: 11:20-1:00pm
and by appointment.
Students, postdocs
and visiting scholars:
Photo 1999
|
Photo 2002
|
Photo 2006
|
Photo 2007
|
Photo 2008
|
Some recent
Yuta Hozumi, Postdoc at Georgia Tech (PhD 2024).
Yuchi Qiu, Assistant Professor (tenure track), University of Illinois Chicago (Research Associate 2020-2023).
Azzam Alfarraj, Assistant Professor (tenure track), 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, MSU 2022-).
Kaifu Gao, Senior machine learning scientist, Ensem 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, Associate Professor, the University of Tennessee, Knoxville (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, Riverwoods, IL (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,
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 (Research Associate, 2001-2002).
Zhenhai Shao, Professor, University of Electronic Science Technology of China (Research Associate, 2000-2001).
Baofeng Feng,
Professor,
Prasad Patnaik, Professor, Indian Institute of
Technology,
Decheng Wan, Professor, Shanghai Jiao Tong University, China (Research Associate, 1999-2001).
Positions available:
Mathematical
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
The Unreasonable
Effectiveness of Mathematics in the Natural Sciences ---
Eugene Wigner