Welcome to Guo-Wei Wei's Home Page
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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:
- Mathematical foundations of biosciences: Differential geometry based solvation models; Geometric algebra-based docking; Persistent topology of biomolecules; Variational multiscale models for ion channel transport; Differential geometry-based density functional theory (DFT) of proton transport; Curvature based biomolecular surfaces; Multiscale virus capsid modeling; Geometric modeling of protein complexes; Mechanoelectrical transducers; Graph theory-based flexibility-rigidity index (FRI) for proteins; Stochastic B-factor prediction; Electrostatic binding analysis; Reeb graph based protein pocket detection; Genomic data; Cahn-Hilliard for mitochondria; Geometric algebra for protein modeling, Geometric topology modeling; Mayer topology modeling; Topological phylogenetic.
- Mathematical foundations of AI and data science: Mathematical representations of data; Topological data analysis; Topological deep learning; Combinatorial commutative algebra; Topological learning; Evolutionary de Rham-Hodge theory; Persistent spectral graph; Persistent Laplacian; Homotopy continuation; Unified topological approach ; Persistent sheaf Laplacians; Persistent path Laplacian; Path topology; Persistent hyperdigraph homology and persistent hyperdigraph Laplacians; Persistent Mayer homology; Persistent Dirac of path and hypergraph; Generative network complex (GNC); Graph neural network (GNN); Multiscale manifold regularization; Champion; Persistent homology; PDE transform; Parametrization via convex optimization; Machine learning; Multitask learning; Autoencoder; Transformer; UMAP-assisted K-means clustering; Dimensionality reduction; CCP dimension reduction; Interaction topology; Persistent Jones polynomial; Persistent Khovanov homology.
- Drug discovery, bioinformatics, and quantitative systems pharmacology: Protein-ligand binding affinity; Pose prediction; MathDL; Virtual screening; Partition coefficient; Solubility; Toxicity; Scoring, ranking, docking, and screening; Protein folding stability change upon mutation; Protein-protein binding affinity; Genotyping; Automated generation of drug-like molecules; Proteome-informed AI for drug adduction; Deep mutational scanning; Multiscale transformer.
- Mathematical virology, virus evolution, infectivity, vaccine breakthrough and antibody resistance
- Biomedical imaging and engineering: Geometric flow approaches to images and surfaces; PDE transform; Image edge analysis by coupled PDEs; Bioluminescence tomography.
- High order interface methods: Matched interface and boundary (MIB); Multidomain interface problems.
- Nano modeling and simulation: Nano-electronic devices; Nanofluidic systems.
- Quantum kinetic theory: Quantum Boltzmann theory; Transport theory; Reaction rate theory.
- Wavelet local spectral methods and applications: Computational electromagnetics; Computational fluid dynamics; Richtmyer-Meshkov instability; Structural stability analysis.
- Dynamical systems: Controlling chaos; Controlling turbulence; Controlling pattern formation.
Publication (Google
Scholar):
- COMPLETE LIST
- Mathematical molecular bioscience and biophysics
- Machine learning, big data, signals, images and surfaces
- Mathematical
virology, virus evolution, infectivity, vaccine breakthrough, and antibody
resistance.
- Matched interface and boundary (MIB)
- Scientific and engineering computations
- Quantum kinetic theory & quantum scattering theory
- Nano and
material sciences
- Controlling chaos, turbulence and pattern
formation
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 Executive
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 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, Data
Analytics and Topology.
o Editorial Board, Mathematics of Data, Learning, and Intelligence
o Editorial Board, SIAM Journal on Life Sciences (SIALS)
o Associate Editor, Frontiers in Molecular Biosciences, Biomolecular Modeling and Simulation, 2019-2025.
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 Associate Editor, Journal of Chemical Information and Modeling, 2020-2024.
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:
- National Institute of Health (NIGMS, NIAID)
- National Science Foundation (DMS, CISE, DGE)
- Department of Energy (DOE)
- National Aeronautics and Space Administration (NASA)
- Bristol-Myers Squibb
- Pfizer
- Michigan Economic Development Corporation
- George Mason University
- MSU Foundation
- COVID-19 High
Performance Computing Consortium
Teaching:
o
Fall 2025: MTH994-001, Mathematics-Assisted
AI and AI-inspired Mathematics. MW 10:40-12:00am Wells Hall C117
o
Fall 2025: MTH850, Numerical Analysis I.
M/W/F 9:10AM-10:00AM
Office hour:
Friday 10:40-12:00pm and by appointment.
Students, postdocs
and visiting scholars:
- Currently 8 Ph.D. candidates, 5 research associates, 3 visiting scholars, 5 undergraduate research students, and 2 high scholar students.
- Graduated 27 Ph.D. students.
- Graduated 11 MSc students.
- Advised 65 undergraduate research students.
- Supported 30 postdoctoral associates.
- Supported 29 visiting scholars.
Photo 1999
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Photo 2002
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Photo 2025
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Some recent
Ø Zhe Su, Assistant Professor (tenure track), Auburn University (Research Associate 2023-2025).
Ø Hongsong Feng, Assistant Professor (tenure track), University of North Carolina at Charlotte (Research Associate 2021-2025).
Ø Li
Shen, NITMB Fellow, Northwestern University/University of Chicago (Ph.D. 2025).
Ø Xiaoqi Wei, postdoc at North Carolina State University (Ph.D. 2024).
Ø Yuta Hozumi, Hale Visiting Assistant Professor, Georgia Institute of Technology (Ph.D. 2024).
Ø Yuchi Qiu, Assistant Professor (tenure track), University of Illinois Chicago (Research Associate 2020-2023).
Ø Azzam Alfarraj, Assistant Professor (tenure track), King Fahd University of Petroleum & Minerals (Ph.D. 2018-2023).
Ø Jiahui Chen, Assistant Professor (tenure-track), University of Arkansas (Visiting assistant professor 2019-2023).
Ø Rui Wang, Simons Center Postdoctoral Fellow, New York University (PhD 2022, Visiting assistant professor 2022-2023).
Ø Dong Chen (Ph.D. 2022, Visiting assistant professor, MSU 2022-).
Ø Kaifu Gao, Senior machine learning scientist, Ensem Therapeutics (Research associate 2018-2022).
Ø Timothy Szocinski, Data scientist at Auray (Ph.D. 2021).
Ø Menglun Wang, The United States Food and Drug Administration (Ph.D. 2021).
Ø David Bramer, Instructor, Michigan State University (Ph.D., 2019).
Ø Duc Nguyen, Associate Professor, the University of Tennessee, Knoxville (Visiting assistant professor, 2015-2018).
Ø Zixuan Cang, Assistant Professor (tenure-track), North Carolina State University (Ph.D. 2018).
Ø Kedi Wu, Principal Quantitative Analyst, Capital One Financial Corporation, Plano, Texas (Ph.D. 2018).
Ø Yin Cao, R&D Analyst, Progressive Insurance, Cleveland, (Ph.D. 2017).
Ø Zhixiong Zhao, Assistant Professor, Foshan University (Research Associate, 2014-2016)
Ø Bao Wang, Assistant Professor (tenure-track), the University of Utah, (PhD 2016).
Ø Kristopher Opron, Senior Bioinformatician and Computational Biologist, University of Michigan Health System (Ph.D. 2016).
Ø Lin Mu, Associate Professor, University of Georgia, Athens (Visiting assistant professor, 2012-2015).
Ø Kelin Xia, Associate Professor, Nanyang Technological University (Ph.D. 2012 and postdoc 2013-2016).
Ø Jin Kyoung Park, Associate Professor, Ivy Tech Community College, Indiana (Ph.D. 2014).
Ø Langhua Hu, Analyst (first job), Discovery Financial Services, Riverwoods, IL (Ph.D. 2013).
Ø Zhan Chen, Professor, Georgia Southern University (Ph.D. 2011).
Ø Duan Chen, Professor, University of North Carolina, Charlotte (Ph.D. 2010).
Ø Siyang Yang, Assistant Professor (tenure-track), City University of Hong Kong (Declined due to family reasons) (Visiting assistant professor, 2010-2012).
Ø Weihua Geng, Professor, South Methodist University (Ph.D. 2008).
Ø Changjun Chen, Associate Professor, Huazhong University of Science and Technology (Research Associate, 2008-2009).
Ø Manfeng Hu, Professor, Jiangnan University (Visiting scholar, 2008-2009).
Ø Yuhui Sun, Analyst (first job), Eli Lilly, Indianapolis, IN (Ph.D. 2007).
Ø Sining Yu, Structured transaction analyst (first job), International Power America (Ph.D. 2007).
Ø Yongcheng Zhou, Professor, Colorado State University (Ph.D. 2006).
Ø
Yibao Zhao, Senior Lecturer,
Ø
Shan Zhao, Professor,
Ø Zujun Hou, Research Scientist, Singapore Bioimaging Consortium (Ph.D. 2003).
Ø Shuguang Guan, Professor, East China Normal University (Ph.D. 2002).
Ø Meng Zhan, Professor, Huazhong University of Science and Technology (Research Associate, 2001-2002).
Ø Zhenhai Shao, Professor, University of Electronic Science Technology of China (Research Associate, 2000-2001).
Ø
Baofeng Feng, Professor,
Ø
Prasad Patnaik, Professor, Indian Institute of
Technology,
Ø Decheng Wan, Professor, Shanghai Jiao Tong University, China (Research Associate, 1999-2001).
Positions available:
- Internships and research assistantships.
- Research associate (Offer to candidates who are trained on mathematical or computational biosciences).
Mathematical
- Biweekly seminars on
Mathematical Molecular Biosciences
- Biweekly seminars in
Computational Topology/Geometry/Graph
- Mathematical
Biology, Fall 2010
- Mathematical
Biology, Spring
2010
Conferences organized:
- Scientific
Committee, "Applied Geometry for Data Sciences, Part
I", IMS, NUS, Singapore, September 30 - October 4, 2024.
- The selection committee in Algebraic and Geometric Topology, 2024 ICBS Frontiers of Science Award, July 2024.
- The nomination committee in Algebraic and Geometric Topology, 2024 ICBS Frontiers of Science Award, July 2024.
- Organizing
Committee, "IMS-NTU joint workshop on Biomolecular Topology: Modelling and Data Analysis",
IMS, NUS, Singapore, June 24-28, 2024.
- International Advisory Committee, 8th International Conference on Computational and Mathematical Biomedical Engineering (CMBE24) will be held at George Mason University, Arlington, Virginia, United States between 24-26 June 2024.
- Organizer, Computational Topology and Application, Tsinghua Sanya International Mathematics Forum (TSIMF), Sanya, China, December 18-22, 2023.
- Lead organizer, 2023 MSU Workshop
on Spatial and Time-Resolved Single-Cell Transcriptomics Analysis,
Michigan State University, November 12 - 13, 2023.
- Lead organizer: Workshop on scRNA-Seq,
Spatiotemporal Transcriptomic, and Genomic Data Analysis, Michigan State
University, August 24 - 26, 2023.
- Organizer, Biweekly Online
Seminar on Mathematical Molecular Biosciences, Michigan State University,
2022-2024.
- Organizer, The 6th Conference on Computational and
Mathematical Bioinformatics and Biophysics, Tsinghua Sanya International
Mathematics Forum (TSIMF), Sanya, China, December 16-20, 2024.
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.
- Organizing Committee, "Applied geometry for data
sciences",
Mathematical Science Research Center, Chongqing, China, July 25-29, 2022.
- Organizing
Committee, "Applied Topology in Frontier
Sciences", IMS, NUS, July 11-22, 2022.
- Organizer, Presidential Workshop:
Everything Chemists Always Wanted To Know About
Machine Learning* (*But Were Afraid To Ask), The
ACS meeting in San Diego, March 19, 2022.
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