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 foundation 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.
- Mathematical foundation of AI and data science: Mathematical representations of data; Topological data analysis; Topological deep learning; 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.
- 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
- 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 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:
- National Institute of Health (NIGMS, NIAID)
- National Science Foundation (DMS, CISE, DGE)
- National Aeronautics and Space Administration
- Bristol-Myers Squibb
- Pfizer
- Michigan Economic Development Corporation
- George Mason University
- MSU Foundation
- COVID-19 High
Performance Computing Consortium
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:
- Currently 9 Ph.D. candidates, 5 research associates, 3 visiting scholars, 5 undergraduate research students, and 2 high scholar students.
- Graduated 26 Ph.D. students.
- Graduated 11 MSc students.
- Advised 61 undergraduate research students.
- Supported 29 postdoctoral associates.
- Supported 26 visiting scholars.
Photo 1999
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Photo 2002
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Photo 2006
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Some recent
Xiaoqi Wei, postdoc at North Carolina State University (Ph.D. 2024).
Yuta Hozumi, Postdoc at Georgia Tech (Ph.D.
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 (Ph.D. 2022, Visiting assistant
professor, MSU 2022-).
Kaifu Gao, Senior machine learning scientist, Ensem Therapeutics (Research
associate 2018-2022).
Timothy Szocinski, Data scientist at Auray (Ph.D.
2021).
Menglun Wang, The United States Food and Drug Administration (Ph.D. 2021).
David Bramer, Instructor, Michigan State
University (Ph.D., 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
(Ph.D. 2018).
Kedi Wu, Principal
Quantitative Analyst, Capital One Financial
Corporation, Plano, Texas (Ph.D. 2018).
Yin Cao, R&D Analyst,
Progressive Insurance, Cleveland, (Ph.D. 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 (Ph.D. 2016).
Lin Mu, Associate Professor, University of
Georgia, Athens (Visiting assistant professor, 2012-2015).
Kelin Xia, Associate Professor, Nanyang
Technological University (Ph.D. 2012 and postdoc 2013-2016).
Jin Kyoung Park, Associate Professor, Ivy Tech
Community College, Indiana (Ph.D. 2014).
Langhua Hu, Analyst (first job), Discovery
Financial Services, Riverwoods, IL (Ph.D. 2013).
Zhan Chen, Associate Professor, Georgia Southern
University (Ph.D. 2011).
Duan Chen, Associate Professor, University of
North Carolina, Charlotte (Ph.D. 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 (Ph.D. 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 (Ph.D. 2007).
Sining Yu, Structured transaction analyst (first
job), International Power America (Ph.D. 2007).
Yongcheng Zhou, Professor, Colorado State
University (Ph.D. 2006).
Yibao Zhao, Senior Lecturer,
Shan Zhao, Professor,
Zujun Hou, Research Scientist, Singapore Bioimaging Consortium (Ph.D. 2003).
Shuguang Guan,
Professor, East China Normal University (Ph.D. 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:
- 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