Welcome to Guo-Wei Wei's Home Page
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Guowei
MSU 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:
Third party YouTube about
our work on SARS-CoV-2
SARS-CoV-2
RBD Mutations in the US.
Persistent Laplacian
projected Omicron BA.4 and BA.5 to become new dominating variants, (2022).
Omicron
BA.2 (B.1.1.529.2): high potential to becoming the next dominating variant,
The Journal of Physical Chemistry Letters, 13,
3840-3849 (2022).
Artificial
intelligence design of mutation-proof COVID-19 antibody therapies, Communications in Information and Systems,
accepted, (2022).
Review
of the mechanisms of SARS-CoV-2 evolution and transmission, Chemical
Science, (2021).
Emerging vaccine-breakthrough
SARS-CoV-2 variants, ACS Infectious
Diseases, 8,
3, 546–556 (2022).
Methodology-centered review of
molecular modeling, simulation, and prediction of SARS-CoV-2, Chemical
Reviews, accepted (2022).
Mechanisms of
SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and
America, The Journal of Physical Chemistry
Letters, 12, 11850-11857 (2021).
Perspective of SARS-CoV-2 main protease inhibitors,
Journal of Medicinal Chemistry, 64, 16922-16955 (2021).
Revealing
the threat of emerging SARS-CoV-2 mutations to antibody therapies, Journal
of Molecular Biology, 433, 167155 (2021).
Vaccine-escape
and fast-growing mutations in the United Kingdom, the United States, Singapore,
Spain, South Africa, and other COVID-19-devastated countries,
Genomics, 11, 2158-2170 (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).
Research Interests:
- Mathematical molecular biosciences: Differential geometry based solvation models; 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; Topological fingerprints of biomolecules; Electrostatic binding analysis; Reeb graph based protein pocket detection; Genomic data; Cahn-Hilliard for mitochondria; Geometric algebra
- AI, machine learning, and data science: Mathematical representations of data; Deep learning; Topological learning; Generative network complex (GNC); Graph neural network (GNN); Multiscale manifold regularization; Topological data analysis; Champion; Persistent homology; PDE transform; Parametrization via convex optimization; Machine learning; Multitask learning; Autoencoder; Transformer; UMAP-assisted K-means clustering; Evolutionary de Rham-Hodge theory; Persistent spectral graph; Persistent Laplacian; Homotopy continuation; Unified topological approach ; Persistent sheaf Laplacians;
- 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
- 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:
- COMPLETE LIST
- Mathematical molecular bioscience and biophysics
- Machine learning, big data, signals, images and
surfaces
- 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 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 Member of Editorial Board, Journal of Modeling in Mechanics and Materials.
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:
- National Institute of Health (NIGMS, NIAID)
- National Science Foundation (DMS, CISE)
- National Aeronautics and Space Administration
- Bristol-Myers Squibb
- Pfizer
- Michigan Economic Development Corporation
- George Mason University
- Michigan State University
- COVID-19 High
Performance Computing Consortium
Teaching:
·
Fall 2022: MTH994-002, Machine learning, TueThu: 2:00-3:30pm, D517WH and hybrid with online.
·
Fall
2022: MTH496-002, Machine Learning, (TueThu:
12:40-2:00pm), A330WH.
Students, postdocs
and visiting scholars:
- Currently 12 PhD candidates, 5 research associates, 0 visiting scholars and 2 undergraduate research students.
- Graduated 24 PhD students
- Graduated 10 MSc students
- Advised 52 undergraduate research students
- Supported 26 postdoctoral associates
- Supported 24 visiting scholars
Photo 2000
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Photo 2002
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Photo 2006
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Photo 2007
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Photo 2008
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Some recent
Rui Wang (PhD 2022, postdoc 2022-)
Dong Chen (PhD 2022, postdoc 2022-).
Kaifu Gao (Research
associate 2018-2022) BAKX Therapeutics.
Timothy Szocinski,
(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 (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).
Kelin Xia, Assistant
Professor (tenure-track), 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 (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
Technology,
Decheng Wan,
Professor, Shanghai Jiao Tong University, China (Postdoc, 1999-2001).
Positions available:
- Internships and research assistantships.
- Postdoctoral associate (Offer to candidates who are trained on mathematical or computational biosciences).
Mathematical
- Biweekly seminars in
Computational Topology/Geometry/Graph
- Mathematical
Biology, Fall 2010
- Mathematical
Biology, Spring
2010
Conferences organized:
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