PUBLICATION
Guo-Wei Wei
Editorials
(29) Guo-Wei Wei, Commutative Algebra Meets Data Science: A New Paradigm in Mathematical Artificial Intelligence, SIAM News, Issue 02 March 2026 March 02, (2026).
(28) Topological Deep Learning: An Emerging Paradigm in Data Science, SIAM News, November 22, (2024).
(27) Tamar Schlick and Guo-Wei Wei, Machine Learning Tools Advance Biophysics, Biophysical Journal, Volume 123, Issue 17, Pages E1-E3 (2024).
(26) Guo-Wei Wei, Jie Wu, Duc Nguyen, and Kelin Xia, Preface Special Issue on Recent Advances in Topological Deep Learning, Foundation of Data Science, 6 (2), i-iii, (2024).
(25) KM Merz, Guo-Wei Wei, F Zhu, Cutting-Edge Methodologies in Omics Data Analysis, Journal of Chemical Information and Modeling 64 (13), 4939-4940, (2024).
(24) KM Merz, YS Choong, Z Cournia, O Isayev, TA Soares, Guo-Wei Wei, F Zhu, Machine Learning in Materials Science, Journal of Chemical Information and Modeling 64 (10), 3959-3960, (2024).
(23) KM Merz, Guo-Wei Wei, F Zhu, Machine Learning in Bio-cheminformatics, Journal of Chemical Information and Modeling 64 (7), 2125-2128, (2024).
(22) Mathematics-assisted Directed Evolution and Protein Engineering, SIAM News, June 6, (2023).
(21) Characterizing Musical Sounds with Topological Data Analysis, SIAM News, 56(2), Mach (2023).
(20) KJ Naidoo, KM Merz, Guo-Wei Wei, Modeling Reactions from Chemical Theories to Machine Learning, Journal of Chemical Information and Modeling 63 (23), 7273-7273, (2023).
(19) KM Merz, Guo-Wei Wei, F Zhu, Harnessing the Power of Large Language Model-Based Chatbots for Scientific Discovery, Journal of Chemical Information and Modeling 63 (17), 5395-5395, (2023).
(17) KM Merz, Guo-Wei Wei, F Zhu, Machine learning in bio-cheminformatics, Journal of Chemical Information and Modeling 63 (1), 1-1, (2023).
(16) Guo-Wei Wei, TA Soares, H Wahab, F Zhu, Computational Chemistry in Asia, Journal of Chemical Information and Modeling 62 (21), 5035-5037, (2022).
(15) Guo-Wei Wei, F Zhu, KM Merz, Editorial on Machine Learning, Journal of Chemical Information and Modeling, 62 (17), 3941-3941, (2022).
(14) Guo-Wei Wei, Topological Artificial Intelligence Forecasting of Future Dominant Viral Variants, SIAM News, August 9, (2022).
(13) Guo-Wei Wei, TA Soares, H Wahab, R Wang, Computational Chemistry in Asia, Journal of Chemical Information and Modeling 61 (2), 547-547, (2021).
(12) KM Merz Jr, G De Fabritiis, Guo-Wei Wei, Generative models for molecular design, Journal of Chemical Information and Modeling, 60 (12), 5635-5636, (2020).
(11) KM Merz Jr, G De Fabritiis, Guo-Wei Wei, JCIM special issue on generative models for molecular design, Journal of Chemical Information and Modeling 60 (3), 1072-1072, (2020).
(10) Guo-Wei Wei, Persistent Homology Analysis of Biomolecular Data, SIAM News, 50(10) December, (2017).
(9) Guo-Wei Wei, Mathematics at the eve of a historic transition in biology, Computational and Mathematical Biophysics, 5, 138-141, (2017).
(7) Mathematical Molecular Bioscience and Biophysics, SIAM News, 49 (7), September (2016).
(6) Emil Alexov and Guo-Wei Wei, Preface: Special Issue on Modeling Electrostatics in Molecular Biology (MEMB), Communications in Computational Physics 13 (1), i-v, (2013).
(5) W Guo, L Udpa, Y Wang, Guo-Wei Wei, S Zhao, Mathematical methods for images and surfaces, International Journal of Biomedical Imaging (2012).
(4) Guo-Wei Wei, L Udpa, Y Wang, S Zhao, Mathematical methods for images and surfaces, International Journal of Biomedical Imaging 2010(1), 918467 (2010).
(3) Guo-Wei Wei and Ge Wang, Special issue on recent advances in computational techniques for biomedical imaging, Communications in Numerical Methods in Engineering, 25(6), 581-582 (2009).
(2) Guo-Wei Wei and Ge Wang, Call for Papers: Special Issue on ‘Recent Advances in Computational Techniques for Biomedical Imaging, Communications in Numerical Methods in Engineering (CNM), Numerical Linear Algebra with Applications, 15(1) (2008).
(1) Guo-Wei and Ge Wang, Special Issue on ‘Recent Advances in Computational Techniques for Biomedical Imaging’, International Journal for Numerical Methods in Engineering (NME), International journal for numerical methods in engineering 73 (4), 596-596 (2008).
PAPERS
(400) Kelin Xia and Guo-Wei Wei, A review of geometric, topological and graph theory apparatuses for the modeling and analysis of biomolecular data (2016) arXiv:1612.01735.
(399) Duc Nguyen, Kaifu Gao, Jiahui Chen, Rui Wang, and Guo-Wei Wei, Potentially highly potent drugs for 2019-nCoV, (2020).
(398) Kaifu Gao, Duc Nguyen, Rui Wang and Guo-Wei Wei, Machine intelligence design of 2019-nCoV drugs, (2020).
(397) Jian Liu, Dong Chen, and Guo-Wei Wei, Interaction homotopy and interaction homology, (2023).
(396) Saumya Nigam, Dong Chen, Elvira Gjelaj, Rui Wang, Aaroh Shyam Tak, Manvir Bamrah, Tyrese T. Byrd, Adoniram Johnson, Ossaid Ahmed, Hanaan Hayat, Hassan H. Hayat, Jinxing Li, Guo-Wei Wei, Ping Wang, Deep Learning-Assisted Iron Content Quantification in Magnetic Particle Imaging, (2025).
(395) Jiahui Chen, Rui Wang and Guo-Wei Wei, Review of the mechanisms of SARS-CoV-2 evolution and transmission, Chemical Science (2022).
(394) Jian Liu, Dong Chen, Guo-Wei Wei, Parametrization of Symmetry in Data, (2025).
(393) Nicole Hayes, Ekaterina Merkurjev, and Guo-Wei Wei, Predicting Protein-Nucleic Acid Flexibility Using Persistent Sheaf Laplacians, (2025).
(392) Benjamin Jones and Guo-Wei Wei, PETLS: Persistent Topological Laplacian Software, (2025).
(391) Jian Liu, Li Shen, and Guo-Wei Wei, Persistent Khovanov homology of tangles, Journal of Knot Theory and Its Ramifications, (2024).
(390) Yiming Ren, Junjie Wee, Xi Chen, Grace Qian, and Guo-Wei Wei, Persistent Sheaf Laplacian Analysis of Protein Stability and Solubility Changes upon Mutation, (2026).
(389) Xiang Xiang Wang and Guo-Wei Wei, A Hierarchical Sheaf Spectral Embedding Framework for Single-Cell Analysis, (2026).
(388) Xiang Xiang Wang and Guo-Wei Wei, Multi-dimensional Persistent Sheaf Laplacians for Image Analysis, (2026).
(387) Xiang Xiang Wang and Guo-Wei Wei, Multiscale Grassmann Manifolds for Single-Cell Data Analysis, (2025).
(386) JunJie Wee, Faisal Suwayyid, Mushal Zia, Hongsong Feng, Yuta Hozumi, Guo-Wei Wei, Commutative algebra neural network reveals genetic origins of diseases, (2025).
(385) Mushal Zia1, Faisal Suwayyid, and Guo-Wei Wei, GBNL: Graded Betti Number Learning of Complex Biological Data, (2025).
(384) Li Shen, Jian Liu, and Guo-Wei Wei, Computing Khovanov homology of tangles, (2025).
(383) Li Shen, Jian Liu, and Guo-Wei Wei, Khovanov homology of tangles: algorithm and computation, (2025).
(382) Jian Jiang, Guilin Wang, Daixin Li, Nicole Hayes, Benjamin Jones, Yazhou Shi, Huahai Qiu, Bengong Zhang, Tianshou Zhou, and Guo-Wei Wei, Unexpected Applications of AlphaFold in Molecular Sciences: A Review, Annual review of Biochemistry, accepted (2025).
(381) Emilee Walden, Jiahui Chen, and Guo-Wei Wei, Dimensionality reduction for k-means clustering of large-scale influenza mutation datasets, Communication in Information and Systems, accepted (2025).
(380) Yuta Hozumi, Rui Wang, Guo-Wei Wei, CCP: Correlated Clustering and Projection for Dimensionality Reduction, Machine Learning: Science and Technology, (2022).
(379) Dong Chen, Jian Liu, Chunlong Chen, Guo-Wei Wei, Interaction topological transformer for multiscale learning in porous materials, Science Advances (2026).
(378) Faisal Suwayyid, Yuta Hozumi, Hongsong Feng, Mushal Zia, JunJie Wee, Guo-Wei Wei, CAKL: Commutative algebra k-mer learning of genomics, Nature Communication, (2025).
(377) Xiang Liu, Zhe Su, Yongyi Shi, Yiying Ton, Ge Wang, and Guo-Wei Wei, Manifold Topological Deep Learning for Biomedical Data, Nature Communication, accepted (2026).
(376) Jian Liu, Li Shen, Mushal Zia, Guo-Wei Wei, Topological Sequence Analysis of Genomes: Category Theory Approaches, Journal of Computational Biophysics and Chemistry, 25 (12), 3125-3138 (2026).
(375) Xiang Liu, Xuefei Huang, and Guo-Wei Wei, Machine-Learning Prediction of Virus-like Particle Stoichiometry and Stability using Persistent Topological Laplacians, Biophysical Journal, https://doi.org/10.1016/j.bpj.2025.10.013 (2025).
(374) Jian Jiang, Daixin Li, Guilin Wang, Nicole Hayes, Yazhou Shi, Huahai Qiu, Bengong Zhang, Tianshou Zhou, Guo-Wei Wei, A review of recent advances in generative artificial intelligence models for biomolecular sciences, Acta Pharmaceutica Sinica B, 16 (3), 1201-1218 (2026).
(373) Jian Liu, Li Shen, Dong Chen, and Guo-Wei Wei, Topological Sequence Analysis of Genomes: Delta Complex Approaches, Foundations of Data Science, doi: 10.3934/fods.2026003 (2025).
(372) Caleb Simiyu Khaemba, Hongsong Feng, Dong Chen, Chun-Long Chen, and Guo-Wei Wei, Commutative Algebra Modeling in Materials Science -- A Case Study on Metal-Organic Frameworks (MOFs), Journal of Chemical Information and Modeling, 66(5), 2584-2596, (2026).
(371) Sean Cottrell, Seungmin Yoon, Xiaoqi Wei, Alex Dickson, and Guo-Wei Wei, Computational Drug Repurposing for Alzheimer’s Disease via Sheaf Theoretic Population-Scale Analysis of snRNA-Seq Data, Journal of Medicinal Chemistry, 69 (4), 4221-4238 (2026).
(370) Faisal Suwayyid and Guo-Wei Wei, Persistent Stanley-Reisner theory, Foundations of Data Science, 8, 287-312 (2026).
(369) Jian Liu, Dong Chen, and Guo-Wei Wei, Persistent interaction topology in data analysis, Foundations of Data Science, 9, 34-60, (2026).
(368) Zhe Su, Xiang Liu, Layal Bou Hamdan, Vasileios Maroulas, Jie Wu, Gunnar Carlsson and Guo-Wei Wei, Topological Data Analysis and Topological Deep Learning Beyond Persistent Homology–A Review, Artificial Intelligence Review, 59:58, (2026).
(367) Yimin Ren and Guo-Wei Wei, Interpretability and Representability of Commutative Algebra, Algebraic Topology, and Topological Spectral Theory for Real-World Data, Advanced Intelligence Discovery, e202500207 (2025).
(366) Jian Jiang, Daixin Li, Guilin Wang, and Guo-Wei Wei, Recent Advances in Machine Learning Predictions of Protein-Ligand Binding Affinities, Current Opinion in Structural Biology, 96: 103193 (2026).
(365) Mushal Zia, Faisal Suwayyid, Yuta Hozumi, JunJie Wee, Hongsong Feng, and Guo-Wei Wei, CAP: Commutative Algebra Prediction of Protein-Nucleic Acid Binding Affinities,, Machine Learning: Science and Technology, 6, 045068 (2025).
(364) Xiang Liu, Junjie Wee and Guo-Wei Wei, Topological Machine Learning for Protein-Nucleic Acid Binding Affinity Changes Upon Mutation, Machine Learning: Science and Technology, 6, 045035 (2025).
(363) Sean Cottrell and Guo-Wei Wei, Multiscale Cell-Cell Interactive Spatial Transcriptomics Analysis, Advanced Science, 12 (44), e08358 (2025).
(362) Jian Jiang, Lu ke, Long Chen, Bozheng Dou, Yueying Zhu, Yazhou Shi, Huahai Qiu, Bengong Zhang, Tianshou Zhou, and Guo-Wei Wei, Machine learning predictions from unpredictable chaos, Journal of the Royal Society Interface, 22 (231), 20250441, (2025).
(361) Dong Chen, Gengzhuo Liu, Hongyan Du, Ben Jones, Junjie Wee, Rui Wang, Jiahui Chen, Jana Shen, and Guo-Wei Wei, Drug Resistance Predictions Based on a Directed Flag Transformer, Advanced Sciences, 12 (36), e02756 (2025).
(360) Hongsong Feng, Faisal Suwayyid, Mushal Zia, JunJie Wee, Yuta Hozumi, Chunlong Chen, Guo-wei Wei, CAML: Commutative algebra machine learning --- A case study on protein-ligand binding affinity prediction, Journal of Chemical Information and Modeling, 65 (13), 6732-6743 (2025).
(359) Xingjian Xu, Chunmei Wang, Guo-Wei Wei, and Jiahui Chen, PLNet: Persistent Laplacian Neural Network for Protein-Protein Binding Free Energy Prediction, Protein Science, 34: e70377 (2025).
(358) Dong Chen, Rui Wang, Guo-Wei Wei, and Feng Pan, Enhancing Energy Predictions in Multi-Atom Systems with Multiscale Topological Learning, Journal of Materials Chemistry A, 13 (27), 21555-21563 (2025).
(357) Dong Chen, Bingxu Wang, Shunning Li, Wentao Zhang, Kai Yang, Yongli Song, Guo-Wei Wei, and Feng Pan, Superionic Ionic Conductor Discovery via Multiscale Topological Learning, Journal of the American Chemical Society, 147, 20888-20898 (2025).
(356) Dong Chen, Jian Jiang, Nicole Hayes, Zhe Su, Guo-Wei Wei, Artificial Intelligence Approaches for Anti-Addiction Drug Discovery, Digital Discovery, 4, 1404-1416 (2025).
(355) JunJie Wee and Guo-Wei Wei, Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning, Virus Evolution, 11(1), veaf026 (2025).
(354) Benjamin Jones and Guo-Wei Wei, Khovanov Laplacian and Khovanov Dirac for Knots and Links, Journal of Physics: Complexity, 6(2), 025014 (2025).
(353) Zhe Su, Yiying Tong and Guo-Wei Wei, Topology-preserving Hodge Decomposition in the Eulerian Representation, Beijing Journal of Pure and Applied Mathematics, 2(2),619-657 (2025).
(352) Nicole Hayes, Xiaoqi Wei, Hongsong Feng, Ekaterina Merkurjev, Guo-Wei Wei, Persistent Sheaf Laplacian Analysis of Protein Flexibility, The Journal of Physical Chemistry, 129, 17, 4169–4178 (2025).
(351) Wanying Bi, Hongsong Feng, Jie Wu, Jingyan Li, Guo-Wei Wei, Topological magnitude for protein flexibility analysis, R Soc Open Sci., 12 (12): 251599 (2025).
(350) Jian Jiang, Chunhuan Zhang, Lu Ke, Yueying Zhu, Nicole, Hayse, Huahai Qiu, Bengong Zhang, Tianshou Zhou, and Guo-Wei Wei, A Review of Imbalanced Data Challenge in Chemistry, Chemical Science, 16, 7637-7658 (2025).
(349) Mushal Zia, Benjamin Jones, Hongsong Feng, Guo-Wei Wei, Persistent Directed Flag Laplacian (PDFL)-Based Machine Learning for Protein–Ligand Binding Affinity Prediction, Journal of Chemical Theory and Computation, 21(8) 4276-4285 (2025).
(348) Hongsong Feng, Jeffrey Y Zhao, Guo-Wei Wei, Multiscale differential geometry learning for protein flexibility analysis, Journal of Computational Chemistry, 46, e70073, (2025).
(347) Dong Chen, Chunlong Chen, and Guo-Wei Wei, Category-Specific Topological Learning of Metal-Organic Frameworks, Journal of Materials Chemistry A, 13, 9292 - 9303 (2025).
(346) Ruzhi Song, Fengling Li, Jie Wu, Fengchun Lei and Guo-Wei Wei, Multisacle Jones Polynomial and Persistent Jones Polynomial for Knot Data Analysis, AIMS Mathematics, 10(1), 1463-1487 (2025).
(345) Xiaoqi Wei and Guo-Wei Wei, Persistent topological Laplacians --- A survey, Mathematics, 13(2), 208 (2025).
(344) Ben Jones and Guo-Wei Wei, Persistent Directed Flag Laplacians, Foundations of Data Science, 7(3), 737-758 (2025).
(343) J. Jiang, L Chen, Y Zhu, Y Shi, H Qiu, B Zhang, T Zhou, GW Wei, Proteomic Learning of Gamma-Aminobutyric Acid (GABA) Receptor-Mediated Anesthesia, Journal of Chemical Information and Modeling, 65 (7), 3655-3668 (2025).
(342) Hongsong Feng, Li Shen, Jian Liu, and Guo-Wei Wei, Mayer homology learning prediction of protein-ligand binding affinities, Journal of Computational Biophysics and Chemistry, 24(2), 253-266 (2025).
(341) Xiaoqi Wei and Guo-Wei Wei, Persistent sheaf Laplacians, Foundations of Data Science, 7(2), 446-463 (2025).
(340) Saumya Nigam, Elvira Gjelaj, Rui Wang, Guo-Wei Wei, Ping Wang, Machine Learning and Deep Learning Applications in Magnetic Particle Imaging, Journal of Magnetic Resonance Imaging 61(1),42-51 (2025).
(339) Jian Jiang, Chunhuan Zhang, Long Chen, Lu Ke, Bozheng Dou, Yueying Zhu, Jie Liu, Huahai Qiu, Hongsong Feng, Bengong Zhang, Guo-Wei Wei, A Review of Transformer Models in Drug Discovery and Beyond, Journal Pharmaceutical Analysis, 15(6), 101081 (2025).
(338) Yuta Hozumi and Guo-Wei Wei, Analyzing scRNA-seq data by CCP-assisted UMAP and t-SNE, PLOS One, 19(12), e0311791 (2024).
(337) JunJie Wee, Jiahui Chen, and Guo-Wei Wei, Preventing future zoonosis: SARS-CoV-2 mutations enhance human-animal cross-transmission, Computers in Biology and Medicine, 182, 109101 (2024).
(336) Zhe Su, Yiying Tong, and Guo-Wei Wei, Hodge decomposition of vector fields in Cartesian grids, SA’24: SIGGRAPH Asia 2024 Conference Papers, Article No.:90, pages 1-10, (2024).
(335) Gokul Bhusal, Ekaterina Merkurjev, and Guo-Wei Wei, Persistent Laplacian-enhanced Algorithm for Scarcely Labeled Data Classification, Machine Learning, 113, 7267-7292 (2024).
(334) Nicole Hayes, Ekaterina Merkurjev, and Guo-Wei Wei, Graph-Based Bidirectional Transformer Decision Threshold Adjustment Algorithm for Class-Imbalanced Molecular Data, Journal of Computational Biophysics and Chemistry, 23(10), 1339-1358 (2024).
(333) Zhe Su, Yiying Tong and Guo-Wei Wei, Persistent de Rham-Hodge Laplacians in Eulerian representation for manifold topological learning, AIMS Mathematics, 9(10) 27438-27470 (2024).
(332) JunJie Wee and Guo-Wei Wei, Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation, Journal of Chemical Information and Modeling, 64(16), 6676-6683 (2024).
(331) Jian Jiang, Long Chen, Bozheng Dou, Lu Ke, Yueying Zhu, Jie Liu, Bengong Zhang, Tianshou Zhou, and Guo-Wei Wei, Transformer Technology in Molecular Science, WIREs Computational Molecular Science, 14(4) e1725, (2024).
(330) Li Shen, Hongsong Feng, Funglian Li, Fundchun Lei, Jie Wu, and Guo-Wei Wei, Knot data analysis using multiscale Gauss link integral, Proceedings of the National Academy of Sciences, 121 (42) e2408431121 (2024).
(329) Li Shen, Jian Liu, and Guo-Wei Wei, Persistent Mayer Homology and Persistent Mayer Laplacian, Foundation of Data Science, 6(4), 584-612 (2024).
(328) Faisal Suwayyid and Guo-Wei Wei, Persistent Mayer Dirac, Journal of Physics: Complexity, 5, 045005 (2024).
(327) Theodore Papamarkou, Tolga Birdal, Michael Bronstein, Gunnar Carlsson, Justin Curry, Yue Gao, Mustafa Hajij, Roland Kwitt, Pietro Liò, Paolo Di Lorenzo, Vasileios Maroulas, Nina Miolane, Farzana Nasrin, Karthikeyan Natesan Ramamurthy, Bastian Rieck, Simone Scardapane, Michael T Schaub, Petar Veličković, Bei Wang, Yusu Wang, Guo-Wei Wei, Ghada Zamzmi, Position: Topological Deep Learning is the New Frontier for Relational Learning, The International Conference on Machine Learning, Position: Topological Deep Learning is the New Frontier for Relational Learning (openreview.net) (2024).
(326) Dong Chen, Jian Liu and Guo-Wei Wei, Multiscale Topology-enabled Structure-to-Sequence Transformer for Protein-Ligand Interaction Predictions, Nature Machine Intelligence, 6, 799-810 (2024).
(325) Sean Cottrell, Yuta Hozumi, and Guo-Wei Wei, K-Nearest-Neighbors Induced Topological PCA for scRNA Sequence Data Analysis, Computers in Biology and Medicine, 175, 108497 (2024).
(324) Jiahui Chen, Yongjia Xu, Xin Yang, Zixuan Cang, Weihua Geng, and Guo-Wei Wei, Poisson-Boltzmann based machine learning (PBML) model for electrostatic analysis, Biophysical Journal, 123(17) 2801-28-14 (2024).
(323) Li Shen, Jian Liu, and Guo-Wei Wei, Evolutionary Khovanov homology, AIMS Mathematics, 9(9): 26139-26165 (2024).
(322) Zhe Su, Yiying Tong, and Guo-Wei Wei, Hodge decomposition of single cell RNA velocity, Journal of Chemical Information and Modeling, 64, 3558--3568 (2024).
(321) Hongsong Feng; Sean Cottrell; Yuta Hozumi; Guo-Wei Wei, Multiscale differential geometry learning of networks with applications to single-cell RNA sequencing data, Computers in Biology and Medicine, 171, 108211 (2024).
(320) Yuta Hozumi, Guo-Wei Wei, Analyzing Single Cell RNA Sequencing with Topological Nonnegative Matrix Factorization, Journal of Computational and Applied Mathematics, 445, 115842 (2024).
(319) Jian Liu, Li Shen, and Guo-Wei Wei, ChatGPT for Computational Topology, Foundations of Data Science, 6, 221-250 (2024).
(318) Faisal Suwayyid and Guo-Wei Wei, Persistent Dirac of Paths in Digraphs and Hypergraphs, Foundation of Data Science, 6, 124-153 (2024).
(317) Emily Ribando-Gros, Rui Wang, Jiahui Chen, Yiying Tong, and Guo-Wei Wei, Combinatorial and Hodge Laplacians: Similarity and difference, SIAM Review, 66 (3), 575-601 (2024).
(316) Hongyan Du, Guo-Wei Wei, and Tingjun Hou, Multiscale Topology in Interactomic Network: From Transcriptome to Antiadiction Drug Repurposing, Briefings in Bioinformatics, 25 (2), bbae054 (2024).
(315) JunJie Wee, Jiahui Chen, Kelin Xia, and Guo-Wei Wei, Integration of persistent Laplacian and pre-trained transformer for protein solubility changes upon mutation, Computers in Biology and Medicine, 169, 107918 (2024).
(314) Sheik Ahmed Ullah, Xin Yang, Ben Jones, Shan Zhao, Weihua Geng, and Guo-Wei Wei, Bridging Eulerian and Lagrangian Poisson-Boltzmann solvers by ESES, Journal of Computational Chemistry, 45, 306-320 (2024).
(313) Sean Cottrell, Rui Wang, and Guo-Wei Wei, PLPCA: Persistent Laplacian-enhanced PCA for Microarray Data Analysis, Journal of Chemical Information and Modeling, 64, 7, 2405–2420 (2024).
(312) Long Chen, Jian Jiang, Bozheng Dou, Hongsong Feng, Jie Liu, Yueying Zhu, Bengong Zhang, Tianshou Zhou, and Guo-Wei Wei, Machine Learning Study of the Extended Drug-target Interaction Network informed by Pain Related Voltage-Gated Sodium Channels, Pain, 165 (4), 306-320 (2024).
(311) Saumya Nigam, Jeotikanta Mohapatra, Ashley V. Makela, Jessi Mercedes Rodriguez, Aixia Sun, Hanaan Hayat, Elizabeth Kenyon, Nathan A. Redman, George Jabin, Bin Gu, Mohamed Ashry, Lorenzo F. Sempere, Jiahui Chen, Guo-Wei Wei, Steven Bolin, Brett Etchebarne, J. Ping Liu, Christopher H. Contag, and Ping Wang, Shape anisotropy-governed high performance nanomagnetosol for in vivo magnetic particle imaging of lungs, Small, 20 (5) 2305300 (2024).
(310) Yuta Hozumi, Kiyoto, Tanemura, and Guo-Wei Wei, Preprocessing of single cell RNA sequencing data using Correlated Clustering and Projection, Journal of Chemical Information and Modeling, 64, 7, 2829–2838 (2024).
(309) Rui Wang, Hongsong Feng, and Guo-Wei Wei, ChatGPT in drug discovery: A case study on anti-cocaine addiction drug development with chatbots, Journal of Chemical Information and Modeling, 63, 22, 7189–7209 (2023).
(308) Feng, Hongsong; Wang, Rui; Zhan, Chang-Guo, and Guo-Wei Wei, Multi-objective Molecular Optimization for Opioid Use Disorder Treatment Using Generative Network Complex, Journal of Medicinal Chemistry, 66, 17, 12479–12498 (2023).
(307) Yuchi Qiu and Guo-Wei Wei, Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models, Briefings in Bioinformatics, 24 (5) bbad289 (2023).
(306) Jiahui Chen, Daniel R. Woldring, Faqing Huang, Xuefei Huang, and Guo-Wei Wei, Topological deep learning based deep mutational scanning, Computers in Biology and Medicine, 164, 107258 (2023).
(305) Dong Chen, Jian Liu, Jie Wu, and Guo-Wei Wei, Persistent hyperdigraph homology and persistent hyperdigraph Laplacians, Foundation of Data Science, 5, 558-588 (2023).
(304) Bozheng Dou, Zailiang Zhu, Ekaterina Merkurjev, Lu Ke, Long Chen, Jian Jiang, Yueying Zhu, Jie Liu, Bengong Zhang, and Guo-Wei Wei, Machine Learning methods for Small Data Challenges in Molecular Science, Chemical Reviews, 123, 13, 8736–8780 (2023).
(303) Hongsong Feng, Jian Jiang, and Guo-Wei Wei, Machine-learning Repurposing of DrugBank Compounds for Opioid Use Disorder, Computers in Biology and Medicine, 160, 106921 (2023).
(302) Li Shen, Hongsong Feng, Yuchi Qiu and Guo-Wei Wei, SVSBI: Sequence-based virtual screening of biomolecular interactions, Communications Biology, 6, 536, (2023).
(301) Dong Chen, Jian Liu, Jie Wu, Guo-Wei Wei, Feng Pan, and Shing-Tung Yau, Path topology in molecular and materials sciences, The Journal of Physical Chemistry Letters, 14, 954-964, (2023).
(300) Hongsong Feng, Rana Elladki, Jian Jiang, and Guo-Wei Wei, Machine-learning Analysis of Opioid Use Disorder Informed by MOR, DOR, KOR, NOR and ZOR-Based Interactome Networks, Computers in Biology and Medicine, 157, 106745 (2023).
(299) Hasaan Hayat, Rui Wang, Aixia Sun, Christiane L. Mallett, Saumya Nigam, Nathan Redman, Demarcus Bunn, Elvira Gjelaj, Nazanin Talebloo, Adam Alessio, Anna Moore, Kurt Zinn, Guo-Wei Wei; Jinda Fan, and Ping Wang, Deep learning-enabled quantification of simultaneous PET/MRI for cell transplantation monitoring, iScience, 26,107083 (2023).
(298) Zailiang Zhu, Bozheng Dou,Yukang Cao, Jian Jiang, Yueying Zhu, Dong Chen, Hongsong Feng, Jie Liu, Bengong Zhang, Tianshou Zhou, Guo-Wei Wei, TIDAL: Topology-Inferred Drug Addiction Learning, Journal of Chemical Information and Modeling, 63, 5, 1472–1489 (2023).
(297) Xiaoqi Wei, Jiehui Chen and Guo-Wei Wei, Persistent topological Laplacian analysis of SARS-Cov-2 variants, Journal of Computational Biophysics and Chemistry, 22, 569-587, (2023).
(296) Yao Zhang, Kaifu Gao, Dexin Sui, Tuo Zhang, Peixuan Yu, Yuhan Jiang, Min Su, Guo-Wei Wei, Jian Hu, Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter, Nature Communication, 14(1), 385 (2023).
(295) Hongsong Feng and Guo-Wei Wei, Virtual screening of DrugBank database for hERG blockers using topological Laplacian-assisted AI models, Computers in Biology and Medicine, 153, 106491 (2023).
(294) Yuchi Qiu and Guo-Wei Wei, Persistent spectral theory-guided protein engineering, Nature Computational Science, 3, 149-163 (2023).
(293) Jiahui Chen, Rui Wang, Yuta Hozumi, Gengzhuo Liu, Yuchi Qiu, Xiaoqi Wei and Guo-Wei Wei, Emerging dominant SARS-CoV-2 variants, Journal of Chemical Information and Modeling, 63, 335–342, (2023).
(292) Nicole Hayes, Ekaterina Merkurjev, and Guo-Wei Wei, Integrating Transformer and Autoencoder Techniques with Spectral Graph Algorithms for the Prediction of Scarcely Labeled Molecular Data, Computers in Biology and Medicine, 153, 106479 (2023).
(291) Ekaterina Merkurjev, Duc Duy Nguyen, and Guo-Wei Wei, Multiscale Laplacian Learning, Applied Intelligence, 53, 15727-15746, (2023).
(290) Rui Wang and Guo-Wei Wei, Persistent path Laplacian, Foundations of Data Science, 5, 26-55, (2023).
(289) Jiahui Chen, Yuchi Qiu, Rui Wang and Guo-Wei Wei, Persistent Laplacian projected Omicron BA.4 and BA.5 to become new dominating variants, Computers in Biology and Medicine, 151, 106262, (2022).
(288) Yuchi Qiu and Guo-Wei Wei, CLADE 2.0: Evolution-driven cluster learning-assisted directed evolution, Journal of Chemical Information and Modeling, 62, 19, 4629–4641 (2022).
(287) Jian Liu, Kelin Xia, Jie Wu, Stephen Yau, and Guo-Wei Wei, Biomolecular Topology: modelling and data analysis. Acta Mathematica Sinica, English Series, 38, 1901-1938 (2022).
(286) Jiahui Chen and Guo-Wei Wei, Artificial intelligence design of mutation-proof COVID-19 antibody therapies, Communications in Information and Systems, 22 (3), 339-361 (2022).
(285) Jiahui Chen and Guo-Wei Wei, 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).
(284) Azzam Alfarraj and Guo-Wei Wei, Geometric algebra generation of molecular surfaces, Journal of the Royal Society Interface, 19 (189), 20220117 (2022).
(283) Kaifu Gao, Rui Wang, Jiahui Chen, Limei Cheng, Jaclyn Frishcosy, Yuta Huzumi, Yuchi Qiu, Tom Schluckbier, Xiaoqi Wei, and Guo-Wei Wei, Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2, Chemical Reviews, 122, 13, 11287–11368 (2022).
(282) Hongsong Feng, Kaifu Gao, Dong Chen, Li Shen, Alfred J Robison, Edmund Ellsworth and Guo-Wei Wei, Machine learning analysis of cocaine addiction informed by DAT, SERT, and NET-based interactome networks, Journal of Chemical Theory and Computation, 18(4), 2703–2719 (2022).
(281) J Grbić, Jie Wu, Kelin Xia, and Guo-Wei Wei, Aspects of topological approaches for data science, Foundation of Data Science, 4(2), 165-216 (2022).
(280) Rui Wang, Jiahui Chen, Yuta Hozumi, Changchuan Yin, and Guo-Wei Wei, Emerging vaccine-breakthrough SARS-CoV-2 variants, ACS Infectious Diseases, 8, 3, 546–556 (2022).
(279) Jiahui Chen, Rui Wang, Nancy Benovich Gilby, and Guo-Wei Wei, Omicron variant (B.1.1.529): Infectivity, vaccine breakthrough, and antibody resistance, Journal of Chemical Information and Modeling, 62 (2), 412-422 (2022).
(278) Limei Cheng, Yuchi Qiu, Brian J. Schmidt, and Guo-Wei Wei, Review of applications and challenges of quantitative systems pharmacology modeling and machine learning for heart failure, Journal of Pharmacokinetics and Pharmacodynamics, 49, 39-50, (2021).
(277) Yuchi Qiu, Jian Hu, Guo-Wei Wei, Cluster learning-assisted directed evolution, Nature Computational Science, 1(12), 809-818 (2021).
(276) Kaifu Gao, Rui Wang, Jiahui Chen, Jetze Tepe, Faqing Huang, and Guo-Wei Wei, Perspectives of SARS-CoV-2 main protease inhibitors, Journal of Medicinal Chemistry, 64, 16922-16955 (2021).
(275) Dong Chen, Jiaxin Zheng, Guo-Wei Wei, and Feng Pan, Extracting Predictive Representations from Hundreds of Millions of Molecules, The Journal of Physical Chemistry Letters, 12, 10793-10801 (2021).
(274) Kaifu Gao, Dong Chen, Alfred J. Robison, and Guo-Wei Wei, Proteome-informed machine learning studies of cocaine addiction, The Journal of Physical Chemistry Letters, 12, 11122-11134 (2021).
(273) Jiahui Chen, Weihua Geng, and Guo-Wei Wei, MLIMC: Machine learning-based implicit-solvent Monte Carlo, Chinese Journal of Chemical Physics, 34(6) 683-694 (2021).
(272) Rui Wang, Jiahui Chen, and Guo-Wei Wei, Mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America, The Journal of Physical Chemistry Letters, 12, 11850-11857 (2021).
(271) Qing Zhu, Yuzhe Du, Yoshiko Nomura, Rong Gao, Zixuan Cang, Guo-Wei Wei, Dalia Gordon, Michael Gurevitz, James Groome and Ke Dong, The voltage-sensing module of domain III in an insect sodium channel modulates the action of both α and β toxins, Insect Biochemistry and Molecular Biology, 137, 103625 (2021).
(270) Xiaoqi Wei and Guo-Wei Wei, Homotopy continuation for the spectra of persistent Laplacians, Foundations of Data Science, 3(4) 677-700 (2021).
(269) Jiahui Chen, Kaifu Gao, Rui Wang, and Guo-Wei Wei, Revealing the threat of emerging SARS-CoV-2 mutations to antibody therapies, Journal of Molecular Biology, 433, 167155 (2021).
(268) Rui Wang, Kaifu Gao, Jiahui Chen, and Guo-Wei Wei, 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).
(267) Dong Chen, Kaifu Gao, Duc D Nguyen, Yi Jiang, Guo-Wei Wei, and Feng Pan, Algebraic Graph-assisted Bidirectional Transformers for Molecular Prediction, Nature Communications, 12, 3527 (2021).
(266) Timothy Szocinski; Duc D Nguyen; Guo-Wei Wei, AweGNN: Auto-parametrized weighted element-specific graph neural networks, Computers in Biology and Medicine, 134, 104460 (2021).
(265) Jiahui Chen, Kaifu Gao, Rui Wang, and Guo-Wei Wei, Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies, Chemical Science, 12, 6929 - 6948 (2021).
(264) Rui Wang, Rundong Zhao, Emily Ribando-Gros, Jiahui Chen, Yiying Tong, and Guo-Wei Wei, HERMES: Persistent spectral graph software, Foundations of Data Science, 3, 67-97 (2021).
(263) Yuta Hozumi, Rui Wang, Changchuan Yin, and Guo-Wei Wei, UMAP-assisted K-means clustering of large-scale SARS-CoV-2 mutation datasets, Computers in Biology and Medicine, 131, 104264 (2021).
(262) Jasiel O. Strubbe-Rivera, Jiahui Chen, Benjamin A. West, Kristin N. Parent, Guo-Wei Wei, Jason N. Bazil, Modeling the effects of calcium overload on mitochondrial ultrastructural remodeling, Applied Sciences, 11, 2071 (2021).
(261) Jian Jiang, Rui Wang and Guo-Wei Wei, GGL-Tox: Geometric graph learning for toxicity prediction, Journal of Chemical Information and Modeling, 61, 1691-1700 (2021).
(260) Rui Wang, Jiahui Chen, Kaifu Gao, Yuta Hozumi, Changchuan Yin, and Guo-Wei Wei, Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants, Communications Biology, 4, 228 (2021).
(259) Yi Jiang, Dong Chen, Xin Chen, Guo-Wei Wei and Feng Pan, Topological representations of crystalline compounds for the machine-learning prediction of materials properties, npj Computational Materials, 7(1) 1-8 (2021).
(258) Jiahui Chen, Rui Wang, and Guo-Wei Wei, SARS-CoV-2 becoming more infectious as revealed by algebraic topology and deep learning, Communications in Information and Systems, 21(1), 31-36 (2021).
(257) Jiahui Chen, Kaifu Gao, Rui Wang, Duc Nguyen, and Guo-Wei Wei, Review of COVID-19 antibody therapies, Annual Review of Biophysics, 50, 1-30 (2021).,
(256) Jiahui Chen, Rundong Zhao, Yiying Tong and Guo-Wei Wei, Evolutionary de Rham-Hodge method, Discrete and Continuous Dynamical Systems Series B, 26, 3785-3821 (2021).
(255) KM Merz Jr, G De Fabritiis, and GW Wei, Generative models for molecular design, Journal of Chemical Information and Modeling 60 (12), 5635-5636 (2020).
(254) Rui Wang, Jiahui Chen, Yuta Hozumi, Changchuan Yin, and Guo-Wei Wei, Decoding Asymptomatic COVID-19 infection and transmission, The Journal of Physical Chemistry Letters, 11, 10007-10015 (2020).
(253) Duc Duy Nguyen, Kaifu Gao, Jiahui Chen, Rui Wang, and Guo-Wei Wei, Unveiling the molecular mechanism of SARS-CoV-2 main protease inhibition from 137 crystal structures using algebraic topology and deep learning, Chemical Sciences, 11, 12036 - 12046 (2020).
(252) Rui Wang, Yuta Hozumi, Yong-Hui Zheng, Changchuan Yin, and Guo-Wei Wei, Host immune response driving SARS-CoV-2 evolution, Viruses, 12, 1095 (2020).
(251) Rui Wang, Yuta Hozumi, Changchuan Yin, Guo-Wei Wei, Mutations on COVID-19 diagnostic targets, Genomics, 112, 5204-5213 (2020).
(250) Zixuan Cang, Elizabeth Munch, and Guo-Wei Wei, Evolutionary homology on coupled dynamical systems with applications to protein flexibility analysis, Journal of Applied and Computational Topology, 4, 481-507 (2020).
(249) Kaifu Gao, Duc Nguyen, Meihua Tu, and Guo-Wei Wei, Generative network complex for the automated generation of druglike molecules, Journal of Chemical Information and Modeling, 60 5682-5698 (2020).
(248) Ruiqiong Guo, Zixuan Cang, Jiaqi Yao, M. Kim, Erin Deans, Guo-Wei Wei, Seung-gu Kang, and Heedeok Hong, Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme. Proceedings of the National Academy of Sciences, 117 (36), 22146-22156 (2020).
(247) Rundong Zhao, Menglun Wang, Jiahui Chen, Yiying Tong and Guo-Wei Wei, The de Rham–Hodge Analysis and Modeling of Biomolecules, Bulletin of Mathematical Biology, 82, 1-38 (2020).
(246) Jiahui Chen, Rui Wang, Menglun Wang, and Guo-Wei Wei, Mutations strengthened SARS-CoV-2 infectivity, Journal of Molecular Biology, 432, 5212-5226 (2020).
(245) K Gao, DD Nguyen, J Chen, R Wang, GW Wei, Repositioning of 8565 existing drugs for COVID-19. The Journal of Physical Chemistry Letters, 11, 13, 5373–5382 (2020).
(244) Rui Wang, Yuta Hozumi, Changchuan Yin, and Guo-Wei Wei, 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).
(243) Rui Wang, Duc D Nguyen and Guo-Wei Wei, Persistent spectral graph, International Journal for Numerical Methods in Biomedical Engineering, 36(9), e3376 (2020).
(242) Duc D. Nguyen and Guo-Wei Wei, Math and AI-based Repositioning of Existing Drugs for COVID-19, SIAM News, 53(4) (2020).
(241) Xin Chen, Dong Chen, Mouyi Weng, Yi, Jiang, Guo-Wei Wei and Feng Pan, Topology-Based Machine Learning Strategy for Cluster Structure Prediction, The Journal of Physical Chemistry Letters, 11, 11, 4392–4401 (2020).
(240) Zixuan Cang and Guo-Wei Wei, Persistent cohomology for datasets with heterogeneous information, SIAM Journal on Mathematics of Data Science, 2 (2), 396-418 (2020).
(239) Kaifu Gao, Duc Duy Nguyen, Vishnu Sresht, Alan M. Mathiowetz, Meihua Tu, and Guo-Wei Wei, Are 2D fingerprints still valuable for drug discovery? Physical Chemistry Chemical Physics, 2 (16), 8373-8390 (2020).
(238) Jian Jiang, Rui Wang, Menglun Wang, Kaifu Gao, Duc D Nguyen and Guo-Wei Wei, Boosting tree-assisted multitask deep learning for small scientific datasets. Journal of Chemical Information and Modeling, 60 (3), 1235-1244 (2020).
(237) David Bramer and Guo-Wei Wei, Atom-specific persistent homology and its application to protein flexibility analysis, Computational and Mathematical Biophysics, 8, 1-35 (2020).
(236) Duc Nguyen, Zixuan Cang, and Guo-Wei Wei, A review of mathematical representations of biomolecular data, Physical Chemistry Chemical Physics,22, 4343-4367(2020).
(235) Menglun Wang, Z. X. Cang, and Guo-Wei Wei, A topology-based network tree for the prediction of protein-protein binding free energy changes following mutation, Nature Machine Intelligence, 2, 116-123 (2020).
(234) Duc Duy Nguyen, Kaifu Gao, Menglun Wang, and Guo-Wei Wei, MathDL: Mathematical deep learning for D3R Grand Challenge 4, Journal of Computer Aided Molecular Design, 34, 131-147 (2020).
(233) Limei Cheng, Guo-Wei Wei and Tarek Leil, Review of quantitative systems pharmacological modeling of thrombosis, Communications in Information and Systems, 19, 219-240 (2019).
(232) Christopher Grow, Kaifu Gao, Duc D Nguyen and Guo-Wei Wei, Generative network complex (GNC) for drug discovery, Communications in Information and Systems, 19, 241-277 (2019).
(231) Rundong Zhao, Mathieu Desbrun, Guo-Wei Wei and Yiying Tong, 3D Hodge Decompositions of Edge- and Face-based Vector Fields, ACM Transactions on Graphics (TOG) 38 (6), 181 (2019).
(230) Guo-Wei Wei, Protein structure prediction beyond AlphaFold, Nature Machine Intelligence, Vol. 1, 336-337, (2019).
(229) Duc D Nguyen and Guo-Wei Wei, AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening, Journal of Chemical Information and Modeling, 59, 3291-3304, (2019).
(228) Duc D. Nguyen and Guo-Wei Wei, DG-GL: Differential geometry based geometric learning of molecular datasets, International Journal for Numerical Methods in Biomedical Engineering, 35 (3), e3179 (2019).
(227) Duc Duy Nguyen, Zixuan Cang, Kedi Wu, Menglun Wang, Yin Cao and Guo-Wei Wei, Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges, Journal of Computer Aided Molecular Design, 33, 71-82 (2019).
(226) David Bramer and G. W. Wei, Blind prediction of protein B-factor and flexibility, Journal of Chemical Physics, 149, 134107 (2018).
(225) Rundong Zhao, Menglun Wang, Yiying Tong and Guo-Wei Wei, A divide-and-conquer strategy for large-scale Eulerian solvent excluded surface, Communications in Information and Systems, 18, 299-329 (2018).
(224) Rundong Zhao, Zixuan Cang, Yiying Tong and Guo-Wei Wei, Protein Pocket Detection via Convex Hull Surface Evolution and Associated Reeb Graph, Bioinformatics, 24 (17), i830-i837 (2018).
(223) Kedi Wu, Zhixiong Zhao, Renxiao Wang and Guo-Wei Wei, TopP–S: Persistent Homology-Based Multi-Task Deep Neural Networks for Simultaneous Predictions of Partition Coefficient and Aqueous Solubility, Journal of Computational Chemistry, 39, 1444-1454 (2018).
(222) Kedi Wu and Guo-Wei Wei, Quantitative toxicity prediction using topology based multi-task deep neural networks, Journal of Chemical Information and Modeling, 58, 520-531 (2018).
(221) David Bramer and G. W. Wei, Multiscale weighted colored graphs for protein flexibility and rigidity analysis, Journal of Chemical Physics, 148, 054103 (2018). (This workwas featured in AIP Scilight)
(220) Ahmet Erdemir, Peter J. Hunter, Gerhard A. Holzapfel, Leslie M. Loew, John Middleton, Christopher R. Jacobs, Perumal Nithiarasu, Rainlad Löhner, Guowei Wei, Beth A. Winkelstein, Victor H. Barocas, Farshid Guilak, Joy P. Ku, Jennifer L. Hicks, Scott L. Delp, Michael Sacks, Jeffrey A. Weiss, Gerard A. Ateshian, Steven A. Maas, and Andrew D. McCulloch, Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research, Journal of Biomechanical Engineering, 140, 024701, (2018).
(219) Z. X. Cang, Lin Mu and Guo-Wei Wei, Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening, PLOS Computational Biology, 14(1), e100592 (2018).
(218) Yuri A. Nedialkov, Kristopher Opron, Hailey L. Caudill1, Fadi Assaf, Amanda J. Anderson, Robert I. Cukier, Guo-Wei Wei and Zachary F. Burton, Hinge action versus grip in translocation by RNA polymerase, Transcription, 9,1-16 (2018)
(217) Elizabeth Jurrus, Dave Engel, Keith Star, Kyle Monson, Juan Brandi, Lisa E Felberg, David H Brookes, Leighton Wilson, Jiahui Chen, Karina Liles, Minju Chun, Peter Li, Todd Dolinsky, Robert Konecny, David R Koes, Jens Erik Nielsen, Teresa Head-Gordon, Weihua Geng, Robert Krasny, Guo-Wei Wei, Michael J Holst, J Andrew McCammon, and Nathan A Baker, Improvements to the APBS biomolecular solvation software suite, Protein Science, 27, 112-128 (2018)
(216) Bao Wang, Chengzhang Wang, Kedi Wu and Guo-Wei Wei, Breaking the polar-nonpolar division in solvation free energy prediction, Journal of Computational Chemistry, 39, 217–232 (2018).
(215) Z. X. Cang and Guo-Wei Wei, Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction, International Journal for Numerical Methods in Biomedical Engineering, 34 (2), e2914 (2018).
(214) Guo-Wei Wei, Mathematics at the eve of a historic transition in biology, Molecular Based Mathematical Biology, 5, 138-141 (2017).
(213) Guo-Wei Wei, Persistent homology analysis of biomolecular data, SIAM News, 50 (10) December (2017).
(212) Z. X. Cang and Guo-Wei Wei, TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions
, PLOS Computational Biology, 13(7), e1005690 (2017).
(211) Z. X. Cang and Guo-Wei Wei, Element specific persistent homology for the analysis and prediction of protein folding stability upon mutation, Bioinformatics, 33, 3549-3557 (2017).
(210) Duc D Nguyen, Tian Xiao, Menglun Wang and Guo-Wei Wei, Rigidity strengthening: A mechanism for protein-ligand binding, Journal of Chemical Information and Modeling, 57, 1715-1721 (2017).
(209) Bao Wang, Zhixiong Zhao, Duc Nguyen and Guo-Wei Wei, Feature functional theory - binding predictor (FFT-BP) for the blind prediction of binding free energy, Theoretical Chemistry Account, 136, 55 (2017).
(208) Yin Cao, Bao Wang, Kelin Xia and Guo-Wei Wei, Finite volume formulation of the MIB method for elliptic interface problems, Journal of Computational and Applied Mathematics, 321, 60-77 (2017).
(207) Duc D Nguyen, Bao Wang and Guo-Wei Wei, Accurate, robust and reliable calculations of Poisson-Boltzmann binding energies, Journal of Computational Chemistry, 38, 941-948 (2017).
(206) Duan Chen and Guo-Wei Wei, A Review of Mathematical Modeling, Simulation and Analysis of Membrane Channel Charge Transport, Reference Module in Life Sciences, (2017).
(205) Yongcheng Zhou and Guo-Wei Wei, Variational Methods for Biomolecular Modeling, in Variational Methods in Molecular Modeling, Edited by Jianzhong Wu, Springer Science+Business Media Singapore, 181-221, (2017).
(204) Beibei Liu, Bao Wang, Rundong Zhao, Yiying Tong and Guo-Wei Wei, ESES: software for Eulerian solvent excluded surface, Journal of Computational Chemistry, 38, 446-466 (2017).
(203) Lin Mu, Kelin Xia and Guo-Wei Wei, Geometric and electrostatic modeling using molecular rigidity functions,Journal of Computational and Applied Mathematics, 313, 18-37 (2017).
(202) Duc D Nguyen and Guo-Wei Wei, The impact of surface area, volume, curvature and Lennard-Jones potential to solvation modeling, Journal of Computational Chemistry, 38, 24–36 (2017).
(201) Guo-Wei Wei and Nathan A. Baker, Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: A review. In Many-Body Effects and Electrostatics in Biomolecules, edited by Qiang Cui, Markus Meuwly, and Pengyu Ren, Pan Stanford, 417-464, (2016).
(200) Guo-Wei Wei, Mathematical Molecular Bioscience and Biophysics, SIAM News, 49 (7), (2016).
(199) Bao Wang, Zhixiong Zhao and Guo-Wei Wei, Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies, Journal of Chemical Physics, 145, 124110 (2016).
(198) Duc D Nguyen, Kelin Xia and Guo-Wei Wei, Generalized flexibility-rigidity index, Journal of Chemical Physics, 144, 234106 (2016).
(197) Kristopher Opron, Kelin Xia, Zachary F. Burton and Guo-Wei Wei, Flexibility-Rigidity Index for Protein-Nucleic Acid Flexibility and Fluctuation Analysis, Journal of Computational Chemistry, 37, 1283–1295 (2016).
(196) Zachary F. Burton, Kristopher Opron, Guowei Wei and James H. Geiger, A model for genesis of transcription systems, Transcription, 7, 1-13 (2016).
(195) Bao Wang and Guo-Wei Wei, Object-oriented persistent homology, Journal of Computational Physics, 305, 276-299 (2016).
(194) Zixuan Cang, Lin Mu, Kedi Wu, Kris Opron, Kelin Xia and Guo-Wei Wei, A topological approach to protein classification, Molecular based Mathematical Biology, 3, 140-162 (2015)
(193) Kelin Xia, Kristopher Opron and Guo-Wei Wei, Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM), Journal of Chemical Physics, 143, 204106 (2015).
(192) Bao Wang and Guo-Wei Wei, Parameter optimization in differential geometry based solvation models, Journal of Chemical Physics, 143, 134119 (2015).
(191) Kelin Xia, Zhixiong Zhao and Guo-Wei Wei, Multiresolution persistent homology for excessively large biomolecular datasets, Journal of Chemical Physics, 143, 134103 (2015).
(190) Kristopher Opron, Kelin Xia, and Guo-Wei Wei, Communication: Capturing protein multiscale thermal fluctuations, Journal of Chemical Physics, 142, 211101 (2015).
(189) Jinkyoung Park, Kelin Xia and G.W. Wei, Atomic scale design and three-dimensional simulations of nanofluidic systems, Microfluidics and Nanofluidics, 19, 665-692 (2015).
(188) Kelin Xia and Guo-Wei Wei, Multidimensional persistence in biomolecular data, Journal of Computational Chemistry, 36, 1502-1520 (2015).
(187) Kelin Xia, Zhixiong Zhao and Guo-Wei Wei, Multiresolution topological simplification, Journal of Computational Biology,22, 9, 1-5 (2015).
(186) Bao Wang, Kelin Xia and Guo-Wei Wei, Matched interface and boundary method for 3D elastic interface problems, Journal of Computational Physics, 294, 405-438 (2015).
(185) Kelin Xia and Guo-Wei Wei, Persistent topology for cryo-EM data analysis, International Journal for Numerical Methods in Biomedical Engineering, 31, e02719 (2015).
(184) Langhua Hu, Duan Chen and Guo-Wei Wei, Geometric and phonon effects on nano transistors, Journal of Computational Physics, 290, 169-187 (2015).
(183) Bao Wang, Kelin Xia and Guo-Wei Wei, Matched interface and boundary method for irregular elastic interface problems, Journal of Computational and Applied Mathematics, 285, 203-225 (2015).
(182) Kelin Xia, X. Feng, Yiying Tong and Guo-Wei Wei, Persistent homology for the quantitative prediction of fullerene stability, Journal of Computational Chemistry, 36, 408-422 (2015).
(181) Langhua Hu, Siyang Yang and Guo-Wei Wei, Simulation of inviscid compressible flows using PDE transform. Commun. Comput. Phys., 16, 1201-1238 (2014).
(180) Kelin Xia and Guo-Wei Wei, A Galerkin formulation of the MIB method for three dimensional elliptic interface problems, Computers and Mathematics with Applications, 68, 719–745, (2014).
(179) Kelin Xia, Meng Zhan, and Guo-Wei Wei, MIB Galerkin method for elliptic interface problems, Journal of Computational and Applied Mathematics, 272. 195-220 (2014).
(178) Kelin Xia and Guo-Wei Wei, Persistent homology analysis of protein structure, flexibility and folding, International Journal for Numerical Methods in Biomedical Engineering, 30, 814-844 (2014).
(177) Kristopher Opron, Kelin Xia, and Guo-Wei Wei, Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis, Journal of Chemical Physics, 140(23), 234105, (2014).
(176) Kelin Xia and Guo-Wei Wei, Molecular nonlinear dynamics and protein thermal uncertainty quantification, Chaos, 24, 013103 (2014).
(175) Shan Zhao and Guo-Wei Wei, A unified discontinuous Galerkin framework for time integration, Mathematical Methods in the Applied Sciences, 37, 1042-1071 (2014).
(174) Kelin Xia, Xin Feng, Zhan Chen, Yiying Tong and Guo-Wei Wei, Multiscale geometric modeling of macromolecules I: Cartesian representation, Journal of Computational Physics, 257, 912-936 (2014).
(173) Kelin Xia, and Guo-Wei Wei, A stochastic model for protein flexibility analysis, Physical Review E, 88, 062709 (2013).
(172) X. Feng, Kelin Xia, Zhan Chen, Yiying Tong and Guo-Wei Wei, Multiscale geometric modeling of macromolecules II: Lagrangian representation, Journal of Computational Chemistry, 34, 2100-2120 (2013).
(171) Kelin Xia, Kristopher Opron and Guo-Wei Wei, Multiscale multiphysics and multidomain models — Flexibility and rigidity, Journal of Chemical Physics, 139, 194109 (2013).
(170) L. Mu, J. P. Wang, G. W. Wei, X. Ye and S. Zhao, Weak Galerkin methods for second order elliptic interface problems, Journal of Computational Physics, 250, 106-125 (2013).
(169) Michael Daily, Jaehun Chun, Alejandro Heredia-Langner, Guo-Wei Wei, and Nathan Baker, Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies. Journal of Chemical Physics, 139, 204108 (2013).
(168) Guo-Wei Wei, Multiscale multiphysics and multidomain models I: Basic theory, Journal of Theoretical and Computational Chemistry, 12(8), 1341006 (2013)
(167) Jinkyoung Park and G.W. Wei, A molecular level prototype for mechanoelectrical transducers in mammalian hair cells, Journal of Computational Neuroscience, 35, 231-241, (2013).
(166) Dennis G. Thomas, Jaehun Chun, Zhan Chen, Guo-Wei Wei, Nathan A. Baker, Parameterization of a geometric flow implicit solvation model, Journal of Computational Chemistry, 24, 687-695 (2013)
(165) Emil Alexov and Guo-Wei Wei, Preface: Special issue on modeling electrostatics in molecular biology (MEMB), Commun. Comput. Phys., 13(1) 1-5, (2013).
(164) Duan Chen and Guo-Wei Wei, Quantum dynamics in continuum models for proton transport I: Basic formulation, Communication in Computational Physics, 13, 285-324 (2013)
(163) Langhua Hu, Duan Chen and Guo-Wei Wei, High-order fractional partial differential equations for molecular surface construction, Molecular Based Mathematical Biology, 1-25 (2012).
(162) X. Feng, Kelin Xia, Yiying Tong and Guo-Wei Wei, Geometric modeling of organelles, subcellular structures and multiprotein complexes, International Journal for Numerical Methods in Biomedical Engineering, 28, 1198-1223 (2012).
(161) Zhan Chen, Shan Zhao, Jaehun Chun, Dennis G. Thomas, Nathan Baker, Peter Bates and Guo-Wei Wei, Variational approach for nonpolar solvation analysis, Journal of Chemical Physics, 137, 084101 (2012).
(160) Anita T. Layton and Guo-Wei Wei, Editorials: Interface methods for biological and biomedical problems, International Journal for Numerical Methods in Biomedical Engineering, 28, 289–290, (2012)
(159) Duan Chen and Guo-Wei Wei, Quantum dynamics in continuum models for proton transport --- Generalized correlation, Journal of Chemical Physics, 136, 134109 (2012)
(158) Guo-Wei Wei, Qiong Zheng, Zhan Chen, and Kelin Xia, Variational multiscale models for charge transport, SIAM Review. 54(4), 699-754 (2012).
(157) Yang Wang, Guo-Wei Wei and Siyang Yang, Selective extraction of entangled textures via adaptive PDE transform, Int. J. Biomed Imaging, Volume 2012 (2012), Article ID 958142 (2012).
(156) Langhua Hu and Guo-Wei Wei, Nonlinear Poisson equation for heterogeneous media. Biophysical Journal, 103, 758–766 (2012).
(155) Duan Chen, Zhan Chen and Guo-Wei Wei, Quantum dynamics in continuum models for proton transport II: Variational solvent-solute interface, International Journal for Numerical Methods in Biomedical Engineering, 28, 25-51 (2012)
(154) Qiong Zheng, Siyang Yang and Guo-Wei Wei, Molecular surface generation using PDE transform. International Journal for Numerical Methods in Biomedical Engineering, 28, 291-316 (2012)
(153) Yang Wang, Guo-Wei Wei and Siyang Yang, Model decomposing evolution equations, Journal of Scientific Computing, 50, 495-518 (2012).
(152) Yang Wang, Guo-Wei Wei and Siyang Yang, Empirical model decomposition using local spectral evolution kernels, Journal of Scientific Computing, 50, 629-664 (2012).
(151) Kelin Xia, Meng Zhan, Decheng Wan and Guo-Wei Wei, Adaptively deformed mesh based matched interface and boundary (MIB) method for elliptic interface problems, Journal of Computational Physics, 231, 1440–1461 (2012).
(150) Zhan Chen and G. W. Wei, Differential geometry based salvation model III: Quantum formulation, Journal of Chemical Physics, 135, 194108 (2011).
(149) Qiong Zheng and Guo-Wei Wei, Poisson-Boltzmann-Nernst-Planck model. Journal of Chemical Physics, 134 (19), 194101, (2011) (It was the most downloaded in JCP in May 2011)
(148) Kelin Xia, Meng Zhan and Guo-Wei Wei, The matched interface and boundary (MIB) method for multi-domain elliptic interface problems. Journal of Computational Physics, 230, 8231–8258 (2011)
(147) Yang Wang, Guo-Wei Wei and Siyang Yang, Partial differential equation transform --- variational formulation and Fourier analysis, International Journal for Numerical Methods in Biomedical Engineering, 27, 1996-2020, (2011).
(146) Qiong Zheng, Duan Chen and Guo-Wei Wei, Second-order Poisson-Nernst-Planck solver for ion transport. Journal of Computational Physics, 230, 5239-5262 (2011)
(145) Zhan Chen, Nathan Baker and G. W. Wei, Differential geometry based salvation model II: Lagrangian formulation (62 pages), Journal of Mathematical Biology, 63, 1139–1200, (2011).
(144) Weihua Geng and G.W. Wei, Multiscale molecular dynamics via the matched interface and boundary (MIB) method, Journal of Computational Physics, 230, 435-457 (2011).
(143) Duan Chen, Zhan Chen, Changjun Chen, Weihua Geng and Guo-Wei Wei, MIBPB: A software package for electrostatic analysis, Journal of Computational Chemistry, 32, 756–770 (2011).
(142) G. W. Wei, Lalita Udpa, Yang Wang and Shan Zhao, Editorial: Mathematical methods for images and surfaces, International Journal of Biomedical Imaging, Volume 2010, Article ID 918467, 3 pages (2010).
(141) Zhan Chen, Nathan Baker and G. W. Wei, Differential geometry based solvation model I: Eulerian formulation, Journal of Computational Physics, 229, 8231-8258 (2010).
(140) Duan Chen and Guo-Wei Wei, Modeling and simulation of nano-electronic devices, Journal of Computational Physics, 229, 4431-4460, (2010).
(139) Changjun Chen, Rishu Saxena, and Guo-Wei Wei, Differential geometry based multiscale model for virus capsid dynamics, Int. J. Biomed Imaging, Volume 2010, Article ID 308627, 9 pages (2010).
(138) Guo-Wei, Wei, Differential geometry based multiscale models, Bulletin of Mathematical Biology, volume 72, 1562-1622, (2010).
(137) C.H.W. Ng, Y.B. Zhao, Y. Xiang and G.W. Wei, On the accuracy and stability of a few differential quadrature formulations for the vibration analysis of beams, Int. J. Engng. Applied Sci. 1 (4), 1-25 (2009).
(136) G.W. Wei and G. Wang, Editorial: Special issue on recent advances in computational techniques for biomedical imaging, Commun. Numer. Methods Engng, 25, 581-582 (2009)
(135) P. Bates, Z. Chen, Y.H. Sun, G.W. Wei and S. Zhao, Geometric and potential driving formation and evolution of biomolecular surfaces, J. Math. Biol. 59, 193-231 (2009)
(134) Shan Zhao and G.W. Wei, Matched interface and boundary (MIB) for the implementation of boundary conditions in high order central finite differences, Int. J. Numer. Meth. Engng. 77, 1690-1730 (2009)
(133) Duan Chen, G.W. Wei, X. Cong and Ge Wang, Computational methods for optical molecular imaging, Commun. Numer. Methods Engng, 25, 1137-1161(2008).
(132) S.N. Yu, Y. Xiang and G.W. Wei, Matched interface and boundary (MIB) method for the vibration analysis of plates, Commun. Numer. Methods Engng, 25, 923-950 (2009).
(131) S.N. Yu and G.W. Wei, Three dimensional matched interface and boundary (MIB) method for geometric singularities, J. Comput. Phys. 227, 602-632 (2007).
(130) W.H. Geng, S.N. Yu and G.W. Wei, Treatment of charge singularities in implicit solvent models, J. Chem. Phys., 127, 114106 (20 pages) (2007). Also available at the Virtual Journal of Biological Physics Research October 1, 2007
(129) P. Bates, G.W. Wei and S. Zhao, Minimal molecular surfaces and their applications, J. Comput. Chem., 29, 380-391 (2008).
(128) S. N. Yu, W. H. Geng and G.W. Wei, Treatment of geometric singularities in implicit solvent models, J. Chem. Phys., 126, 244108 (13 pages) (2007). Also available at the Virtual Journal of Biological Physics Research July 1, 2007.
(127) Y.C. Zhou, M. Feig and G.W. Wei, Highly accurate biomolecular electrostatics in continuum dielectric environments, J. Comput. Chem. 29, 87-97 (2008).
(126) G.W. Wei and S. Zhao, On the validity of ``A proof that the discrete singular convolution (DSC)/Langrange-distributed approximation function (LDAF) method is inferior to high order finite differences '', J. Comput. Phys., 226, 2389-2392 (2007).
(125) S. N. Yu, Y. C. Zhou and G. W. Wei, Matched interface and boundary (MIB) method for elliptic problems with sharp-edged interfaces, J. Comput. Phys. 224, 729-756 (2007).
(124) G.W. Wei, Editoral: Recent advances in mathematical methods for the analysis of biomedical image, International Journal of Biomedical Imaging, vol. 2006, 70578, 1, (2006).
(123) S.F. Shieh, Y.Q. Wang, G.W. Wei and C.-H. Lai, Mathematical analysis of the wavelet method of chaos control, J. Math. Phys., 47, 082701 (2006).
(122) Y.C. Zhou and G.W. Wei, On the fictitious-domain and interpolation formulations of the matched interface and boundary (MIB) method, J. Comput. Phys. 219, 228-246 (2006).
(121) Ge Wang, Haiou Shen Wenxiang Cong, Shan Zhao and G.W. Wei, Temperature modulated bioluminescence tomography, Optics Express, 14 (17) 7852-7871 (2006).
(120) L. Zhang, Y. Xiang and G.W. Wei, Local adaptive differential quadrature for free vibration analysis of cylindrical shells with various boundary conditions, International Journal of Mechanical Sciences, 48, 1126-1138 (2006).
(119) Y.H. Sun, P.R. Wu, G.W. Wei and G. Wang, Evolution operator based single-step method for image processing, Int. J. Biomed. Imaging, 83847, 1-27 (2006).
(118) Y.H. Sun, Y.C. Zhou, S. G. Li and G.W. Wei, A windowed Fourier spectral scheme for hyperbolic conservation laws, J. Comput. Phys., 214, 466-490 (2006).
(117) Y.C. Zhou, S. Zhao, M. Feig and G. W. Wei, High order matched interface and boundary (MIB) schemes for elliptic equations with discontinuous coefficients and singular sources, J. Comput. Phys., 213, 1-30, (2006).
(116) C.W. Lim, Z.R. Li, Y. Xiang, G.W. Wei and C.M. Wang, On the missing modes when using the exact frequency relationship between Kirchhoff and Mindlin plates, Advances in Vibration Engineering, 4, 221-248, (2005).
(115) Y.-C. Lai, Z. Liu, G.-W. Wei, C. H. Lai, Reply to ``Comment on `Shadowability of statistical averages in chaotic systems''', Physical Review Letters, 94, 219403 (2005).
(114) S.G. Guan, C.H. Lai and G.W. Wei, Phase synchronization between two essentially different chaotic systems, Phys. Rev. E, 72, 016205 (2005).
(113) S.G. Guan, C.H. Lai and G.W. Wei, Bistable chaos without symmetry in generalized synchronization, Phys. Rev. E, 71, 036209 (2005).
(112) S.N. Yu, S. Zhao and G.W. Wei, Local spectral time splitting method for first and second order partial differential equations, J. Comput. Phys., 206, 727-780 (2005).
(111) S. Zhao, G.W. Wei and Y. Xiang, DSC analysis of free-edged beams by an iteratively matched boundary method, J. Sound Vibr., 284, 487-493 (2005).
(110) S. Zhao and G.W. Wei, Option valuation by using discrete singular convolution, Appl. Math. Comput., 167, 383-418 (2005).
(109) C.W. Lim, Z.R. Li and G.W. Wei, DSC-Ritz method for the high frequency mode analysis of thick shallow shells, Int. J. Numer. Meth. Engng., 62, 205-232 (2005).
(108) Y.S. Hou, G.W. Wei and Y. Xiang, DSC-Ritz method for the vibration analysis of Mindlin plates, Int. J. Numer. Meth. Engng., 62, 262-288 (2005).
(107) S. Zhao and G.W. Wei, Tensor product derivative matching for wave propagation in inhomogeneous media, Microwave Optical Techn. Lett., 43(1), 69-77 (2004).
(106) S. Guan, G.W. Wei and C.H. Lai, Controllability of flow turbulence, Phys. Rev. E, 69, 066214 (2004).
(105) S. Zhao and G.W. Wei, High order FDTD methods via derivative matching for Maxwell's equations with material interfaces, J. Comput. Phys., 200, 60-103, (2004).
(104) C.H.W. Ng, Y.B. Zhao and G.W. Wei, Comparison of the DSC and GDQ methods for the vibration analysis of plates, Comput. Methods Appl. Mech. Engng., 193, 2483-2506 (2004).
(103) G. Bao, G.W. Wei, and S. Zhao, Numerical solution of the Helmholtz equation with high wave numbers, Int. J. Numer. Meth. Engng., 59, 389-408 (2004).
(102) Y. Xiang and G.W. Wei, Exact solution for buckling and vibration of stepped rectangular Mindlin plates, Int. J. Solid Struct., 41, 279-294 (2004).
(101) M. Zhan, X. Wang, X. Gong, G.W. Wei, and C.-H. Lai, Complete synchronization and generalized synchronization of one -way coupled time-delayed systems, Phys. Rev. E, 68, 036208 (2003).
(100) S. Guan, C.-H. Lai and G.W. Wei, A new wavelet method for characterizing turbulence, Comput. Phys. Commun. 155, 77-91 (2003).
(99) Ying Wang, Y.B. Zhao and G.W. Wei, A note on the numerical solution of high-order differential equations, J. Comput. Appl. Math., 159, 387-398 (2003).
(98) W.Z. Bao, F.F. Sun and G.W. Wei, Numerical methods for the generalized Zakharov system, J. Comput. Phys., 190, 201-228 (2003).
(97) Z.H. Shao, G.W. Wei and S. Zhao, DSC time-domain solution of Maxwell's equations, J. Comput. Phys., 189, 427-453 (2003).
(96) Y.C. Zhou and G.W. Wei, High-resolution conjugate filters for the simulation of flows, J. Comput. Phys., 189, 150-179 (2003).
(95) S. Zhao and G.W. Wei, Comparison of the discrete singular convolution and three other numerical schemes for Fisher's equation, SIAM J. Sci. Comput.,25, 127-147 (2003).
(94) G. Bao, G.W. Wei and S. Zhao, Local spectral time-domain method for electromagnetic wave propagation, Optics Letters, 28, 513-515 (2003).
(93) Z. H. Shao, Z. Shen, Q. He and G.W. Wei, A generalized higher-order finite difference time domain method and its application in guided-wave problems, IEEE T. Microwave Theory Tech., 51, 856-861 (2003).
(92) Y.C. Zhou, Y. Gu and G.W. Wei, Shock-capturing with natural high frequency oscillations, Int. J. Numer. Methods in Fluid, 41, 1319-1338 (2003).
(91) Y. Gu, Y.C. Zhou and G.W. Wei, Conjugate filters with spectral-like resolution for 2D incompressible flows, Computers and Fluids, 33, 777-794 (2003).
(90) S. Guan, Y.C. Zhou, G.W. Wei and C.-H. Lai, Controlling flow turbulence, Chaos, 13, 64-70 (2003).
(89) S. Guan, C.-H. Lai and G.W. Wei, On geometry and boundary control of pattern formation and competition, Physica D, 176, 19-43 (2003).
(88) Y. Gu and G.W. Wei, Conjugated filter approach for shock capturing, Commun. Numer. Meth. Engng., 19, 99-110 (2003).
(87) Y.C. Zhou, B. S. V. Patnaik, D.C. Wan and G. W. Wei, DSC solution for flow in a staggered double lid driven cavity, Int. J. Numer. Methods in Engng.,57, 211-234 (2003).
(86) S. Zhao and G.W. Wei, Jump process analysis for the trend estimation of time series, Comput. Statist. Data Anal., 42, 219-241 (2003).
(85) G.W. Wei, M. Zhan, and C.-H. Lai, Tailoring wavelets for chaos control, Phys. Rev. Lett. 89, 284103 (2002). This workwas highlighted in Physical Review Letters and featured in Nature.
(84) G. W. Wei and Y. Q. Jia, Synchronization based image edge detection, Europhys. Lett. 59, 814-819 (2002).
(83) Y.-C. Lai, Z.H. Liu, G.W. Wei, and C.-H. Lai, Shadowing of statistical averages in chaotic systems, Phys. Rev. Lett. 89, 184101 (2002).
(82) M. Zhan, G.W. Wei, C.-H. Lai, Y.-C. Lai and Z.H. Liu, Coherent resonance near Hopf bifurcation from chaos, Phys. Rev. E 66, 036201 (2002).
(81) G.W. Wei, and Y. Gu, Conjugated filter approach for solving Burger's equation, J. Comput. Appl. Math., 149, 439-456 (2002).
(80) Y. Xiang, Y.B. Zhao and G.W. Wei, Closed form solutions for vibration of multi-span rectangular plates, Int. J. Mech. Sci., 44, 1195-1218 (2002).
(79) D.C. Wan, B.S.V. Patnaik and G.W. Wei, Discrete singular convolution-finite subdomain method for the solution of incompressible viscous flows, J. Comput. Phys. 180, 229-255 (2002).
(78) Y. Xiang and G.W. Wei, Exact solutions for the vibration of multi-span rectangular Mindlin plates, Journal of Vibration and Acoustics, Trans. ASME, 124, 545-551 (2002).
(77) G.W. Wei, Oscillation reduction by anisotropic diffusions, Comput. Phys. Commun., 144, 417-342 (2002).
(76) G.W. Wei, Y.B. Zhao, and Y. Xiang, A novel approach for the analysis of high frequency vibrations, J. Sound and Vibration, 257, 207-246 (2002).
(75) Y.B. Zhao and G.W. Wei, DSC analysis rectangular plates with nonuniform boundary conditions, J. Sound and Vibration, 255, 203-225 (2002).
(74) G.W. Wei and S. Zhao, Synchronization and information processing by an on-off coupling, Phys. Rev. E, 65, 056210 (2002).
(73) Y. Xiang, Y.B. Zhao and G.W. Wei, Discrete singular convolution and its application to the analysis of plates with internal supports. II Complex supports, Int. J. Numer. Methods Engng., 55, 947-971 (2002).
(72) G.W. Wei, Y.B. Zhao and Y. Xiang, Discrete singular convolution and its application to the analysis of plates with internal supports, I Theory and algorithm, Int. J. Numer. Methods Engng., 55, 913-946 (2002).
(71) B.F. Feng and G.W. Wei, A comparison of the spectral and the discrete singular convolution schemes for the KdV-type equations, J. Comput. Appl. Math., 145, 183-188 (2002).
(70) Z.J. Hou and G.W. Wei, A new approach for edge detection, Pattern Recognition, 35(7), 1559-1570 (2002).
(69) B. S. V. Patnaik and G.W. Wei, Controlling wake turbulence [Phys. Rev. Lett. 88, 054502 (2002)], Phys. Rev. Lett., 88, 127901 (2002).
(68) Y.B. Zhao, G.W. Wei, and Y. Xiang, Plate vibration under irregular internal supports, Int. J. Solids and Structures, 39, 1361-1383 (2002).
(67) S. Guan, C.-H. Lai and G.W. Wei, A wavelet method for the characterization of spatiotemporal patterns, Physica D, 163, 49-79 (2002).
(66) D.C. Wan, Y.C. Zhou and G.W. Wei, Numerical solution of incompressible flows by the discrete singular convolution, Int. J. Numer. Methods Fluid, 38,789-810 (2002).
(65) M. Zhan, G.W. Wei and C.-H. Lai, Transition from intermittence to periodicity in lag synchronization in coupled Rossler oscillators, Phys. Rev. E, 65, 036202 (2002).
(64) S. Y. Yang, Y. C. Zhou and G.W. Wei, Comparison of the discrete singular convolution algorithm and the Fourier pseudospectral methods for solving partial differential equations, Comput. Phys. Commun., 143, 113-135 (2002).
(63) B. S. V. Patnaik, and G.W. Wei, Controlling wake turbulence, Phys. Rev. Lett., 88, 054502 (2002). This workwas featured in Physical Review Focus and Wissenschat-online.
(62) Y.B. Zhao, G.W. Wei, and Y. Xiang, Discrete singular convolution for the prediction of high frequency vibration of plates, Int. J. Solids and Struct., 39, 65-88 (2002).
(61) G.W. Wei, H. Wang, D.J. Kouri, M. Papadakis, I.A. Kakadiaris, and D.K. Hoffman, On the mathematical properties of distributed approximating functionals, J. Math. Chem., 30, 83-107 (2001).
(60) Z. Shi, G.W. Wei, D.J. Kouri, D.K. Hoffman, Z. Bao, Lagrange wavelets for signal processing, IEEE T. Image Processing, 10, 1488-1508 (2001).
(59) D.C. Wan, B.S.V. Patnaik and G.W. Wei, A new benchmark quality solution for the buoyancy driven cavity by discrete singular convolution, Numer. Heat Transfer B - Fundamentals, 40, 199-228 (2001).
(58) G.W. Wei, Y.B. Zhao and Y. Xiang, The determination of the natural frequencies of rectangular plates with mixed boundary conditions by discrete singular convolution, Int. J. Mech. Sci., 43, 1731-1746 (2001).
(57) S. Guan, C.-H. Lai and G.W. Wei, Fourier-Bessel analysis of patterns in a circular domain, Physica D, 151, 83-98 (2001).
(56) G.W. Wei, Discrete singular convolution for beam analysis, Engineering Structures, 23, 1045-1053 (2001).
(55) G.W. Wei, Vibration analysis by discrete singular convolution, J. Sound Vibration, 244, 535-553 (2001).
(54) G.W. Wei, Synchronization of single-side locally averaged adaptive coupling and its application to shock capturing, Phys. Rev. Lett., 86, 3542-3545 (2001).
(53) G.W. Wei, A new algorithm for solving some mechanical problems, Comput. Methods Appl. Mech. Engng., 190, 2017-2030 (2001).
(52) D.C. Wan and G.W. Wei, The study of quasi wavelets based numerical method applied to Burgers' equations, Appl. Math. Mech-Engl, 21, 1099-1110 (2000).
(51) D.C. Wan and G.W. Wei, Numerical solution of incompressible Euler and Navier-Stokes equations by efficient discrete singular convolution method, Acta Mechanica Sinica, 16, 223-239 (2000).
(50) G.W. Wei, Wavelets generated by using discrete singular convolution kernels, J. Phys. A, Mathematical and General, 33, 8577-8596 (2000).
(49) G.W. Wei, A unified approach for the solution of the Fokker-Planck equation, J. Phys. A, Mathematical and General, 33, 4935-4953 (2000).
(48) G.W. Wei, Solving quantum eigenvalue problems by discrete singular convolution, J. Phys. B, 33, 343-352 (2000).
(47) G.W. Wei, Discrete singular convolution for the sine-Gordon equation, Physica D, 137, 247-259 (2000).
(46) D. K. Hoffman, G. W. Wei, and D. J. Kouri, A variation approach to the Dirichlet--Gabor wavelet-distributed approximating functional, J. Math. Chem., 25, 235-244 (1999).
(45) D.S. Zhang, G.W. Wei, D.J.Kouri, David K. Hoffman, Michael Gorman, Antonio Palacios, and Gemunu H. Gunaratne, Integrating the Kuramoto-Sivashinsky equation in polar coordinates: Application of the distributed approximating functional approach, Phys. Rev. E., 60, 3353-3360 (1999).
(44) Zhuoer Shi, D.J. Kouri, G.W. Wei, and David K. Hoffman, Generalized symmetric interpolating wavelets, Comput. Phys. Commun., 119, 194-218 (1999).
(43) D.J. Kouri, D.S. Zhang, G.W. Wei, and D.K. Hoffman, Numerical solutions of nonlinear wave equations, Phys. Rev., E 59, 1274-1277 (1999).
(42) G.W. Wei, Generalized Perona-Malik equation for Image Restoration, IEEE Signal Processing Lett., 6, 165-167 (1999).
(41) G.W. Wei, Discrete singular convolution for the solution of the Fokker-Planck equations, J. Chem. Phys., 110, 8930-8942 (1999).
(40) G.W. Wei, Generalized reaction-diffusion equations, Chem. Phys. Lett., 303, 531-536 (1999).
(39) S. Alavi, G.W. Wei and R.F. Snider, Chain relations of reduced distribution functions and their associated correlation functions, J. Chem. Phys., 108, 706-714 (1998).
(38) D.S. Zhang, G.W. Wei, D.J. Kouri and D.K. Hoffman, Lagrange distributed approximating functional method for the solution of the Schrodinger equation, Chem. Phys. Lett., 284, 56-62 (1998).
(37) D.K. Hoffman, G.W. Wei, D.S. Zhang, and D.J. Kouri, Interpolating distributed approximating functionals, Phys. Rev., E 57, 6152-6160 (1998).
(36) D.K. Hoffman, G.W. Wei, and D.J. Kouri, Shannon-Gabor wavelet distributed approximating functional, Chem. Phys. Lett., 287, 119-124 (1998).
(35) G.W. Wei, D.S. Zhang, D.J. Kouri and D.K. Hoffman, Distributed approximating functional approach to Burgers' equation in one and two space dimensions, Comput. Phys. Commun., 111, 87-92 (1998).
(34) G.W. Wei, S. Althorpe, D.J. Kouri and D.K. Hoffman, Lagrange-distributed approximating-functional approach to wave-packet propagation: Application to the time-independent wave-packet reactant-product decoupling method, Phys. Rev. A 57 (5), 3309-3316 (1998).
(33) G.W. Wei, D.J. Kouri, and D.K. Hoffman, Wavelets and distributed approximating functionals, Comput. Phys. Commun., 112, 1-6 (1998).
(32) G.W. Wei, D.S. Zhang, D.J. Kouri, and D.K. Hoffman, Wavelet-distributed approximating functional method for solving the Navier-Stokes equation, Comput. Phys. Commun., 115, 18-24 (1998).
(31) G.W. Wei, D.S. Zhang, D.J. Kouri and D.K. Hoffman, A robust and reliable approach to nonlinear dynamical problems, Comput. Phys. Commun., 111, 93-109 (1998).
(30) G.W. Wei, Quasi wavelets and quasi interpolating wavelets, Chem. Phys. Lett., 296, 215-222 (1998).
(29) G.W. Wei, S. Althorpe, D.J. Kouri and D.K. Hoffman, An application of distributed approximating functional-wavelets to reactive scattering, J. Chem. Phys., 108, 7065-7069 (1998).
(28) G.W. Wei, D.S. Zhang, D.J. Kouri and D.K. Hoffman, Lagrange distributed approximating functionals, Phys. Rev. Lett.,79, 775-779 (1997).
(27) G.W. Wei, S. Alavi and R.F. Snider, Equal reaction rates for all recombination pathways, J. Chem. Phys, 106, 1463-1466 (1997).
(26) D.S. Zhang, G.W. Wei, D.J. Kouri and D.K. Hoffman, Distributed approximating functional approach to the Fokker-Planck equation: Eigenfunction expansion, J. Chem. Phys., 106, 5216-5224 (1997).
(25) D.S. Zhang, G.W. Wei, D.J. Kouri and D.K. Hoffman, Burgers' equation with high Reynolds number, Phys. Fluids, 9, 1853-1855 (1997).
(24) D.S. Zhang, G.W. Wei, D.J. Kouri and D.K. Hoffman, Numerical method for the nonlinear Fokker-Planck equation, Phys. Rev. E 56, 1197-1206 (1997).
(23) G.W. Wei, D.S. Zhang, D.J. Kouri and D.K. Hoffman, Distributed approximating functional approach to the Fokker-Planck equation: Time propagation, J. Chem. Phys., 107, 3239-3246 (1997).
(22) J.G. Muga, G.W. Wei and R.F. Snider, Short-time behaviour of the quantum survival probability, Europhys. Lett., 35, 247-252 (1996).
(21) J.G. Muga, G.W. Wei and R.F. Snider, Survival probability for the Yamaguchi potential, Ann. Phys., 252, 336-356 (1996).
(20) R.F. Snider, G.W. Wei and J.G. Muga, Moderately dense gas quantum kinetic theory: Transport coefficient expressions, J. Chem. Phys., 105, 3066-3078 (1996).
(19) R.F. Snider, G.W. Wei and J.G. Muga, Moderately dense gas quantum kinetic theory: Aspects of pair correlations, J. Chem. Phys., 105, 3057-3065 (1996).
(18) G.W. Wei and R.F. Snider, Discrete basis representation of Ursell operators, Phys. Rev., E 54, 2414-2418, (1996).
(17) G.W. Wei and R. F. Snider, Correlated state evaluation of the second virial coefficient, Phys. Rev. A, 52(4), 2925-2936 (1995).
(16) G. Wei and R. F. Snider, A pictorial representation for multispin evolutions, Concepts in Magn. Reson., 7(2), 153-163 (1995).
(15) R. F. Kiefl, J. W. Schneider, A. McFarlane, K. Chow, T. L. Duty, T. L. Estle, B. Hitti, R. L.Lichti, E. J. Ansaldo, C. Schwab, P. W. Percival, G. Wei, S. Wlodek, K. Kojima, W. J. Romanow, J. P. McCauley, Jr, N. Coustel, J. E. Fischer, and A. B. Smith, III, Molecular dynamics of the Muonium-C60 radical in solid C60, Phys. Rev. Lett., 68, 2708-2712 (1992).
(14) R. F. Kiefl, J. W. Schneider, A. McFarlane, K. Chow, T. L. Duty, T. L. Estle, B. Hitti, R. L. Lichti, E. J. Ansaldo, C. Schwab, P. W. Percival, G. Wei, S. Wlodek, K. Kojima, W. J. Romanow, J. P. McCauley, Jr, N. Coustel, J. E. Fischer, and A. B. Smith, III, Molecular dynamics of the (Mu+)- C60 radical in solid C60, Phys. Rev. Lett., 68, 1347-1350 (1992).
(13) F.L. Jiang, G.W. Wei, Z.Y. Huang, X.J. Lei, M.C. Hong, B.S. Kang and H.Q. Liu, Syntheses and crystal structures of 2 thiolato-organophosphino cobalt(II) complexes, (Et4N)[Co(SC6H5)3(PPh3)] and [Co(S-meta- C6H4CH3)2(Ph2PCH2CH2P(Ph)CH2CH2PPh2)], J. Coord. Chem., 25, 183-191 (1992).
(12) G.W. Wei, Z.Y. Huang, X.J. Lei, R. Cao, F.L. Jiang, M.C. Hong, L.R. Huang and H.Q. Liu, Structure of [Bis(2-diphenylphospinoethyl)phenylphospine-P, P, P] carbonyl-(phenylthiolato)Cobalt(I), [Co(Ph2PCH2CH2P(Ph)CH2CH2PPh2)(SPh)(CO)], ActaCrystallogr. C, 48, 2130-2132 (1992).
(11) G. Wei, M. Hong, Z. Huang, and H. Liu, Synthesis and crystal structure of a platinum(II) complex with mixed diphosphine and thiolate ligands, Pt(dppm)(SPh)_2, J. Struct. Chem., 11(5), 334-338 (1992).
(10) M.C. Hong, Z.Y. Huang, X.J. Lei, G.W. Wei, B.S. Kang and H.Q. Liu, Syntheses, properties and X-ray crystal structures of hexa-nuclear cobalt chalcogen clusters Co6S8(PPh3)6 and Co6Se8(PPh3)6.THF, Polyhedron, 10, 927-934 (1991).
(9) F.L. Jiang, G.W. Wei, X.J. Lei, L.R. Huang, M.C. Hong and H.Q. Liu, Synthesis, characterization and polymorphic crystal structures of Bis(para-tolylthiolato)bis(tri-n-butylphosphine)-Nickel(II), J. Chem. Res. S, 9, 238-239 (1991).
(8) G.W. Wei, M.C. Hong, Z.Y. Huang, and H.Q. Liu, Stereochemistry of mixed thiolate and ditertiary phosphine cobalt (II) complexes -- Crystal structures of [Co(Ph2P(CH2)3-PPh2)(SPh)2] and [Co(Ph2PCH2CH2P(Ph)CH2CH2PPh2)(SPh)2], J. Chem. Soc. Dalton, 11, 3145-3148 (1991).
(7) G.W. Wei, H.Q. Liu, Z.Y. Huang, M.C. Hong, L.R. Huang and B.S. Kang, Syntheses and stereochemistry of Dicobalt (II) complexes, [Co2(dppm)(mu-SR)2(SR)2] (dppm=Ph2PCH2PPh2 - R=C6H5, m-C6H4CH3, p-C6H4CH3 and p-C6H4-TC4H9) and [Co2(dppe)(mu-SPh)3(SPh)] (dppe=Ph2PCH2CH2PPh2), Polyhedron, 10, 553-560 (1991).
(6) M. Hong, Z. Huang, X. Lei, G. Wei, B. Kang, and H. Liu, A cobalt-selenium cluster with triethylphophine: Preparation an structure of Co6(v3-Se)8(PEt_3)_6.THF, Chin. J. Chem., (English), 9(5), 421-428 (1991).
(5) G.W. Wei and H.Q. Liu, Structure of [1,2-Bis(diphenylphosphino)Ethane] -Di(phenylthio)Palladium(II), Acta Crystallogr. C, 46, 2457-2458 (1990).
(4) H.Q. Liu R. Cao, X.J. Liu D. Wu, G.W. Wei, Z.Y. Huang, M.C. Hong, and B.S. Kang, Syntheses and structural characterizations of a series of Mo(W)-Cu-S compounds of bidentat dialkyldithiocarbamate ligands-- Crystal structure of [NET4]2{Mo2Cu5S6O2(Me2NCS2)3], J. Chem. Soc. Dalton, 3, 1023-1026 (1990).
(3) M.C. Hong, Z.Y. Huang, X.J. Lei, G.W. Wei, B.S. Kang and H.Q. Liu, A new cobalt sulfur cluster with triphenylphosphine - Preparation and structure of CO6S8(PPh3)6, Inorg. Chem. Acta, 159, 1-2 (1989).
(2) H. Liu, R. Cao, X. Lei, G. Wei, and B. Kang, NMR study of some molybdenum (tungsten)-copper-sulfur compounds, Bull. Magn. Reson., 11(3-4), 395 (1989).
(1) G.W. Wei, H.Q. Liu, Z.Y. Huang, L.R. Huang and B.S. Kang, Synthesis and X-ray structure of an asymmetrical dicobalt (II) complex CO2(dppe)(mu-SPH)3SPh (dppe=Ph2PCH2CH2PPh2), J. Chem Soc. Chem. Commun., 23, 1839-1840 (1989).
PATENTS
1. Donald K Kouri, David K Hoffman, Mark Arnold, Ioannis A Kakadiaris, Zhuoer Shi, DeSheng Zhang, Gemunu H Gunaratne, Haixiang Wang, Guowei W Wei, Methods for performing DAF data filtering and padding – US Patent 7272265 (2007).
2. Guowei Wei, Duc D Nguyen and Zixuan Cang, System and methods for machine learning for drug design and discovery - US Patent App. 16/372,239 (2019).
3. GW Wei, DD Nguyen, Z Cang, Systems and methods for drug design and discovery comprising applications of machine learning with differential geometric modeling, US Patent App. 17/043,551 (2021).
4. Guowei Wei, Jiahui Chen, Zixuan Cang and Weihua Geng, Machine learning based implicit solvent models for molecular simulations, Pending, US Patent App. 17/637,440, (2022).