Publications

(*equal contribution, ^†corresponding author) | Google Scholar Profile

2025

1. JMCA

   Enhancing Energy Predictions in Multi-Atom Systems with Multiscale Topological Learning

   Dong Chen, Rui Wang , Guo-Wei Wei^†, and Feng Pan^†

   Journal of Materials Chemistry A 2025
2. JMRI

   Machine Learning and Deep Learning Applications in Magnetic Particle Imaging

   Saumya Nigam, Elvira Gjelaj, Rui Wang , Guo-Wei Wei^†, and Ping Wang^†

   Journal of Magnetic Resonance Imaging 61(1) 42–51 2025
3. PLOS Comp Biol

   How Large Is the Universe of RNA-like Motifs? A Clustering Analysis of RNA Graph Motifs Using Topological Descriptors

   Rui Wang , and Tamar Schlick^†

   PLOS Computational Biology 21(7) e1013230 2025
4. CommChem

   Topological Deep Learning for Enhancing Peptide-Protein Complex Prediction

   Xuhang Dai*, Rui Wang* , and Yingkai Zhang^†

   Communications Chemistry () Accepted 2025

2024

1. JMRI

   Machine Learning and Deep Learning Applications in Magnetic Particle Imaging

   Saumya Nigam, Elvira Gjelaj, Rui Wang , Guo-Wei Wei^†, and Ping Wang^†

   Journal of Magnetic Resonance Imaging () Accepted 2024
2. AdvSci

   Drug resistance revealed by in silico deep mutational scanning and mutation tracker

   Dong Chen, Gengzhuo Liu, Hongyan Du, Junjie Wee, Rui Wang , Jiahui Chen, Jana Shen^†, and Guo-Wei Wei^†

   Advanced Science () e02756 2024
3. SIREV

   Combinatorial and Hodge Laplacians: Similarities and Differences

   Emily Ribando-Gros, Rui Wang , Jiahui Chen, Yiying Tong^†, and Guo-Wei Wei^†

   SIAM Review 66(3) 575-601 2024

2023

1. JCIM

   ChatGPT in Drug Discovery: A Case Study on Anticocaine Addiction Drug Development with Chatbots

   Rui Wang , Hongsong Feng, and Guo-Wei Wei^†

   Journal of Chemical Information and Modeling 66(3) 575-601 2023
2. JMC

   Multiobjective Molecular Optimization for Opioid Use Disorder Treatment Using Generative Network Complex

   Hongsong Feng, Rui Wang , Chang-Guo Zhan, and Guo-Wei Wei^†

   Journal of Medicinal Chemistry 66(3) 575-601 2023
3. JCIM

   PLPCA: Persistent Laplacian Enhanced-PCA for Microarray Data Analysis

   Sean Cottrell, Rui Wang , and Guo-Wei Wei^†

   Journal of Chemical Information and Modeling 66(3) 575-601 2023
4. iScience

   Deep Learning Enabled Quantification of Simultaneous PET/MRI for Cell Transplantation Monitoring

   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^†

   iScience 66(3) 575-601 2023

2022

1. ChemRev

   Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2

   Kaifu Gao*, Rui Wang* , Jiahui Chen, Limei Cheng, Jaclyn Frishcosy, Yuta Huzumi, Yuchi Qiu, Tom Schluckbier, Xiaoqi Wei, and Guo-Wei Wei^†

   Chemical Reviews 122(13) 11287–11368 2022
2. ACS ID

   Emerging vaccine-breakthrough SARS-CoV-2 variants

   Rui Wang , Jiahui Chen, Yuta Hozumi, Changchuan Yin, and Guo-Wei Wei^†

   ACS Infectious Diseases 8(3) 546–556 2022
3. JCIM

   Omicron variant (B. 1.1. 529): Infectivity, vaccine breakthrough, and antibody resistance

   Jiahui Chen, Rui Wang , Nancy Benovich Gilby, and Guo-Wei Wei^†

   Journal of Chemical Information and Modeling 62(2) 412–422 2022
4. FoDS

   Persistent Laplacian projected Omicron BA. 4 and BA. 5 to become new dominating variants

   Jiahui Chen, Yuchi Qiu, Rui Wang , and Guo-Wei Wei^†

   Computers in Biology and Medicine 151(2) 106262 2022
5. FoDS

   Persistent Path Laplacian

   Rui Wang , and Guo-Wei Wei^†

   Foundation of Data Science 151(2) 106262 2022
6. arXiv

   CCP: Correlated Clustering and Projection for Dimensionality Reduction

   Yuta Hozumi, Rui Wang , and Guo-Wei Wei^†

   arXiv preprint arXiv:2206.04189 151(2) 106262 2022
7. JCIM

   Emerging dominant SARS-CoV-2 variants

   Jiahui Chen, Rui Wang , Yuta Hozumi, Gengzhuo Liu, Yuchi Qiu, Xiaoqi Wei, and Guo-Wei Wei^†

   Journal of Chemical Information and Modeling 63(1) 335–342 2022

2021

1. AR of Biophy

   Review of COVID-19 antibody therapies

   Jiahui Chen*, Kaifu Gao*, Rui Wang* , Duc Duy Nguyen, and Guo-Wei Wei^†

   Annual Review of Biophysics 50(1) 1 2021
2. ChemSci

   Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies

   Jiahui Chen*, Kaifu Gao*, Rui Wang , and Guo-Wei Wei^†

   Chemical Science 12(20) 6929–6948 2021
3. CBM

   UMAP-assisted K-means clustering of large-scale SARS-CoV-2 mutation datasets

   Yuta Hozumi, Rui Wang , Changchuan Yin, and Guo-Wei Wei^†

   Computers in Biology and Medicine 131(20) 104264 2021
4. CIS

   SARS-CoV-2 becoming more infectious as revealed by algebraic topology and deep learning

   Jiahui Chen, Rui Wang , and Guo-Wei Wei^†

   Communications in Information and Systems 21(1) 31 2021
5. CommBio

   Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants

   Rui Wang , Jiahui Chen, Kaifu Gao, Yuta Hozumi, Changchuan Yin, and Guo-Wei Wei^†

   Communications Biology 4(1) 1–14 2021
6. JCIM

   GGL-Tox: geometric graph learning for toxicity prediction

   Jian Jiang, Rui Wang , and Guo-Wei Wei^†

   Journal of Chemical Information and Modeling 61(4) 1691–1700 2021
7. FoDS

   HERMES: Persistent spectral graph software

   Rui Wang , Rundong Zhao, Emily Ribando-Gros, Jiahui Chen, Yiying Tong^†, and Guo-Wei Wei^†

   Fondations of Data Science (Springfield, Mo.) 3(1) 67 2021
8. JMB

   Revealing the threat of emerging SARS-CoV-2 mutations to antibody therapies

   Jiahui Chen, Kaifu Gao, Rui Wang , and Guo-Wei Wei^†

   Journal of Molecular Biology 433(18) 167155 2021
9. Genomics

   Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries

   Rui Wang , Jiahui Chen, Kaifu Gao, and Guo-Wei Wei^†

   Genomics 113(4) 2158–2170 2021
10. arXiv

    Review of the mechanisms of SARS-CoV-2 evolution and transmission

    Jiahui Chen, Rui Wang , and Guo-Wei Wei^†

    ArXiv 113(4) 2158–2170 2021
11. JPCL

    Mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America

    Rui Wang , Jiahui Chen, and Guo-Wei Wei^†

    The Journal of Physical Chemistry Letters 12(49) 11850–11857 2021
12. JMC

    Perspectives on SARS-CoV-2 main protease inhibitors

    Kaifu Gao, Rui Wang , Jiahui Chen, Jetze J Tepe, Faqing Huang, and Guo-Wei Wei^†

    Journal of Medicinal Chemistry 64(23) 16922–16955 2021

2020

1. IJNMBE

   Persistent spectral graph

   Rui Wang , Duc Duy Nguyen, and Guo-Wei Wei^†

   International Journal for Numerical Methods in Biomedical Engineering 36(9) e3376 2020
2. JCIM

   Boosting tree-assisted multitask deep learning for small scientific datasets

   Jian Jiang, Rui Wang , Menglun Wang, Kaifu Gao, Duc Duy Nguyen, and Guo-Wei Wei^†

   Journal of Chemical Information and Modeling 60(3) 1235–1244 2020
3. BioRxiv

   Machine intelligence design of 2019-nCoV drugs

   Kaifu Gao, Duc Duy Nguyen, Rui Wang , and Guo-Wei Wei^†

   BioRxiv 60(3) 1235–1244 2020
4. JCIM

   Decoding SARS-CoV-2 transmission and evolution and ramifications for COVID-19 diagnosis, vaccine, and medicine

   Rui Wang , Yuta Hozumi, Changchuan Yin^†, and Guo-Wei Wei^†

   Journal of Chemical Information and Modeling 60(12) 5853–5865 2020
5. Genomics

   Mutations on COVID-19 diagnostic targets

   Rui Wang , Yuta Hozumi, Changchuan Yin^†, and Guo-Wei Wei^†

   Genomics 112(6) 5204–5213 2020
6. JPCL

   Repositioning of 8565 existing drugs for COVID-19

   Kaifu Gao, Duc Duy Nguyen, Jiahui Chen, Rui Wang , and Guo-Wei Wei^†

   The Journal of Physical Chemistry Letters 11(13) 5373–5382 2020
7. JMB

   Mutations strengthened SARS-CoV-2 infectivity

   Jiahui Chen, Rui Wang , Menglun Wang, and Guo-Wei Wei^†

   Journal of Molecular Biology 432(19) 5212–5226 2020
8. JPCL

   Decoding asymptomatic COVID-19 infection and transmission

   Rui Wang , Jiahui Chen, Yuta Hozumi, Changchuan Yin^†, and Guo-Wei Wei^†

   The Journal of Physical Chemistry Letters 11(23) 10007–10015 2020
9. Viruses

   Host immune response driving SARS-CoV-2 evolution

   Rui Wang , Yuta Hozumi, Yong-Hui Zheng, Changchuan Yin, and Guo-Wei Wei^†

   Viruses 12(10) 1095 2020
10. ChemSci

    Unveiling the molecular mechanism of SARS-CoV-2 main protease inhibition from 137 crystal structures using algebraic topology and deep learning

    Duc Duy Nguyen, Kaifu Gao, Jiahui Chen, Rui Wang , and Guo-Wei Wei^†

    Chemical Science 11(44) 12036–12046 2020

2019