Publications

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 2024
2. arXiv

   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

   ArXiv 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 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 2023
3. JCIM

   PLPCA: Persistent Laplacian Enhanced-PCA for Microarray Data Analysis

   Sean Cottrell, Rui Wang , and Guowei Wei

   Journal of Chemical Information and Modeling 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, and  others

   iScience 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 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 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 2022
4. arXiv

   Graph and Hodge Laplacians: Similarity and Difference

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

   arXiv preprint arXiv:2204.12218 2022
5. 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 2022
6. FoDS

   Persistent Path Laplacian

   Rui Wang , and Guo-Wei Wei

   Foundation of Data Science 2022
7. arXiv

   CCP: Correlated Clustering and Projection for Dimensionality Reduction

   Yuta Hozumi, Rui Wang , and Guo-Wei Wei

   arXiv preprint arXiv:2206.04189 2022
8. 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 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 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 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 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 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 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 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.) 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 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 2021
10. arXiv

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

    Jiahui Chen, Rui Wang , and Guo-Wei Wei

    ArXiv 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 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 2021

2020

1. IJNMBE

   Persistent spectral graph

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

   International Journal for Numerical Methods in Biomedical Engineering 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 2020
3. BioRxiv

   Machine intelligence design of 2019-nCoV drugs

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

   BioRxiv 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 2020
5. Genomics

   Mutations on COVID-19 diagnostic targets

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

   Genomics 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 2020
7. JMB

   Mutations strengthened SARS-CoV-2 infectivity

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

   Journal of Molecular Biology 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 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 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 2020

2019