Publications

† indicates equal contribution
Citations to these papers in Google Scholar; code/data freely available for various papers on GitHub and on GitHub(Vfold-RNA)

In press

  1. Harnessing Computational Approaches for RNA-Targeted Drug Discovery
    Yuanzhe Zhou, Shi-Jie Chen
    RNA and Nanomedicine, 2024
    DOI

2024

  1. RNA-Puzzles Round V: blind predictions of 23 RNA structures
    Fan Bu, Yagoub Adam, Ryszard W Adamiak, Maciej Antczak, Belisa Rebeca H de Aquino, Nagendar Goud Badepally, Robert T Batey, Eugene F Baulin, Pawel Boinski, Michal J Boniecki, Janusz M Bujnicki, Kristy A Carpenter, Jose Chacon, Shi-Jie Chen, Wah Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne K Dawson, Frank DiMaio, Feng Ding, Anne-Catherine Dock-Bregeon, Nikolay V Dokholyan, Ron O Dror, Stanisław Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Amiri Farsani, Adrian R Ferré-D’Amaré, Caleb Geniesse, George E Ghanim, Horacio V Guzman, Iris V Hood, Lin Huang, Dharm Skandh Jain, Farhang Jaryani, Lei Jin, Astha Joshi, Masha Karelina, Jeffrey S Kieft, Wipapat Kladwang, Sebastian Kmiecik, Deepak Koirala, Markus Kollmann, Rachael C Kretsch, Mateusz Kurciński, Jun Li, Shuang Li, Marcin Magnus, BenoÎt Masquida, S Naeim Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Hoang Duong Nguyen, Grigory Nikolaev, Chandran Nithin, Grace Nye, Iswarya PN Pandaranadar Jeyeram, Alberto Perez, Phillip Pham, Joseph A Piccirilli, Smita Priyadarshini Pilla, Radosław Pluta, Simón Poblete, Almudena Ponce-Salvatierra, Mariusz Popenda, Lukasz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzynska, Congzhou Mike Sha, Filip Stefaniak, Zhaoming Su, Krishna C Suddala, Marta Szachniuk, Raphael Townshend, Robert J Trachman, Jian Wang, Wenkai Wang, Andrew Watkins, Tomasz K Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph David Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Zok, Dong Zhang, Sicheng Zhang, Adriana Żyła, Eric Westhof, Zhichao Miao
    Nature Methods, 2024
    DOI

  2. mRNA vaccine sequence and structure design and optimization: Advances and challenges
    Lei Jin†, Yuanzhe Zhou†, Sicheng Zhang†, Shi-Jie Chen
    Journal of Biological Chemistry, 2024
    DOI

  3. Modeling the reactive oxygen species (ROS) wave in Chlamydomonas reinhardtii colonies
    Yuanzhe Zhou, Yosef Fichman, Sicheng Zhang, Ron Mittler, Shi-Jie Chen
    Free Radical Biology and Medicine, 2024
    DOI

  4. SPRank - A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual Screening
    Yuanzhe Zhou†, Yangwei Jiang†, Shi-Jie Chen
    Journal of chemical Theory and Computation, 2024
    DOI • GitHub • Presented at the American Chemical Society (ACS) national meeting, August 18-22, 2024

  5. Embracing exascale computing in nucleic acid simulations
    Jun Li, Yuanzhe Zhou, Shi-Jie Chen
    Current Opinion in Structural Biology, 2024
    DOI

  6. Advances in machine-learning approaches to RNA-targeted drug design
    Yuanzhe Zhou, Shi-Jie Chen
    Artificial Intelligence Chemistry, 2024
    DOI

2022

  1. An RNA aptamer that shifts the reduction potential of metabolic cofactors
    John S. Samuelian, Thomas J. Gremminger, Zhenwei Song, Raghav R. Poudyal, Jun Li, Yuanzhe Zhou, Seth A. Staller, Johan A. Carballo, Manami Roychowdhury-Saha, Shi-Jie Chen, Donald H. Burke, Xiao Heng, Dana A. Baum
    Nature Chemical Biology, 2022
    DOI

  2. RNA-ligand molecular docking: Advances and challenges
    Yuanzhe Zhou†, Yangwei Jiang†, Shi-Jie Chen
    Wiley Interdisciplinary Reviews: Computational Molecular Science, 2022
    DOI

  3. Graph deep learning locates magnesium ions in RNA
    Yuanzhe Zhou, Shi-Jie Chen
    QRB Discovery, 2022
    DOI • GitHub

2021

  1. Theoretical and Computational Modeling of RNA-Ligand Interactions
    Yuanzhe Zhou
    Doctoral dissertation, University of Missouri-Columbia, 2021

  2. SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction
    Yuanzhe Zhou, Jun Li, Travis Hurst, Shi-Jie Chen
    Frontiers in Molecular Biosciences, 2021
    DOI • Link

  3. A Bayes-inspired theory for optimally building an efficient coarse-grained folding force field
    Travis Hurst, Dong Zhang, Yuanzhe Zhou, Shi-Jie Chen
    Communications in Information and Systems, 2021
    DOI

2020

  1. RLDOCK: A New Method for Predicting RNA-Ligand Interactions
    Li-Zhen Sun, Yangwei Jiang, Yuanzhe Zhou, Shi-Jie Chen
    Journal of Chemical Theory and Computation, 2020
    DOI • GitHub

  2. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
    Zhichao Miao, Ryszard W. Adamiak, Maciej Antczak, Michał J. Boniecki, Janusz Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Yi Cheng, Fang-Chieh Chou, Rhiju Das, Nikolay V. Dokholyan, Feng Ding, Caleb Geniesse, Yangwei Jiang, Astha Joshi, Andrey Krokhotin, Marcin Magnus, Olivier Mailhot, Francois Major, Thomas H. Mann, Paweł Piątkowski, Radoslaw Pluta, Mariusz Popenda, Joanna Sarzynska, Lizhen Sun, Marta Szachniuk, Siqi Tian, Jian Wang, Jun Wang, Andrew M. Watkins, Jakub Wiedemann, Yi Xiao, Xiaojun Xu, Joseph D. Yesselman, Dong Zhang, Yi Zhang, Zhenzhen Zhang, Chenhan Zhao, Peinan Zhao, Yuanzhe Zhou, Tomasz Zok, Adriana Żyła, Aiming Ren, Robert T. Batey, Barbara L. Golden, Lin Huang, David M. Lilley, Yijin Liu, Dinshaw J. Patel, Eric Westhof
    RNA, 2020
    DOI

2019

  1. Predicting Monovalent Ion Correlation Effects in Nucleic Acids
    Li-Zhen Sun, Yuanzhe Zhou, Shi-Jie Chen
    ACS Omega, 2019
    DOI

  2. Analytical modeling and deep learning approaches to estimating RNA SHAPE reactivity from 3D structure
    Travis Hurst†, Yuanzhe Zhou†, Shi-Jie Chen
    Communications in Information and Systems, 2019
    DOI


© Yuanzhe Zhou,