Shi‐Jie Chen

Also affiliated with University of Missouri, Chongqing Medical University

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 38 papers. Top paper: “Kinetic pathway of HIV-1 TAR cotranscriptional folding”.

Kinetic pathway of HIV-1 TAR cotranscriptional folding

Nucleic Acids Research(2024)10.1093/nar/gkae362

N/A

0.254DataRank · unranked

4 citations

Sicheng Zhang, Zhenwei Song, Xiao Heng, Shi‐Jie Chen, Lei Jin

Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer

Nucleic Acids Research(2020)10.1093/nar/gkaa494

N/A

0DataRank · unranked

65 citations

Dong Zhang, Liming Qiu, Sven Kruspe, L. Motlova, Petr Kolenko +9 more

Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction

Nucleic Acids Research(2020)10.1093/nar/gkaa463

N/A

0DataRank · unranked

22 citations

Shi‐Jie Chen, Xiaojun Xu

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

UNC Libraries(2020)10.17615/4xwy-qb25

N/A

0DataRank · unranked

19 citations

I. Tuszynska, J. Santalucia, Rhiju Das, F. Ding, P. Sripakdeevong +27 more

Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase

Nucleic Acids Research(2020)10.1093/nar/gkz1224

N/A

0DataRank · unranked

32 citations

Jie Zheng, Thomas Gremminger, Liming Qiu, Dong Zhang, Steve Tuske +8 more

Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability

Biophysical Journal(2020)10.1016/j.bpj.2020.07.042

N/A

0DataRank · unranked

10 citations

Dong Zhang, Yangwei Jiang, Shi‐Jie Chen, Chenhan Zhao

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

UNC Libraries(2020)10.17615/rh9e-gx23

N/A

0DataRank · unranked

5 citations

Janusz M. Bujnicki, Feng Ding, Greggory M. Rice, Wipapat Kladwang, J.J. Trausch +41 more

Cas9-specific immune responses compromise local and systemic AAV CRISPR therapy in multiple dystrophic canine models

Nature Communications(2021)10.1038/s41467-021-26830-7

N/A

0DataRank · unranked

171 citations

Sandeep Kumar, Dennis O. Pérez‐López, Nalinda B. Wasala, Dong Zhang, Yongping Yue +19 more

RNA–ligand molecular docking: Advances and challenges

Wiley Interdisciplinary Reviews Computational Molecular Science(2021)10.1002/wcms.1571

N/A

0DataRank · unranked

81 citations

Yangwei Jiang, Shi‐Jie Chen, Yuanzhe Zhou

RNA 3D Structure Prediction Using Coarse-Grained Models

Frontiers in Molecular Biosciences(2021)10.3389/fmolb.2021.720937

N/A

0DataRank · unranked

47 citations

Shi‐Jie Chen, Jun Li

RLDOCK method for predicting RNA-small molecule binding modes

Methods(2021)10.1016/j.ymeth.2021.01.009

N/A

0DataRank · unranked

26 citations

Shi‐Jie Chen, Yangwei Jiang

The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity

Nucleic Acids Research(2021)10.1093/nar/gkab342

N/A

0DataRank · unranked

24 citations

Thomas Gremminger, Gatikrushna Singh, Yi Cheng, Jun Li, Liming Qiu +8 more

Graph, pseudoknot, and SARS-CoV-2 genomic RNA: A biophysical synthesis

Biophysical Journal(2021)10.1016/j.bpj.2021.01.030

N/A

0DataRank · unranked

7 citations

Shi‐Jie Chen

SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction

Frontiers in Molecular Biosciences(2021)10.3389/fmolb.2021.721955

N/A

0DataRank · unranked

6 citations

Jun Li, Travis Hurst, Shi‐Jie Chen, Yuanzhe Zhou

Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences

Bioinformatics(2022)10.1093/bioinformatics/btac426

N/A

0DataRank · unranked

42 citations

Sicheng Zhang, Dong Zhang, Shi‐Jie Chen, Jun Li

Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions

Computational and Structural Biotechnology Journal(2022)10.1016/j.csbj.2022.11.007

N/A

0DataRank · unranked

23 citations

Damian Beasock, Yang Wang, Yao-Gen Shu, Jonathan D. Dinman, Tamar Schlick +13 more

RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling

Nucleic Acids Research(2023)10.1093/nar/gkad122

N/A

0DataRank · unranked

43 citations

Shi‐Jie Chen, Jun Li

Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15

Proteins Structure Function and Bioinformatics(2023)10.1002/prot.26583

N/A

0DataRank · unranked

23 citations

Sicheng Zhang, Shi‐Jie Chen, Jun Li

RNA-Puzzles Round V: blind predictions of 23 RNA structures

Nature Methods(2024)10.1038/s41592-024-02543-9

N/A

0DataRank · unranked

65 citations

Yagoub Adam, Ryszard W. Adamiak, Maciej Antczak, Belisa R. H. de Aquino, Nagendar Goud Badepally +94 more

mRNA vaccine sequence and structure design and optimization: Advances and challenges

Journal of Biological Chemistry(2024)10.1016/j.jbc.2024.108015

N/A

0DataRank · unranked

60 citations

Yuanzhe Zhou, Sicheng Zhang, Shi‐Jie Chen, Lei Jin

Machine learning in RNA structure prediction: Advances and challenges

Biophysical Journal(2024)10.1016/j.bpj.2024.01.026

N/A

0DataRank · unranked

30 citations

Jun Li, Shi‐Jie Chen, Sicheng Zhang

Advances in machine-learning approaches to RNA-targeted drug design

Artificial Intelligence Chemistry(2024)10.1016/j.aichem.2024.100053

N/A

0DataRank · unranked

20 citations

Shi‐Jie Chen, Yuanzhe Zhou

Propagation of a rapid cell-to-cell H2O2 signal over long distances in a monolayer of cardiomyocyte cells

Redox Biology(2024)10.1016/j.redox.2024.103069

N/A

0DataRank · unranked

9 citations

Linda Rowland, Thi Thao Nguyen, Shi‐Jie Chen, Ron Mittler, Yosef Fichman

SPRank─A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual Screening

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00681

N/A

0DataRank · unranked

9 citations

Yangwei Jiang, Shi‐Jie Chen, Yuanzhe Zhou

Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology

ACS Applied Bio Materials(2024)10.1021/acsabm.4c00432

N/A

0DataRank · unranked

8 citations

Laura P. Rebolledo, Elizabeth Skelly, Renata de Freitas Saito, Hui Wei, David M.J. Lilley +16 more

Modeling the reactive oxygen species (ROS) wave in Chlamydomonas reinhardtii colonies

Free Radical Biology and Medicine(2024)10.1016/j.freeradbiomed.2024.06.003

N/A

0DataRank · unranked

7 citations

Yosef Fichman, Sicheng Zhang, Ron Mittler, Shi‐Jie Chen, Yuanzhe Zhou

Embracing exascale computing in nucleic acid simulations

Current Opinion in Structural Biology(2024)10.1016/j.sbi.2024.102847

N/A

0DataRank · unranked

4 citations

Yuanzhe Zhou, Shi‐Jie Chen, Jun Li

smFRET-assisted RNA structure prediction

Communications in Information and Systems(2024)10.4310/cis.241021213225

N/A

0DataRank · unranked

1 citations

Nils G. Walter, Shi‐Jie Chen, Jun Li

Machine learning-inferred and energy landscape-guided analyses reveal kinetic determinants of CRISPR/Cas9 gene editing

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.30.591525

N/A

0DataRank · unranked

0 citations

Risi Liyanage, Dongsheng Duan, Shi‐Jie Chen, Lei Jin

Enhancing RNA 3D Structure Prediction in CASP16 : Integrating Physics‐Based Modeling With Machine Learning for Improved Predictions

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.26856

N/A

0DataRank · unranked

6 citations

Jun Li, Yuanzhe Zhou, Shi‐Jie Chen, Sicheng Zhang

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.70079

N/A

0DataRank · unranked

1 citations

Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki, Giovanni Bussi, Thomas E. Cheatham +46 more

Circulatory CCL2 distinguishes Duchenne muscular dystrophy dogs

Disease Models & Mechanisms(2025)10.1242/dmm.052137

N/A

0DataRank · unranked

1 citations

Matthew J. Burke, Chady H. Hakim, James Teixeira, Jin-Young Han, Yongping Yue +7 more

Computational modeling of cotranscriptional RNA folding

Computational and Structural Biotechnology Journal(2025)10.1016/j.csbj.2025.06.005

N/A

0DataRank · unranked

1 citations

Shi‐Jie Chen, Lei Jin

Template-based RNA structure prediction advanced through a blind code competition

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.30.696949

N/A

0DataRank · unranked

2 citations

Shujun He, Toshiyuki Oda, G Gangadhareswar Rao, Yehyun Kim, Raehyun Kim +54 more

Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.28.656632

N/A

0DataRank · unranked

1 citations

Adrien Chauvier, Serena S. Teh, Vincent A. Reed, Sicheng Zhang, Courtney E. Szyjka +4 more

Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch

Research Square(2025)10.21203/rs.3.rs-6999249/v1

N/A

0DataRank · unranked

0 citations

Rosa Romero Franco, Adrien Chauvier, Serena S. Teh, Vincent A. Reed, Sicheng Zhang +4 more

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

RNA(2020)10.1261/rna.075341.120

N/A

0DataRank · unranked

173 citations

Ryszard W. Adamiak, Maciej Antczak, M. Boniecki, Janusz M. Bujnicki, Shi‐Jie Chen +45 more

Blind prediction of complex water and ion ensembles around RNA in CASP16

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.03.685595

N/A

0DataRank · unranked

0 citations

Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki, Giovanni Bussi, Thomas E. Cheatham +46 more