Hong-Bin Shen

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 22

Top Topics

Electron Microscopy

Top Venues

Nature communications

Journal of chemical information and modeling

Bioinformatics (Oxford, England)

Nature computational science

This page only lists publications with an associated author ORCID identifier.

Publications

Jiachen Li, Xiaoyong Pan, Ye Yuan, Hong-Bin Shen
TFvelo: gene regulation inspired RNA velocity estimation. Nature communications 15 (1) (2024)
Jiachen Li, Xiaoyong Pan, Ye Yuan, Hong-Bin Shen
TFvelo: gene regulation inspired RNA velocity estimation. Nature communications 15 (1) (2024)
Jiachen Li, Xiaoyong Pan, Ye Yuan, Hong-Bin Shen
TFvelo: gene regulation inspired RNA velocity estimation. Nature communications 15 (1) (2024)
Jiachen Li, Xiaoyong Pan, Ye Yuan, Hong-Bin Shen
TFvelo: gene regulation inspired RNA velocity estimation. Nature communications 15 (1) (2024)
Jiachen Li, Xiaoyong Pan, Ye Yuan, Hong-Bin Shen
TFvelo: gene regulation inspired RNA velocity estimation. Nature communications 15 (1) (2024)
Hailong Yang, Yue Chen, Yun Zuo, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Dong-Jun Yu
MINDG: a drug-target interaction prediction method based on an integrated learning algorithm. Bioinformatics (Oxford, England) 40 (4) (2024)
Yuxuan Wang, Ying Xia, Junchi Yan, Ye Yuan, Hong-Bin Shen, Xiaoyong Pan
ZeroBind: a protein-specific zero-shot predictor with subgraph matching for drug-target interactions. Nature communications 14 (1) (2023)
Chunqiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen
Fast protein structure comparison through effective representation learning with contrastive graph neural networks. PLoS computational biology 18 (3) (2022)
Jiachen Li, Siheng Chen, Xiaoyong Pan, Ye Yuan, Hong-Bin Shen
Cell clustering for spatial transcriptomics data with graph neural networks. Nature computational science 2 (6) (2022)
Jin-Xian Hu, Yang Yang, Ying-Ying Xu, Hong-Bin Shen
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images. Bioinformatics (Oxford, England) 38 (21) (2022)
Jiachen Li, Siheng Chen, Xiaoyong Pan, Ye Yuan, Hong-Bin Shen
Cell clustering for spatial transcriptomics data with graph neural networks. Nature computational science 2 (6) (2022)
Ying Xia, Chunqiu Xia, Xiaoyong Pan, Hong-Bin Shen
BindWeb: A web server for ligand binding residue and pocket prediction from protein structures. Protein science : a publication of the Protein Society 31 (12) (2022)
Yu-Xuan Chen, Rui Xie, Yang Yang, Lin He, Dagan Feng, Hong-Bin Shen
Fast Cryo-EM Image Alignment Algorithm Using Power Spectrum Features. Journal of chemical information and modeling 61 (9) (2021)
Biao Zhang, Wenyi Zhang, Robin Pearce, Yang Zhang, Hong-Bin Shen
Fitting Low-Resolution Protein Structures into Cryo-EM Density Maps by Multiobjective Optimization of Global and Local Correlations. The journal of physical chemistry. B 125 (2) (2021)
Ying Xia, Chun-Qiu Xia, Xiaoyong Pan, Hong-Bin Shen
GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues. Nucleic acids research 49 (9) (2021)
Xiaoyong Pan, Jasper Zuallaert, Xi Wang, Hong-Bin Shen, Elda Posada Campos, Denys O Marushchak, Wesley De Neve
ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity. Bioinformatics (Oxford, England) 36 (21) (2021)
Wei-Xun Zhang, Xiaoyong Pan, Hong-Bin Shen
Signal-3L 3.0: Improving Signal Peptide Prediction through Combining Attention Deep Learning with Window-Based Scoring. Journal of chemical information and modeling 60 (7) (2020)
Rui Xie, Yu-Xuan Chen, Jia-Ming Cai, Yang Yang, Hong-Bin Shen
SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment. Journal of chemical information and modeling 60 (5) (2020)
Shuo Yin, Biao Zhang, Yang Yang, Yan Huang, Hong-Bin Shen
Clustering Enhancement of Noisy Cryo-Electron Microscopy Single-Particle Images with a Network Structural Similarity Metric. Journal of chemical information and modeling 59 (4) (2019)
Yang Yang, Qingwei Fang, Hong-Bin Shen
Predicting gene regulatory interactions based on spatial gene expression data and deep learning. PLoS computational biology 15 (9) (2019)
Yu-Jiao Yang, Shuai Wang, Biao Zhang, Hong-Bin Shen
Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis. Journal of chemical information and modeling 58 (6) (2018)
Yi-Ze Zhang, Hong-Bin Shen
Signal-3L 2.0: A Hierarchical Mixture Model for Enhancing Protein Signal Peptide Prediction by Incorporating Residue-Domain Cross-Level Features. Journal of chemical information and modeling 57 (4) (2017)