Xiaoyong Pan

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 24

Top Topics

Binding Protein

Top Venues

Briefings in bioinformatics

Nature communications

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)
Yao Dai, Manja Idorn, Manutea C Serrero, Xiaoyong Pan, Emil Aagaard Thomsen, Ryo Narita, Muyesier Maimaitili, Xiaoqing Qian, Marie B Iversen, Line S Reinert, Rasmus K Flygaard, Muwan Chen, Xiangning Ding, Bao-Cun Zhang, Madalina E Carter-Timofte, Qing Lu, Zhuofan Jiang, Yiye Zhong, Shuhui Zhang, Lintai Da, Jinwei Zhu, Mark Denham, Poul Nissen, Trine Hyrup Mogensen, Jacob Giehm Mikkelsen, Shen-Ying Zhang, Jean-Laurent Casanova, Yujia Cai, Soren Riis Paludan
TMEFF1 is a neuron-specific restriction factor for herpes simplex virus. Nature 632 (8024) (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)
Yao Dai, Manja Idorn, Manutea C Serrero, Xiaoyong Pan, Emil Aagaard Thomsen, Ryo Narita, Muyesier Maimaitili, Xiaoqing Qian, Marie B Iversen, Line S Reinert, Rasmus K Flygaard, Muwan Chen, Xiangning Ding, Bao-Cun Zhang, Madalina E Carter-Timofte, Qing Lu, Zhuofan Jiang, Yiye Zhong, Shuhui Zhang, Lintai Da, Jinwei Zhu, Mark Denham, Poul Nissen, Trine Hyrup Mogensen, Jacob Giehm Mikkelsen, Shen-Ying Zhang, Jean-Laurent Casanova, Yujia Cai, Soren Riis Paludan
TMEFF1 is a neuron-specific restriction factor for herpes simplex virus. Nature 632 (8024) (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)
Yao Dai, Manja Idorn, Manutea C Serrero, Xiaoyong Pan, Emil Aagaard Thomsen, Ryo Narita, Muyesier Maimaitili, Xiaoqing Qian, Marie B Iversen, Line S Reinert, Rasmus K Flygaard, Muwan Chen, Xiangning Ding, Bao-Cun Zhang, Madalina E Carter-Timofte, Qing Lu, Zhuofan Jiang, Yiye Zhong, Shuhui Zhang, Lintai Da, Jinwei Zhu, Mark Denham, Poul Nissen, Trine Hyrup Mogensen, Jacob Giehm Mikkelsen, Shen-Ying Zhang, Jean-Laurent Casanova, Yujia Cai, Soren Riis Paludan
TMEFF1 is a neuron-specific restriction factor for herpes simplex virus. Nature (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)
Chunqiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen
Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network. Briefings in bioinformatics 24 (1) (2023)
Chunqiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen
Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network. Briefings in bioinformatics (2023)
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
Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network. Briefings in bioinformatics 24 (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)
Qunzhuo Wu, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Shitong Wang, Jing Wu, Dong-Jun Yu
MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction. Briefings in bioinformatics 23 (5) (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, 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)
Hui Li, Zhaohong Deng, Haitao Yang, Xiaoyong Pan, Zhisheng Wei, Hong-Bin Shen, Kup-Sze Choi, Lei Wang, Shitong Wang, Jing Wu
circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier. Briefings in bioinformatics (2021)
Yongxian Fan, Meijun Chen, Xiaoyong Pan
GCRFLDA: scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field. Briefings in bioinformatics (2021)
Xiaoyong Pan, Yi Fang, Xianfeng Li, Yang Yang, Hong-Bin Shen
RBPsuite: RNA-protein binding sites prediction suite based on deep learning. BMC genomics 21 (1) (2020)
Xiaoyong Pan, Yang Yang, Chun-Qiu Xia, Aashiq H Mirza, Hong-Bin Shen
Recent methodology progress of deep learning for RNA-protein interaction prediction. Wiley interdisciplinary reviews. RNA 10 (6) (2019)
Fei Yuan, Xiaoyong Pan, Lei Chen, Yu-Hang Zhang, Tao Huang, Yu-Dong Cai
Analysis of Protein-Protein Functional Associations by Using Gene Ontology and KEGG Pathway. BioMed research international 2019 (2019)