Xiaoyong Pan

Publication Activity (10 Years)

Years Active: 2012-2024
Publications (10 Years): 37

Top Topics

Subcellular Localization

Top Venues

Briefings Bioinform.

Publications

Bin Liu, Huiya Huang, Weixi Liao, Xiaoyong Pan, Cheng Jin, Ye Yuan
DeepSipred: A deep-learning-based approach on siRNA inhibition prediction. BIC (2024)
Hehe Wu, Xiaojian Liu, Yi Fang, Yang Yang, Yan Huang, Xiaoyong Pan, Hong-Bin Shen
Decoding protein binding landscape on circular RNAs with base-resolution transformer models. Comput. Biol. Medicine 171 (2024)
Yi Fang, Xiaoyong Pan, Hong-Bin Shen
drug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment. Bioinform. 39 (4) (2023)
Chun-Qiu 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 Bioinform. 24 (1) (2023)
Yongxian Fan, Guicong Sun, Xiaoyong Pan
ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (2) (2023)
Qunzhuo Wu, Zhaohong Deng, Wei Zhang, Xiaoyong Pan, Kup-Sze Choi, Yun Zuo, Hong-Bin Shen, Dong-Jun Yu
MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering. Bioinform. 39 (8) (2023)
Ye Yuan, Qushuo Chen, Jun Mao, Guipeng Li, Xiaoyong Pan
DG-Affinity: predicting antigen-antibody affinity with language models from sequences. BMC Bioinform. 24 (1) (2023)
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 Bioinform. 23 (1) (2022)
Yi Fang, Xiaoyong Pan, Hong-Bin Shen
Recent Deep Learning Methodology Development for RNA-RNA Interaction Prediction. Symmetry 14 (7) (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 Bioinform. 23 (5) (2022)
Yongxian Fan, Meijun Chen, Xiaoyong Pan
GCRFLDA: scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field. Briefings Bioinform. 23 (1) (2022)
Xiaoyong Pan, Lei Chen, Min Liu, Zhibin Niu, Tao Huang, Yu-Dong Cai
Identifying Protein Subcellular Locations With Embeddings-Based node2loc. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (2) (2022)
Jiachen Li, Siheng Chen, Xiaoyong Pan, Ye Yuan, Hong-Bin Shen
Cell clustering for spatial transcriptomics data with graph neural networks. Nat. Comput. Sci. 2 (6) (2022)
Nianzu Yang, Huaijin Wu, Junchi Yan, Xiaoyong Pan, Ye Yuan, Le Song
Molecule Generation for Drug Design: a Graph Learning Perspective. CoRR (2022)
Chun-Qiu 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 Comput. Biol. 18 (3) (2022)
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. Bioinform. 36 (21) (2021)
Yang Lin, Xiaoyong Pan, Hong-Bin Shen
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning. Bioinform. 37 (16) (2021)
Haitao Yang, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Lei Wang, Shitong Wang, Jing Wu
RNA-binding protein recognition based on multi-view deep feature and multi-label learning. Briefings Bioinform. 22 (3) (2021)
Hehe Wu, Xiaoyong Pan, Yang Yang, Hong-Bin Shen
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network. Briefings Bioinform. 22 (6) (2021)
Yu-Hang Zhang, Tao Zeng, Xiaoyong Pan, Wei Guo, Zijun Gan, Yunhua Zhang, Tao Huang, Yu-Dong Cai
Screening Dys-Methylation Genes and Rules for Cancer Diagnosis by Using the Pan-Cancer Study. IEEE Access 8 (2020)
Chun-Qiu Xia, Xiaoyong Pan, Hong-Bin Shen
Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data. Bioinform. 36 (10) (2020)
Xiaoyong Pan, Hong-Bin Shen
Scoring disease-microRNA associations by integrating disease hierarchy into graph convolutional networks. Pattern Recognit. 105 (2020)
Junchi Yan, Xiaoyong Pan, Liangda Li, Changsheng Li, Peng Cui, Chao Ma
IEEE Access Special Section: Sequential Data Modeling and Its Emerging Applications. IEEE Access 8 (2020)
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. J. Chem. Inf. Model. 60 (7) (2020)
Xiaoyong Pan, Yong-Xian Fan, Jue Jia, Hong-Bin Shen
Identifying RNA-binding proteins using multi-label deep learning. Sci. China Inf. Sci. 62 (1) (2019)
Yang Jiang, Xiaoyong Pan, Yu-Hang Zhang, Tao Huang, Yufei Gao
Gene Expression Difference Between Primary and Metastatic Renal Cell Carcinoma Using Patient-Derived Xenografts. IEEE Access 7 (2019)
Yong-Xian Fan, Yongzhen Li, Huihua Yang, Xiaoyong Pan
CNNPSP: Pseudouridine Sites Prediction Based on Deep Learning. IDEAL (1) (2019)
Zhi-Hai Zhang, Gemma Berenguer, Xiaoyong Pan
Location, inventory and testing decisions in closed-loop supply chains: A multimedia company. IISE Trans. 51 (1) (2019)
Lei Chen, Xiaoyong Pan, Tao Zeng, Yu-Hang Zhang, Tao Huang, Yu-Dong Cai
Identifying Essential Signature Genes and Expression Rules Associated With Distinctive Development Stages of Early Embryonic Cells. IEEE Access 7 (2019)
Xiaoyong Pan, Lars Juhl Jensen, Jan Gorodkin
Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles. Bioinform. 35 (9) (2019)
Xiaoyong Pan, Hong-Bin Shen
Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network. Neurocomputing 305 (2018)
Kaiming Zhang, Yiqun Xiao, Xiaoyong Pan, Yang Yang
Prediction of RNA-protein interactions with distributed feature representations and a hybrid deep model. ICIMCS (2018)
Zhen Cao, Xiaoyong Pan, Yang Yang, Yan Huang, Hong-Bin Shen
The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. Bioinform. 34 (13) (2018)
Xiaoyong Pan, Hong-Bin Shen
Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks. Bioinform. 34 (20) (2018)
Xiaoyong Pan, Hong-Bin Shen
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach. BMC Bioinform. 18 (1) (2017)
Xiaoyong Pan, Junchi Yan
Attention based convolutional neural network for predicting RNA-protein binding sites. CoRR (2017)
Alexander Junge, Jan C. Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan, Christian Anthon, Christian von Mering, Christopher T. Workman, Lars Juhl Jensen, Jan Gorodkin
RAIN: RNA-protein Association and Interaction Networks. Database J. Biol. Databases Curation 2017 (2017)
Xiaoyong Pan, Lin Zhu, Yong-Xian Fan, Junchi Yan
Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection. Comput. Biol. Chem. 53 (2014)
Xiaoyong Pan, Yanyan Du, Lian Wang, Chuntang Lei, Gang Zhou, Bing Zhou
Particle-Stabilized High Internal Phase Emulsions as Templates for Porous Nanocomposite Materials. ICDMA (2012)
Xiaoyong Pan, Jie Wang, Weihua Chen, Ling Peng, Yong Liu
Highly Efficient Method to Recover Silver from Discarded Plasma Display Panels. ICDMA (2012)
Hongcheng Li, Huajun Cao, Xiaoyong Pan
A carbon emission analysis model for electronics manufacturing process based on value-stream mapping and sensitivity analysis. Int. J. Comput. Integr. Manuf. 25 (12) (2012)