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2020 – today
- 2024
[j35]Jiabei Cheng, Xiaoyong Pan, Yi Fang, Kaiyuan Yang, Yiming Xue, Qingran Yan, Ye Yuan:
GexMolGen: cross-modal generation of hit-like molecules via large language model encoding of gene expression signatures. Briefings Bioinform. 25(6) (2024)- [j34]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: 108175 (2024) - [c5]Bin Liu, Huiya Huang, Weixi Liao, Xiaoyong Pan, Cheng Jin, Ye Yuan:
DeepSipred: A deep-learning-based approach on siRNA inhibition prediction. BIC 2024 - [i3]Zhinuo Zhou, Peng Zhou, Xiaoyong Pan:
FLIER: Few-shot Language Image Models Embedded with Latent Representations. CoRR abs/2410.07648 (2024) - 2023
- [j33]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) - [j32]Yi Fang, Xiaoyong Pan, Hong-Bin Shen:
De novodrug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment. Bioinform. 39(4) (2023) - [j31]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) - [j30]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): 430 (2023) - [j29]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): 944-954 (2023) - 2022
- [j28]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) - [j27]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) - [j26]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) - [j25]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): 399-408 (2022) - [j24]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) - [j23]Yi Fang, Xiaoyong Pan, Hong-Bin Shen:
Recent Deep Learning Methodology Development for RNA-RNA Interaction Prediction. Symmetry 14(7): 1302 (2022) - [j22]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): 666-675 (2022) - [i2]Nianzu Yang, Huaijin Wu, Junchi Yan, Xiaoyong Pan, Ye Yuan, Le Song:
Molecule Generation for Drug Design: a Graph Learning Perspective. CoRR abs/2202.09212 (2022) - 2021
- [j21]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) - [j20]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) - [j19]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): 5159-5168 (2021) - [j18]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): 2308-2316 (2021) - 2020
- [j17]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: 489-501 (2020) - [j16]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: 210167-210170 (2020) - [j15]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): 3018-3027 (2020) - [j14]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): 3679-3686 (2020) - [j13]Xiaoyong Pan, Hong-Bin Shen:
Scoring disease-microRNA associations by integrating disease hierarchy into graph convolutional networks. Pattern Recognit. 105: 107385 (2020)
2010 – 2019
- 2019
- [j12]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: 128570-128578 (2019) - [j11]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: 142586-142594 (2019) - [j10]Xiaoyong Pan, Lars Juhl Jensen, Jan Gorodkin:
Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles. Bioinform. 35(9): 1494-1502 (2019) - [j9]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): 19103:1-19103:3 (2019) - [j8]Zhi-Hai Zhang, Gemma Berenguer, Xiaoyong Pan:
Location, inventory and testing decisions in closed-loop supply chains: A multimedia company. IISE Trans. 51(1): 41-56 (2019) - [c4]Yong-Xian Fan, Yongzhen Li, Huihua Yang, Xiaoyong Pan:
CNNPSP: Pseudouridine Sites Prediction Based on Deep Learning. IDEAL (1) 2019: 291-301 - 2018
- [j7]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): 2185-2194 (2018) - [j6]Xiaoyong Pan, Hong-Bin Shen:
Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks. Bioinform. 34(20): 3427-3436 (2018) - [j5]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: 51-58 (2018) - [c3]Kaiming Zhang, Yiqun Xiao, Xiaoyong Pan, Yang Yang:
Prediction of RNA-protein interactions with distributed feature representations and a hybrid deep model. ICIMCS 2018: 27:1-27:5 - 2017
- [j4]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: baw167 (2017) - [j3]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): 136:1-136:14 (2017) - [i1]Xiaoyong Pan, Junchi Yan:
Attention based convolutional neural network for predicting RNA-protein binding sites. CoRR abs/1712.02270 (2017) - 2014
- [j2]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: 324-330 (2014) - 2012
- [j1]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): 1102-1110 (2012) - [c2]Xiaoyong Pan, Jie Wang, Weihua Chen, Ling Peng, Yong Liu:
Highly Efficient Method to Recover Silver from Discarded Plasma Display Panels. ICDMA 2012: 471-476 - [c1]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: 602-607
Coauthor Index
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