Particle-Stabilized High Internal Phase Emulsions as Templates for Porous Nanocomposite Materials. - Xiaoyong Pan; Yanyan Du; Lian Wang; Chuntang Lei; Gang Zhou; Bing Zhou (ICDMA, 2012)

Highly Efficient Method to Recover Silver from Discarded Plasma Display Panels. - Xiaoyong Pan; Jie Wang; Weihua Chen; Ling Peng; Yong Liu (ICDMA, 2012)

A carbon emission analysis model for electronics manufacturing process based on value-stream mapping and sensitivity analysis. - Hongcheng Li; Huajun Cao; Xiaoyong Pan (Int. J. Comput. Integr. Manuf., 2012)

Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection. - Xiaoyong Pan; Lin Zhu; Yong-Xian Fan; Junchi Yan (Comput. Biol. Chem., 2014)

RAIN: RNA-protein Association and Interaction Networks. - 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 (Database J. Biol. Databases Curation, 2017)

RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach. - Xiaoyong Pan; Hong-Bin Shen (BMC Bioinform., 2017)

Attention based convolutional neural network for predicting RNA-protein binding sites. - Xiaoyong Pan; Junchi Yan (CoRR, 2017)

Prediction of RNA-protein interactions with distributed feature representations and a hybrid deep model. - Kaiming Zhang; Yiqun Xiao; Xiaoyong Pan; Yang Yang 030 (ICIMCS, 2018)

The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. - Zhen Cao; Xiaoyong Pan; Yang Yang 030; Yan Huang; Hong-Bin Shen (Bioinform., 2018)

Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks. - Xiaoyong Pan; Hong-Bin Shen (Bioinform., 2018)

Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network. - Xiaoyong Pan; Hong-Bin Shen (Neurocomputing, 2018)

CNNPSP: Pseudouridine Sites Prediction Based on Deep Learning. - Yong-Xian Fan; Yongzhen Li; Huihua Yang; Xiaoyong Pan (IDEAL (1), 2019)

Identifying Essential Signature Genes and Expression Rules Associated With Distinctive Development Stages of Early Embryonic Cells. - Lei Chen 007; Xiaoyong Pan; Tao Zeng 003; Yu-Hang Zhang; Tao Huang 004; Yu-Dong Cai 001 (IEEE Access, 2019)

Gene Expression Difference Between Primary and Metastatic Renal Cell Carcinoma Using Patient-Derived Xenografts. - Yang Jiang; Xiaoyong Pan; Yu-Hang Zhang; Tao Huang; Yufei Gao (IEEE Access, 2019)

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles. - Xiaoyong Pan; Lars Juhl Jensen; Jan Gorodkin (Bioinform., 2019)

Identifying RNA-binding proteins using multi-label deep learning. - Xiaoyong Pan; Yong-Xian Fan; Jue Jia; Hong-Bin Shen (Sci. China Inf. Sci., 2019)

Location, inventory and testing decisions in closed-loop supply chains: A multimedia company. - Zhi-Hai Zhang; Gemma Berenguer; Xiaoyong Pan (IISE Trans., 2019)

IEEE Access Special Section: Sequential Data Modeling and Its Emerging Applications. - Junchi Yan; Xiaoyong Pan; Liangda Li; Changsheng Li; Peng Cui; Chao Ma (IEEE Access, 2020)

Screening Dys-Methylation Genes and Rules for Cancer Diagnosis by Using the Pan-Cancer Study. - Yu-Hang Zhang; Tao Zeng 003; Xiaoyong Pan; Wei Guo 039; Zijun Gan; Yunhua Zhang; Tao Huang 004; Yu-Dong Cai 001 (IEEE Access, 2020)

Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data. - Chun-Qiu Xia; Xiaoyong Pan; Hong-Bin Shen (Bioinform., 2020)

Signal-3L 3.0: Improving Signal Peptide Prediction through Combining Attention Deep Learning with Window-Based Scoring. - Wei-Xun Zhang; Xiaoyong Pan; Hong-Bin Shen (J. Chem. Inf. Model., 2020)

Scoring disease-microRNA associations by integrating disease hierarchy into graph convolutional networks. - Xiaoyong Pan; Hong-Bin Shen (Pattern Recognit., 2020)

Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network. - Hehe Wu; Xiaoyong Pan; Yang Yang 030; Hong-Bin Shen (Briefings Bioinform., 2021)

RNA-binding protein recognition based on multi-view deep feature and multi-label learning. - Haitao Yang; Zhaohong Deng; Xiaoyong Pan; Hong-Bin Shen; Kup-Sze Choi; Lei Wang; Shitong Wang 001; Jing Wu 030 (Briefings Bioinform., 2021)

lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning. - Yang Lin; Xiaoyong Pan; Hong-Bin Shen (Bioinform., 2021)

ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity. - Xiaoyong Pan; Jasper Zuallaert; Xi Wang; Hong-Bin Shen; Elda Posada Campos; Denys O. Marushchak; Wesley De Neve (Bioinform., 2021)

GCRFLDA: scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field. - Yongxian Fan; Meijun Chen; Xiaoyong Pan (Briefings Bioinform., 2022)

circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier. - Hui Li; Zhaohong Deng; Haitao Yang; Xiaoyong Pan; Zhisheng Wei; Hong-Bin Shen; Kup-Sze Choi; Lei Wang; Shitong Wang 001; Jing Wu 030 (Briefings Bioinform., 2022)

MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction. - Qunzhuo Wu; Zhaohong Deng; Xiaoyong Pan; Hong-Bin Shen; Kup-Sze Choi; Shitong Wang 001; Jing Wu 030; Dong-Jun Yu (Briefings Bioinform., 2022)

Molecule Generation for Drug Design: a Graph Learning Perspective. - Nianzu Yang; Huaijin Wu; Junchi Yan; Xiaoyong Pan; Ye Yuan; Le Song (CoRR, 2022)

Cell clustering for spatial transcriptomics data with graph neural networks. - Jiachen Li; Siheng Chen; Xiaoyong Pan; Ye Yuan; Hong-Bin Shen (Nat. Comput. Sci., 2022)

Fast protein structure comparison through effective representation learning with contrastive graph neural networks. - Chun-Qiu Xia; Shi-Hao Feng; Ying Xia; Xiaoyong Pan; Hong-Bin Shen (PLoS Comput. Biol., 2022)

Recent Deep Learning Methodology Development for RNA-RNA Interaction Prediction. - Yi Fang; Xiaoyong Pan; Hong-Bin Shen (Symmetry, 2022)

Identifying Protein Subcellular Locations With Embeddings-Based node2loc. - Xiaoyong Pan; Lei Chen 007; Min Liu 020; Zhibin Niu; Tao Huang 004; Yu-Dong Cai 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites. - Yongxian Fan; Guicong Sun; Xiaoyong Pan (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network. - Chun-Qiu Xia; Shi-Hao Feng; Ying Xia; Xiaoyong Pan; Hong-Bin Shen (Briefings Bioinform., 2023)

De novodrug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment. - Yi Fang; Xiaoyong Pan; Hong-Bin Shen (Bioinform., 2023)

MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering. - Qunzhuo Wu; Zhaohong Deng; Wei Zhang 221; Xiaoyong Pan; Kup-Sze Choi; Yun Zuo 001; Hong-Bin Shen; Dong-Jun Yu (Bioinform., 2023)

DG-Affinity: predicting antigen-antibody affinity with language models from sequences. - Ye Yuan; Qushuo Chen; Jun Mao; Guipeng Li; Xiaoyong Pan (BMC Bioinform., 2023)

RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs. - Yichong Li; Xiaojian Liu; Fan Cheng; Xiaoyong Pan; Yang Yang 030 (BIBM, 2024)

DeepSipred: A deep-learning-based approach on siRNA inhibition prediction. - Bin Liu; Huiya Huang; Weixi Liao; Xiaoyong Pan; Cheng Jin; Ye Yuan (BIC, 2024)

GexMolGen: cross-modal generation of hit-like molecules via large language model encoding of gene expression signatures. - Jiabei Cheng; Xiaoyong Pan; Yi Fang; Kaiyuan Yang 009; Yiming Xue; Qingran Yan; Ye Yuan (Briefings Bioinform., 2024)

Predicting transcriptional changes induced by molecules with MiTCP. - Kaiyuan Yang 009; Jiabei Cheng; Shenghao Cao; Xiaoyong Pan; Hong-Bin Shen; Ye Yuan (Briefings Bioinform., 2024)

Decoding protein binding landscape on circular RNAs with base-resolution transformer models. - Hehe Wu; Xiaojian Liu; Yi Fang; Yang Yang 030; Yan Huang; Xiaoyong Pan; Hong-Bin Shen (Comput. Biol. Medicine, 2024)

FLIER: Few-shot Language Image Models Embedded with Latent Representations. - Zhinuo Zhou; Peng Zhou; Xiaoyong Pan (CoRR, 2024)

ProtDAT: A Unified Framework for Protein Sequence Design from Any Protein Text Description. - Xiao-Yu Guo; Yi-Fan Li; Yuan Liu; Xiaoyong Pan; Hong-Bin Shen (CoRR, 2024)

DRAG: design RNAs as hierarchical graphs with reinforcement learning. - Yichong Li; Xiaoyong Pan; Hongbin Shen; Yang Yang 030 (Briefings Bioinform., 2025)

Explainable RNA-Small Molecule Binding Affinity Prediction Based on Multiview Enhancement Learning. - Zeyu Wu; Zhaohong Deng; Qunzhuo Wu; Yun Zuo 001; Xiaoyong Pan; Hongbin Shen; Xingze Fang; Yuxi Ge; Shudong Hu (J. Chem. Inf. Model., 2025)

Discovering the nuclear localization signal universe through a deep learning model with interpretable attention units. - Yi-Fan Li; Xiaoyong Pan; Hong-Bin Shen (Patterns, 2025)

Loc4Lnc: Accurate prediction of long noncoding RNA subcellular localization via enhanced RNA sequence representation. - Yujia Cheng; Xiaoyong Pan; Yang Yang (Quant. Biol., 2025)

Modeling enzyme temperature stability from sequence segment perspective. - Ziqi Zhang; Shiheng Chen; Runze Yang; Zhisheng Wei; Wei Zhang 221; Lei Wang; Zhanzhi Liu; Fengshan Zhang; Jing Wu 030; Xiaoyong Pan; Hongbin Shen; Longbing Cao; et al. (CoRR, 2025)