Xiaoyong Pan

发表

Identification of the copy number variant biomarkers for breast cancer subtypes

Xiaoyong Pan, Lei Chen, Tao Huang, 2018, Molecular Genetics and Genomics.

Hybrid deep learning for predicting hypertensive disorder onset using temporal and non-temporal data

Xiaoyong Pan, P. Rijnbeek, 2017 .

Inferring Disease-Associated MicroRNAs Using Semi-supervised Multi-Label Graph Convolutional Networks

Hongbin Shen, Xiaoyong Pan, 2019, iScience.

OUGENE: a disease associated over-expressed and under-expressed gene database

Hongbin Shen, Xiaoyong Pan, 2016 .

Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks

Junchi Yan, Hongbin Shen, Xiaoyong Pan, 2017, BMC Genomics.

Adaptive compressive learning for prediction of protein-protein interactions from primary sequence.

Hong-Bin Shen, Hongbin Shen, Xiaoyong Pan, 2011, Journal of theoretical biology.

WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA

Jan Gorodkin, Lars Juhl Jensen, Xiaoyong Pan, 2018, Genes.

Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection

Xiaoyong Pan, Lei Chen, Tao Huang, 2017, Zeitschrift für Induktive Abstammungs- und Vererbungslehre.

Recent methodology progress of deep learning for RNA–protein interaction prediction

Hong-Bin Shen, Xiaoyong Pan, Yang Yang, 2019, Wiley interdisciplinary reviews. RNA.

Identification of Protein Subcellular Localization With Network and Functional Embeddings

Tao Zeng, Yu-Dong Cai, Tao Huang, 2021, Frontiers in Genetics.

Identifying the RNA signatures of coronary artery disease from combined lncRNA and mRNA expression profiles.

Tao Zeng, Yu-Dong Cai, Tao Huang, 2020, Genomics.

Investigating the gene expression profiles of cells in seven embryonic stages with machine learning algorithms.

Yu-Dong Cai, Tao Huang, Lei Chen, 2020, Genomics.

Identifying Cell-Type Specific Genes and Expression Rules Based on Single-Cell Transcriptomic Atlas Data

Tao Zeng, Yu-Dong Cai, Tao Huang, 2020, Frontiers in Bioengineering and Biotechnology.

New computational tool based on machine-learning algorithms for the identification of rhinovirus infection-related genes.

Xiaoyong Pan, Tao Huang, Yu-Dong Cai, 2019, Combinatorial chemistry & high throughput screening.

Identifying Methylation Pattern and Genes Associated with Breast Cancer Subtypes

Xiaoyong Pan, Lei Chen, Tao Huang, 2019, International journal of molecular sciences.

Primary Tumor Site Specificity is Preserved in Patient-Derived Tumor Xenograft Models

Xiaohua Hu, Xiaoyong Pan, Lei Chen, 2019, Front. Genet..

Analysis of Protein–Protein Functional Associations by Using Gene Ontology and KEGG Pathway

Yu-Dong Cai, Tao Huang, Lei Chen, 2019, BioMed research international.

Copy Number Variation Pattern for Discriminating MACROD2 States of Colorectal Cancer Subtypes

Tao Zeng, Yu-Dong Cai, Tao Huang, 2019, Front. Bioeng. Biotechnol..

Screening of Methylation Signature and Gene Functions Associated With the Subtypes of Isocitrate Dehydrogenase-Mutation Gliomas

Tao Zeng, Yu-Dong Cai, Tao Huang, 2019, Front. Bioeng. Biotechnol..

Identification of the Gene Expression Rules That Define the Subtypes in Glioma

Xiaoyong Pan, Lei Chen, Tao Huang, 2018, Journal of clinical medicine.

HIV infection alters the human epigenetic landscape

Xiaoyong Pan, Lei Chen, Tao Huang, 2018, Gene Therapy.

Tissue Expression Difference between mRNAs and lncRNAs

Xiaoyong Pan, Lei Chen, Tao Huang, 2018, International journal of molecular sciences.

Tissue differences revealed by gene expression profiles of various cell lines

Xiaoyong Pan, Lei Chen, Tao Huang, 2018, Journal of cellular biochemistry.

Inferring Disease-Associated MicroRNAs Using Semi-supervised Multi-Label Graph Convolutional Networks

Hongbin Shen, Xiaoyong Pan, 2019, bioRxiv.

Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features.

Hongbin Shen, Xiaoyong Pan, Ya-Nan Zhang, 2010, Journal of proteome research.

Inferring novel genes related to oral cancer with a network embedding method and one-class learning algorithms

Yu-Dong Cai, Tao Huang, Lei Chen, 2019, Gene Therapy.

IEEE Access Special Section: Sequential Data Modeling and Its Emerging Applications

Changsheng Li, Junchi Yan, Chao Ma, 2020, IEEE Access.

Identification of Type 2 Diabetes Biomarkers From Mixed Single-Cell Sequencing Data With Feature Selection Methods

Xiaoyong Pan, Zhandong Li, Yunpeng Cai, 2022, Frontiers in Bioengineering and Biotechnology.

Alternative Polyadenylation Modification Patterns Reveal Essential Posttranscription Regulatory Mechanisms of Tumorigenesis in Multiple Tumor Types

Tao Zeng, Yu-Dong Cai, Tao Huang, 2020, BioMed research international.

Recent Deep Learning Methodology Development for RNA-RNA Interaction Prediction

Hongbin Shen, Xiaoyong Pan, Yi Fang, 2022, Symmetry.

Identifying Functions of Proteins in Mice With Functional Embedding Features

Tao Huang, Lei Chen, Hao Li, 2022, Frontiers in Genetics.

A Novel Fusion Strategy for E-MAP Missing Value Imputation

Hongbin Shen, Xiaoyong Pan, Lixiu Yao, 2011 .

Identification of cortical interneuron cell markers in mouse embryos based on machine learning analysis of single-cell transcriptomics

Tao Huang, Lei Chen, Yu-Hang Zhang, 2022, Frontiers in neuroscience.

OUGene 2.0: An updated disease-associated over- and under-expressed gene database by mining full-text articles

Hongbin Shen, Xiaoyong Pan, Erdi Qin, 2022, bioRxiv.

Leveraging Scaffold Information to Predict Protein-ligand Binding Affinity with an Empirical Graph Neural Network

Hongbin Shen, Xiaoyong Pan, Chun-Qiu Xia, 2022, bioRxiv.

MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction

Zhaohong Deng, K. Choi, Shitong Wang, 2022, Briefings Bioinform..

CRIP: predicting circRNA – RBP-binding sites using a codon-based encoding and hybrid deep neural networks

Hongbin Shen, Xiaoyong Pan, Yang Yang, 2019 .

Identifying Protein Subcellular Locations With Embeddings-Based node2loc

Yu-Dong Cai, Tao Huang, Lei Chen, 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

LabCaS for Ranking Potential Calpain Substrate Cleavage Sites from Amino Acid Sequence.

Yang Zhang, Hongbin Shen, Xiaoyong Pan, 2019, Methods in molecular biology.

RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach

Hongbin Shen, Xiaoyong Pan, 2016, bioRxiv.

Transcriptomic landscape of lncRNAs in inflammatory bowel disease

J. Gorodkin, F. Pociot, S. Seemann, 2015, Genome Medicine.

BindWeb: A web server for ligand binding residue and pocket prediction from protein structures

Hongbin Shen, Xiaoyong Pan, Chun-Qiu Xia, 2022, Protein science : a publication of the Protein Society.

Immunosignature Screening for Multiple Cancer Subtypes Based on Expression Rule

Lei Chen, XiaoYong Pan, Tao Zeng, 2019, Front. Bioeng. Biotechnol..

Analysis of Expression Pattern of snoRNAs in Different Cancer Types with Machine Learning Algorithms

Lei Chen, Tao Huang, Yu-Dong Cai, 2019, International journal of molecular sciences.

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles

Jan Gorodkin, Lars Juhl Jensen, Xiaoyong Pan, 2018, Bioinform..

lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning

Hong-Bin Shen, Xiaoyong Pan, Yang Lin, 2021, Bioinform..

The lncLocator: a subcellular localization predictor for long non‐coding RNAs based on a stacked ensemble classifier

Zhen Cao, Yan Huang, Hong-Bin Shen, 2018, Bioinform..

Gene expression differences among different MSI statuses in colorectal cancer

Xiaoyong Pan, Lei Chen, Tao Huang, 2018, International journal of cancer.

Identifying Patients with Atrioventricular Septal Defect in Down Syndrome Populations by Using Self-Normalizing Neural Networks and Feature Selection

Xiaohua Hu, Xiaoyong Pan, Yu Hang Zhang, 2018, Genes.

IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction

Hong-Bin Shen, Junchi Yan, Yong-Xian Fan, 2016, BMC Genomics.

Transcriptomic landscape of lncRNAs in inflammatory bowel disease

Jan Gorodkin, Xiaoyong Pan, Stefan E Seemann, 2015, Genome Medicine.

Classification of Widely and Rarely Expressed Genes with Recurrent Neural Network

Yu-Dong Cai, Tao Huang, Lei Chen, 2018, Computational and structural biotechnology journal.

PredcircRNA: computational classification of circular RNA from other long non-coding RNA using hybrid features.

Xiaoyong Pan, Xiaoyong Pan, K. Xiong, 2015, Molecular bioSystems.

Gene Expression Difference Between Primary and Metastatic Renal Cell Carcinoma Using Patient-Derived Xenografts

Xiaoyong Pan, Tao Huang, Yang Jiang, 2019, IEEE Access.

Recognizing Pattern and Rule of Mutation Signatures Corresponding to Cancer Types

Tao Zeng, Yu-Dong Cai, Tao Huang, 2021, Frontiers in Cell and Developmental Biology.

GCRFLDA: scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field

Xiaoyong Pan, Yongxian Fan, Meijun Chen, 2021, Briefings Bioinform..

Lentiviral delivery of co-packaged Cas9 mRNA and a Vegfa-targeting guide RNA prevents wet age-related macular degeneration in mice

Xiaodong Sun, S. Paludan, Xiaoyong Pan, 2021, Nature Biomedical Engineering.

Lentiviral delivery of co-packaged Cas9 mRNA and a Vegfa-targeting guide RNA prevents wet age-related macular degeneration in mice

Xiaodong Sun, S. Paludan, Xiaoyong Pan, 2021, Nature Biomedical Engineering.

Predicting RNA‐protein binding sites and motifs through combining local and global deep convolutional neural networks

Hong-Bin Shen, Xiaoyong Pan, Hongbin Shen, 2018, Bioinform..

Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks

Junchi Yan, Hongbin Shen, Xiaoyong Pan, 2017, bioRxiv.

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

Jan Gorodkin, Lars Juhl Jensen, Anne Wenzel, 2018, PloS one.

RAIN: RNA–protein Association and Interaction Networks

Christian von Mering, Jan Gorodkin, Lars Juhl Jensen, 2017, Database J. Biol. Databases Curation.

Distinguishing Glioblastoma Subtypes by Methylation Signatures

Tao Zeng, Yu-Dong Cai, Tao Huang, 2020, Frontiers in Genetics.

Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network

Hong-Bin Shen, Xiaoyong Pan, Hongbin Shen, 2018, Neurocomputing.

Analysis of Gene Expression Differences between Different Pancreatic Cells

Yu-Dong Cai, Tao Huang, Lei Chen, 2019, ACS Omega.

Signal-3L 3.0: Improving Signal Peptide Prediction through Combining Attention Deep Learning with Window-Based Scoring

Hong-Bin Shen, Xiaoyong Pan, Wei-Xun Zhang, 2020, J. Chem. Inf. Model..

Towards better accuracy for missing value estimation of epistatic miniarray profiling data by a novel ensemble approach.

Hong-Bin Shen, Hongbin Shen, Xiaoyong Pan, 2011, Genomics.

Cell clustering for spatial transcriptomics data with graph neural networks

Siheng Chen, Hongbin Shen, Xiaoyong Pan, 2022, Nature Computational Science.

Predicting protein subcellular location with network embedding and enrichment features.

Lin Lu, Xiaoyong Pan, Yu-Dong Cai, 2020, Biochimica et biophysica acta. Proteins and proteomics.

Identification of Gene Signatures and Expression Patterns During Epithelial-to-Mesenchymal Transition From Single-Cell Expression Atlas

Xiangtian Yu, Yu-Dong Cai, Tao Huang, 2021, Frontiers in Genetics.

Screening Dys-Methylation Genes and Rules for Cancer Diagnosis by Using the Pan-Cancer Study

Tao Huang, Tao Zeng, Xiaoyong Pan, 2020, IEEE Access.

Prediction of RNA-protein interactions with distributed feature representations and a hybrid deep model

Xiaoyong Pan, Yang Yang, Kaiming Zhang, 2018, ICIMCS '18.

CRIP: predicting circRNA–RBP-binding sites using a codon-based encoding and hybrid deep neural networks

Hong-Bin Shen, Yang Yang, Xiaoyong Pan, 2019, RNA.

Predicting circRNA-RBP interaction sites using a codon-based encoding and hybrid deep neural networks

Hong-Bin Shen, Yang Yang, Xiaoyong Pan, 2018, bioRxiv.

Robust prediction of B-factor profile from sequence using two-stage SVR based on random forest feature selection.

Hong-Bin Shen, Xiao-Yong Pan, Hongbin Shen, 2009, Protein and peptide letters.

Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data

Hong-Bin Shen, Xiaoyong Pan, Chun-Qiu Xia, 2020, Bioinform..

LigBind: identifying binding residues for over 1000 ligands with relation-aware graph neural networks.

Hongbin Shen, Xiaoyong Pan, Ying Xia, 2023, Journal of molecular biology.

GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues

Hongbin Shen, Xiaoyong Pan, Chun-Qiu Xia, 2021, Nucleic acids research.

RNA-binding protein recognition based on multi-view deep feature and multi-label learning

Zhaohong Deng, Kup-Sze Choi, Shitong Wang, 2020, Briefings Bioinform..

Molecule Generation for Drug Design: a Graph Learning Perspective

Junchi Yan, Xiaoyong Pan, Ye Yuan, 2022, ArXiv.

EchoAI: A deep-learning based model for classification of echinoderms in global oceans

Hongbin Shen, Peng Zhou, Xue-Wei Xu, 2023, Frontiers in Marine Science.

circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier

Zhaohong Deng, K. Choi, Shitong Wang, 2021, Briefings Bioinform..

Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection

Yu-Dong Cai, Tao Huang, Lei Chen, 2018, Molecular Genetics and Genomics.

RBPsuite: RNA-protein binding sites prediction suite based on deep learning

Hongbin Shen, Xiaoyong Pan, Yang Yang, 2020, BMC Genomics.

Identification of the copy number variant biomarkers for breast cancer subtypes

Yu-Dong Cai, Tao Huang, Lei Chen, 2018, Molecular Genetics and Genomics.

ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity

Hong-Bin Shen, Wesley De Neve, Xiaoyong Pan, 2020, Bioinform..

Fast protein structure comparison through effective representation learning with contrastive graph neural networks

Hongbin Shen, Xiaoyong Pan, Chun-Qiu Xia, 2022, PLoS Comput. Biol..

Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection

Junchi Yan, Yong-Xian Fan, Xiaoyong Pan, 2014, Comput. Biol. Chem..

Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network

Hong-Bin Shen, Hehe Wu, Yang Yang, 2021, Briefings Bioinform..

Investigation and Prediction of Human Interactome Based on Quantitative Features

Kaiyan Feng, Tao Huang, Lei Chen, 2020, Frontiers in Bioengineering and Biotechnology.

Predicting protein subcellular location using learned distributed representations from a protein-protein network

Lei Chen, Tao Huang, Min Liu, 2019, bioRxiv.

Identifying Essential Signature Genes and Expression Rules Associated With Distinctive Development Stages of Early Embryonic Cells

Tao Huang, Tao Zeng, Xiaoyong Pan, 2019, IEEE Access.

Recent Progresses of Computational Analysis of RNA-Protein Interactions

Hongbin Shen, Xiaoyong Pan, Yang Yang, 2021 .

CNNPSP: Pseudouridine Sites Prediction Based on Deep Learning

Yongzhen Li, Yong-Xian Fan, Xiaoyong Pan, 2019, IDEAL.

Inferring novel genes related to oral cancer with a network embedding method and one-class learning algorithms

Yu-Dong Cai, Tao Huang, Lei Chen, 2019, Gene Therapy.

ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites

Xiaoyong Pan, Yongxian Fan, Guicong Sun, 2022, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

TFvelo: gene regulation inspired RNA velocity estimation

Hongbin Shen, Xiaoyong Pan, Ye Yuan, 2023, bioRxiv.

Fusing Multiple Biological Networks to Effectively Predict miRNA-disease Associations

Xiaoyong Pan, Qingqi Zhu, Yong-Xian Fan, 2020, Current Bioinformatics.

Scoring disease-microRNA associations by integrating disease hierarchy into graph convolutional networks

Hong-Bin Shen, Xiaoyong Pan, Hongbin Shen, 2020, Pattern Recognit..

Protein Structure Refinement Using Multi-Objective Particle Swarm Optimization with Decomposition Strategy

Hongbin Shen, Di Wang, Xiaoyong Pan, 2021, International journal of molecular sciences.

RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach

Hong-Bin Shen, Xiaoyong Pan, Hongbin Shen, 2016, BMC Bioinformatics.

Decoding protein binding landscape on circular RNAs with base-resolution Transformer models

Hongbin Shen, Xiaoyong Pan, Yang Yang, 2022, bioRxiv.

TFvelo: gene regulation inspired RNA velocity estimation

Hongbin Shen, Xiaoyong Pan, Ye Yuan, 2023, bioRxiv.

IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction

Junchi Yan, Hongbin Shen, Xiaoyong Pan, 2016, BMC Genomics.

Attention based convolutional neural network for predicting RNA-protein binding sites pdf

Junchi Yan, Xiaoyong Pan, Junchi Yan, 2017, ArXiv.

Identifying RNA-binding proteins using multi-label deep learning

Hong-Bin Shen, Yong-Xian Fan, Xiaoyong Pan, 2018, Science China Information Sciences.

Investigating the biological relevance in trained embedding representations of protein sequences

Wesley De Neve, Yvan Saeys, Xiaoyong Pan, 2019, ICML 2019.