Xing-Ming Zhao

发表

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information

Xing-Ming Zhao, Jin-Kao Hao, Le Lu, 2012, Bioinform..

Differential network analysis from cross-platform gene expression data

Hong Yan, Xing-Ming Zhao, Xiao-Fei Zhang, 2016, Scientific Reports.

Joint Learning of Multiple Differential Networks With Latent Variables

Hong Yan, Xing-Ming Zhao, Fu Lee Wang, 2019, IEEE Transactions on Cybernetics.

A Survey on the Computational Approaches to Identify Drug Targets in the Postgenomic Era

Xing-Ming Zhao, Yan-Fen Dai, Xingming Zhao, 2015, BioMed research international.

A Novel Hybrid GA/SVM System for Protein Sequences Classification

Xing-Ming Zhao, Xin Huang, De-Shuang Huang, 2004, IDEAL.

Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"

Xing-Ming Zhao, Peer Bork, Vera van Noort, 2014, PLoS Comput. Biol..

Drug-target network in myocardial infarction: A structural analysis

Xing-Ming Zhao, Huiru Zheng, Haiying Wang, 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine.

Classifying G-Protein Coupled Receptors with Hydropathy Blocks and Support Vector Machines

Xing-Ming Zhao, De-Shuang Huang, Yiu-ming Cheung, 2006, ICIC.

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility

Xing-Ming Zhao, Jiangning Song, De-Shuang Huang, 2010, BMC Bioinformatics.

Victors: a web-based knowledge base of virulence factors in human and animal pathogens

Xing-Ming Zhao, Bin Zhao, Xiaoqin Zhang, 2018, Nucleic Acids Res..

A Novel Clustering Analysis Based on PCA and SOMs for Gene Expression Patterns

Xing-Ming Zhao, Xin Huang, De-Shuang Huang, 2004, ISNN.

DeepPhos: prediction of protein phosphorylation sites with deep learning

Xing-Ming Zhao, Yu Liu, Ao Li, 2019, Bioinform..

Gene Expression Data Classification Using Consensus Independent Component Analysis

Xing-Ming Zhao, De-Shuang Huang, Xiangzhen Kong, 2008, Genom. Proteom. Bioinform..

Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics

Xing-Ming Zhao, Jin-Kao Hao, Alioune Ngom, 2008 .

NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference

Xing-Ming Zhao, Jin-Kao Hao, Béatrice Duval, 2013, Bioinform..

Exploring functional variant using a deep learning framework

Xing-Ming Zhao, Rui Jiang, Zhuo Liu, 2017, 2017 13th IEEE Conference on Automation Science and Engineering (CASE).

The Imbalanced Problem in Mass-spectrometry Data Analysis

Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, 2008 .

DeepTL-Ubi: a novel deep transfer learning method for effectively predicting ubiquitination sites of multiple species.

Xing-Ming Zhao, Ao Li, Yu Liu, 2020, Methods.

Pattern recognition in bioinformatics

Xing-Ming Zhao, Jin-Kao Hao, Alioune Ngom, 2014, Neurocomputing.

Classifying protein sequences using hydropathy blocks

Xing-Ming Zhao, De-Shuang Huang, Yiu-ming Cheung, 2006, Pattern Recognit..

A novel Markov pairwise protein sequence alignment method for sequence comparison.

Xing-Ming Zhao, De-Shuang Huang, Yiu-ming Cheung, 2005, Protein and peptide letters.

Prediction of Drug Response with a Topology Based Dual-Layer Network Model

Xing-Ming Zhao, Suyun Huang, 2018, ISBRA.

EmDL: Extracting miRNA-Drug Interactions from Literature

Hong Yan, Xing-Ming Zhao, Wenbin Xie, 2019, TCBB.

Identifying cancer-related microRNAs based on gene expression data

Xing-Ming Zhao, Changjun Jiang, Jin-Kao Hao, 2015, Bioinform..

Identifying dysregulated pathways in cancers from pathway interaction networks

Xing-Ming Zhao, Jin-Kao Hao, Keqin Liu, 2012, BMC Bioinformatics.

A new technique for selecting features from protein sequences

Xing-Ming Zhao, Yixue Li, Yunping Zhu, 2006, Int. J. Pattern Recognit. Artif. Intell..

Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs

Xing-Ming Zhao, Peer Bork, Vera van Noort, 2013, PLoS Comput. Biol..

Predicting Therapeutic Targets with Integration of Heterogeneous Data Sources

Xing-Ming Zhao, Yan-Fen Dai, Yin-Ying Wang, 2013, PRIB.

The drug cocktail network

Xing-Ming Zhao, Jiangning Song, Ke-Jia Xu, 2012, BMC Systems Biology.

Comparative analysis of protein-coding genes and long non-coding RNAs of prostate cancer between Caucasian and Chinese populations

Xing-Ming Zhao, Yan Zhang, Luonan Chen, 2012, 2012 IEEE 6th International Conference on Systems Biology (ISB).

PPIM: A Protein-Protein Interaction Database for Maize1

Xing-Ming Zhao, Rui Jiang, Guanghui Zhu, 2015, Plant Physiology.

Editorial - Data mining in bioinformatics

Xing-Ming Zhao, 2015, J. Bioinform. Comput. Biol..

FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures

Xing-Ming Zhao, Luonan Chen, Weihua Tang, 2010, BMC Systems Biology.

A hybrid sequential feature selection approach for the diagnosis of Alzheimer's Disease

Xing-Ming Zhao, Yang Han, Xingming Zhao, 2016, 2016 International Joint Conference on Neural Networks (IJCNN).

Data Mining in Systems Biology

Xing-Ming Zhao, 2016, TCBB.

Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data

Xing-Ming Zhao, Peer Bork, Georg Zeller, 2011, PLoS Comput. Biol..

Editorial: part 2: network construction and mining for systems biology.

Xing-Ming Zhao, 2014, IET systems biology.

PhosD: inferring kinase‐substrate interactions based on protein domains

Xing-Ming Zhao, Gui-Min Qin, Rui-Yi Li, 2016, Bioinform..

GANcon: Protein Contact Map Prediction With Deep Generative Adversarial Network

Xing-Ming Zhao, Ao Li, Zhenhua Yu, 2020, IEEE Access.

A survey on biomarker identification based on molecular networks

Xing-Ming Zhao, Guanghui Zhu, Jun Wu, 2016, Quantitative Biology.

Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks

Xing-Ming Zhao, Kazuyuki Aihara, Luonan Chen, 2008, APBC.

Microarray data analysis using rival penalized EM algorithm in normal mixture models

Xing-Ming Zhao, De-Shuang Huang, Yiu-ming Cheung, 2005, Proceedings of 2005 IEEE International Workshop on VLSI Design and Video Technology, 2005..

Identifying Disease Associated miRNAs Based on Protein Domains

Xing-Ming Zhao, Gui-Min Qin, Rui-Yi Li, 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Domain-Domain Interaction Identification with a Feature Selection Approach

Xing-Ming Zhao, Luonan Chen, 2008, PRIB.

Identifying disease genes and module biomarkers by differential interactions

Xing-Ming Zhao, Zhi-Ping Liu, Luonan Chen, 2012, J. Am. Medical Informatics Assoc..

Analysis of Gene Expression Data Using Rpem Algorithm in Normal Mixture Model with Dynamic Adjustment of Learning Rate

Xing-Ming Zhao, De-Shuang Huang, Yiu-ming Cheung, 2010, Int. J. Pattern Recognit. Artif. Intell..

Exploring drug combinations in a drug-cocktail network

Xing-Ming Zhao, Jiangning Song, Ke-Jia Xu, 2011, 2011 IEEE International Conference on Systems Biology (ISB).

Data mining in systems biology

Xing-Ming Zhao, Shuigeng Zhou, Ao Li, 2016, Neurocomputing.

Predicting contact map using Radial Basis Function Neural Network with Conformational Energy Function

Xing-Ming Zhao, De-Shuang Huang, Peng Chen, 2008, Int. J. Bioinform. Res. Appl..

EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning

Hong Yan, Xing-Ming Zhao, Le Ou-Yang, 2019, Bioinform..

Improved method for predicting phi-turns in proteins using a two-stage classifier.

Xing-Ming Zhao, Shu-Lin Wang, Min Wu, 2010, Protein and peptide letters.

eFG: an electronic resource for Fusarium graminearum

Xing-Ming Zhao, Xiaodong Zhang, Luonan Chen, 2013, Database J. Biol. Databases Curation.

Drug-Domain Interaction Networks in Myocardial Infarction

Xing-Ming Zhao, Huiru Zheng, Haiying Wang, 2013, IEEE Transactions on NanoBioscience.

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets

Xing-Ming Zhao, Jiangning Song, Tatsuya Akutsu, 2014, Bioinform..

scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation

Hong Yan, Xing-Ming Zhao, Le Ou-Yang, 2020, Bioinform..

A New Balanced Ensemble Classifier for Predicting Fungi Protein Subcellular Localization Based on Protein Primary Structures

Xing-Ming Zhao, Luonan Chen, Xingming Zhao, 2009, 2009 2nd International Conference on Biomedical Engineering and Informatics.

A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks

Xing-Ming Zhao, Min Wu, Le Ou-Yang, 2020, Bioinform..

Prediction of beta-hairpins in proteins using physicochemical properties and structure information.

Xing-Ming Zhao, Min Wu, Jun-Feng Xia, 2010, Protein and peptide letters.

A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer

Xing-Ming Zhao, Weiguo Liu, Xiaoyu Zhang, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

CSTEA: a webserver for the Cell State Transition Expression Atlas

Xing-Ming Zhao, Jun Wu, Xiao Chen, 2017, Nucleic Acids Res..

Modeling and Dynamical Analysis of Molecular Networks

Xing-Ming Zhao, Ruiqi Wang, Zengrong Liu, 2009, Complex.

MVP: a microbe–phage interaction database

Xing-Ming Zhao, Zhi Liu, Peer Bork, 2017, Nucleic Acids Res..

Gene function prediction using labeled and unlabeled data

Xing-Ming Zhao, Kazuyuki Aihara, Luonan Chen, 2008, BMC Bioinformatics.

Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study

Hong Yan, Xing-Ming Zhao, Kang Ning, 2017, Oncotarget.

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines

Xing-Ming Zhao, Xiao Chen, Peer Bork, 2016, Nucleic Acids Res..

PCID: A Novel Approach for Predicting Disease Comorbidity by Integrating Multi-Scale Data

Xing-Ming Zhao, Feng He, De-Shuang Huang, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

A systematic exploration of the associations between amino acid variants and post-translational modifications

Xing-Ming Zhao, Gui-Min Qin, Yi-Bo Hou, 2016, Neurocomputing.

Exploring drug combinations in genetic interaction network

Xing-Ming Zhao, Jiangning Song, Yin-Ying Wang, 2012, BMC Bioinformatics.

A systems biology approach to identify effective cocktail drugs

Xing-Ming Zhao, Luonan Chen, Zikai Wu, 2010, BMC Systems Biology.

Predicting drug-disease associations with heterogeneous network embedding.

Xing-Ming Zhao, Kai Yang, David Waxman, 2019, Chaos.

Understanding tissue-specificity with human tissue-specific regulatory networks

Xing-Ming Zhao, De-Shuang Huang, Lin Zhu, 2016, Science China Information Sciences.

Automatic Modeling of Signaling Pathways by Network Flow Model

Xing-Ming Zhao, Kazuyuki Aihara, Luonan Chen, 2009, J. Bioinform. Comput. Biol..

Protein function prediction with the shortest path in functional linkage graph and boosting

Xing-Ming Zhao, Kazuyuki Aihara, Luonan Chen, 2008, Int. J. Bioinform. Res. Appl..

The exploration of functional divergence between human and macaque brains based on gene networks

Xing-Ming Zhao, Peipei Xiao, Xingming Zhao, 2016, 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

DrPOCS: Drug Repositioning Based on Projection Onto Convex Sets

Hong Yan, Xing-Ming Zhao, Chunfeng Cui, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

jNMFMA: a joint non-negative matrix factorization meta-analysis of transcriptomics data

Xing-Ming Zhao, Hong-Qiang Wang, Chun-Hou Zheng, 2015, Bioinform..

A novel approach to extracting features from motif content and protein composition for protein sequence classification

Xing-Ming Zhao, De-Shuang Huang, Yiu-ming Cheung, 2005, Neural Networks.

MAT2: manifold alignment of single-cell transcriptomes with cell triplets

Xing-Ming Zhao, Ying Wang, Jinglong Zhang, 2021, Bioinform..

mMGE: a database for human metagenomic extrachromosomal mobile genetic elements

Xing-Ming Zhao, Yanqi Dong, Long-Hao Jia, 2020, Nucleic Acids Res..

STAB: a spatio-temporal cell atlas of the human brain

Xing-Ming Zhao, Long-Hao Jia, Shaojun Pan, 2020, Nucleic Acids Res..

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines

Xing-Ming Zhao, Peer Bork, Robin B. Gasser, 2020, Nucleic Acids Res..

FPPI: Fusarium graminearum protein-protein interaction database.

Xing-Ming Zhao, Luonan Chen, Xingming Zhao, 2009, Journal of proteome research.

A novel hybrid GA/RBFNN technique for protein sequences classification.

Xing-Ming Zhao, De-Shuang Huang, Yiu-Ming Cheung, 2005, Protein and peptide letters.

Gene Function Prediction with the Shortest Path in Functional Linkage Graph

Xing-Ming Zhao, Kazuyuki Aihara, Luonan Chen, 2007 .

The exploration of network motifs as potential drug targets from post-translational regulatory networks

Xing-Ming Zhao, Jiangning Song, Peer Bork, 2016, Scientific Reports.

Predicting drug targets based on protein domains.

Xing-Ming Zhao, Jose C Nacher, Xingming Zhao, 2012, Molecular bioSystems.

FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model

Xing-Ming Zhao, Jiangning Song, Tatsuya Akutsu, 2012, PloS one.

A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

Xing-Ming Zhao, Liying Kang, Xingming Zhao, 2014, BioMed research international.

Inferring gene regulatory networks from gene expression data by PC-algorithm based on conditional mutual information

Xing-Ming Zhao, Jin-Kao Hao, Luonan Chen, 2011 .

Integrative analysis of mutational and transcriptional profiles reveals driver mutations of metastatic breast cancers

Xing-Ming Zhao, Jin-Kao Hao, Wonshik Han, 2016, Cell Discovery.

GMrepo: a database of curated and consistently annotated human gut metagenomes

Xing-Ming Zhao, Pengyu Luo, Long-Hao Jia, 2019, Nucleic Acids Res..

Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers

Xing-Ming Zhao, Xiaoping Liu, Luonan Chen, 2013, BMC Medical Genomics.

DIPOS: database of interacting proteins in Oryza sativa.

Xing-Ming Zhao, Xiaoping Liu, Luonan Chen, 2011, Molecular bioSystems.

PPIM: A Protein-Protein Interaction Database for Maize1

Xing-Ming Zhao, Xin-Jian Xu, Luonan Chen, 2015, Plant Physiology.

Prediction of S-Glutathionylation Sites Based on Protein Sequences

Xing-Ming Zhao, Luonan Chen, Xiaobo Zhou, 2013, PloS one.

Protein Subcellular Localization Prediction for Fusarium graminearum ∗

Xing-Ming Zhao, Luonan Chen, Chenglei Sun, 2009 .

mTD: A database of microRNAs affecting therapeutic effects of drugs.

Xing-Ming Zhao, Hong Yan, Wen-Bin Xie, 2017, Journal of genetics and genomics = Yi chuan xue bao.

Network-based biomarkers for complex diseases.

Xing-Ming Zhao, Luonan Chen, Xingming Zhao, 2014, Journal of theoretical biology.

A Survey on Computational Approaches to Predicting Adverse Drug Reactions.

Xing-Ming Zhao, Yin-Ying Wang, Yun-Gu Chen, 2016, Current topics in medicinal chemistry.

Computational Approaches for Identifying Signaling Pathways from Molecular Interaction Networks

Xing-Ming Zhao, Xiao-Dong Zhang, 2013 .