Xingming Zhao

发表

Computational Systems Biology

Xingming Zhao, Weidong Tian, R. Jiang, 2013, TheScientificWorldJournal.

Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks

Xingming Zhao, Luonan Chen, Jin-Kao Hao, 2014, Nucleic acids research.

Drug discovery in the age of systems biology: the rise of computational approaches for data integration.

P. Bork, G. Zeller, Xingming Zhao, 2012, Current opinion in biotechnology.

Uncovering signal transduction networks from high-throughput data by integer linear programming

K. Aihara, Xingming Zhao, Luonan Chen, 2008, Nucleic acids research.

Predicting protein–protein interactions from protein sequences using meta predictor

Xingming Zhao, De-shuang Huang, Jun-Feng Xia, 2010, Amino Acids.

Identifying responsive functional modules from protein-protein interaction network

Zikai Wu, Luonan Chen, Xingming Zhao, 2009, Molecules and cells.

Identifying Biomarkers with Differential Analysis

Xingming Zhao, Guimin Qin, 2013 .

A Network Approach to Predict Pathogenic Genes for Fusarium graminearum

Xingming Zhao, Luonan Chen, Xiaoping Liu, 2010, PloS one.

Inferring the miRNA-disease associations based on domain-disease associations

Xingming Zhao, Guimin Qin, Rui-Yi Li, 2015 .

A survey on computational approaches to identifying disease biomarkers based on molecular networks.

Xingming Zhao, Guimin Qin, 2014, Journal of theoretical biology.

A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

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

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.

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.

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.

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.

A discriminative approach for identifying domain–domain interactions from protein–protein interactions

K. Aihara, Xingming Zhao, Luonan Chen, 2010, Proteins.

Breakthrough Technologies PPIM : A Protein-Protein Interaction Database for Maize 1

Xingming Zhao, Luonan Chen, Peipei Xiao, 2016 .

Database tool eFG: an electronic resource for Fusarium graminearum

Xingming Zhao, Luonan Chen, Xiaoping Liu, 2013 .

Predicting drug targets based on protein domains.

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

Protein domain annotation with predicted domain-domain interaction networks.

K. Aihara, Xingming Zhao, Luonan Chen, 2008, Protein Peptide Letters.

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.

Analysis of Transcriptome of Rice Anther

Xingming Zhao, Zhiping Liu, Jiguang Wang, 2009 .

A Network Biology Approach to Understand Combination of Drugs

Xingming Zhao, Jiangning Song, Ke-Jia Xu, 2010 .

Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana

Xingming Zhao, Luonan Chen, Yong Wang, 2019, npj Systems Biology and Applications.

Network Flow Model Based Analysis of Mouse Hepatocarcinogenesis

Xingming Zhao, Luonan Chen, Chaochao Wu, 2010 .

Gene expression Identifying cancer-related microRNAs based on gene expression data

Xingming Zhao, Luonan Chen, Jin-Kao Hao, 2015 .

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.

MVP: a microbe–phage interaction database

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

Consistent alterations of human fecal microbes after transplanted to germ-free mice

Na L. Gao, Xingming Zhao, Wei-Hua Chen, 2018 .

Repositioning drugs for breast cancer based on the identification of cancer related signaling pathways

Xingming Zhao, Yinyu Wang, Xiaodong Zhang, 2013, Proceedings of the 32nd Chinese Control Conference.

Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment

Xingming Zhao, Puzi Jiang, Wei-Hua Chen, 2020, BMC Genomics.

Detecting B-cell lymphomas dysregulation modules based on molecular interaction network

Xingming Zhao, Fuyan Hu, 2011, 2011 IEEE International Conference on Systems Biology (ISB).

Construction of human tissue-specific phosphorylation networks with protein expression data

Xingming Zhao, Luonan Chen, Yinyu Wang, 2013, 2013 7th International Conference on Systems Biology (ISB).

Protein Function Prediction with Data‐Mining Techniques

Xingming Zhao, Luonan Chen, 2010 .

Understanding the aristolochic acid toxicities in rat kidneys with regulatory networks.

Xingming Zhao, Zhiguang Li, Tao Chen, 2015, IET systems biology.

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

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

Advances in genome informatics.

Ming Li, Xingming Zhao, Yixue Li, 2010, Journal of bioinformatics and computational biology.

Macrel: antimicrobial peptide screening in genomes and metagenomes

Xing-Ming Zhao, Shaojun Pan, Luis Pedro Coelho, 2019, bioRxiv.

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..

A survey on biomarker identification based on molecular networks

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

Network-based biomarkers for complex diseases.

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

Identifying disease genes and module biomarkers by differential interactions

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

Identifying dysregulated pathways in cancers from pathway interaction networks

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

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).

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

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

metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies

Luis Pedro Coelho, Xingming Zhao, Wei-Hua Chen, 2021, bioRxiv.

Gene Expression Data Classification Using Consensus Independent Component Analysis

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

Identification of Functional Gene Modules Associated With STAT-Mediated Antiviral Responses to White Spot Syndrome Virus in Shrimp

Xingming Zhao, Fuhua Li, Guanghui Zhu, 2019, Front. Physiol..

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

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

Automatic Modeling of Signaling Pathways by Network Flow Model

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

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

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

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..

Compromised intestinal barrier underlies gut microbiota dysbiosis of intestinal diseases

Xingming Zhao, Xiushan Yin, Puzi Jiang, 2019 .

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..

FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures

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

Protein Subcellular Localization Prediction for Fusarium graminearum ∗

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

Understanding tissue-specificity with human tissue-specific regulatory networks

Xingming Zhao, De-shuang Huang, Suping Deng, 2016, Science China Information Sciences.

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

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

GEAR: A database of Genomic Elements Associated with drug Resistance

P. Bork, Xingming Zhao, Peipei Xiao, 2017, Scientific Reports.

Differential network analysis from cross-platform gene expression data

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

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).

The drug cocktail network

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

Identifying cancer-related microRNAs based on gene expression data

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

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

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

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.

Chapter 2 Identifying Biomarkers with Differential Analysis

Xingming Zhao, Guimin Qin, 2015 .

Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs

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

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.

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.

mBodyMap: a curated database for microbes across human body and their associations with health and diseases

Xingming Zhao, Wei-Hua Chen, Zhi Liu, 2021, Nucleic Acids Res..

SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)

Luis Pedro Coelho, Xingming Zhao, Shaojun Pan, 2021, bioRxiv.

Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models

Xingming Zhao, Puzi Jiang, Wei-Hua Chen, 2019, mSystems.

Gene function prediction using labeled and unlabeled data

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

mMGE: a database for human metagenomic extrachromosomal mobile genetic elements

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

Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data

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

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.

Exploring drug combinations in genetic interaction network

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

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..

OGEE v 2 : an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines

P. Bork, Xingming Zhao, Wei-Hua Chen, 2016 .

metaMIC: reference-free Misassembly Identification and Correction

Luis Pedro Coelho, Xingming Zhao, Wei-Hua Chen, 2021 .

Protein domain annotation with integration of heterogeneous information sources

Kazuyuki Aihara, Luonan Chen, Yong Wang, 2008, Proteins.

PPIM: A Protein-Protein Interaction Database for Maize1

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

A systems biology approach to identify effective cocktail drugs

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

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

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

HISP: a hybrid intelligent approach for identifying directed signaling pathways

Xingming Zhao, Shan Li, 2017, Journal of molecular cell biology.

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.

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.

PhosD: inferring kinase‐substrate interactions based on protein domains

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

eFG: an electronic resource for Fusarium graminearum

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

Predicting Therapeutic Targets with Integration of Heterogeneous Data Sources

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

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.

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).

Protein classification with imbalanced data

Xin Li, Kazuyuki Aihara, Luonan Chen, 2007, Proteins.

Protein function prediction with high-throughput data

Kazuyuki Aihara, Luonan Chen, Xing-Ming Zhao, 2008, Amino Acids.

Exploring drug combinations in genetic interaction network

Xingming Zhao, Jiangning Song, Ke-Jia Xu, 2012, BMC Bioinformatics.

Prediction of S-Glutathionylation Sites Based on Protein Sequences

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

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

Xing-Ming Zhao, Min Wu, 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 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.

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..

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.

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 .

EmDL: Extracting miRNA-Drug Interactions from Literature

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

Deep convolutional neural network for accurate segmentation and quantification of white matter hyperintensities

Xiaofeng Zhu, Jianxin Wang, Fang-Xiang Wu, 2020, Neurocomputing.

AMPSphere : the worldwide survey of prokaryotic antimicrobial peptides

Luis Pedro Coelho, P. Bork, Xingming Zhao, 2021 .

Drug-Domain Interaction Networks in Myocardial Infarction

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

Identifying rice arsenic stress response pathways based on molecular interaction network

Xingming Zhao, Luonan Chen, Jingdong Liu, 2012, 2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications.

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

Xingming Zhao, Luonan Chen, Jin-Kao Hao, 2013, Bioinform..

FPPI: Fusarium graminearum protein-protein interaction database.

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

A systems biology approach to identify the signalling network regulated by Rho-GDI-γ during neural stem cell differentiation.

Xingming Zhao, Hua Cheng, T. Wen, 2012, Molecular bioSystems.

Joint Learning of Multiple Differential Networks With Latent Variables

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