Xing-Ming Zhao

Orcid: 0000-0002-4531-3970

According to our database1, Xing-Ming Zhao authored at least 84 papers between 2004 and 2024.

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Bibliography

2024
Enhancing Generalized Fetal Brain MRI Segmentation using A Cascade Network with Depth-wise Separable Convolution and Attention Mechanism.
CoRR, 2024

2023
Improving Alzheimer's Disease Diagnosis With Multi-Modal PET Embedding Features by a 3D Multi-Task MLP-Mixer Neural Network.
IEEE J. Biomed. Health Informatics, August, 2023

A survey on computational strategies for genome-resolved gut metagenomics.
Briefings Bioinform., May, 2023

Deciphering the genetic architecture of human brain structure and function: a brief survey on recent advances of neuroimaging genomics.
Briefings Bioinform., March, 2023

SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing.
Bioinform., 2023

Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022
CITEdb: a manually curated database of cell-cell interactions in human.
Bioinform., November, 2022

Co-VAE: Drug-Target Binding Affinity Prediction by Co-Regularized Variational Autoencoders.
IEEE Trans. Pattern Anal. Mach. Intell., 2022

mBodyMap: a curated database for microbes across human body and their associations with health and diseases.
Nucleic Acids Res., 2022

GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison.
Nucleic Acids Res., 2022

Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice.
Genom. Proteom. Bioinform., 2022

An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease.
Briefings Bioinform., 2022

MorbidGCN: prediction of multimorbidity with a graph convolutional network based on integration of population phenotypes and disease network.
Briefings Bioinform., 2022

2021
Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

STAB: a spatio-temporal cell atlas of the human brain.
Nucleic Acids Res., 2021

mMGE: a database for human metagenomic extrachromosomal mobile genetic elements.
Nucleic Acids Res., 2021

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.
Nucleic Acids Res., 2021

MAT2: manifold alignment of single-cell transcriptomes with cell triplets.
Bioinform., 2021

PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein-protein interaction information.
Bioinform., 2021

nMAGMA: a network-enhanced method for inferring risk genes from GWAS summary statistics and its application to schizophrenia.
Briefings Bioinform., 2021

2020
GMrepo: a database of curated and consistently annotated human gut metagenomes.
Nucleic Acids Res., 2020

Deep convolutional neural network for accurate segmentation and quantification of white matter hyperintensities.
Neurocomputing, 2020

A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks.
Bioinform., 2020

scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation.
Bioinform., 2020

GANcon: Protein Contact Map Prediction With Deep Generative Adversarial Network.
IEEE Access, 2020

2019
Joint Learning of Multiple Differential Networks With Latent Variables.
IEEE Trans. Cybern., 2019

EmDL: Extracting miRNA-Drug Interactions from Literature.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

DrPOCS: Drug Repositioning Based on Projection Onto Convex Sets.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Victors: a web-based knowledge base of virulence factors in human and animal pathogens.
Nucleic Acids Res., 2019

EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning.
Bioinform., 2019

DeepPhos: prediction of protein phosphorylation sites with deep learning.
Bioinform., 2019

2018
MVP: a microbe-phage interaction database.
Nucleic Acids Res., 2018

Prediction of Drug Response with a Topology Based Dual-Layer Network Model.
Proceedings of the Bioinformatics Research and Applications - 14th International Symposium, 2018

2017
PCID: A Novel Approach for Predicting Disease Comorbidity by Integrating Multi-Scale Data.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017

CSTEA: a webserver for the Cell State Transition Expression Atlas.
Nucleic Acids Res., 2017

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.
Nucleic Acids Res., 2017

PhosD: inferring kinase-substrate interactions based on protein domains.
Bioinform., 2017

PPIM: A protein-protein interaction database for Maize.
Proceedings of the 13th IEEE Conference on Automation Science and Engineering, 2017

Exploring functional variant using a deep learning framework.
Proceedings of the 13th IEEE Conference on Automation Science and Engineering, 2017

2016
Data Mining in Systems Biology.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016

Identifying Disease Associated miRNAs Based on Protein Domains.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016

A survey on biomarker identification based on molecular networks.
Quant. Biol., 2016

A systematic exploration of the associations between amino acid variants and post-translational modifications.
Neurocomputing, 2016

Data mining in systems biology.
Neurocomputing, 2016

Understanding tissue-specificity with human tissue-specific regulatory networks.
Sci. China Inf. Sci., 2016

A hybrid sequential feature selection approach for the diagnosis of Alzheimer's Disease.
Proceedings of the 2016 International Joint Conference on Neural Networks, 2016

The exploration of functional divergence between human and macaque brains based on gene networks.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015
Editorial - Data mining in bioinformatics.
J. Bioinform. Comput. Biol., 2015

Identifying cancer-related microRNAs based on gene expression data.
Bioinform., 2015

<i>j</i>NMFMA: a joint non-negative matrix factorization meta-analysis of transcriptomics data.
Bioinform., 2015

2014
Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication".
PLoS Comput. Biol., 2014

Pattern recognition in bioinformatics.
Neurocomputing, 2014

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets.
Bioinform., 2014

2013
Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs.
PLoS Comput. Biol., 2013

NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference.
Bioinform., 2013

<i>eFG</i>: an electronic resource for <i>Fusarium graminearum</i>.
Database J. Biol. Databases Curation, 2013

Predicting Therapeutic Targets with Integration of Heterogeneous Data Sources.
Proceedings of the Pattern Recognition in Bioinformatics, 2013

2012
Identifying disease genes and module biomarkers by differential interactions.
J. Am. Medical Informatics Assoc., 2012

The drug cocktail network.
BMC Syst. Biol., 2012

Exploring drug combinations in genetic interaction network.
BMC Bioinform., 2012

Identifying dysregulated pathways in cancers from pathway interaction networks.
BMC Bioinform., 2012

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information.
Bioinform., 2012

Comparative analysis of protein-coding genes and long non-coding RNAs of prostate cancer between Caucasian and Chinese populations.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

Drug-target network in myocardial infarction: A structural analysis.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011
Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data.
PLoS Comput. Biol., 2011

2010
Analysis of Gene Expression Data Using Rpem Algorithm in Normal Mixture Model with Dynamic Adjustment of Learning Rate.
Int. J. Pattern Recognit. Artif. Intell., 2010

A systems biology approach to identify effective cocktail drugs.
BMC Syst. Biol., 2010

FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures.
BMC Syst. Biol., 2010

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility.
BMC Bioinform., 2010

2009
Automatic Modeling of Signaling Pathways by Network Flow Model.
J. Bioinform. Comput. Biol., 2009

Modeling and Dynamical Analysis of Molecular Networks.
Proceedings of the Complex Sciences, 2009

A New Balanced Ensemble Classifier for Predicting Fungi Protein Subcellular Localization Based on Protein Primary Structures.
Proceedings of the 2nd International Conference on BioMedical Engineering and Informatics, 2009

2008
Protein function prediction with the shortest path in functional linkage graph and boosting.
Int. J. Bioinform. Res. Appl., 2008

Predicting contact map using Radial Basis Function Neural Network with Conformational Energy Function.
Int. J. Bioinform. Res. Appl., 2008

Gene Expression Data Classification Using Consensus Independent Component Analysis.
Genom. Proteom. Bioinform., 2008

Gene function prediction using labeled and unlabeled data.
BMC Bioinform., 2008

Domain-Domain Interaction Identification with a Feature Selection Approach.
Proceedings of the Pattern Recognition in Bioinformatics, 2008

Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

2006
Classifying protein sequences using hydropathy blocks.
Pattern Recognit., 2006

A new technique for selecting features from protein sequences.
Int. J. Pattern Recognit. Artif. Intell., 2006

Classifying G-Protein Coupled Receptors with Hydropathy Blocks and Support Vector Machines.
Proceedings of the Computational Intelligence and Bioinformatics, 2006

2005
A novel approach to extracting features from motif content and protein composition for protein sequence classification.
Neural Networks, 2005

2004
A Novel Clustering Analysis Based on PCA and SOMs for Gene Expression Patterns.
Proceedings of the Advances in Neural Networks, 2004

A Novel Hybrid GA/SVM System for Protein Sequences Classification.
Proceedings of the Intelligent Data Engineering and Automated Learning, 2004


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