Zhongming Zhao

Orcid: 0000-0002-3477-0914

According to our database1, Zhongming Zhao authored at least 161 papers between 2003 and 2024.

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Bibliography

2024
Improved liver disease prediction from clinical data through an evaluation of ensemble learning approaches.
BMC Medical Informatics Decis. Mak., December, 2024

Correction: VER-Net: a hybrid transfer learning model for lung cancer detection using CT scan images.
BMC Medical Imaging, December, 2024

VER-Net: a hybrid transfer learning model for lung cancer detection using CT scan images.
BMC Medical Imaging, December, 2024

An improved method for diagnosis of Parkinson's disease using deep learning models enhanced with metaheuristic algorithm.
BMC Medical Imaging, December, 2024

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup.
J. Am. Medical Informatics Assoc., January, 2024

GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console.
CoRR, 2024

2023
Advances and challenges in Bioinformatics and Biomedical Engineering: IWBBIO 2020.
BMC Bioinform., December, 2023

Optimal ranking and directional signature classification using the integral strategy of multi-objective optimization-based association rule mining of multi-omics data.
Frontiers Bioinform., May, 2023

Benchmark of embedding-based methods for accurate and transferable prediction of drug response.
Briefings Bioinform., May, 2023

<i>deCS</i>: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues.
Genom. Proteom. Bioinform., April, 2023

Deep learning for detecting and elucidating human T-cell leukemia virus type 1 integration in the human genome.
Patterns, February, 2023

SMLBT: secure machine learning and blockchain-based telemedicine model for the remote areas of developing countries.
Int. J. Comput. Biol. Drug Des., 2023

2022
NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes.
Genom. Proteom. Bioinform., October, 2022

Unsupervised Feature Selection Using an Integrated Strategy of Hierarchical Clustering With Singular Value Decomposition: An Integrative Biomarker Discovery Method With Application to Acute Myeloid Leukemia.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Designing optimal convolutional neural network architecture using differential evolution algorithm.
Patterns, 2022

WebCSEA: web-based cell-type-specific enrichment analysis of genes.
Nucleic Acids Res., 2022

Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer.
BMC Bioinform., 2022

KCOSS: an ultra-fast k-mer counter for assembled genome analysis.
Bioinform., 2022

Grid-Search Integrated Optimized Support Vector Machine Model for Breast Cancer Detection.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

Detection of Chronic Kidney Disease Using Neuro-Fuzzy Rule-based Classifier.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021
EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data.
Patterns, 2021

Artificial image objects for classification of schizophrenia with GWAS-selected SNVs and convolutional neural network.
Patterns, 2021

Integration of millions of transcriptomes using batch-aware triplet neural networks.
Nat. Mach. Intell., 2021

DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner.
Nucleic Acids Res., 2021

CSEA-DB: an omnibus for human complex trait and cell type associations.
Nucleic Acids Res., 2021

KinaseMD: kinase mutations and drug response database.
Nucleic Acids Res., 2021

Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning.
Briefings Bioinform., 2021

Landscape of drug-resistance mutations in kinase regulatory hotspots.
Briefings Bioinform., 2021

Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity.
Briefings Bioinform., 2021

Negatively-Associated Maximal Frequent Geneset Mining on DNA Methylation Profile.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

Mining Cancer Cell Line-Based Drugs to Benefit KRAS<sup>(G12D)</sup> Pancreatic Adenocarcinoma Patients.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020
The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions.
BMC Medical Informatics Decis. Mak., March, 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
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Nat., 2020

VISDB: a manually curated database of viral integration sites in the human genome.
Nucleic Acids Res., 2020

TSEA-DB: a trait?tissue association map for human complex traits and diseases.
Nucleic Acids Res., 2020

Informatics and machine learning methods for health applications.
BMC Medical Informatics Decis. Mak., 2020

Correction to: The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions.
BMC Medical Informatics Decis. Mak., 2020

SURE-based optimum-length S-G filter to reconstruct NDVI time series iteratively with outliers removal.
Int. J. Wavelets Multiresolution Inf. Process., 2020

Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation.
CoRR, 2020

Correction to: The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases.
BMC Bioinform., 2020

In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells.
BMC Bioinform., 2020

Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020.
BMC Bioinform., 2020

6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes.
Bioinform., 2020

Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data.
Briefings Bioinform., 2020

Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice.
Briefings Bioinform., 2020

2019
Computational Approaches for Modeling Signal Transduction Networks.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019

The International Conference on Intelligent Biology and Medicine 2018: Medical Informatics Thematic Track (MedicalInfo2018).
BMC Medical Informatics Decis. Mak., 2019

Distance based knowledge retrieval through rule mining for complex biomarker recognition from tri-omics profiles.
Int. J. Comput. Biol. Drug Des., 2019

Correction to: circular RNA expression profiles during the differentiation of mouse neural stem cells.
BMC Syst. Biol., 2019

The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases.
BMC Bioinform., 2019

deTS: tissue-specific enrichment analysis to decode tissue specificity.
Bioinform., 2019

CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures.
Bioinform., 2019

Translational bioinformatics in mental health: open access data sources and computational biomarker discovery.
Briefings Bioinform., 2019

Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor.
Briefings Bioinform., 2019

A Multi-classifier Model to Identify Mitochondrial Respiratory Gene Signatures in Human Cancer.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018
TissGDB: tissue-specific gene database in cancer.
Nucleic Acids Res., 2018

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications.
BMC Bioinform., 2018

ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence.
Database J. Biol. Databases Curation, 2018

Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study.
Briefings Bioinform., 2018

2017
Towards integrated oncogenic marker recognition through mutual information-based statistically significant feature extraction: an association rule mining based study on cancer expression and methylation profiles.
Quant. Biol., 2017

mutLBSgeneDB: mutated ligand binding site gene DataBase.
Nucleic Acids Res., 2017

SZGR 2.0: a one-stop shop of schizophrenia candidate genes.
Nucleic Acids Res., 2017

Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data.
BMC Medical Informatics Decis. Mak., 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work.
BMC Syst. Biol., 2017

Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer.
BMC Bioinform., 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools.
BMC Bioinform., 2017

Impacts of somatic mutations on gene expression: an association perspective.
Briefings Bioinform., 2017

No-Boundary Thinking in Bioinformatics.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Representation Learning for Retinal Vasculature Embeddings.
Proceedings of the Fetal, Infant and Ophthalmic Medical Image Analysis, 2017

TrapRM: Transcriptomic and proteomic rule mining using weighted shortest distance based multiple minimum supports for multi-omics dataset.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016
Two Algorithms for the Detection and Tracking of Moving Vehicle Targets in Aerial Infrared Image Sequences.
Remote. Sens., 2016

Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis.
PLoS Comput. Biol., 2016

TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes.
Nucleic Acids Res., 2016

ccmGDB: a database for cancer cell metabolism genes.
Nucleic Acids Res., 2016

An informatics research agenda to support precision medicine: seven key areas.
J. Am. Medical Informatics Assoc., 2016

A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes.
J. Am. Medical Informatics Assoc., 2016

Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015.
BMC Syst. Biol., 2016

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach.
BMC Syst. Biol., 2016

Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types.
Briefings Bioinform., 2016

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes.
Briefings Bioinform., 2016

2015
SGDriver: a novel structural genomics-based approach to prioritize cancer related and potentially druggable somatic mutations.
BMC Bioinform., December, 2015

Continuous Change Detection and Classification Using Hidden Markov Model: A Case Study for Monitoring Urban Encroachment onto Farmland in Beijing.
Remote. Sens., 2015

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.
PLoS Comput. Biol., 2015

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3, 000 Cancer Genomes across 9 Cancer Types.
PLoS Comput. Biol., 2015

A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case.
BMC Syst. Biol., 2015

Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation.
Bioinform., 2015

EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles.
Bioinform., 2015

Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm.
BioData Min., 2015

2014
Parcel-Based Change Detection in Land-Use Maps by Adopting the Holistic Feature.
IEEE J. Sel. Top. Appl. Earth Obs. Remote. Sens., 2014

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.
PLoS Comput. Biol., 2014

The oncogenic and prognostic potential of eight microRNAs identified by a synergetic regulatory network approach in lung cancer.
Int. J. Comput. Biol. Drug Des., 2014

Integrated Approach in Systems Biology.
Comput. Math. Methods Medicine, 2014

Evaluating four major algorithms for identifying differential regulators in condition-specific transcriptional responses.
BMC Bioinform., 2014

2013
TSGene: a web resource for tumor suppressor genes.
Nucleic Acids Res., 2013

Dynamic protein interaction modules in human hepatocellular carcinoma progression.
BMC Syst. Biol., 2013

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives.
BMC Bioinform., 2013

Differential coexpression network modules observed in human hepatocellular carcinoma progression.
BMC Bioinform., 2013

A short tutorial in analyzing NGS data of cancer genomes for somatic mutation calling.
BMC Bioinform., 2013

Identifying transcription factor and microRNA mediated synergetic regulatory networks in lung cancer.
BMC Bioinform., 2013

Network analysis of gene fusions in human cancer.
BMC Bioinform., 2013

No-boundary thinking in bioinformatics research.
BioData Min., 2013

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives.
Briefings Bioinform., 2013

Correlating adverse drug reactions with biological pathways in humans.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Network-based mutation analysis of putative cancer genes from next-generation sequencing data.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

2012
Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma.
PLoS Comput. Biol., 2012

Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia.
PLoS Comput. Biol., 2012

Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs.
J. Am. Medical Informatics Assoc., 2012

Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer.
BMC Syst. Biol., 2012

Advances in systems biology: computational algorithms and applications.
BMC Syst. Biol., 2012

DTome: a web-based tool for drug-target interactome construction.
BMC Bioinform., 2012

BioEve Search: A Novel Framework to Facilitate Interactive Literature Search.
Adv. Bioinformatics, 2012

Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

Comprehensive analyses of tumor suppressor genes in protein-protein interaction networks: A topological perspective.
Proceedings of the Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, 2012

A comparative study of methods for detecting small somatic variants in disease-normal paired next generation sequencing data.
Proceedings of the Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, 2012

A network and functional investigation of illicit drugs and their targets.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

2011
Multiple-cue saliency measurement and optimized image composition for image retargeting.
J. Comput. Appl. Math., 2011

MentalSquares: A generic bipolar Support Vector Machine for psychiatric disorder classification, diagnostic analysis and neurobiological data mining.
Int. J. Data Min. Bioinform., 2011

Virus interactions with human signal transduction pathways.
Int. J. Comput. Biol. Drug Des., 2011

Gene regulation in glioblastoma: a combinatorial analysis of microRNAs and transcription factors.
Int. J. Comput. Biol. Drug Des., 2011

Do cancer proteins really interact strongly in the human protein-protein interaction network?
Comput. Biol. Chem., 2011

A comprehensive network and pathway analysis of candidate genes in major depressive disorder.
BMC Syst. Biol., 2011

Identifying the key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma using a systems biology approach.
BMC Bioinform., 2011

An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies.
Bioinform., 2011

dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.
Bioinform., 2011

Do MicroRNAs Preferentially Target the Genes with Low DNA Methylation Level at the Promoter Region?
Proceedings of the Bio-Inspired Computing and Applications, 2011

Network-assisted causal gene detection in genome-wide association studies: an improved module search algorithm.
Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011

Development and implementation of a novel computational tool for an efficient construction of drug-target interactome.
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

2010
Assessing gene length biases in gene set analysis of Genome-Wide Association Studies.
Int. J. Comput. Biol. Drug Des., 2010

Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues.
Int. J. Comput. Biol. Drug Des., 2010

A Novel microRNA and transcription factor mediated regulatory network in schizophrenia.
BMC Syst. Biol., 2010

Pathway- and network-based analysis of GWAS data revealed susceptibility gene sets to schizophrenia.
BMC Bioinform., 2010

Application of Pearson correlation coefficient (PCC) and Kolmogorov-Smirnov distance (KSD) metrics to identify disease-specific biomarker genes.
BMC Bioinform., 2010

Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.
Artif. Intell. Medicine, 2010

Genome-Wide DNA Methylation Profiling in 40 Breast Cancer Cell Lines.
Proceedings of the Advanced Intelligent Computing Theories and Applications, 2010

Investigating microRNA-transcription factor mediated regulatory network in glioblastoma.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010

2009
ERGR: An ethanol-related gene resource.
Nucleic Acids Res., 2009

CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?
BMC Bioinform., 2009

A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases-schizophrenia as a case.
Bioinform., 2009

Global Network Features of Cancer Genes in the Human Interactome.
Proceedings of the International Joint Conferences on Bioinformatics, 2009

Pathway and Network Analysis of Schizophrenia Candidate Genes under Meta-Analysis Linkage Peaks.
Proceedings of the International Joint Conferences on Bioinformatics, 2009

SmartWarf - A portable automated warfarin dosing tool.
Proceedings of the 2009 International Symposium on Collaborative Technologies and Systems, 2009

2008
A fast two-step deblurring method for satellite images.
Proceedings of the IEEE International Conference on Systems, 2008

An SVM-Based Algorithm for Classifying Promoter-Associated CpG Islands in the Human and Mouse Genomes.
Proceedings of the Advanced Intelligent Computing Theories and Applications. With Aspects of Artificial Intelligence, 2008

FindSUMO: A PSSM-Based Method for Sumoylation Site Prediction.
Proceedings of the Advanced Intelligent Computing Theories and Applications. With Aspects of Artificial Intelligence, 2008

Building Change Detection Based on Similarity Calibration.
Proceedings of the Fifth International Conference on Fuzzy Systems and Knowledge Discovery, 2008

Schizophrenia Genes: Characteristics of Function and Protein Interaction Networks.
Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics, 2008

2007
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes.
BMC Bioinform., 2007

2005
SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).
Bioinform., 2005

A fused road detection approach in high resolution multi-spectrum remote sensing imagery.
Proceedings of the IEEE International Geoscience & Remote Sensing Symposium, 2005

The indigenous remote sensing image processing system and its exertion strategy.
Proceedings of the IEEE International Geoscience & Remote Sensing Symposium, 2005

Multi-scale segmentation of the high resolution remote sensing image.
Proceedings of the IEEE International Geoscience & Remote Sensing Symposium, 2005

Clouds and cloud shadows removal from high-resolution remote sensing images.
Proceedings of the IEEE International Geoscience & Remote Sensing Symposium, 2005

Image compression based on unrestrained sized wavelet transform.
Proceedings of the IEEE International Geoscience & Remote Sensing Symposium, 2005

A new identification method for artificial objects based on various features.
Proceedings of the Color Imaging X: Processing, Hardcopy, and Applications, San Jose, 2005

2004
Urban building extraction from high-resolution satellite panchromatic image using clustering and edge detection.
Proceedings of the 2004 IEEE International Geoscience and Remote Sensing Symposium, 2004

An algorithm for eliminating the isolated regions based on connected area in image classification.
Proceedings of the 2004 IEEE International Geoscience and Remote Sensing Symposium, 2004

Texture image segmentation based on wavelet-domain hidden Markov models.
Proceedings of the 2004 IEEE International Geoscience and Remote Sensing Symposium, 2004

Remote sensing study based on IRSA Remote Sensing Image Processing System.
Proceedings of the 2004 IEEE International Geoscience and Remote Sensing Symposium, 2004

An integrated classification strategy of hyperspectral imaging spectrometer data.
Proceedings of the 2004 IEEE International Geoscience and Remote Sensing Symposium, 2004

2003
Road detection from Quickbird fused image using IHS transform and morphology.
Proceedings of the 2003 IEEE International Geoscience and Remote Sensing Symposium, 2003

Automatic change detection of artificial objects in multitemporal high spatial resolution remotely sensed imagery.
Proceedings of the 2003 IEEE International Geoscience and Remote Sensing Symposium, 2003


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