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List of works by Zhongming Zhao

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

scientific article published on 24 February 2020

A Convergent Study of Genetic Variants Associated With Crohn's Disease: Evidence From GWAS, Gene Expression, Methylation, eQTL and TWAS

article

A Frameshift Variant in the CHST9 Gene Identified by Family-Based Whole Genome Sequencing Is Associated with Schizophrenia in Chinese Population

scientific article published on 03 September 2019

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

scientific article

A Linear Regression and Deep Learning Approach for Detecting Reliable Genetic Alterations in Cancer Using DNA Methylation and Gene Expression Data

scientific article published on 12 August 2020

A bias-reducing pathway enrichment analysis of genome-wide association data confirmed association of the MHC region with schizophrenia

scientific article

A comprehensive network and pathway analysis of candidate genes in major depressive disorder

scientific article

A developmental stage specific network approach for studying dynamic transcription factor-microRNA co-regulation during craniofacial development

scientific article published on 24 November 2020

A meta-analysis of somatic mutations from next generation sequencing of 241 melanomas: a road map for the study of genes with potential clinical relevance

scientific article

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

scientific article published on 14 July 2009

A novel microRNA and transcription factor mediated regulatory network in schizophrenia

scientific article

ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence

article

Acquired resistance of EGFR-mutant lung adenocarcinomas to afatinib plus cetuximab is associated with activation of mTORC1.

scientific article

Adenoma formation following limited ablation of p120-catenin in the mouse intestine.

scientific article

Adipose tissue-specific ablation of Ces1d causes metabolic dysregulation in mice

scientific article published on 22 April 2022

Age-associated telomere attrition in adipocyte progenitors predisposes to metabolic disease

scientific article published on 14 December 2020

Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis

scientific article published on 16 July 2020

An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies ⬇️

scientific article published on January 25, 2011

An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies.

scientific article published on 29 January 2018

An integrative, genomic, transcriptomic and network-assisted study to identify genes associated with human cleft lip with or without cleft palate

scientific article published on 03 April 2020

Anemia and Red Blood Cell Indices Predict HIV-Associated Neurocognitive Impairment in the Highly Active Antiretroviral Therapy Era

scientific article published on 21 December 2015

Angiogenic gene networks are dysregulated in opioid use disorder: evidence from multi-omics and imaging of postmortem human brain

scientific article published on 12 August 2021

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

scientific article published on 09 August 2012

Application of systems biology approach identifies and validates GRB2 as a risk gene for schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample ⬇️

scientific article published on December 30, 2010

Asprosin is a centrally acting orexigenic hormone.

scientific article

Assessing gene length biases in gene set analysis of Genome-Wide Association Studies

scientific article published on January 1, 2010

Association of FAS, a TNF-α receptor gene, with treatment resistant schizophrenia ⬇️

scientific article published on 05 May 2011

Association signals unveiled by a comprehensive gene set enrichment analysis of dental caries genome-wide association studies

scientific article

Association study of 167 candidate genes for schizophrenia selected by a multi-domain evidence-based prioritization algorithm and neurodevelopmental hypothesis

scientific article

BRAF(L597) mutations in melanoma are associated with sensitivity to MEK inhibitors

scientific article

Beyond histology: translating tumor genotypes into clinically effective targeted therapies

scientific article

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

scientific article published on 01 December 2019

CSEA-DB: an omnibus for human complex trait and cell type associations

scientific article published on 19 November 2020

Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults

scientific article

Changes in the Microbial Community Diversity of Oil Exploitation

scientific article published on 24 July 2019

Characterization of Tumor-Suppressor Gene Inactivation Events in 33 Cancer Types

scientific article published on 01 January 2019

Clinically relevant genes and regulatory pathways associated with NRASQ61 mutations in melanoma through an integrative genomics approach

scientific article

Clonal architectures predict clinical outcome in clear cell renal cell carcinoma

scientific article published on 18 March 2019

Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data

scientific article

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

scientific article

ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis

scientific article published on 28 December 2017

Consensus rules in variant detection from next-generation sequencing data

scientific article

Convergent genomic and pharmacological evidence of PI3K/GSK3 signaling alterations in neurons from schizophrenia patients

scientific article published on 07 December 2020

Convergent roles of de novo mutations and common variants in schizophrenia in tissue-specific and spatiotemporal co-expression network.

scientific article

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

scientific article published on 07 October 2019

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action

scientific article (publication date: June 2015)

Deciphering the Unique MicroRNA Signature in Human Esophageal Adenocarcinoma ⬇️

scientific article published on May 28, 2013

Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition

scientific article published on 17 November 2017

Decoding regulatory structures and features from epigenomics profiles: A Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model

scientific article published on 28 October 2019

Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network

scientific article published on 11 June 2020

Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning

scientific article published on 24 June 2020

Dense module searching for gene networks associated with multiple sclerosis

scientific article published on 03 April 2020

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

scientific article

Differential Expression of Viral Transcripts From Single-Cell RNA Sequencing of Moderate and Severe COVID-19 Patients and Its Implications for Case Severity

scientific article published on 16 October 2020

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

scientific article published on 20 March 2018

Diverse types of genomic evidence converge on alcohol use disorder risk genes

scientific article published on 13 March 2020

Do cancer proteins really interact strongly in the human protein-protein interaction network?

scientific article

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

scientific article published on 24 March 2015

Enriched pathways for major depressive disorder identified from a genome-wide association study

scientific article published on 16 January 2012

Estrogen receptor-α expressing neurons in the ventrolateral VMH regulate glucose balance

scientific article published on 01 May 2020

Gastric adenocarcinoma has a unique microRNA signature not present in esophageal adenocarcinoma ⬇️

scientific article published on June 1, 2013

Gene expression imputation and cell type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders

scientific article published on 03 December 2020

Gene set analysis of genome-wide association studies: methodological issues and perspectives

scientific article published on 30 April 2011

Gene2vec: distributed representation of genes based on co-expression

article

Genes and microRNAs associated with mouse cleft palate: A systematic review and bioinformatics analysis

scientific article published on 20 February 2018

Genetic Relationship between Schizophrenia and Nicotine Dependence

scientific article published on 10 May 2016

Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy

scientific article

Genome-Wide Correlation of DNA Methylation and Gene Expression in Postmortem Brain Tissues of Opioid Use Disorder Patients

scientific article published on 01 November 2021

Genome-Wide Meta-Analyses of FTND and TTFC Phenotypes

scientific article published on 11 July 2019

Genome-wide association study of HIV-associated neurocognitive disorder (HAND): A CHARTER group study

scientific article published on 26 April 2017

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

scientific article published in April 2018

Genomic landscape of a metastatic malignant proliferating tricholemmal tumor and its response to PI3K inhibition

scientific article published on 15 February 2019

H19, a Long Non-coding RNA, Mediates Transcription Factors and Target Genes through Interference of MicroRNAs in Pan-Cancer

scientific article published on 27 May 2020

Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer

scientific article published on 19 November 2014

Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat.

scientific article

Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts

scientific article published on 01 September 2020

Impacts of somatic mutations on gene expression: an association perspective

scientific article published on 28 April 2016

Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer

scientific article published on 23 April 2015

Integrated approach in systems biology

scientific article published on 31 December 2014

Integrative genomics and computational systems medicine

scientific article

Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer ⬇️

scientific article published on December 17, 2012

Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics

scientific article published on 04 February 2019

Key regulators in prostate cancer identified by co-expression module analysis

scientific article

Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study

scientific article published on 24 December 2016

KinaseMD: kinase mutations and drug response database

scientific article published on 02 November 2020

Lung Cancer: One Disease or Many

scientific article published on 05 June 2018

MET Exon 14 Skipping in Non-Small Cell Lung Cancer.

scientific article published on 28 March 2016

MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis

scientific article

Machine learning to predict delayed cerebral ischemia and outcomes in subarachnoid hemorrhage

scientific article published on 12 November 2020

Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties

scientific article

Mega-analysis of Odds Ratio: A Convergent Method for a Deep Understanding of the Genetic Evidence in Schizophrenia

scientific article published on 01 April 2019

MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors

scientific article published on 21 January 2020

MicroRNA-124-3p suppresses mouse lip mesenchymal cell proliferation through the regulation of genes associated with cleft lip in the mouse

scientific article published on 14 November 2019

MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip

article

Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumors

scientific article published on 02 July 2020

Multi-Objective Optimized Fuzzy Clustering for Detecting Cell Clusters from Single-Cell Expression Profiles

scientific article published on 13 August 2019

Multi-dimensional prioritization of dental caries candidate genes and its enriched dense network modules

scientific article

Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression

scientific article published on 06 January 2020

Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study

scientific article

Multiple transcription factors contribute to inter-chromosomal interaction in yeast

scientific article published on 21 December 2018

NGS catalog: A database of next generation sequencing studies in humans

scientific article published on 19 April 2012

Network analysis of EtOH-related candidate genes

scientific article

Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia ⬇️

scientific article published on July 5, 2012

Network-assisted Causal Gene Detection in Genome-wide Association Studies: An Improved Module Search Algorithm

scientific article

Network-assisted prediction of potential drugs for addiction

scientific article

Network-based identification of critical regulators as putative drivers of human cleft lip

scientific article published on 31 January 2019

Network.assisted analysis to prioritize GWAS results: principles, methods and perspectives

scientific article published on February 2014

Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance

scientific article published on 03 June 2013

Oncolytic HSV therapy modulates vesicular trafficking inducing cisplatin sensitivity and anti-tumor immunity

scientific article published on 21 October 2020

Optimizing the sequence of anti-EGFR-targeted therapy in EGFR-mutant lung cancer

scientific article

Pathway and Network Analysis of Schizophrenia Candidate Genes under Meta-Analysis Linkage Peaks

article

Pathway- and network-based analysis of GWAS data revealed susceptibility gene sets to schizophrenia

scientific article published on 23 July 2010

Pathway-based analysis of GWAS datasets: effective but caution required ⬇️

scientific article published on December 16, 2010

Patient-derived iPSCs link elevated mitochondrial respiratory complex I function to osteosarcoma in Rothmund-Thomson syndrome

scientific article published on 29 December 2021

Patterns and processes of somatic mutations in nine major cancers

scientific article

Personalized Pathway Enrichment Map of Putative Cancer Genes from Next Generation Sequencing Data ⬇️

scientific article (publication date: 2012)

Prioritization of Epilepsy Associated Candidate Genes by Convergent Analysis ⬇️

scientific article published on February 24, 2011

Prioritization of risk genes in multiple sclerosis by a refined Bayesian framework followed by tissue-specificity and cell type feature assessment

scientific article published on 11 May 2022

Protein-Protein Interaction and Pathway Analyses of Top Schizophrenia Genes Reveal Schizophrenia Susceptibility Genes Converge on Common Molecular Networks and Enrichment of Nucleosome (Chromatin) Assembly Genes in Schizophrenia Susceptibility Loci ⬇️

scientific article published on May 12, 2013

Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy

scientific article

Rationale for co-targeting IGF-1R and ALK in ALK fusion-positive lung cancer

scientific article

Retraction Note: Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts

scientific article published on 01 December 2020

SZGR 2.0: a one-stop shop of schizophrenia candidate genes

scientific article published on 12 October 2016

Schizophrenia gene networks and pathways and their applications for novel candidate gene selection

scientific article

Searching joint association signals in CATIE schizophrenia genome-wide association studies through a refined integrative network approach ⬇️

scientific article published on October 26, 2012

Splicing QTL of human adipose-related traits.

scientific article published on 10 January 2018

Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome

scientific article

Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis

scientific article

TET2 stabilization by 14-3-3 binding to the phosphorylated Serine 99 is deregulated by mutations in cancer

scientific article published on 03 January 2019

TSEA-DB: a trait-tissue association map for human complex traits and diseases

scientific article published on 01 January 2020

Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury

scientific article published on 16 February 2016

Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer

scientific article

Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma

scientific article published on 10 September 2020

TissGDB: tissue-specific gene database in cancer.

scientific article published on 25 September 2017

Top associated SNPs in prostate cancer are significantly enriched in cis-expression quantitative trait loci and at transcription factor binding sites

scientific article

Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder

scientific article

Translational bioinformatics in mental health: open access data sources and computational biomarker discovery

scientific article published on 27 November 2017

Two non-synonymous markers in PTPN21, identified by genome-wide association study data-mining and replication, are associated with schizophrenia

scientific article

Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening

scientific article published on 3 October 2017

VERSE: a novel approach to detect virus integration in host genomes through reference genome customization

scientific article

VISDB: a manually curated database of viral integration sites in the human genome

scientific article published on 01 January 2020

VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data

scientific article

VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data

scientific article

Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels

scientific article published on 27 February 2018

White matter deficits in cocaine use disorder: convergent evidence from in vivo diffusion tensor imaging and ex vivo proteomic analysis

scientific article published on 29 April 2021

Whole-genome sequencing reveals oncogenic mutations in mycosis fungoides

scientific article published on 16 June 2015

deTS: tissue-specific enrichment analysis to decode tissue specificity

scientific article published on 01 October 2019

dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks ⬇️

scientific article published on November 2, 2010

scGWAS: landscape of trait-cell type associations by integrating single-cell transcriptomics-wide and genome-wide association studies

scientific article published in 2022

scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells

scientific article published on 5 December 2017

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