List of works - Zhongming Zhao

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

scientific article published on September 13, 2013

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

scientific article published on November 2, 2010

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

scientific article

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

scientific article

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

scientific article published on 30 April 2011

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

scientific article

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

scientific article published in April 2018

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

scientific article

A novel microRNA and transcription factor mediated regulatory network in schizophrenia

scientific article

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

scientific article

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

scientific article published on July 5, 2012

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

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

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

scientific article

Whole-genome sequencing reveals oncogenic mutations in mycosis fungoides

scientific article published on June 16, 2015

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

scientific article

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

scientific article published on 09 August 2012

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

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

scientific article

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

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

scientific article

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

scientific article published on 17 November 2017

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

scientific article published on February 1, 2014

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

scientific article

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

Deciphering the Unique MicroRNA Signature in Human Esophageal Adenocarcinoma

scientific article published on May 28, 2013

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

scientific article published on December 16, 2010

Patterns and processes of somatic mutations in nine major cancers

scientific article published on February 19, 2014

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

scientific article

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

scientific article

Beyond histology: translating tumor genotypes into clinically effective targeted therapies

scientific article

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

scientific article published on June 1, 2013

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

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

scientific article published on January 25, 2011

Asprosin is a centrally acting orexigenic hormone.

scientific article

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

scientific article

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

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

scientific article published on 19 April 2012

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

scientific article published on 16 January 2012

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

scientific article published on 24 March 2015

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

scientific article published on December 17, 2012

Genetic Relationship between Schizophrenia and Nicotine Dependence

scientific article published on 10 May 2016

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

scientific article

Consensus rules in variant detection from next-generation sequencing data

scientific article

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

scientific article

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

scientific article

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

scientific article published on 28 March 2016

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

scientific article

Prioritization of Epilepsy Associated Candidate Genes by Convergent Analysis

scientific article published on February 24, 2011

List of works by Zhongming Zhao

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

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

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

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

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

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

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

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

A novel microRNA and transcription factor mediated regulatory network in schizophrenia

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

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

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

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

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

Whole-genome sequencing reveals oncogenic mutations in mycosis fungoides

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

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

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

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

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

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

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

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

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

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

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

Deciphering the Unique MicroRNA Signature in Human Esophageal Adenocarcinoma

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

Patterns and processes of somatic mutations in nine major cancers

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

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

Beyond histology: translating tumor genotypes into clinically effective targeted therapies

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

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

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

Asprosin is a centrally acting orexigenic hormone.

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

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

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

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

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

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

Genetic Relationship between Schizophrenia and Nicotine Dependence

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

Consensus rules in variant detection from next-generation sequencing data

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

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

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

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

Prioritization of Epilepsy Associated Candidate Genes by Convergent Analysis