Zhongming Zhao

Zhongming Zhao, Jingchun Sun, Po-Hsiu Kuo, 2008, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

Pancreatic cancer ductal cell of origin drives CD73-dependent generation of immunosuppressive adenosine

Zhongming Zhao, P. Brown, D. Bar-Sagi, 2021, bioRxiv.

Prioritization and Evaluation of Depression Candidate Genes by Combining Multidimensional Data Resources

Zhongming Zhao, Po-Hsiu Kuo, Chung-Feng Kao, 2011, PloS one.

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

William Pao, Zhongming Zhao, Ronglai Shen, 2014, Nature Medicine.

Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs

Peilin Jia, Zhongming Zhao, Patrick F. Sullivan, 2010, Molecular Psychiatry.

IL-15 Regulates Homeostasis and Terminal Maturation of NKT Cells

Jelena S. Bezbradica, Zhongming Zhao, Jingchun Sun, 2011, The Journal of Immunology.

Racial differences in genomic features and new trans-ancestry prognosis subtypes in bladder cancer

Zhongming Zhao, X. Yi, P. Jia, 2021 .

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

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature.

A comparative study of cancer proteins in the human protein-protein interaction network

Zhongming Zhao, Jingchun Sun, Zhongming Zhao, 2010, BMC Genomics.

Global Network Features of Cancer Genes in the Human Interactome

Peilin Jia, Zhongming Zhao, Jingchun Sun, 2009, 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing.

MicroRNA-138 suppresses glioblastoma proliferation through downregulation of CD44

Zhongming Zhao, G. Calin, Young-Jun Jeon, 2021, Scientific Reports.

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

Zhongming Zhao, M. Washington, P. Jia, 2013, Cancer.

MitoTrace: A Computational Framework for Analyzing Mitochondrial Variation in Single-Cell RNA Sequencing Data

D. Samuels, Wankun Deng, Mingqiang Wang, 2023, Genes.

Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration

Fabian J Theis, Zhongming Zhao, L. Simon, 2019, bioRxiv.

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

Zhongming Zhao, P. Jia, B. Fang, 2020, Frontiers in Microbiology.

Cell-Type-Specific Profibrotic Scores across Multi-Organ Systems Predict Cancer Prognosis

Zhongming Zhao, P. Jia, Huihui Fan, 2021, Cancers.

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

Fabian J. Theis, Zhongming Zhao, Fabian J Theis, 2020, Nature Communications.

Causal Inference of Genetic Variants and Genes in Amyotrophic Lateral Sclerosis

Zhongming Zhao, P. Jia, Yulin Dai, 2022, Frontiers in Genetics.

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.

Zhongming Zhao, P. Jia, B. Su, 2014, Schizophrenia bulletin.

The dystrobrevin-binding protein 1 gene: features and networks

K. Kendler, Jingchun Sun, B. Riley, 2009, Molecular Psychiatry.

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

Zhongming Zhao, P. Jia, Huiping Zhang, 2020, Journal of Medical Genetics.

Transcriptome Sequencing and Genome-wide Association Analyses Reveal Lysosomal Function and Actin Cytoskeleton Remodeling in Schizophrenia and Bipolar Disorder

Peilin Jia, Zhongming Zhao, Jingchun Sun, 2014, Molecular Psychiatry.

Integrative Analysis of Common Neurodegenerative Diseases Using Gene Association, Interaction Networks and mRNA Expression Data

Zhongming Zhao, Mehmet Koyutürk, Sean Maxwell, 2012, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

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

Peilin Jia, Zhongming Zhao, Bairong Shen, 2014, Oncotarget.

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

Zhongming Zhao, N. Cox, F. Cheng, 2018, Genome Medicine.

Genetic Variation in Iron Metabolism Is Associated with Neuropathic Pain and Pain Severity in HIV-Infected Patients on Antiretroviral Therapy

Zhongming Zhao, P. Jia, I. Grant, 2014, PloS one.

Integration of millions of transcriptomes using batch-aware triplet neural networks

Zhongming Zhao, Lukas M. Simon, Yin-Ying Wang, 2021, Nature Machine Intelligence.

Meta-analyses of genome-wide linkage scans of anxiety-related phenotypes

N. Wray, Zhongming Zhao, P. Sham, 2012, European Journal of Human Genetics.

The current Salmonella‐host interactome

Zhongming Zhao, J. Klein-Seetharaman, Jingchun Sun, 2012, Proteomics. Clinical applications.

Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana

Zhongming Zhao, Yuhua Li, K. Chong, 2008, Cell Research.

Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer

Jing Wang, Hao Wang, Hua Xu, 2017, BMC Bioinformatics.

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

Zhongming Zhao, A. Franco, S. Lane, 2021, Translational Psychiatry.

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

Zhongming Zhao, P. Jia, Yulin Dai, 2021, Briefings Bioinform..

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

Zhongming Zhao, P. Jia, Guangsheng Pei, 2019, Nucleic Acids Res..

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

Zhongming Zhao, P. Jia, Xiaoming Liu, 2019, BMC Genomics.

Deep generative neural network for accurate drug response imputation

Zhongming Zhao, P. Jia, Guangsheng Pei, 2021, Nature Communications.

Prioritization and Association Analysis of Murine-Derived Candidate Genes in Anxiety-Spectrum Disorders

Zhongming Zhao, J. Flint, K. Kendler, 2011, Biological Psychiatry.

Distinct lithium-induced gene expression effects in lymphoblastoid cell lines from patients with bipolar disorder

Zhongming Zhao, C. Bowden, Junfei Zhao, 2017, European Neuropsychopharmacology.

Investigating association of four gene regions (GABRB3, MAOB, PAH, and SLC6A4) with five symptoms in schizophrenia

Zhongming Zhao, Jingchun Sun, H. Meltzer, 2012, Psychiatry Research.

Association study of 83 candidate genes for bipolar disorder in chromosome 6q selected using an evidence‐based prioritization algorithm

F. McMahon, Zhongming Zhao, C. Pato, 2013, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

Clonal architectures predict clinical outcome in clear cell renal cell carcinoma

Z. Cai, X. Fang, X. Yi, 2019, Nature Communications.

Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome.

Zhongming Zhao, Fengkai Zhang, Zhongming Zhao, 2006, Gene.

Landscape of drug-resistance mutations in kinase regulatory hotspots

Zhongming Zhao, Pora Kim, Hanyang Li, 2020, Briefings Bioinform..

Genome-wide association study of antipsychotic induced QTc interval prolongation

Peilin Jia, Zhongming Zhao, Patrick F. Sullivan, 2010, The Pharmacogenomics Journal.

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

Peilin Jia, Zhongming Zhao, Pora Kim, 2016, Briefings Bioinform..

Informatics and machine learning methods for health applications

Kai Wang, Li Shen, Zhongming Zhao, 2020, BMC Medical Informatics and Decision Making.

NOTCH induced MDSC recruitment after oHSV virotherapy in CNS cancer models modulates anti-tumor immunotherapy.

Zhongming Zhao, S. Lawler, H. Nakashima, 2022, Clinical cancer research : an official journal of the American Association for Cancer Research.

Comprehensive characterization of tumor immune landscape following oncolytic virotherapy by single-cell RNA sequencing

Zhongming Zhao, Xiaoliu Zhang, Guangsheng Pei, 2021, Cancer Immunology, Immunotherapy.

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

Zhongming Zhao, P. Jia, E. Galea, 2016, Glia.

Consensus Rules in Variant Detection from Next-Generation Sequencing Data

Fei Li, Peilin Jia, William Pao, 2012, PloS one.

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

Peilin Jia, Zhongming Zhao, Fazil Aliev, 2012, BMC Genomics.

Dense module searching for gene networks associated with multiple sclerosis

Zhongming Zhao, P. Jia, Yulin Dai, 2020, BMC Medical Genomics.

Frequent gene conversion between human red and green opsin genes

Zhongming Zhao, D. Hewett‐Emmett, Wen-Hsiung Li, 1998, Journal of Molecular Evolution.

DNA Methylation Profiling Distinguishes Three Clusters of Breast Cancer Cell Lines

Zhongming Zhao, Siyuan Zheng, Zhongming Zhao, 2012, Chemistry & biodiversity.

Schizophrenia Gene Networks and Pathways and Their Applications for Novel Candidate Gene Selection

Peilin Jia, Zhongming Zhao, Jingchun Sun, 2010, PloS one.

Single-cell RNA sequencing reveals a strong connection between Gadd45g upregulation and oncolytic HSV infection in tumor tissue

Zhongming Zhao, Xiaoliu Zhang, Guangsheng Pei, 2021, Molecular therapy oncolytics.

Co-delivery of novel bispecific and trispecific engagers by an amplicon vector augments the therapeutic effect of an HSV-based oncolytic virotherapy

Zhongming Zhao, P. Gunaratne, Xiaoliu Zhang, 2021, Journal for ImmunoTherapy of Cancer.

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

Martin J. Aryee, Zhongming Zhao, A. Iafrate, 2016, The oncologist.

Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues

Zhongming Zhao, Kellie J. Archer, Tobias Guennel, 2010, Int. J. Comput. Biol. Drug Des..

FOXK1 Participates in DNA Damage Response by Controlling 53BP1 Function

Zhongming Zhao, Junjie Chen, Xu Li, 2020, Cell reports.

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

Peilin Jia, Zhongming Zhao, Wei Zhao, 2017, BMC Genomics.

Dynamic protein interaction modules in human hepatocellular carcinoma progression

Chen-Ching Lin, Hui Yu, Zhongming Zhao, 2013, BMC Systems Biology.

Characterization of genome-wide association study data reveals spatiotemporal heterogeneity of mental disorders

Zhongming Zhao, P. Jia, Guangsheng Pei, 2020, BMC Medical Genomics.

Nucleotide Variation and Haplotype Diversity in a 10-kb Noncoding Region in Three Continental Human Populations

Zhongming Zhao, Yun-Xin Fu, Wen-Hsiung Li, 2006, Genetics.

Progression of prostate carcinoma is promoted by adipose stromal cell-secreted CXCL12 signaling in prostate epithelium

Zhongming Zhao, Achinto Saha, J. DiGiovanni, 2021, npj Precision Oncology.

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

Hua Sun, Peilin Jia, Zhongming Zhao, 2019, Briefings Bioinform..

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

Zhongming Zhao, Xiaoqian Jiang, S. Savitz, 2020, Research square.

Drug repurposing for COVID-19 using graph neural network and harmonizing multiple evidence

Zhongming Zhao, Xiaoqian Jiang, Jing Tang, 2020, Scientific Reports.

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

Jing Tang, Zhongming Zhao, Yejin Kim, 2020, Research square.

Tissue-Specific Signaling Networks Rewired by Major Somatic Mutations in Human Cancer Revealed by Proteome-Wide Discovery.

Zhongming Zhao, Feixiong Cheng, Junfei Zhao, 2017, Cancer research.

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

Zhongming Zhao, P. Jia, J. Iwata, 2020, BMC Medical Genomics.

Lung Cancer: One Disease or Many

Zhongming Zhao, P. Jia, M. Aldrich, 2018, Human Heredity.

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

Zhongming Zhao, P. Jia, M. Landi, 2018, Genome Medicine.

Functional Features, Biological Pathways, and Protein Interaction Networks of Addiction‐Related Genes

Zhongming Zhao, Jingchun Sun, Zhongming Zhao, 2010, Chemistry & biodiversity.

Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach*

Zhongming Zhao, Feixiong Cheng, Junfei Zhao, 2015, Molecular & Cellular Proteomics.

Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach

Zhongming Zhao, F. Cheng, Chen-Ching Lin, 2014, Genome Medicine.

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

Zhongming Zhao, C. Coarfa, Sohaib A. Khan, 2020, Nature Communications.

Cell-type deconvolution analysis identifies cancer-associated myofibroblast component as a poor prognostic factor in multiple cancer types

Zhongming Zhao, Jun Yao, P. Jia, 2021, Oncogene.

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

Zhongming Zhao, P. Jia, Guangsheng Pei, 2019, Front. Genet..

Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020

Zhongming Zhao, Xinghua Shi, Yulin Dai, 2020, BMC Bioinformatics.

Detecting methylation signatures in neurodegenerative disease by density-based clustering of applications with reducing noise

Zhongming Zhao, Saurav Mallik, Zhongming Zhao, 2020, Scientific Reports.

Splicing QTL of human adipose-related traits

P. Jia, Liang Ma, Zhongming Zhao, 2018, Scientific Reports.

Functional SNPs are enriched for schizophrenia association signals

M C O'Donovan, K. Kendler, Jingchun Sun, 2014, Molecular Psychiatry.

Genetic overlap of schizophrenia and bipolar disorder in a high‐density linkage survey in the Portuguese Island population

Zhongming Zhao, F. Middleton, C. Pato, 2012, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

Conservation and divergence of DNA methylation in eukaryotes

Zhongming Zhao, Leng Han, Zhixi Su, 2011, Epigenetics.

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

Junfeng Xia, Peilin Jia, William Pao, 2015, Methods.

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

Zhongming Zhao, Junjie Zhu, Yuan Cao, 2017, Genes.

scRNASeqDB: a database for gene expression profiling in human single cell by RNA-seq

Peilin Jia, Zhongming Zhao, Junjie Zhu, 2017, bioRxiv.

Hypoxia‐inducible factor‐dependent induction of myeloid‐derived netrin‐1 attenuates natural killer cell infiltration during endotoxin‐induced lung injury

Zhongming Zhao, Guangsheng Pei, H. Eltzschig, 2021, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Glucocorticoids enhance the anti-leukemic activity of FLT3 inhibitors in FLT3 mutant acute myeloid leukemia.

Zhongming Zhao, Zhenqiu Liu, Hong-Gang Wang, 2020, Blood.

Overexpression of miR-1306-5p, miR-3195, and miR-3914 Inhibits Ameloblast Differentiation through Suppression of Genes Associated with Human Amelogenesis Imperfecta

J. Iwata, A. Suzuki, Yin-Ying Wang, 2021, International journal of molecular sciences.

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

P. Jia, Quan Wang, Min Zhao, 2013, BMC Bioinformatics.

p52 expression enhances lung cancer progression

Zhongming Zhao, P. Massion, L. Gleaves, 2018, Scientific Reports.

Investigating Cellular Trajectories in the Severity of COVID-19 and Their Transcriptional Programs Using Machine Learning Approaches

Zhongming Zhao, L. Simon, Hyun-hwan Jeong, 2021, Genes.

INSCT: Integrating millions of single cells using batch-aware triplet neural networks

Lukas M. Simon, Yin-Ying Wang, Zhongming Zhao, 2020, bioRxiv.

Optimizing the Sequence of Anti-EGFR–Targeted Therapy in EGFR-Mutant Lung Cancer

X. Chen, Zhongming Zhao, M. Ladanyi, 2014, Molecular Cancer Therapeutics.

L-arginine Supplementation Improves Responses to Injury and Inflammation in Dextran Sulfate Sodium Colitis

Zhongming Zhao, M. Kay Washington, Kshipra Singh, 2012, PloS one.

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

Peilin Jia, William Pao, Zhongming Zhao, 2014, Cell reports.

An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC)

Z. Ding, Xingyi Guo, Yuanyuan Wang, 2016, BMC Genomics.

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers

Zhongming Zhao, Feixiong Cheng, Jun Li, 2018, Cell reports.

Protein tyrosine phosphatase receptor δ serves as the orexigenic asprosin receptor.

Zhongming Zhao, P. Jia, C. Flask, 2022, Cell metabolism.

CpG islands: algorithms and applications in methylation studies.

Zhongming Zhao, Leng Han, Zhongming Zhao, 2009, Biochemical and biophysical research communications.

Methylation-dependent transition rates are dependent on local sequence lengths and genomic regions.

Zhongming Zhao, Cizhong Jiang, Zhongming Zhao, 2007, Molecular biology and evolution.

Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology

Zhongming Zhao, Lei Xie, Hua Xu, 2016, Scientific Reports.

SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)

Zhongming Zhao, Fengkai Zhang, Fengkai Zhang, 2005, Bioinform..

Genetic Variation in VEGF Family Genes and Breast Cancer Risk: A Report from the Shanghai Breast Cancer Genetics Study

Zhongming Zhao, J. Long, X. Shu, 2010, Cancer Epidemiology, Biomarkers & Prevention.

ERGR: An ethanol-related gene resource

An-Yuan Guo, Zhongming Zhao, Kenneth S. Kendler, 2008, Nucleic Acids Res..

Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome.

Zhongming Zhao, Eric Boerwinkle, Zhongming Zhao, 2002, Genome research.

Concordance of copy number loss and down-regulation of tumor suppressor genes: a pan-cancer study

Zhongming Zhao, Min Zhao, Zhongming Zhao, 2016, BMC Genomics.

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

P. Jia, G. Jun, J. Iwata, 2019, BMC Medical Genomics.

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

Zhongming Zhao, P. Jia, I. Grant, 2017, Fluids and Barriers of the CNS.

Association Study of 167 Candidate Genes for Schizophrenia Selected by a Multi-Domain Evidence-Based Prioritization Algorithm and Neurodevelopmental Hypothesis

Peilin Jia, Zhongming Zhao, Ayman H. Fanous, 2013, PloS one.

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

Peilin Jia, Zhongming Zhao, Jingchun Sun, 2011, Schizophrenia Research.

Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis

Zhongming Zhao, Jingchun Sun, Leng Han, 2010, Artif. Intell. Medicine.

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

Peilin Jia, Zhongming Zhao, Jingchun Sun, 2009, Bioinform..

Schizophrenia Genes: Characteristics of Function and Protein Interaction Networks

Zhongming Zhao, Jingchun Sun, Leng Han, 2008, 2008 International Conference on BioMedical Engineering and Informatics.

DCGL v2.0: An R Package for Unveiling Differential Regulation from Differential Co-expression

Zhongming Zhao, Bao-Hong Liu, Yi-Xue Li, 2013, PloS one.

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

Peilin Jia, Zhongming Zhao, Zhongming Zhao, 2012, PloS one.

Common variants in the MKL1 gene confer risk of schizophrenia.

Zhongming Zhao, E. Oord, Yong-Gang Yao, 2015, Schizophrenia bulletin.

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

Zhongming Zhao, Jiayang Sun, Xingyi Guo, 2015, Bioinform..

Advances in systems biology: computational algorithms and applications

Hua Xu, Yufei Huang, Zhongming Zhao, 2012, BMC Systems Biology.

Exploring schizophrenia drug-gene interactions through molecular network and pathway modeling.

Daniel K. Putnam, Zhongming Zhao, Jingchun Sun, 2011, AMIA ... Annual Symposium proceedings. AMIA Symposium.

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics with bigger data and wider applications

Jingwen Yan, Jianhua Ruan, Zhijin Wu, 2019, BMC Genomics.

Intravenous Glial Growth Factor 2 (GGF2) Isoform of Neuregulin-1β Improves Left Ventricular Function, Gene and Protein Expression in Rats after Myocardial Infarction

Zhongming Zhao, F. Harrell, D. Sawyer, 2013, PloS one.

Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs

Hua Xu, Mei Liu, Zhongming Zhao, 2012, J. Am. Medical Informatics Assoc..

Concordant dysregulation of miR-5p and miR-3p arms of the same precursor microRNA may be a mechanism in inducing cell proliferation and tumorigenesis: a lung cancer study

Zhongming Zhao, S. Bandyopadhyay, Chen-Ching Lin, 2015, RNA.

Network-Assisted Prediction of Potential Drugs for Addiction

Zhongming Zhao, Jingchun Sun, Hua Xu, 2014, BioMed research international.

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

Zhongming Zhao, P. Jia, Bairong Shen, 2014, BMC Genomics.

Circular RNA expression profiles and features in human tissues: a study using RNA-seq data

Zhongming Zhao, Xiaofeng Song, Jing Wu, 2017, BMC Genomics.

Functional Implications of Biochemical and Molecular Characteristics of Donation After Circulatory Death Livers

Zhongming Zhao, L. Marnett, Hui Yu, 2015, Transplantation direct.

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

Zhongming Zhao, C. Lovly, J. Gilbert, 2019, npj Precision Oncology.

Connectivity map analysis of nonsense-mediated decay-positive BMPR2-related hereditary pulmonary arterial hypertension provides insights into disease penetrance.

Zhongming Zhao, Siyuan Zheng, J. Cogan, 2012, American journal of respiratory cell and molecular biology.

Virus interactions with human signal transduction pathways

Jaime G. Carbonell, Judith Klein-Seetharaman, Junfeng Xia, 2011, Int. J. Comput. Biol. Drug Des..

Systematic dissection of dysregulated transcription factor–miRNA feed-forward loops across tumor types

Wei Jiang, Chen-Ching Lin, Zhongming Zhao, 2015, Briefings Bioinform..

MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets

Zhongming Zhao, S. Bandyopadhyay, D. Ghosh, 2015, Scientific Reports.

The oncogenic and prognostic potential of eight microRNAs identified by a synergetic regulatory network approach in lung cancer

Zhongming Zhao, Ramkrishna Mitra, Zhongming Zhao, 2014, Int. J. Comput. Biol. Drug Des..

A Tri-Component Conservation Strategy Reveals Highly Confident MicroRNA-mRNA Interactions and Evolution of MicroRNA Regulatory Networks

Zhongming Zhao, Chen-Ching Lin, R. Mitra, 2014, PloS one.

OP-BIBJ150107 996..1008

Zhongming Zhao, F. Cheng, Quan Wang, 2016 .

Effects of tamoxifen inducible MerCreMer on gene expression in cardiac myocytes in mice

Zhongming Zhao, A. Marian, Hyun-hwan Jeong, 2022, The journal of cardiovascular aging.

Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data

Zhongming Zhao, Bairong Shen, Jiajia Chen, 2015, BMC Genomics.

Oncogenes and tumor suppressor genes: comparative genomics and network perspectives

Zhongming Zhao, Jingchun Sun, Qi Liu, 2015, BMC Genomics.

Exploring drug-target interaction networks of illicit drugs

Jingchun Sun, R. Atreya, Zhongming Zhao, 2013, BMC Genomics.

Characterization of Schizophrenia Adverse Drug Interactions through a Network Approach and Drug Classification

Zhongming Zhao, A. Fanous, Jingchun Sun, 2013, BioMed research international.

A network and functional investigation of illicit drugs and their targets

Zhongming Zhao, Jingchun Sun, Ravi V. Atreya, 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops.

DTome: a web-based tool for drug-target interactome construction

Hua Xu, Zhongming Zhao, Yonghui Wu, 2012, BMC Bioinformatics.

Network‐Assisted Investigation of Antipsychotic Drugs and Their Targets

Zhongming Zhao, Jingchun Sun, Hua Xu, 2012, Chemistry & biodiversity.

Development and implementation of a novel computational tool for an efficient construction of drug-target interactome

Zhongming Zhao, Paul Hart, Jingchun Sun, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

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

Junfeng Xia, Peilin Jia, Zhongming Zhao, 2011, Comput. Biol. Chem..

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes

Chuan Wang, Qi Liu, Zhongming Zhao, 2007, BMC Bioinformatics.

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

Peilin Jia, Zhongming Zhao, Guangsheng Pei, 2019, Bioinform..

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data

Peilin Jia, Zhongming Zhao, Zhongming Zhao, 2014, PLoS Comput. Biol..

Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes.

Qiancheng Shen, Jian Zhang, F. Cheng, 2017, American Journal of Human Genetics.

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

Yaomin Xu, Xingyi Guo, Jiayang Sun, 2015, Bioinform..

Objective Radiographic Response to MEK Inhibitor Therapy in a Patient with a Metastatic Melanoma with a BRAF

Zhongming Zhao, J. Netterville, P. Jia, 2012 .

A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts.

Vladimir I. Vladimirov, J. Nurnberger, Zhongming Zhao, 2010, Human molecular genetics.

Apoptotic Engulfment Pathway and Schizophrenia

Zhongming Zhao, A. Fanous, K. Kendler, 2009, PloS one.

Epidemic Clostridioides difficile Ribotype 027 Lineages: Comparisons of Texas Versus Worldwide Strains

Zhongming Zhao, K. Garey, T. Savidge, 2019, Open forum infectious diseases.

mutLBSgeneDB: mutated ligand binding site gene DataBase

Zhongming Zhao, Pinyi Lu, Pora Kim, 2016, Nucleic Acids Res..

Genome-Wide Meta-Analyses of FTND and TTFC Phenotypes.

Ming D. Li, L. Bierut, Zhongming Zhao, 2019, Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco.

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

Peilin Jia, Zhongming Zhao, Yulin Dai, 2018, Database J. Biol. Databases Curation.

Genome-Wide DNA Methylation Profiling in 40 Breast Cancer Cell Lines

Tim Hui-Ming Huang, Zhongming Zhao, Leng Han, 2010, ICIC.

Extracellular Matrix/Integrin Signaling Promotes Resistance to Combined Inhibition of HER2 and PI3K in HER2+ Breast Cancer.

F. Cheng, Junfei Zhao, M. V. Estrada, 2017, Cancer research.

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

Zhongming Zhao, Feixiong Cheng, Junfei Zhao, 2016, PLoS Comput. Biol..

Oncolytic HSV Therapy Modulates Vesicular Trafficking Inducing Cisplatin Sensitivity and Antitumor Immunity

Zhongming Zhao, A. Sood, Z. Siddik, 2020, Clinical Cancer Research.

Algorithms for network-based identification of differential regulators from transcriptome data: a systematic evaluation

Hui Yu, Jing Yang, Ramkrishna Mitra, 2014, Science China Life Sciences.

Evaluating four major algorithms for identifying differential regulators in condition-specific transcriptional responses

Hui Yu, Zhongming Zhao, Zhongming Zhao, 2014, BMC Bioinformatics.

Hdac3 is essential for the maintenance of chromatin structure and genome stability.

Andrew J. Wilson, Christina E. Wells, M. Washington, 2010, Cancer cell.

Convergent evidence for Wnt signaling pathway in psychotic disorders

P. Jia, Zhongming Zhao, 2010, 2010 Biomedical Sciences and Engineering Conference.

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

P. Jia, G. Jun, J. Iwata, 2019, BMC Genomics.

Methylation of promoters of microRNAs and their host genes in myelodysplastic syndromes

Annette S. Kim, W. El-Rifai, Leng Han, 2013, Leukemia & lymphoma.

Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC.

E. Olejniczak, S. Fesik, C. M. Eischen, 2015, Molecular cell.

The WNT/β-catenin pathway regulates expression of the genes involved in cell cycle progression and mitochondrial oxidative phosphorylation in the postmitotic cardiac myocytes

Zhongming Zhao, A. Marian, Hyun-hwan Jeong, 2022, The journal of cardiovascular aging.

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

Zhongming Zhao, Peilin Jia, Ruifeng Hu, 2021, Methods.

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

Zhongming Zhao, P. Jia, A. Fanous, 2011, Journal of Medical Genetics.

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

Zhongming Zhao, J. Gingold, Dung-Fang Lee, 2021, PLoS genetics.

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

Zhongming Zhao, N. Schork, P. Jia, 2017, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

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

Zhongming Zhao, P. Jia, I. Grant, 2016, The Journal of infectious diseases.

Gene2vec: distributed representation of genes based on co-expression

Jingcheng Du, Peilin Jia, Zhongming Zhao, 2018, BMC Genomics.

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

Zhongming Zhao, Saurav Mallik, Zhongming Zhao, 2017, Genes.

Identification of gene signatures from RNA-seq data using Pareto-optimal cluster algorithm

Zhongming Zhao, Saurav Mallik, Zhongming Zhao, 2018, BMC Systems Biology.

Presence of three different paternal lineages among North Indians: A study of 560 Y chromosomes

S. Agrawal, F. Khan, M. Borkar, 2009, Annals of human biology.

Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms?

Zhongming Zhao, Jingchun Sun, Zhongming Zhao, 2007, Biochemical and biophysical research communications.

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

Qingxia Chen, Peilin Jia, William Pao, 2014, Genome Biology.

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

Zhongming Zhao, Saurav Mallik, Zhongming Zhao, 2017, Quantitative Biology.

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

Zhongming Zhao, Lukas M. Simon, Fangfang Yan, 2021, Patterns.

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

Zhongming Zhao, Saurav Mallik, Tapas Bhadra, 2020, Genes.

Genetics and Population Analysis an Efficient Hierarchical Generalized Linear Mixed Model for Pathway Analysis of Genome-wide Association Studies

Britney L. Grayson, X. Chen, P. Jia, 2022 .

Correction to: The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics

Xia Ning, E. Mathé, Yan Guo, 2019, BMC Genomics.

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

Peilin Jia, Zhongming Zhao, Ruifeng Hu, 2020, Nucleic Acids Res..

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers

J. Weinstein, F. Cheng, Jun Li, 2018, Cell reports.

A cross-cancer differential co-expression network reveals microRNA-regulated oncogenic functional modules.

Chen-Ching Lin, Zhongming Zhao, Feixiong Cheng, 2015, Molecular bioSystems.

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

Zhongming Zhao, P. Jia, Zhongming Zhao, 2013, Human Genetics.

Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma

Siyuan Zheng, S. Hiebert, W. Tansey, 2011, BMC Medical Genomics.

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

F. Cheng, P. Jia, Quan Wang, 2014, Oncotarget.

p52 expression enhances lung cancer progression

P. Massion, L. Gleaves, Hui Yu, 2018, Scientific Reports.

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

P. Jia, Han Liang, P. Kim, 2019, Briefings Bioinform..

Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science

Yufei Huang, Lang Li, Jianhua Ruan, 2016, BMC Genomics.

KCOSS: an ultra-fast k-mer counter for assembled genome analysis

Deyou Tang, Daqiang Tan, Juan Fu, 2021, Bioinform..

A Multi-classifier Model to Identify Mitochondrial Respiratory Gene Signatures in Human Cancer

Saurav Mallik, Zhongming Zhao, Tapas Bhadra, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Gene Profiling of Cancer Stem Cells-like Cells Reveals IGF-1R and IGFBP3 Pathway as a Promising Therapeutic Target for Lung Cancer

Siyuan Zheng, B. Lu, C. Speirs, 2010 .

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

Zhongming Zhao, P. Jia, W. Pao, 2012, Human mutation.

An informatics research agenda to support precision medicine: seven key areas

Marge M. Benham-Hutchins, Matthew K. Breitenstein, R. Nagarajan, 2016, J. Am. Medical Informatics Assoc..

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

Zhongming Zhao, Siyuan Zheng, Siyuan Zheng, 2011, BMC Bioinformatics.

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

Hui Yu, Peilin Jia, Zhongming Zhao, 2015, Bioinform..

0 : Edge-weighted dense module search for genome-wide association studies and gene expression profiles

P. Jia, Quan Wang, Hui Yu, 2015 .

Prioritization of Epilepsy Associated Candidate Genes by Convergent Analysis

Peilin Jia, Zhongming Zhao, Zhongming Zhao, 2011, PloS one.

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

P. Jia, Junfeng Jiang, Zhongming Zhao, 2014, Oncotarget.

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

Zhongming Zhao, P. Jia, Zhongming Zhao, 2012, BMC Genomics.

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

Zhongming Zhao, P. Jia, Qingguo Wang, 2015, Genome Medicine.

Linking Biochemical Pathways and Networks to Adverse Drug Reactions

Zhongming Zhao, Huiru Zheng, Haiying Wang, 2014, IEEE Transactions on NanoBioscience.

Spectrum of Point Mutations in the Human Genome and Major Subpopulations

P. Jia, H. Vuong, Zhongming Zhao, 2013 .

Features of Recent Codon Evolution: A Comparative Polymorphism-Fixation Study

Zhongming Zhao, Cizhong Jiang, Zhongming Zhao, 2010, Journal of biomedicine & biotechnology.

Comparative Analysis of CpG Islands in Four Fish Genomes

Zhongming Zhao, Leng Han, Zhongming Zhao, 2008, Comparative and functional genomics.

A novel statistical method to estimate the effective SNP size in vertebrate genomes and categorized genomic regions

Zhongming Zhao, Cizhong Jiang, Daekwan Seo, 2006, BMC Genomics.

Sequence context analysis in the mouse genome: single nucleotide polymorphisms and CpG island sequences.

Zhongming Zhao, Fengkai Zhang, Zhongming Zhao, 2006, Genomics.

EmptyNN: A neural network based on positive-unlabeled learning to remove cell-free droplets and recover lost cells in single-cell RNA sequencing data

Zhongming Zhao, L. Simon, Fangfang Yan, 2021, bioRxiv.