Publications by authors named "Zhongming Zhao"

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Genes and microRNAs associated with mouse cleft palate: A systematic review and bioinformatics analysis.
Mech Dev 2018 Apr 21;150:21-27. Epub 2018 Feb 21.
Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA; Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA. Electronic address:


Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers.
Cell Rep 2018 Apr;23(1):255-269.e4
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:


Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening.
BMC Genomics 2017 Oct 3;18(Suppl 6):678. Epub 2017 Oct 3.
Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA.



Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes.
Am J Hum Genet 2017 Jan 8;100(1):5-20. Epub 2016 Dec 8.
Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China. Electronic address:

A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes.
J Am Med Inform Assoc 2016 Jul 28;23(4):681-91. Epub 2016 Mar 28.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37212, USA Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA


Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury.
Glia 2016 May 16;64(5):853-74. Epub 2016 Feb 16.
Institut De Neurociències and Unitat De Bioquímica, Facultat De Medicina, Universitat Autònoma De Barcelona, Bellaterra, Barcelona, 08193, Spain.


Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach.
Mol Cell Proteomics 2016 Feb 9;15(2):642-56. Epub 2015 Dec 9.
From the ‡Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37203; ‖Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232; **Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232; ¶¶School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas 77030

ccmGDB: a database for cancer cell metabolism genes.
Nucleic Acids Res 2016 Jan 30;44(D1):D959-68. Epub 2015 Oct 30.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37212, USA

TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes.
Nucleic Acids Res 2016 Jan 20;44(D1):D1023-31. Epub 2015 Nov 20.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37212, USA School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA

Systematic Integration of Brain eQTL and GWAS Identifies ZNF323 as a Novel Schizophrenia Risk Gene and Suggests Recent Positive Selection Based on Compensatory Advantage on Pulmonary Function.
Schizophr Bull 2015 Nov 10;41(6):1294-308. Epub 2015 Mar 10.
Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; CAS Center for Excellence in Brain Science, Chinese Academy of Sciences, Shanghai, 200031, China.

ERBB activation modulates sensitivity to MEK1/2 inhibition in a subset of driver-negative melanoma.
Oncotarget 2015 Sep;6(26):22348-60
Department of Medicine/Division of Hematology-Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.

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 Sep 9;11(9):e1004497. Epub 2015 Sep 9.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer.
Methods 2015 Jul 23;83:118-27. Epub 2015 Apr 23.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States. Electronic address:

Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers.
Sci Rep 2015 Jul 9;5:12063. Epub 2015 Jul 9.
1] Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA [2] Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA [3] Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA.

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.
RNA 2015 Jun 7;21(6):1055-65. Epub 2015 Apr 7.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, USA Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee 37232, USA.

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.
PLoS Comput Biol 2015 Jun 17;11(6):e1004202. Epub 2015 Jun 17.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America; Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.


Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC.
Mol Cell 2015 May 26;58(3):440-52. Epub 2015 Mar 26.
Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Electronic address:


Optimizing the sequence of anti-EGFR-targeted therapy in EGFR-mutant lung cancer.
Mol Cancer Ther 2015 Feb 4;14(2):542-52. Epub 2014 Dec 4.
Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee. Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee. Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.

Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation.
Bioinformatics 2015 Jan 5;31(1):84-93. Epub 2014 Sep 5.
Department of Biomedical Informatics, Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, Department of Psychiatry and Department of Cancer Biology, Vanderbilt University, Nashville, TN 37212, USA Department of Biomedical Informatics, Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, Department of Psychiatry and Department of Cancer Biology, Vanderbilt University, Nashville, TN 37212, USA Department of Biomedical Informatics, Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37232, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, Department of Psychiatry and Department of Cancer Biology, Vanderbilt University, Nashville, TN 37212, USA.


MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets.
Sci Rep 2015 Jan 23;5:8004. Epub 2015 Jan 23.
1] Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA [2] Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA [3] Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37212, USA [4] Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, 37232, USA.


Top associated SNPs in prostate cancer are significantly enriched in cis-expression quantitative trait loci and at transcription factor binding sites.
Oncotarget 2014 Aug;5(15):6168-77
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, USA; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA.

A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks.
PLoS One 2014 23;9(7):e103142. Epub 2014 Jul 23.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America; Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.


Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach.
Genome Med 2014 14;6(10):81. Epub 2014 Oct 14.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 600, Nashville, TN 37203 USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA.


VERSE: a novel approach to detect virus integration in host genomes through reference genome customization.
Genome Med 2015 20;7(1). Epub 2015 Jan 20.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA.

Classification of Cancer Primary Sites Using Machine Learning and Somatic Mutations.
Biomed Res Int 2015 11;2015:491502. Epub 2015 Oct 11.
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37212, USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

Critical Genomic Networks and Vasoreactive Variants in Idiopathic Pulmonary Arterial Hypertension.
Am J Respir Crit Care Med 2016 08;194(4):464-75
6 Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee.



Distinct lithium-induced gene expression effects in lymphoblastoid cell lines from patients with bipolar disorder.
Eur Neuropsychopharmacol 2017 11 20;27(11):1110-1119. Epub 2017 Sep 20.
Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, United States. Electronic address:

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