Zhongming Zhao

Zhongming Zhao

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Zhongming Zhao

Publications by authors named "Zhongming Zhao"

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100Publications

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Subtype-specific signaling pathways and genomic aberrations associated with prognosis of glioblastoma.

Neuro Oncol 2018 Jul 25. Epub 2018 Jul 25.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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July 2018

Lung Cancer: One Disease or Many.

Hum Hered 2018 Jun 5;83(2):65-70. Epub 2018 Jun 5.

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June 2018

Repurposing sertraline sensitizes non-small cell lung cancer cells to erlotinib by inducing autophagy.

JCI Insight 2018 Jun 7;3(11). Epub 2018 Jun 7.

Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.

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June 2018

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

Schizophr Bull 2018 Jun 20. Epub 2018 Jun 20.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX.

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June 2018

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

Brief Bioinform 2018 May;19(3):450-460

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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May 2018

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

Transl Psychiatry 2018 May 24;8(1):105. Epub 2018 May 24.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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May 2018

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:

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April 2018

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:

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April 2018

p52 expression enhances lung cancer progression.

Sci Rep 2018 Apr 17;8(1):6078. Epub 2018 Apr 17.

Department of Cancer Biology, Vanderbilt University, Nashville, TN, 37232, USA.

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April 2018

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

Brief Bioinform 2018 Mar 20. Epub 2018 Mar 20.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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March 2018

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

Genome Med 2018 02 27;10(1):16. Epub 2018 Feb 27.

Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.

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February 2018

Advances on PPARγ Research in the Emerging Era of Precision Medicine.

Curr Drug Targets 2018 ;19(6):663-673

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States.

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January 2018

TissGDB: tissue-specific gene database in cancer.

Nucleic Acids Res 2018 Jan;46(D1):D1031-D1038

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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January 2018

Splicing QTL of human adipose-related traits.

Sci Rep 2018 Jan 10;8(1):318. Epub 2018 Jan 10.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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January 2018

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

Genome Med 2018 01 29;10(1). Epub 2018 Jan 29.

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.

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January 2018

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

Genes (Basel) 2017 Dec 5;8(12). Epub 2017 Dec 5.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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December 2017

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

Genes (Basel) 2017 Dec 28;9(1). Epub 2017 Dec 28.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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December 2017

Domain retention in transcription factor fusion genes and its biological and clinical implications: a pan-cancer study.

Oncotarget 2017 Dec 24;8(66):110103-110117. Epub 2017 Nov 24.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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December 2017

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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November 2017

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

Nat Commun 2017 Nov 17;8(1):1604. Epub 2017 Nov 17.

Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.

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November 2017

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

BMC Bioinformatics 2017 Oct 3;18(Suppl 11):405. Epub 2017 Oct 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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October 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work.

BMC Syst Biol 2017 Oct 3;11(Suppl 5):88. Epub 2017 Oct 3.

The Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA.

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October 2017

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

BMC Genomics 2017 Oct 3;18(Suppl 6):680. Epub 2017 Oct 3.

Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, No. 29 Jiangjun Avenue, Nanjing, Jiangsu, 211106, China.

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October 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics.

BMC Genomics 2017 Oct 3;18(Suppl 6):703. Epub 2017 Oct 3.

Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.

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October 2017

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.

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October 2017

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

BMC Bioinformatics 2017 Sep 2;18(1):388. Epub 2017 Sep 2.

Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.

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September 2017

Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data.

BMC Med Inform Decis Mak 2017 Jul 5;17(Suppl 2):77. Epub 2017 Jul 5.

University of Texas, Health Science Center at Houston, of Biomedical Informatics, Houston, TX, USA.

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July 2017

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

Cancer Res 2017 06 31;77(11):2810-2821. Epub 2017 Mar 31.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas.

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June 2017

NO-BOUNDARY THINKING IN BIOINFORMATICS.

Pac Symp Biocomput 2017 ;22:646-648

Institute for Biomedical Informatics, University of Pennsylvania Philadelphia, PA 19104, USA,

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March 2017

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

Nucleic Acids Res 2017 Jan 12;45(D1):D915-D924. Epub 2016 Oct 12.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA

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January 2017

mutLBSgeneDB: mutated ligand binding site gene DataBase.

Nucleic Acids Res 2017 01 7;45(D1):D256-D263. Epub 2016 Oct 7.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA

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January 2017

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:

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January 2017

The Potential Roles of Long Noncoding RNAs (lncRNA) in Glioblastoma Development.

Mol Cancer Ther 2016 12 26;15(12):2977-2986. Epub 2016 Oct 26.

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA.

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December 2016

Transcriptome- and proteome-oriented identification of dysregulated eIF4G, STAT3, and Hippo pathways altered by PIK3CA in HER2/ER-positive breast cancer.

Breast Cancer Res Treat 2016 12 22;160(3):457-474. Epub 2016 Oct 22.

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.

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December 2016

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

BMC Genomics 2016 10 21;17(1):821. Epub 2016 Oct 21.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA.

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October 2016

Frontiers in Integrative Genomics and Translational Bioinformatics.

Biomed Res Int 2015 28;2015:725491. Epub 2015 Oct 28.

Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249, USA.

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September 2016

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

PLoS Comput Biol 2016 09 15;12(9):e1005074. Epub 2016 Sep 15.

Division of Infectious Disease, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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September 2016

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.

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August 2016

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.

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August 2016

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

BMC Genomics 2016 08 22;17 Suppl 7:524. Epub 2016 Aug 22.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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August 2016

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

BMC Genomics 2016 08 22;17 Suppl 7:532. Epub 2016 Aug 22.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA.

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August 2016

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

BMC Genomics 2016 08 22;17 Suppl 7:515. Epub 2016 Aug 22.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA.

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August 2016

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach.

BMC Syst Biol 2016 08 26;10 Suppl 3:65. Epub 2016 Aug 26.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.

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August 2016

Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015.

BMC Syst Biol 2016 08 26;10 Suppl 3:61. Epub 2016 Aug 26.

Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.

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August 2016

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 07 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

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July 2016

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.

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May 2016

The homing and inhibiting effects of hNSCs-BMP4 on human glioma stem cells.

Oncotarget 2016 Apr;7(14):17920-31

Department of Brain Protection & Plasticity Research, Beijing Institute of Basic Medical Sciences, Beijing 100850, China.

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April 2016

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

Oncologist 2016 Apr 28;21(4):481-6. Epub 2016 Mar 28.

Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA.

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April 2016

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

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February 2016

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

Sci Rep 2016 Feb 4;6:20441. Epub 2016 Feb 4.

Ph.D. Program in Computer Science, Biology, and Biochemistry, The Graduate Center, The City University of New York, New York, New York, United States of America.

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February 2016

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

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January 2016

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

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January 2016

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

Mol Biosyst 2015 Dec;11(12):3244-52

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA. and Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.

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December 2015

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.

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November 2015

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

Genome Biol 2014 ;15(10):489

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.

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October 2015

Integrated approach in systems biology.

Comput Math Methods Med 2014 31;2014:656473. Epub 2014 Dec 31.

Departments of Biomedical Informatics, Psychiatry, and Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

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October 2015

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 25;7(4):384-93. Epub 2014 Dec 25.

Departments of Biomedical Informatics, Psychiatry, and Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.

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September 2015

microRNA regulation in cancer: One arm or two arms?

Int J Cancer 2015 Sep 20;137(6):1516-8. Epub 2015 Apr 20.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN.

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September 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 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.

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September 2015

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

Bioinformatics 2015 Aug 24;31(15):2591-4. Epub 2015 Mar 24.

Department of Biomedical Informatics, Center for Quantitative Sciences.

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August 2015

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:

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July 2015

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.

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July 2015

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.

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June 2015

Bioinformatics drives the applications of next-generation sequencing in translational biomedical research.

Methods 2015 Jun;79-80:1-2

Department of Biomedical Informatics, Vanderbilt University Medical Center, United States.

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June 2015

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

Transplant Direct 2015 Jun 15;1(5):e18. Epub 2015 Jun 15.

The Transplant Center, Department of Surgery, Vanderbilt University Medical Center, Nashville, TN.

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June 2015

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.

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June 2015

Common variants in the MKL1 gene confer risk of schizophrenia.

Schizophr Bull 2015 May 7;41(3):715-27. Epub 2014 Nov 7.

Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China;

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May 2015

In-depth genomic data analyses revealed complex transcriptional and epigenetic dysregulations of BRAFV600E in melanoma.

Mol Cancer 2015 Mar 14;14:60. Epub 2015 Mar 14.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA.

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March 2015

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

Genes Chromosomes Cancer 2015 Feb 19;54(2):110-21. Epub 2014 Nov 19.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN.

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February 2015

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.

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February 2015

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

Oncotarget 2015 Feb;6(4):2496-508

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.

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February 2015

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.

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February 2015

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.

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January 2015

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.

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January 2015

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

Sci China Life Sci 2014 Nov 18;57(11):1090-102. Epub 2014 Oct 18.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232, USA.

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November 2014

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

BMC Genomics 2014 Nov 24;15:1015. Epub 2014 Nov 24.

Center for Systems Biology, Soochow University, Jiangsu, China.

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November 2014

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.

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October 2014