BIOGRAPHICAL SKETCH
NAME
POSITION TITLE
Zhao, Zhongming, Ph.D.
ZZHAO1
Chief Bioinfor. Officer, Vanderbilt-Ingram Cancer Ctr.
Associate Professor of Biomedical Informatics,
Psychiatry, and Cancer Biology
EDUCATION/TRAINING
INSTITUTION AND LOCATION
DEGREE
MM/YY
Zhejiang University
B.S.
07/91
Biology
Peking University
M.S.
07/96
Genetics
University of Texas, Houston
M.S.
08/98
Biomathematics
University of Texas, Houston and MD Anderson
Cancer Center
Ph.D.
08/00
Human and Molecular
Genetics
University of Houston
M.S.
12/02
Computer Science
Post-doc
07/02-08/03
eRA COMMONS USER NAME
The W.M. Keck Center for Computational
and Structural Biology, Houston
FIELD OF STUDY
Bioinformatics
A. Personal Statement
I have the expertise, leadership, and motivation to successfully carry out the proposed work. I have unique
interdisciplinary training and more than 16 years of bioinformatics/biomedical informatics research experience
that is important for this application. I have developed my research program based on the application of
bioinformatics and systems biology to the important but difficult problems of complex disease genetics,
especially cancer and neuropsychiatric disorders. In addition to my productive research, I have successfully
administered many projects (e.g. staffing, research protections, budget), collaborated with other researchers
(more than 50 collaborators in my academic life), and trained more than 25 students and postdocs.
Integrative analysis of genomic datasets, especially those from next generation sequencing platforms, is
shifting our paradigm in the study of complex diseases. The current proposal stands on a unique and productive
interdisciplinary collaboration. I believe my demonstrated record of successful research in the field of integrative
genomics and next generation sequencing and my strong collaboration relationships have prepared me to work
in this exciting but challenging project.
B. Positions and Honors
Positions and Employment
2001-2003
Research Fellow, Human Genetics Center, University of Texas Health Science Center at
Houston, Houston, TX
2003
Faculty Associate, Human Genetics Center, University of Texas Health Science Center at
Houston, Houston, TX
2003-2009
Assistant Professor, Departments of Psychiatry and Human Genetics, and Fellow, Center for the
Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA
2006-pres
Adjunct Professor, Shanghai Center for Bioinformatics Technology, Shanghai, China
2009-2010
Head, Bioinformatics Group, Functional Genomics Shared Resource (FGSR), Vanderbilt Univ
2009-pres
Associate Professor, Dept. of Biomedical Informatics, Vanderbilt University School of Medicine
2009-pres
Associate Professor, Dept. of Psychiatry, Vanderbilt University School of Medicine
2009-pres
Associate Professor, Dept. of Cancer Biology, Vanderbilt University Medical Center
2009-pres
Investigator, Center for Molecular Neuroscience, Vanderbilt University Medical Center
2009-pres
Chief Bioinformatics Officer, Vanderbilt-Ingram Cancer Center (VICC)
2009-pres
Director, Bioinformatics Resource Center (BRC), Vanderbilt University Medical Center
2012-pres
Associate Director, Center for Quantitative Sciences, Vanderbilt University
Honors
1995
Pratthana Life Sciences Scholarship, Peking University, China
1998, 1999, 2000 Travel Award, University of Texas Graduate School of Biomedical Sciences at Houston
2002
The Keck Foundation Post-doctoral Fellowship, The W.M. Keck Center for Computational and
Structural Biology, Houston, TX
2003
2005
2008
2009
2010
2011
2011
2011
2012-pres
The Keck Foundation Post-doctoral Fellowship, The W.M. Keck Center for Computational and
Structural Biology, Houston, TX
NARSAD Young Investigator Award (2005-2007), National Alliance for Research on
Schizophrenia and Depression
NARSAD Young Investigator Award (2008-2010)
VPSD Career Development Award from the GI SPORE Grant (NIH/NCI 50CA95103)
Nick Norgan Award for the best paper published in Annals of Human Biology during 2009
Mentor of the NARSAD Young Investigator Award to Dr. Peilin Jia and Dr. Jingchun Sun
Outstanding Achievement Award, The International Society of Intelligent Biological Medicine
Second Prize, the Best Student Paper Award Competition (received by my student Daniel
Putman), AMIA 2011 Annual Symposium
Ingram Associate Professorship
Other professional activities (2010-)
2010
2010
2010
2010
2010
2010
2010
2011
2011
2012
2012
2012
2012
2013
2013
Panel member, The Ontario Research Fund-Global Leadership in Genomics and Life Sciences
(GL2 competition, $100 million competition), The Ontario Ministry of Research and Innovation
Member, study section ZHDI-MRG C (ID), NIH
ad hoc reviewer, Molecular and Cellular Biosciences Program, National Science Foundation
ad hoc reviewer, Special Emphasis Panel, 2010/08 ZRG1 GGG-F (55) R for NIH RFA-OD-10-005
(RC4), Genes, Genomes and Genetics Study Section
ad hoc reviewer, NIH CHHD-C Developmental Biology Subcommittee
ad hoc reviewer of research proposal to Council's Triage, Medical Research Council, UK
ad hoc reviewer, Neuroscience and Mental Health, The Wellcome Trust, London, UK
ad hoc reviewer, Special Emphasis Panel 2011/10 ZGM1 BRT-X (KR), NIGMS, NIH, July, 2011
Panel member, Clusters of Excellence, German Excellence initiative the German Research
Foundation (DFG), Berlin, Germany
Reviewer for research proposal to CHILDREN with CANCER UK
ad hoc reviewer, Biodata Management and Analysis (BDMA) NIH study section
ad hoc reviewer, Special Emphasis Panel/Scientific Review Group 2012/10 ZMH1 ERB-M (06) S
Panel member, 2012 Ontario Research Fund – Personalized Health Panel
ad hoc reviewer, Special Emphasis Panel 2013/05 ZRG1 GGG-C (50), NIH/NIAMS
ad hoc reviewer, Special Panel ZDA1 SXC-E (13), CEBRA, NIH/NIDA
Editor-in-Chief, International Journal of Computational Biology and Drug Design (2012-)
Associate Editor, BMC Genomics (2010-), Academic Editor, PLoS ONE (2010-)
Editorial Board Member, Current Genomics (2008-), Genomics, Proteomics & Bioinformatics (2012-)
C. Selected Peer-Reviewed Publications (From >150 publications *corresponding author)
Most relevant to the current application
1. Zhao M, Sun J, Zhao Z* (2013) Synergetic regulatory networks mediated by oncogene-driven microRNAs
and transcription factors in serous ovarian cancer. Molecular BioSystems 9 (12): 3187-3198
2. Dahlman KB, Xia J, Hutchinson K, Ng C, Hucks D, Jia P, Atefi M, Su Z, Branch S, Lyle P, Hicks D, Bozon V,
Glaspy J, Netterville JL, Vnencak-Jones C, Sosman J, Ribas A, Zhao Z* [co-corresponding author], Pao W
(2012) BRAF L597 mutations in melanoma are associated with sensitivity to MEK inhibitors. Cancer
Discovery 2(9):791-797
3. Jia P, Li F, Xia J, Chen H, Ji H, Pao W, Zhao Z* (2012) Consensus rules in variant detection from
next-generation sequencing data. PLoS ONE 7(5): e38470
4. Xia J, Wang Q, Jia P, Wang B, Pao W, Zhao Z* (2012) NGS Catalog: A database of next generation
sequencing studies in humans. Human Mutation 33:E2341-2355
5. Xu J, Sun J, Helm M, Li A, Chen J, Zhao Z* [co-corresponding author], Chen X* (2012) RNA-Seq analysis
implicates dysregulation of the immune system in schizophrenia. BMC Genomics 13 (Suppl S8):S2
6. Jia P, Fanous, AH, Kendler, KS, International Schizophrenia Consortium, Zhao Z* (2012) Network-assisted
discovery of combined causal signals from genome-wide association studies (GWAS) in schizophrenia.
PLoS Computational Biology 8(7): e1002587
7. Sun J, Gong X, Purow B, Zhao Z* (2012) Investigating microRNA-transcription factor regulatory network
uncovered key microRNA components in glioblastoma core pathways. PLoS Computational Biology 8(7):
e1002488
8. Jia P, Wang L, Fanous AH, Chen X, Kendler KS, the International Schizophrenia Consortium, Zhao Z*
(2012) A bias-reducing pathway enrichment analysis of GWAS datasets confirmed association of the MHC
region with schizophrenia. Journal of Medical Genetics 49:96-103
9. Beeghly-Fediel A, Shu XO, Lu W, Long J, Cai Q, Xiang Y, Zheng Y, Zhao Z, Gu K, Gao YT, Zheng W (2011)
Genetic variants in VEGF family genes and breast cancer risk: a report from the Shanghai Breast Cancer
Genetics Study. Cancer Epidemiology, Biomarkers & Prevention 20(1):33-41
10. Jia P, Zheng S, Long J, Zheng W, Zhao Z* (2011) dmGWAS: dense module searching for genome-wide
association studies in protein-protein interaction networks. Bioinformatics. 27(1) 95-102 [PMCID:
PMC3008643]
Additional recent publications of importance to the field
11. Wang Q, Xia J, Jia P, Pao W, Zhao Z* (2013) Application of next generation sequencing to human gene
fusion detection: computational tools, features and perspectives. Briefings in Bioinformatics 14(4):506-519
12. Bhaskara S, Knutson SK, Jiang G, Chandrasekharan MB, Wilson AJ, Zheng S, Yenamandra A, Locke K,
Yuan J, Summers A, Washington K, Zhao Z, Sun ZW, Xia F, Khabele D, Hiebert SW (2010) Hdac3 is
essential for maintenance of chromatin structure and genome stability. Cancer Cell 18(5):436-447
13. Wang L, Jia P, Wolfinger RD, Chen X, Grayson BL, Aune TM, Zhao Z* (2011) An efficient hierarchical
generalized linear mixed model for pathway analysis of genome-wide association studies. Bioinformatics.
27:686-692
14. Sun J, Jia P, Fanous AH, Webb BT, van den Oord EJCG, Kendler KS, Zhao Z* (2009) A multi-dimensional
evidence-based candidate gene prioritization approach for complex diseases – Schizophrenia as a case.
Bioinformatics. 25(19):2595-2602 [PMC2752609]
15. Zhao Z, Boerwinkle E (2002) Neighboring-nucleotide effects on single nucleotide polymorphisms: A study of
2.6 million polymorphisms across the human genome. Genome Research 12:1679-1686
D. Research Support
Ongoing
1R01LM011177-01 (Zhao/Wang)
05/01/12–04/30/15
PI
NIH/NLM
“Mapping the Genetic Architecture of Complex Disease via RNA-seq and GWAS data”
We combine statistics, bioinformatics, and genetics to develop novel analytical strategies that maximally
leverage information from both GWAS and RNA-Seq studies to understand the genetic architecture underlying
schizophrenia and other complex diseases.
1R03DE022093-01 (Zhao/Wang)
09/01/11-08/30/14 (NCE)
PI
NIH/NIDCR
“Understanding Genetic Basis of Dental Caries via Integrative Genomic Approaches”
This project aims to develop integrative genomics approaches to identify groups of functionally related genes
with enriched association signals in the GENEVA dental caries genome-wide association studies dataset.
1R21HG006037-01A1 (Wang/Zhao)
05/01/23-04/30/15
PI
NIH/NHGRI
“Integrative Statistical Models for Pathway Analysis of GWAS Data”
To develop integrative mixed effects models and pathway approaches by leveraging information from different
types of genetic variants in GWAS: common and rare, CNVs and SNPs.
2P50CA095103-11 (Coffey)
09/01/12-08/31/17
Co-I
NIH/NCI
SPORE in GI Cancer
This proposal represents the second competing renewal of Vanderbilt’s GI SPORE. This SPORE continues to
focus on colorectal cancer, the second leading cause of cancer deaths in the US, where it affects more men and
women than all other gastrointestinal malignancies combined.
1R01CA158473-01A1 (Zheng)
05/10/12-05/09/17
Co-I
NIH/NCI
Genome Sequencing to Identify Novel Genetics Factors for Breast Cancer Risk
This project is to apply whole exome sequencing to 600 genetically-enriched breast cancer cases and 600
matched controls to identify novel genetic variants associated with breast cancer.
RFP CX-09-008 (Fanous)
04/01/10-03/31/15
Subcontract PI
Department of Veterans Affairs
“Convergent Genetic and Genomic Analyses of Schizophrenia”
This project aims to integrate genetic and genomic data of schizophrenia and then replicate the findings.
2 R01 GM067728-10A1 (Tansey)
04/10/12–03/31/17
Co-I
NIH/NIGMS
“Transcription Control by the Ubiquitin-Proteasome System”
This research program explores transcription control by the ubiquitin-proteasome system (UPS). Results of
these studies will provide paradigms for how the UPS impacts transcription in normal and disease states.
2P30CA068485-14 (Pietenpol)
09/01/10-08/31/15
Investigator
NIH/NCI
“Cancer Center Support Grant”
This is a cancer center support grant from NCI to strategically support Vanderbilt-Ingram Cancer Center.