Jing Zhu, Ph.D.
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Curriculum Vitae
NAME:
JING ZHU
Office Address:
Vanderbilt University Medical Center
D2300 MCN 1161 21st Ave
Nashville, TN 37232
Phone:
Email:
615-999-6403
jing.zhu@vanderbilt.edu
EDUCATION AND TRAINING
Postdoctoral Fellow in Bioinformatics
Vanderbilt University, Nashville, TN
2010 - 2014
Ph.D. in Biomedical Engineering
2010
University of Electronic Science and Technology of China, Chengdu, P. R. China
Master of medicine in Basic Medicine
Harbin Medical University, Harbin, P. R. China
2007
Bachelor of medicine in Basic Medicine
Harbin Medical University, Harbin, P. R. China
2005
ACADEMIC APPOINTMENT
2014 – present
Research Instructor, Department of Surgery, Vanderbilt University,
Nashville, TN
PROFESSIONAL ACTIVITIES
Honors/Awards:
2012
Travel fellowship award
Computational Biology
2009
Outstanding graduate award, University of Electronic Science and
Technology of China
2008
Outstanding graduate award, University of Electronic Science and
Technology of China
Editorial Activities:
from
the
International
Society
for
Jing Zhu, Ph.D.
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Journal Reviewer:
Biology
Conference Reviewer:
2013
International Conference on Intelligent Biology and Medicine (ICIBM
2013)
Invited Talks/Presentations/Tutorials:
2012
20th Annual International Conference on Intelligent Systems for
Molecular Biology. “Deciphering genomic alterations in colorectal
cancer through transcriptional subtype-based network analysis”.
TEACHING ACTIVITIES
Course:
2011
Cancer system biology CANB347, Vanderbilt University.
Research Advisor with Dr. Bing Zhang:
Summer Intern:
2012/2013
Liron Ganel
PUBLICATIONS
Peer Reviewed Articles - Journal:
1. Zhu J, Shi Z, Wang J, Zhang B. Empowering biologist to panomics data: colorectal
cancer as a paradigm. (In preparation)
2. Zhang B, Wang J, Wang X, Zhu J et al. Proteogenomic characterization of human
colon and rectal cancer. Nature. (In press)
3. Tripathi M, Zhu J et al. NFATc1 Activity Regulates Metastatic Behavior in Colorectal
Cancer. (Submitted)
Published papers
2014
4. Codreanu SG, Ullery JC, Zhu J et al. Alkylation damageby lipid electrophilestargets
functional protein systems. Mol Cell Proteomics, 2014. PMID: 24429493.
2013
Jing Zhu, Ph.D.
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5. Zhu J, Wang J, Shi Z, Franklin J, Deane N, Coffey R, Beauchamp R, Zhang B.
Deciphering genomics alterations in colorectal cancer through transcriptional
subtype-based network analysis. Plos One, 8(11), e79282, 2013. PMID: 24260186.
6. Liu Q, Ullery J, Zhu J, Liebler DC, Marnett LJ, Zhang B. RNA-seq data analysis at
the gene and CDS levels provides a comprehensive view of transcriptome responses
induced by 4-hydroxynonenal. Mol Biosyst, 9:3036-3046, 2013. PMID: 24056865.
2012
7. Wang J, Zhou X, Zhu J, Gu Y, Zhao W, Zou J, Guo Z. GO-function: deriving
biologically relevant functions from statistically significant functions. Brief Bioinform,
13(2):216-27, 2012. PMID: 21705405.
2011
8. Wang J, Zhang Y, Shen X, Zhu J, Zhang L, Zou J, Guo Z. Finding co-mutated genes
and candidate cancer genes in cancer genomes by stratified false discovery rate
control. Mol Biosyst, 7(4):1158-66, 2011. PMID: 21279201.
9. Wang J, Zhou X, Zhu J, Zhao W, Guo Y, Guo Z. Analyzing the Co-disruption of
functions related to lung adenocarcinoma based on Gene Ontology. Acta Biophysica
Sinica, 27(11):963-74, 2011.
2010
10. Zhu J, Xiao H, Shen X, Wang J, Zou J, Zhang L, Yang D, Ma W, Yao C, Gong X,
Zhang M, Zhang Y, Guo Z. Viewing cancer genes from co-evolving gene modules.
Bioinformatics, 26(7):919-24, 2010. PMID: 20176579.
11. Wang J, Zhou X, Zhu J, Zhou C, Guo Z. Revealing and avoiding bias in semantic
similarity scores for protein pairs. BMC Bioinformatics, 11:290, 2010. PMID:
20509916.
12. Gong X, Wu R, Zhang Y, Zhao W, Cheng L, Gu Y, Zhang L, Wang J, Zhu J, Guo Z.
Extracting consistent knowledge from highly inconsistent cancer gene data sources.
BMC Bioinformatics, 11:76, 2010. PMID: 20137077.
13. Gu Y, Yang D, Zou J, Ma W, Wu R, Zhao W, Zhang Y, Xiao H, Gong X, Zhang M,
Zhu J, Guo Z. Systematic interpretation of comutated genes in large-scale cancer
mutation profiles. Mol Cancer Ther, 9(8):2186-2195, 2010. PMID: 20663929.
2009
14. Wang D, Wang C, Zhang L, Xiao H, Shen X, Ren L, Zhao W, Hong G, Zhang Y, Zhu
J et al: Evaluation of cDNA microarray data by multiple clones mapping to the same
transcript. Omics,13(6):493-499, 2009. PMID: 19715395.
2008
15. Yang D, Li Y, Xiao H, Liu Q, Zhang M, Zhu J, Ma W, Yao C, Wang J, Wang D, Guo
Z, Yang B. Gaining confidence in biological interpretation of the microarray data: the
functional consistence of the significant GO categories. Bioinformatics, 24(2):265-71,
2008. PMID: 18006543.
Jing Zhu, Ph.D.
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16. Li Y, Guo Z, Peng C, Liu Q, Ma W, Wang J, Yao C, Zhang M, Zhu J. Identifying
cancer genes from cancer mutation profiles by cancer functions. Sci China C Life
Sci, 51(6):569-74, 2008. PMID: 18488178.
17. Zhu J, Guo Z, Yang D, Zhang M, Wang J, Wang C. Discovering the cellular-localized
functional modules and modular interactions in response to liver cancer. High
Technology Letters, 14(4), 2008.
18. Zhang M, Yao C, Guo Z, Zou J, Zhang L, Xiao H, Wang D, Yang D, Gong X, Zhu J
et al: Apparently low reproducibility of true differential expression discoveries in
microarray studies. Bioinformatics, 24(18):2057-2063, 2008. PMID: 18632747.
2007
19. Zhu J, Wang J, Guo Z, Zhang M, Yang D, Li Y, Wang D, Xiao G. GO-2D: identifying
2-dimensional cellular-localized functional modules in Gene Ontology. BMC
Genomics, 2007. PMID: 17250772.
20. Zhu J, Guo Z, Zhang M, Yang D, Wang J, Wang C. Interaction of cellular-localized
signature modules in response to prostate cancer. Progress In Natural Science,
17(11), 2007.
21. Wang J, Li Y, Guo Z, Zhu J, Ma W, Peng C, Liu Q. Finding finer functions for
proteins related to breast cancer based on protein interaction network. YiChuan,
29(9):1061-6, 2007. PMID: 17855254.
22. Guo Z, Wang L, Li Y, Gong X, Yao C, Ma W, Wang D, Li Y, Zhu J, Zhang M, Yang
D, Rao S, Wang J. Edge-based scoring and searching method for identifying
condition-responsive protein-protein interaction sub-network. Bioinformatics,
23(16):2121-8, 2007. PMID: 17545181.
23. Li Y, Guo Z, Ma W, Yang D, Wang D, Zhang M, Zhu J, Zhong G, Li Y, Yao C, Wang
J. Finding finer functions for partially characterized proteins by protein-protein
interaction networks. Chinese Science Bulletin, 52(24):3363-70, 2007.
24. Guo Z, Li Y, Gong X, Yao C, Ma W, Wang D, Li Y, Zhu J, Zhang M, Yang D et al:
Edge-based scoring and searching method for identifying condition-responsive
protein-protein interaction sub-network. Bioinformatics, 23(16):2121-2128, 2007.
PMID: 17545181.
2006
25. Zhang M, Zhu J, Guo Z, Li X, Yang D, Wang L, Rao S: Identifying disease feature
genes based on cellular localized gene functional modules and regulation networks.
Chinese Science Bulletin 51(15):1848-1856, 2006.
26. Wang D, Lv Y, Guo Z, Li X, Li Y, Zhu J, Yang D, Xu J, Wang C, Rao S et al: Effects
of replacing the unreliable cDNA microarray measurements on the disease
classification based on gene expression profiles and functional modules.
Bioinformatics, 22(23):2883-2889, 2006. PMID: 16809389.
Jing Zhu, Ph.D.
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2005
27. Guo Z, Zhang T, Li X, Wang Q, Xu J, Yu H, Zhu J, Wang H, Wang C, Topol EJ et al:
Towards precise classification of cancers based on robust gene functional
expression profiles. BMC Bioinformatics, 6:58, 2005. PMID: 15774002.
Peer Reviewed Articles - Conference:
28. Zhu J, Shen X, Zhang Y, Guo Z, Xiao H, Gu Y: Identifying candidate cancer genes
based on their somatic mutations co-occurring with cancer genes in cancer genome
profiling. The 2nd International Conference on Biomedical Engineering and
Informatics, 1448-1451, 2009.
29. Wang J, Zhou X, Zhu J, Guo Z. Bias of phenotype similarity scores between
diseases. The 4th International Conference on Bioinformatics and Biomedical
Engineering, 2010.
30. Li Y, Ma W, Guo Z, Peng C, Wang J, Gong X, Yang D, Liu Q, Gu Y, Zhang M, Zhu
J, Wang C. Finding finer functions of cancer proteins and rebuilding cancerassociated functional sub-network. The 4th International Conference on
Bioinformatics and Biomedical Engineering, 2010.
31. Wang J, Zhou X, Zhu J, Guo Z. Analysis enrichment algorithms for redundancy
treatment of Gene Ontology ters based on a methylation profile for colorectal cancer.
Proceeding of the 5ht International Congress on Mathematical Biology (ICMB2011),
3:376-80, 2011.
Selected Abstracts/Posters:
1. Zhu J, Shi Z, Wang J, Zhang B. NetGestalt CRC portal: a resource for exploring data
from colorectal cancer genomic and proteomic projects. The Clinical Proteomic
Tumor Analysis Consortium First Annual Scientific Symposium, Bethesda, MD, 2013.
2. Zhu J, Zhang B. Deciphering genomic alterations in colorectal cancer through
subtype-specific driver networks. The 20th Annual International Conference on
Intelligent Systems for Molecular Biology, Long Beach, CA, 2012.
3. Zhu J, Zhang B. Identifying colorectal cancer subtypes and subtype-specific
transcriptional programs and genetic alterations. The Cancer Genome Atlas’ 1st
Annual Scientific Symposium: Enabling Cancer Research Through TCGA, National
Harbor, MD, 2011.