BIOGRAPHICAL SKETCH
Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
POSITION TITLE
Jianhua Ruan
eRA COMMONS USER NAME
Associate Professor
JIANHUA.RUAN
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
DEGREE
(if applicable)
YEAR(s)
Washington University in Saint Louis
Ph.D.
2007
California State University, San Bernardino
University of Science and Technology of China
M.S.
B.S.
2002
1998
INSTITUTION AND LOCATION
FIELD OF STUDY
Computer Science /
Bioinformatics
Computer Science
Biology
A. Personal Statement
My research interests lie in the broad areas of bioinformatics and computational systems biology. More specifically, my
current research is focused on the following three directions: (1) developing computational methods for modeling and
analyzing transcriptional / post-transcriptional regulatory networks (e.g. DNA motif finding and ChIP-seq data analysis); (2)
developing computational methods for analyzing complex biological networks to facilitate understanding of the relationship
between the structure of biological networks and the dynamic behavior of the cell; and (3) network-based cancer
classification and drug target selection via integrated analysis of heterogonous functional genomics data such as gene
expression, protein-protein interactions, and microRNA-mRNA interactions.
I have received a BS in Biology, MS in Computer Science, and PhD in Computer Science emphasizing on Bioinformatics
research. This background gives me a strong edge in tackling biological problems from the computational angle. Since
joining the University of Texas at San Antonio in fall 2007, I have successfully collaborated with many biologists at UTSA
and the UT Health Science Center for a broad spectrum of bioinformatics applications involving genomic, transcriptomic,
proteomic, and epigenomic data. The collaborations have resulted in both peer-reviewed publications as well as NIH and
NSF funded research grants. Therefore, I have a demonstrated record of successful and productive research projects,
and my expertise and experience have prepared me to lead, manage and administrate interdisciplinary research teams.
B. Positions and Honors
Positions and Employment
• 2002 - 2007: Graduate Research Associate, Dept of Computer Science, Washington University in St Louis.
• 2007 - present: Assistant/Associate Professor, Dept of Computer Science, The University of Texas at San Antonio.
• 2014 – present: Core Leader, Computational Systems Biology Core, The University of Texas at San Antonio.
Professional Memberships and Services
• Other Academic Affiliations: Associated Faculty, UTSA/UTHSCSA Joint Graduate Program in Biomedical
Engineering, Oct 2010 – present; Associated member, Cancer Prevention and Population Science (CPPS)
Program, Cancer Therapy and Research Center, UTHSCSA, May 2013 – present.
• Associate Editor: PLoS ONE, Genomics Data, EURASIP Journal on Bioinformatics and Systems Biology
• Conference Organizer: Program Co-chair, Workshop on Graph Techniques for Biomedical Networks, IEEE
International Conference on Bioinformatics and Biomedicine, 2009; Session Chair, IEEE International Workshop
on Genomic Signal Processing and Statistics (GENSIPS), 2011. Publication Committee Chair, International
Conference on Intelligent Biology and Biomedicine (ICIBM), 2014.
• Conference PC Member: AAAI Conference on Artificial Intelligence (AAAI) 2015, Ninth International Meeting on
Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), 2012; International Conference on
Bioinformatics and Biomedicine (BIBM), 2010-2015; International Conference on on Bioinformatics Models,
Methods and Algorithms, 2011,2012; ACM International Workshop on Data Mining in Bioinformatics (BioKDD),
2010-2013; IEEE ICDM workshop on Biological Data Mining and its Applications in Healthcare, 2010-2013;
International Conference on Bioinformatics & Computational Biology, 2008, 2009; Workshop on Data Mining in
•
•
Functional Genomics, IEEE International Conference on Bioinformatics and Biomedicine, 2008, 2009; Mexican
International Conference on Artificial Intelligence (MICAI), 2009-2013
Journal Reviewer: Bioinformatics, Briefings in Bioinformatics, Nucleic Acids Research, PLoS Computational
Biology, PLoS ONE, BMC Systems Biology, BMC Genomics, BMC Medical Genomics, BMC Bioinformatics,
FEBS Letters, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), EURASIP Journal
on Bioinformatics and Systems Biology, EURASIPJournal on Advances in Signal Processing, IEEE Transactions
on Information Technology in BioMedicine, International Journal of Knowledge Discovery in Bioinformatics,
International Journal of Data Mining and Bioinformatics, International Journal of Computational Bioscience,
International Journal of Information Technology & Decision Making, journal of computational bioscience, Journal
of Discrete Algorithms, Annals of Applied Statistics.
Grant Reviewer: UTHSC-SA IIMS/CTSA Pilot Projects (2009); Indiana Alzheimer Disease Center Pilot Projects,
Indiana University School of Medicine (2010). DoD/CDMRP Prostate Cancer Research Program (2014).
NIH/NIGMS ZGM1 TRN-3 (2015).
Honors
• 1993: First Prize, National Chemistry Olympics, Chinese Society of Chemistry
• 2007: Faculty Research Award, University of Texas at San Antonio
• 2008: Top Performer, Third Annual DREAM Reverse Engineering Challenge
• 2012: Tenure-track Research Award, UTSA, 2012
C. Peer-reviewed publications in the last three years and representative earlier publications (selected
from >40 peer-reviewed publications)
1. J Ruan, GD Stormo, and W Zhang. An iterated loop matching approach to the prediction of RNA secondary
structures with pseudoknots. Bioinformatics, 20:58–66, 2004.
2. J Ruan, GD Stormo, and W Zhang. ILM: a web server for predicting RNA secondary structures with pseudoknots.
Nucleic Acids Research, 32:W146–149, 2004.
3. W Zhang, J Ruan, TH Ho, Y You, T Yu, and RS Quatrano. Cis-regulatory element based targeted gene finding:
genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana.
Bioinformatics, 21:3074–3081, 2005.
4. J Ruan and W Zhang. A bi-dimensional regression tree approach to the modeling of gene expression regulation.
Bioinformatics, 22:332–340, 2006.
5. X Zhou, J Ruan (joint-first author), G Wang, and W Zhang. Characterization and identification of microRNA
promoters in four model species. PLoS Computational Biology, 3:412–423, 2007. PMCID:PMC1817659
6. M Ray, J Ruan (joint-first author) and W Zhang. Variations in the transcriptome of Alzheimer's disease reveal
modular networks involved in cardiovascular diseases, Genome Biology, 9:R148, 2008. PMCID:PMC2760875.
7. D Ravi, AM Wiles, S Bhavani, J Ruan, P Leder, and AJR Bishop, A network of conserved damage survival
pathways revealed by a genomic RNAi screen, PLoS Genetics, 5(6): e1000527, 2009. PMCID: PMC2688755
8. J. Ruan, A.K. Dean and W. Zhang, A general co-expression network-based approach to gene expression
analysis: comparison and applications, BMC Systems Biology, 4:8, 2010. PMCID: PMC2829495.
9. S Ghosh, AK Dean, M Walter, Y Bao, Y Hu, J Ruan and R. Li, Cell Density-Dependent Transcriptional Activation
of Endocrine-Related Genes in Human Adipose Tissue-Derived Stem Cells, Experimental Cell Research,
316(13):2087-2098, 2010
10. J. Ruan, A top-performing algorithm for the DREAM3 gene expression prediction challenge, PLoS ONE. 5(2):
e8944, 2010.
11. J Sun, H Pan, C Lei, B Yuan, SJ Nair, C April, B Parameswaran, B Klotzle, JB Fan, J Ruan (co-corresponding
author) and R Li. Genetic and genomic analyses of an RNA polymerase II-pausing factor in regulation of
mammalian transcription and cell growth, Journal of Biological Chemistry, 286(42):36248-57, 2011.
12. MJ Jahid and J Ruan, A Steiner tree-based method for biomarker discovery and classification in breast cancer
metastasis, BMC Genomics, 13 (S6):S8, 2012
13. Z Gao, R Zhao, and J Ruan, A genome-wide cis-regulatory element discovery method based on promoter
sequences and gene co-expression networks, BMC Genomics, 14 (S1):S4, 2013.
14. RL Huang, F Gu, NB Kirma, J Ruan, CL Chen, HC Wang, YP Liao, CC Chang, MH Yu, JM Pilrose, IM
Thompson, HC Huang, THM Huang, HC Lai and KP Nephew, Comprehensive methylome analysis of ovarian
tumors reveals hedgehog signaling pathway regulators as prognostic DNA methylation biomarkers, Epigenetics,
8(6):624-634, 2013
15. C Lei, S Tamim, AJR Bishop and J Ruan, Fully automated protein complex prediction based on topological
similarity and community structure, Proteome Science, 11(S1):S9, 2013
16. MT Weirauch, A Cote, ..., DREAM5 Consortium (..., C Lei, ..., J Ruan, ..., ), ..., QD Morris, ML Bulyk, G
Stolovitzky, and TR Hughes, Evaluation of methods for the modeling of transcription factor sequence specificity.
Nature Biotechnology, 31:126-134, 2013
17. YT Hsu, F Gu, YW Huang, J Liu, J Ruan, RL Huang, CM Wang, CL Chen, R Jadhav, HC Lai, DG Mutch, PJ
Goodfellow, IM Thompson Jr., NB Kirma, and TH Huang, Promoter hypomethylation of EpCAM-regulated bone
morphogenetic protein gene family in recurrent endometrial cancer. Clinical Cancer Research, 19(22):6272-85,
2013
18. S Ghosh, K Ashcraft, MJ Jahid, C April, C Ghajar, J Ruan, H Wang, M Foster, D Hughes, A Ramirez, T Huang,
JB Fan, Y Hu, R Li, Regulation of adipose oestrogen output by mechanical stress, Nature Communications,
4:1821, 2013.
19. C. Lei and J. Ruan, A novel link prediction algorithm for reconstructing protein-protein interaction networks by
topological similarity, Bioinformatics, 29(3):355-364, 2013.
20. MJ Jahid, TH Huang, & J Ruan. A Personalized Committee Classification Approach to Improving Prediction of
Breast Cancer Metastasis. Bioinformatics, 30(13):1858-1866, 2014
21. L Liu, H Chung, G Lacatus, S Baliji, J Ruan (co-corresponding author) & G Sunter. Altered expression of
Arabidopsis genes in response to a multifunctional geminivirus pathogenicity protein. BMC Plant Biology,
14:302, 2014
22. Z Gao & J Ruan. A Structure-based Multiple Instance Learning Approach to Predicting in vitro Transcription
Factor-DNA Interaction. BMC Genomics, to appear.
D. Research Support
Ongoing Research Support

IIS-1218201 (Ruan)
10/2012 - 9/2015
NSF-IIS
$108,000 (annual direct)
Topology-based approaches to integrated analysis of transcriptomic, protein interactomic and phenotypic data
Role: PI
The major goal of this project is to develop computational methods to integrate and analyze omics data.

P20 CA165589 (Robbins & Leach)
1/1/2013 – 12/31/2016
NIH/NCI
$127,564 (annual direct)
Role: Co-I
The Cancer Bioinformatics Initiative: A UTSA/UTHSCSA Partnership
The major goal of this project is to establish a joint degree program emphasizing on cancer bioinformatics.

G12MD007591 (Perry & Tsin)
9/15/2010 - 06/30/2015
NIH/NCRR/RCMI
$1,818,442 (annual direct)
Center for Interdisciplinary Health Research (CIHR): Establishment of interdisciplinary health research for core
facilities and faculty research.
Role: Co-I / Core Leader
The major goal of this project is to develop research infrastructure at UTSA to support interdisciplinary health
research.

1R01CA152063 (PI: Bishop)
09/01/2011 – 07/31/2016
NIH-NCI
$250,000 (annual direct)
Title: Improving etoposide treatment of Ewing's sarcoma.
Role: Collaborator
The major goal of this project is to identify genes involved in surviving etoposide exposure and to determine the utility
of targeting these genes to improve etoposide treatment of Ewing’s sarcoma.
Completed Research Support

SC3 GM086305 (PI: Ruan)
NIH-NIGMS
01/01/2009 – 12/31/2013
$555,449
Title: Computational Discovery and Analysis of Community Structures in Biological Networks.
Role: PI
The major goal of this project is to develop computational algorithms for identifying and analyzing community
structures in biological networks.
IIMS/CTRC/GCCRI/UTSA Pilot Project Program (PI: Ruan)
12/01/13 – 11/30/14
NIH-NCI
$50,000
Title: etwork-based integrative analysis of epigenetic changes in cancer genomes
Role: PI
The major goal of this proposal is to develop computational systems biology approaches to analyze cancer
epigenomics


0848135 (PI: Sponsel)
09/01/2009 – 08/31/2011
NSF- Division of Integrative Organismal Systems
$150,000
Title: A combined biochemical, molecular and computational approach to understanding the regulation of gibberellin
biosynthesis in Arabidopsis.
Role: co-PI
The major goal of this project is to analyze the cis-regulatory elements regulating gibberellin biosynthesis in
Arabidopsis thaliana.

SALSI (PI: Li and Ruan)
02/01/10 – 08/31/11
San Antonio Life Science Institute
$108,000
Title: Molecular Changes in Aging Breast Stroma
Role: PI
The major goal of this proposal is to understand how aging increases risk of ER-positive breast cancer