Bio | Research |
Publications | Teaching | CV |
Links
Jianhua Ruan joined the Department of Computer Science at UTSA as an Assistant Professor in Fall 2007. He received his Ph.D. degree in August 2007 from the Department of Computer Science and Engineering in the
Washington University in Saint Louis, under the direction of Dr.
Weixiong Zhang. He received his M.S. degree in Computer Science in 2002 from the
California State University, San Bernardino. Prior to coming to the United States, He received his B.S. degree in Biology in 1998 from the
University of Science and Technology of China (USTC). His
CV can be found here.
Dr. Ruan's
research interests lie in the broad areas of bioinformatics and computational
biology. He is interested in developing data-analytical methods and tools to
make the vast, diverse and complex biological data more understandable and
useful, and applying mathematical modeling and computational simulation
techniques to address theoretical and experimental questions in biology.
Specifically, he is
currently interested in developing algorithms related to the following areas of
computational biology:
- Functional and structural properties of
biological networks
- Developing algorithms to identify
topological properties that can characterize biological networks
- Relating these topological properties to
biological functions
- Understanding the
high-order organizing principles of biological networks
- Gene transcriptional regulatory networks
- Identifying transcriptional regulatory
elements and modules
- Modeling of transcriptional regulation in model organisms
- Microarray data analysis
- Integration of heterogeneous biological
data
- RNA structures and functions
In his thesis work, he developed graph
algorithms for the detection of natural modules, a.k.a. communities, from
complex networks, and applied the algorithms to study a variety of biological networks,
including protein-protein interaction networks and gene co-expression networks.
He also developed and applied classification and regression tree algorithms to study gene
transcriptional regulatory networks. His another thesis research area is on predicting pseudoknotted RNA secondary structures using dynamic programming and heuristic
algorithms. You can read his work in
Phys Rev E (community structure), Bioinformatics (transcriptional
regulatory networks, and
RNA structure prediction).
2008
2007
- J.E. McDunn, K.D. Husain, A.D. Polpitiya,
A. Burykin, J. Ruan, Q. Li, W. Schierding, N. Lin, D. Dixon, W. Zhang,
C.M. Coopersmith, W.M. Dunne, M. Colonna, B.K. Ghosh, and P. Cobb. Plasticity of the systemic inflammatory response to acute infection during critical illness: Development of the Riboleukogram, PLoS ONE, in press.
- J. Ruan and W. Zhang, An efficient
spectral algorithm for network community discovery and its applications to
biological and social networks, Proc. of IEEE International Conference on Data Mining, ICDM-07, Omaha, NE, USA, Oct. 28-31, 2007. Acceptance rate: 19% Proceeding version | Complete version
- X. Zhou*, J. Ruan*, G. Wang and W. Zhang,
Characterization and identification of microRNA core promoters in four model
species, PLoS Computational Biology, 3(3):e37,
2007.
link (*equal contribution)
2006
-
J. Ruan and W. Zhang, Identification and evaluation of weak community structures in networks, Proc. of National Conference on Artificial Intelligence, (AAAI-06), Boston, MA, July 2006. Acceptance rate: 22% (oral presentation).
preprint
-
J. Ruan and W. Zhang, A Bi-dimensional Regression Tree Approach to the Modeling of Gene Expression Regulation, Bioinformatics, 22(3):332-40, 2006.
preprint | supplementary files
- J. Ruan and W. Zhang, Identification and evaluation of functional modules in gene co-expression networks, Proc. of RECOMB Satellite Conferences on Systems Biology and Computational Proteomics, San Diego, CA, Dec 2006.
Acceptance rate: 40% preprint.
2005
-
X. Zhou*, J. Ruan*, G. Wang and W. Zhang, Characterization of the promoters of microRNA genes: A genome-scale analysis on C. elegans, A. thaliana and H. sapiens, Proc. of RECOMB Satellite Workshop on Systems Biology and Regulatory Genomics, San Diego, CA, Dec. 2005.
preprint (*equal
contribution)
- W. Zhang, J. Ruan, T-h. D. Ho, Y. You, T. Yu and R.S. Quatrano, Cis-regulatory element based targeted gene finding: Genome-wide identification of ABA- and abiotic stress-responsive genes in Arabidopsis thaliana, Bioinformatics, 21(14):3074-81, 2005.
link
-
J. Ruan and W. Zhang, CAGER: Classification Analysis for Gene Expression Regulation, BMC Bioinformatics, 6:114, 2005.
link | Web server
2004
-
J. Ruan, G.D. Stormo and W. Zhang, ILM: a web server for predicting RNA secondary structures with pseudoknots, Nucleic Acids Res., 32, W146-9, 2004.
link | web server
-
J. Ruan, G.D. Stormo and W. Zhang, An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots,
Bioinformatics, 20(1), 58-66, 2004.
link |
software
Fall 2007, CS 5263 Bioinformatics
Spring 2008, CS 3343 Analysis of Algorithms
My previous homepage at WashU
Some useful links that I collected
