Dr. Jianhua Ruan, Department of Computer Science, UTSA

Research Interests

Our research interests lie in the broad areas of bioinformatics and computational biology. We are interested in developing data-analytical methods and tools to make complex biological data more understandable and useful. We are also collaborating with biology labs in UTSA and UT Health Science Center - San Antonio to apply these methods to address theoretical and experimental questions in biology.

Specifically, we are currently developing algorithms in the following areas:

• Functional and structural properties of biological networks
  • Identifying topological properties to characterize biological networks
  • Data mining algorothms for biological networks
• Transcriptional and post-transcriptional regulatory networks
  • Identifying cis-regulatory elements and modules
• Microarray data analysis
  • Knowlege discovery from microarray data by statistical and graph-theoretical methods
• RNA secondary structure prediction

Research Support

Our research is supported by the following sources:

National Institutes of Health National Institute of General Medical Sciences "ARRA Award - Supplemental Funding: Computational Discovery and Analysis of Community Structures in Biological Networks" $124,117, 2009/09/30-2011/08/31, PI

	National Institutes of Health National Institute of General Medical Sciences "Computational Discovery and Analysis of Community Structures in Biological Networks" $443,500, 2009/01/01-2012/12/31, PI
	National Science Foundation Division of Integrative Organismal Systems "A combined biochemical, molecular and computational approach to understanding the regulation of gibberellin biosynthesis in Arabidopsis" $150,000, 2009/09/01-2010/8/31, Co-PI PI: Valerie Sponsel
	National Institutes of Health - National Human Genome Research Institute "Alternative splicing regulation in perspective: A global analysis of exon skipping" $423,090, 2009/04/14-2011/02/28, Co-I PI: Luiz Penalva
	University of Texas at San Antonio Faculty Research Award "Graph-theoretical Approaches to Knowledge Discovery from Gene Expression Microarray Data" $5,000, 2007-2008, PI

Representative publications

Complete listing

J. Ruan and W Zhang, Identifying network community structures with a high resolution, Physical Review E, 77:016104, 2008. link

J. Ruan and W. Zhang, A Bi-dimensional Regression Tree Approach to the Modeling of Gene Expression Regulation, Bioinformatics, 22(3):332-40, 2006. download

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

 

©2008 Jianhua Ruan