Research Description
Our research lies 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 UTHSCSA to apply these methods to address theoretical and experimental questions in human diseases and plant biology.
In recent years, we have been developing algorithms in the following areas:
- Personalized and network-based cancer progonosis
- Biological network-based knowledge discovery from massive biological data
- Functional and structural properties of biological networks
- Identifying topological properties to characterize biological networks
- Community discovery and link prediction algorothms for biological networks
- Transcriptional and post-transcriptional regulatory networks
- Identifying cis-regulatory elements and modules
- Bulk and single-cell omic data analysis
- Knowlege discovery from diverse omic data by statistical and graph-theoretical methods
In his doctoral dissertation research, Dr. Ruan developed two graph algorithms, Qcut and HQcut, for the detection of natural modules (aka communities), from complex networks. He applied the algorithms to study 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. He also developed an algorithm for predicting pseudoknotted RNA secondary structures.
Research Support
Current |
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National Science Foundation Div Of Biological Infrastructure ABI Innovation: Tools and databases for network-based plant systems biology with applications to understanding plant-virus interactions $683,839, 04/15/16-03/31/20, PI |
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National Institutes of Health |
Completed |
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National Science Foundation Division of Intelligent Information Systems "Topology-Based Approaches to Integrated Analysis of Transcriptomic, Protein-Interactomic and Phenotypic Data" $452,657, 10/01/12-09/30/15, PI |
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Institute for Integration of Medicine & Science, Cancer Therapy and Research Center, UTHSCSA |
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National Institutes of Health |
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National Institutes of Health |
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National Institutes of Health |
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National Institutes of Health |
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University of Texas at San Antonio |
SALSI |
San Antonio Life Sciences Institute |
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University of Texas at San Antonio |
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National Institutes of Health |
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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, 09/01/09-8/31/10 (with no-cost extension to 08/31/11), Co-PI PI: Valerie Sponsel |