Dr. Jianhua Ruan, Department of Computer Science, UTSA

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:

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



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

National Institutes of Health
Systems Analysis of Epigenomic Architecture in Cancer Progression
~$2M / year, 5/15/17-4/30/22, co-PI (computational co-leader)
PI: Tim Huang (UTHSCSA)



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
Cancer Therapy & Research Center at The University of Texas Health Science Center

Institute for Integration of Medicine & Science, Cancer Therapy and Research Center, UTHSCSA
"Network-based integrative analysis of epigenetic changes in cancer genomes"
$50,000, 12/01/13-11/30/14, PI

National Institutes of Health
"RCMI Center for Interdiscplinary Health Research CIHR"
$12,657,140, 9/15/10-06/30/15, co-PI (Leader of Computational Systems Biology Core)
PI: George Perry & Andrew Tsin

National Institutes of Health
"Improving Etoposide Treatment of Ewing’s Sarcoma"
$76,631 9/1/11-07/31/16, co-PI
PI: Alexander Bishop (UTHSCSA)

National Institutes of Health
"The Cancer Bioinformatics Initiative: A UTSA/UTHSCSA Partnership"
$575,553, 09/11/12-08/31/16, co-PI
PI: Kay Robbins

National Institutes of Health
National Institute of General Medical Sciences
"Computational Discovery and Analysis of Community Structures in Biological Networks"
$557,617, 1/01/09-12/31/12, PI

University of Texas at San Antonio
Tenure-Track Research Award Competition Program
"Computational systems biology ap-
proaches to the prediction of breast cancer metastasis"
$22,000, 9/1/2012-8/31/2013, PI


San Antonio Life Sciences Institute
"Molecular Changes in Aging Breast Stroma"
$108,000, 02/01/2010-08/31/2011, PI

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

National Institutes of Health
"Environmental epigenetics and stem/progenitor cell injury"
$43,634, 10/01/11-5/31/13, co-PI
PI: Tim Huang (UTHSCSA)

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


©2008 Jianhua Ruan