Jianhua Ruan

 

Department of Computer Science and Engineering

Washington University in St. Louis

Campus Box 1045

One Brookings Drive

St. Louis, MO, 63130-4899

Phone: (314) 359 - 1428

Email : jruan at cse dot wustl dot edu
WWW: http://www.cse.wustl.edu/~jruan
[ Eduction | Research | Publications | Professional Activities | Presentations ]


News: I have successfully defended my dissertation on June 26, 2007, and joined the Department of Computer Science, University of Texas at San Antonio. Visit my new homepage here.

Education

I am a PhD student in the department of Computer Science and Engineering at Washington University in St Louis since 2002. My advisor is Dr. Weixiong Zhang. I received my M.S. degree in Computer Science from California State University, San Bernadino in 2002 and a BS degree in Biology from University of Science and Technology in China in 1998.

Research Interests

My primary research interests are computational biology and machine learning. In particular, I am interested in algorithms in computational biology related to the following areas:

  • Functional and structural properties of biological networks
  • Gene transcriptional regulatory modules and networks
  • Microarray data analysis
  • Integration of heterogeneous biological data
  • RNA structures and functions
I am currently developing graph algorithms for identifying natural modules, a.k.a. communities, in biological networks, and analyzing the biological meaning of such modules in protein-protein interaction networks, gene co-expression networks, as well as other types of graphs constructed from biological data.

Publications

In preparation / under review

  • J. Ruan and W Zhang, "Identifying hierarchical community structures in complex networks", In preparation
  • JE McDunn, KD Husain, AD Polpitiya, A Burykin, J Ruan, ... , Perren Cobb. "Plasticity of the systemic inflammatory response to critical illness", Submittd to PLoS Medicine.

Referred journal publications

  • X Zhou, J Ruan (joint first author), G Wang and W Zhang, "Characterization and identification of microRNA core promoters in four model species", PLoS Computational Biology, 3(3):e37, 2007. 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. pdf | supplementary files
  • 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. Pubmed
  • J. Ruan and W. Zhang, "CAGER: Classification Analysis for Gene Expression Regulation", BMC Bioinformatics, 6:114, 2005. pdf | Web server
  • 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. pubmed | 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. pdf | software

Referred conference papers

  • J. Ruan and W. Zhang, "An efficient spectral algorithm for network community discovery and its applications to biological and social networks", Proc. IEEE Intern. Conf. on Data Mining, ICDM-07, Omaha, NE, USA, Oct. 28-31, 2007. Acceptance rate: 19%. Proceeding version | Complete version
  • 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. pdf.
  • 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). pdf | ps
  • X. Zhou, J. Ruan (joint first author), 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. pdf | ps
  • A. I. Concepcion, J. Ruan and R. Samson. "Spider: a multi-agent architecture for internet distributed computing system", in the proceedings of the 15th International Conference on Parallel and Distributed Computing Systems, Louisville, KY, USA, 147-152, 2002.

Technical Reports

  • J. Ruan and W. Zhang, "Discovering Transcriptional Regulatory Rules from Gene Expression and TF-DNA Binding Data by Decision Tree Learning", WUSTL CSE-Tech. Rep. #43, 2004. pdf

Professional Activities

Reviewer for: Bioinformatics, Nucleic Acids Res., BMC Bioinformatics
Member, International Society for Computational Biology (ISCB)
Member, American Association for Artificial Intelligence (AAAI)

Presentations

  • "Identification and evaluation of functional modules in gene co-expression networks", RECOMB Satellite Conferences on Systems Biology, San Diego, CA, Dec 2006.
  • "Identifying hierarchical community structures in biological networks", poster presentation, Algorithmic Biology 2006, San Diego, CA, Nov 2006.
  • "Community Structure in Biological Networks", Computational biology annual retreat, Washington University, Sept 2006
  • "Identification and evaluation of weak community structures in networks", AAAI-06, Boston, MA, July 2006
  • "Discovering functional modules from gene co-expression networks", Systems Analysis Group, Washington University, Apr 2006
  • "Regulatory networks for abiotic stress and ABA regulation in Arabidopsis", Washington University -- Monsanto Company Plant Science Symposium, Mar 2006
  • "Data mining methods for gene regulatory networks", Computational biology annual retreat, Washington University, Oct 2005
  • "A bi-dimensional regression tree approach to the modeling of gene regulation", poster presentation, RECOMB 2005, Cambridge, MA, May 2005
  • "Mining microarray and sequence data with tree techniques", Monsanto Company, St Louis, MO, Feb 2005
  • "A decision tree approach to mining gene regulatory modules", poster presentation, 4th International Conference on Bioinformatics, Atlanta, GA, Nov 2003
  • "Genome-wide stress gene finding in plants by promoter modeling and analysis", Genetics annual retreat, Washington University, Oct 2003
  • "An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots", poster presentation, CSB 2003, Stanford, CA, Aug 2003



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