Patrick Xuechun Zhao, Ph.D. Assistant Professor pzhao@noble.org 580.224.6725 580.224.6692

Ph.D., Communication and Information Systems, 2000 Shanghai Jiao Tong University, China Joined the Noble Foundation in 2004 Lab: http://bioinfo.noble.org

Research Emphasis: Bioinformatics and Plant Genomics
The Zhao laboratory focuses on research and development in computational biology, bioinformatics and genomics for biological discovery. We are applying statistical pattern recognition, artificial intelligence and machine learning technologies in the study of genome annotation, regulatory mechanism of gene expression, protein-protein interaction and sequence-structure-function relationship, etc.

Research Interests

• Bioinformatics and Plant Genomics
• Machine Learning and Computational Intelligence
• Data Integration, Data Mining for Enabling Systems Biology

Current Projects (partial list)

• Development of bioinformatics tools for the analysis of plant small RNAs focusing on microRNAs (miRNAs), trans-acting small interfering RNAs (siRNAs), long endogenous siRNAs and their target genes / chromatins.
• Building computational models for the study of gene expression regulatory mechanisms in model plants.
• Prediction and functional categorization of transporter proteins in plants and bacteria species.
• Integration and mining of heterogeneous data from high-throughput "omics" platforms for functional and comparative genomics.

Web Services & Databases

• pssRNAMiner: A Plant Short Small RNA Regulatory Cascade Analysis Server.
• PLAN: Personal BLAST Navigator.
• phpSSRMiner: Simple Sequence Repeat Marker Miner.
• MtGene-Atlas: Medicago truncatula Gene Expression Atlas Database.
• TrichOME: A Publicly Available Database of Genes and Metabolites Expressed in Plant Trichomes.
• TransportNN: A Membrane Transport Protein Prediction Server.

Selected Recent Publications
Li, H., Dai, X. and Zhao, P. X. (2008) A Nearest Neighbor Approach for Automated Transporter Prediction and Categorization from Protein Sequences 10.1093/bioinformatics/btn099, Bioinformatics, btn099.

Itaya, A., Bundschuh, R., Archual, A.J., Joung, J.-G., Fei, Z., Dai, X., Zhao, P. X., Tang, Y., Nelson, R.S. and Ding, B. (2008) Small RNAs in tomato fruit and leaf development, Biochim Biophys Acta, 1779, 99-107.

Naoumkina, M., Torres-Jerez, I., Allen, S., He, J., Zhao, P.X., Dixon, R.A. and May, G.D. (2007) Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub), BMC Plant Biology, 7.

Irian, S., Xu, P., Dai, X.B., Zhao, P.X. and Roossinck, M.J. (2007) Regulation of a virus-induced lethal disease in tomato revealed by LongSAGE analysis, Molecular Plant-Microbe Interactions, 20, 1477-1488.

He, J., Dai, X. and Zhao, P. X. (2007) PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results, BMC Bioinformatics, 8.

Dai, X.B., He, J. and Zhao, P.X. (2007) A new systematic computational approach to predicting target genes of transcription factors, Nucleic Acids Research, 35, 4433-4440.

Broz, A.K., Broeckling, C.D., He, J., Dai, X., Zhao, P.X. and Vivanco, J.M. (2007) A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa, BMC Plant Biology, 7, Article No. 25.

Broeckling, C.D., Reddy, I.R., Duran, A.L., Zhao, P.X. and Sumner, L.W. (2006) MET-IDEA: Data extraction tool for mass spectrometry-based metabolomics, Analytical Chemistry, 78, 4334-4341.

Benedito, V.A., Dai, X.B., He, J., Zhao, P.X. and Udvardi, M.K. (2006) Functional genomics of plant transporters in legume nodules, Functional Plant Biology, 33, 731-736.