Zhao Lab

Research

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.

Personnel

Patrick Zhao
Assistant Professor

Xinbin Dai
Sr Research Associate

Rakesh Kaundal
Postdoctoral Fellow

Haiquan Li
Research Associate

Jun Li
Postdoctoral Fellow

Zhaohong Zhuang
Research Assistant

A virus-induced SiRNA gene silencing and PhenoBlast database for Nicotiana benthamiana

Plant Bioinformatics: from Genome to Phoneme, an open framework for visual representation of genotypic-phenotypic associations.

An automated bioinformatics pipeline for plant EST-SSR marker screening and mapping

Medicago truncatula mutagenesis database – an online M. truncatula sequence-indexed fast neutron radiation-induced mutagensis library

TrichOME – an online bioinformatics resource for functional genomics of trichome metabolism

Automated gene prediction and protein analysis of predicted genes using TimeLogic DeCypher® system

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

Recent Publications

Guether, M., Balestrini, R., Hannah, M., He, J., Udvardi, M. K., & Bonfante, P. (2009). Genome-wide reprogramming of regulatory networks, transport, cell wall and membrane biogenesis during arbuscular mycorrhizal symbiosis in Lotus japonicus. New Phytologist, 182, 200-212 DOI:10.1111/j.1469-8137.2008.02725.x.

Tian, L., Peel, G. J., Lei, Z., Aziz, N., Dai, X., He, J., Watson, B. S., Zhao, P. X., Sumner, L. W., & Dixon, R. A. (2009). Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots. BMC Bioinformatics, 9, 1 DOI:10.1186/1471-2229-9-1.

Kaundal, R., & Raghava, G. P. (2009). RSLpred: an integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information. Proteomics, 9 (9), 2324–2342, DOI:10.1002/pmic.200700597.

Mian, M. A. , Zhang, Y., Wang, Z - Y., Zhang, J - Y., Cheng, X., Chen, L., Chekhovskiy, K., Dai, X., Mao, C-H., Cheung, F., Zhao, X., He, J., Scott, A. D., Town, C. D., & May, G. D. (2008). Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages. Plant Biology, 8 (27), DOI:10.1186/1471-2229-8-27.

Zhang, Y., He, J., Zhao, P. X., Bouton, J. H., & Monteros, M. J. (2008). Genome-wide identification of microsatellites in white clover (Trifolium repens L.) using FIASCO and phpSSRMiner. Plant Methods, 4 (19), DOI:doi:10.1186/1746-4811-4-19.