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
Associate Professor

Xinbin Dai
Senior Computational Biologist

Rakesh Kaundal
Postdoctoral Fellow

Jun Li
Bioinformatic Research Analyst

Ruixin Li
Research Technician

James Susaimuthu
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

Kaundal, R., Saina, R., & Zhao, P. X. (2010). Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis thaliana. Plant Physiology, July 20, DOI:10.1104/pp.110.156851.

Wang, M., Benedito, V. A., Zhao, P. X., & Udvardi, M. K. (2010). Inferring large-scale gene regulatory networks using a low-order constraint-based algorithm. Molecular Biosystems, 6 (6), 988-998 DOI: 10.1039/b917571g.

Dai, X., Wang, G., Yang, D - S., Tang, Y., Broun, P., Marks, M. D., Sumner, L. W., Dixon, R. A., & Zhao, P. X. (2010). TrichOME: A comparative omics database for plant trichomes. Plant Physiology, 152, 44-54 DOI: 10.1104/pp.109.145813.

Benedito, V. A., Li, H., Dai, X., He, J., Kaundal, R., Torres-Jerez, I., Harrison, M. J., Tang, Y., Zhao, P. X., & Udvardi, M. K. (2009). Genomic inventory and transcriptional analysis of Medicago truncatula transporters. Plant Physiology, 152, 1716-1730 DOI: 10.1104/pp.109.148684.

Li, H., Benedito, V. A., Udvardi, M. K., & Zhao, P. X. (2009). TransportTP: A two-phase classification approach for membrane transporter prediction and characterization. BMC Bioinformatics, 10 (418), DOI:10.1186/1471-2105-10-418.