• 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

Li, J., Dai, X., Liu, T., & Zhao, P. X. (2012). LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. Nucleic Acids Research, 40 (D1), D1221–D1229 doi:10.1093/nar/gkr939.

Ahmed, F., Benedito, V. A., & Zhao, P. X. (2011). Mining functional elements in messenger RNAs: overview, challenges, and perspectives. Frontiers in Technical Advances in Plant Science, 2, 84 doi:10.3389/fpls.2011.00084.

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Puckette, M., Iyer, N. J., Tang, Y., Dai, X., Zhao, P. X., & Mahalingam, R. (2011). Differential mRNA translation in Medicago truncatula accessions with contrasting responses to ozone-induced oxidative stress. Molecular Plant, August 25, doi: 10.1093/mp/ssr069.

Han, Y., Kang, Y., Torres-Jerez, I., Cheung, F., Town, C. D., Zhao, P. X., Udvardi, M. K., & Monteros, M. J. (2011). Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis. Genomics, 12 (350), doi:10.1186/1471-2164-12-350.