Zhao Lab 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.

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 Plant Biology, 9 (1)DOI:10.1186/1471-2229-9-1.

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:10.1186/1746-4811-4-19.

Wang, G., Tian, L., Aziz, N., Broun, P., Dai, X., He, J., King, A, Zhao, P. X., & Dixon, R. A. (2008). Terpene biosynthesis in glandular trichomes of hop (Humulus lupulus L.). Plant Physiology, 148 (3), 1254-1266 DOI:10.1104/pp.108.125187.

Benedito, V. A., Torres-Jerez, I., Murray, J., Andriankaja, A., Allen, N. S., Kakar, K., Wandrey, M., Verdier, J., Zuber, H., Ott, T., Moreau, S., Niebel, A., Frickey, T., Weiller, G., He, J., Dai, X., Zhao, P. X., Tang, Y., & Udvardi, M. K. (2008). A gene expression atlas of the model legume Medicago truncatula. Plant Journal, 55 (3), 504-513 DOI:10.111/j.1365-313X.2008.03519.x.

Tadege, M., Wen, J. Q., He, J., Tu, H., Kwak, Y., Eschstruth, A., Cayrel, A., Endre, G., Zhao, P. X., Chabaud, M., Ratet, P., & Mysore, K. S. (2008). Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant Journal, 54 (2), 335-347 DOI:10.1111/j.1365-313X.2008.03418.x.

Dai, X., & Zhao, P. X. (2008). pssRNAMiner: A plant short small RNA regulatory cascade analysis server. Nucleic Acids Research, 36 (Suppl. 2), W114-W118 DOI:10.1093/nar/gkn297.

Itaya, A., Bundschuh, R., Archual, A. J., Joung, J. G., Fei, Z., Dai, X., Zhao, P. X., & Tang, Y. (2008). Small RNAs in tomato fruit and leaf development . BBA - Biochimica et Biophysica Acta, 1779 (2), 99-107.

Dai, X., He, J., & Zhao, P. X. (2007). A new systematic computational approach to predicting target genes of transcription factors. Nucleic Acids Research, 35 (13), 4433-4440 DOI:10.1093/nar/gkm454.

Naoumkina, M., Torres-Jerez, I., Allen, S. N., He, J., Zhao, P. X., Dixon, R. A., & May, G. D. (2007). Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub). BMC Plant Biology, 7 (1), 62 DOI:10.1186/1471-2229-7-62/.

Irian, S, Xu, P., Dai, X., Zhao, P. X., & Roossinck, M. J. (2007). Regulation of a virus-induced lethal disease in tomato revealed by LongSAGE analysis. Molecular Plant-Microbe Interactions, 20 (12), 1477-1488 DOI:10.1094 /MPMI -20-12-1477..

Broz, A. K., Broeckling, C. D., He, J., Dai, X., Zhao, P. X., & 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 (25), DOI:10.1186/1471-2229-7-25.

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

Broeckling, C. D., Reddy, I. R., Duran, A. L., Zhao, P. X., & Sumner, L. W. (2006). MET-IDEA: Data extraction tool for mass spectrometry-based metabolomics. Analytical Chemistry, 78 (13), 4334-4341 DOI: 10.1021/ac0521596.