Zhao Lab Publications

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.

Young, N. D. , Debellé, F., Oldroyd, G., Geurts, R., Cannon, S. B. , Udvardi, M. K., Benedito, V. A., Mayer, K.F.X., Gouzy, J., Schoof, H., Van de Peer, Y., Proost, S., Cook, D. R. , Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A.K., Murray, J., Naoumkina, M., Rosen, B., Silverstein, K.A.T., Tang, H., Rombauts, S., Zhao, P. X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Bergès, H., Bidwell, T. G., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Dai, X., Doyle, J.J., Dudez, A-M., Farmer, A. D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Goldstein, S., González, A.J., Green, P.J., Hallab, A., Hartog, M., Hua, A., Humphray, S.J., Jeong, D-H., Jing, Y., Jöcker, A., Kenton, S., Kim, D-J., Klee, K., Lai, H., Lang, C., Lin, S., Macmil, S.L., Magdelenat, G., Matthews, L., McCorrison, J., Monaghan, E.L., Mun, J-H., Najar, F.Z. , Nicholson, C., Noirot, C., O’Bleness, M., Paule, C.R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E. F. , Riddle, C., Sallet, E., Samain, S., Samson, N., Sanders, I., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Severin, A.J., Sherrier, D. J., Shi, R., Sims, S., Singer, S.R. , Sinharoy, S. , Sterck, L., Viollet, A., Wang, B-B., Wang, K., Wang, M., Wang, X-H., Warfsmann, J., Weissenbach, J., White, D.D., White, J. D., Wiley, G. B., Wincker, P., Xing, Y., Yang, L., Yao, Z., Ying, F., Zhai, J., Zhou, L., Zuber, A., Dénarié, J., Dixon, R. A., May, G. D., Schwartz, D.C., Rogers, J., Quétier, F., Town, C. D., & Roe, B. A. (2011). The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, November 16, Published online doi:10.1038/nature10625.

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.

Dai, X., & Zhao, P. X. (2011). psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research, 39, W155–W159 doi:10.1093/nar/gkr319.

Lei, Z., Dai, X., Watson, T., Zhao, P. X., & Sumner, L. W. (2011). A legume specific protein database (LegProt) improves the number of identified peptides, confidence scores and overall protein identification success rates for legume proteomics. Phytochemistry, , doi:10.1016/j.phytochem.2011.01.026 .

Dai, X., Zhuang, Z., & Zhao, P. X. (2011). Computational analysis of miRNA targets in plants: current status and challenges. Briefings in Bioinformatics, 12 (2), 115-121 doi:10.1093/bib/bbq065.

Naoumkina, M., Zhao, Q., Gallego-Giraldo, L., Dai, X., Zhao, P. X., & Dixon, R. A. (2010). Genome-wide analysis of phenylpropanoid defence pathways. Molecular Plant Pathology, 11, 829-846 DOI: 10.1111/j.1364-3703.2010.00648.x.

Kaundal, R., Saina, R., & Zhao, P. X. (2010). Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis . Plant Physiology, 154 (1), 36-54 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.

Benedito, V. A., Li, H., Dai, X., Wandrey, M., He, J., Kaundal, R., Torres-Jerez, I., Gomez, S. K. , Harrison, M. J., Tang, Y., Zhao, P. X., & Udvardi, M. K. (2010). Genomic inventory and transcriptional analysis of Medicago truncatula transporters. Plant Physiology, 152, 1716-1730 DOI: 10.1104/pp.109.148684.

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.

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.

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. BMC 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: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.

Li, H., Li, J., & Zhao, P. X. (2008). Discovery of protein interaction sites. In J. Wang (Ed.), Encyclopedia of Data Warehousing and Mining (2nd ed.). (pp. 1-6). .

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.

Li, H., Dai, X., & Zhao, X. (2008). A nearest neighbor approach for automated transporter prediction and categorization from protein sequences. BMC Bioinformatics, 24 (9), 1129-1136 DOI:10.1093/bioinformatics/btn099.

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-gene Regulatory Mechanisms, 1779 (2), 99-107 DOI:10.1016/j.bbagrm.2007.09.003.

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.

He, J., Dai, X., & Zhao, P. X. (2007). Associative artificial neural network for discovery of highly correlated gene groups based on gene ontology and gene expression. In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (pp. 17-24). .

He, J., Dai, X., & Zhao, X. (2007). PLAN: A web platform for automating high-throughput BLAST searches and for managing and mining results. BMC Bioinformatics, 8 (Feb 9), 53.

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.

He, J., Dai, X., & Zhao, P. X. (2006). A systematic computational approach for transcription factor target gene prediction. In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (pp. 385-391). .

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.