The Zhao Bioinformatics Laboratory
PlantGRN: Modeling and Deciphering Plant Transcriptional Regulatory Networks   
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Published papers

  1. Firoz Ahmed, Muthappa Senthil-Kumar, Seonghee Lee, Xinbin Dai, Kirankumar Mysore and Patrick X. Zhao* (2015). Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in Arabidopsis. RNA Biology 11(11), 1414-1429.
  2. Jamie O'Rourke, Luis Iniguez, Fengli Fu, Bruna Bucciarelli, Susan Miller, Scott Jackson, Philip McClean, Jun Li, Xinbin Dai, Patrick X. Zhao, Georgina Hernandez and Carroll Vance (2014). An RNA-Seq based gene expression atlas of the common bean. BMC Genomics 15(1), 866.
  3. Jun Li, Hairong Wei, Tingsong Liu and Patrick X. Zhao* (2014). GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data. Nucleic Acids Research 42(5), e32.
  4. Nitish K. Mishra, Junil Chang and Patrick X. Zhao* (2014). Prediction of Membrane Transport Proteins and Their Substrate Specificities Using Primary Sequence Information. PLoS ONE 9(6), e100278.
  5. Michael T. Parker, Yuan Zhong, Xinbin Dai, Shiliang Wang and Patrick X. Zhao Comparative genomic and transcriptomic analysis of terpene synthases in Arabidopsis and Medicago. IET Systems Biology, 2014. 8, 146-153.
  6. Wolfgang Goettel, Zongrang Liu, Jing Xia, Weixiong Zhang, Patrick X. Zhao and Yong-Qiang An (2014). Systems and Evolutionary Characterization of MicroRNAs and Their Underlying Regulatory Networks in Soybean Cotyledons. PLoS ONE 9(1), e86153.
  7. Zhipeng Liu, Tianlong Chen, Lichao Ma, Zhiguang Zhao, Patrick X. Zhao, Zhibiao Nan and Yanrong Wang (2013). Global Transcriptome Sequencing Using the Illumina Platform and the Development of EST-SSR Markers in Autotetraploid Alfalfa. PLoS ONE 8(12), e83549.
  8. Xinbin Dai, Senjuti Sinharoy, Michael Udvardi and Patrick X. Zhao* (2013). PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool. BMC Bioinformatics 14(1), 321.
  9. Jun Li, Hairong Wei and Patrick X. Zhao* (2013). DeGNServer: Deciphering Genome-Scale Gene Networks through High Performance Reverse Engineering Analysis. BioMed Research International 2013, 10.
  10. Jun Li, Xinbin Dai, Tingsong Liu and Patrick X. Zhao* (2012). LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. Nucleic Acids Research 40(D1), D1221-D1229.
  11. Nevin D. Young, Frederic Debelle, Giles E. D. Oldroyd, Rene Geurts, Steven B. Cannon, Michael K. Udvardi, Vagner A. Benedito, Klaus F. X. Mayer, Jerome Gouzy, Heiko Schoof, Yves Van de Peer, Sebastian Proost, Douglas R. Cook, Blake C. Meyers, Manuel Spannagl, Foo Cheung, Stephane De Mita, Vivek Krishnakumar, Heidrun Gundlach, Shiguo Zhou, Joann Mudge, Arvind K. Bharti, Jeremy D. Murray, Marina A. Naoumkina, Benjamin Rosen, Kevin A. T. Silverstein, Haibao Tang, Stephane Rombauts, Patrick X. Zhao, Peng Zhou, Valerie Barbe, Philippe Bardou, Michael Bechner, Arnaud Bellec, Anne Berger, Helene Berges, Shelby Bidwell, Ton Bisseling, Nathalie Choisne, Arnaud Couloux, Roxanne Denny, Shweta Deshpande, Xinbin Dai, Jeff J. Doyle, Anne-Marie Dudez, Andrew D. Farmer, Stephanie Fouteau, Carolien Franken, Chrystel Gibelin, John Gish, Steven Goldstein, Alvaro J. Gonzalez, Pamela J. Green, Asis Hallab, Marijke Hartog, Axin Hua, Sean J. Humphray, Dong-Hoon Jeong, Yi Jing, Anika Jocker, Steve M. Kenton, Dong-Jin Kim, Kathrin Klee, Hongshing Lai, Chunting Lang, Shaoping Lin, Simone L. Macmil, Ghislaine Magdelenat, Lucy Matthews, Jamison McCorrison, Erin L. Monaghan, Jeong-Hwan Mun, Fares Z. Najar, Christine Nicholson, Celine Noirot, Majesta O/'Bleness, Charles R. Paule, Julie Poulain, Florent Prion, Baifang Qin, Chunmei Qu, Ernest F. Retzel, Claire Riddle, Erika Sallet, Sylvie Samain, Nicolas Samson, Iryna Sanders, Olivier Saurat, Claude Scarpelli, Thomas Schiex, Beatrice Segurens, Andrew J. Severin, D. Janine Sherrier, Ruihua Shi, Sarah Sims, Susan R. Singer, Senjuti Sinharoy, Lieven Sterck, Agnes Viollet, Bing-Bing Wang, Keqin Wang, Mingyi Wang, Xiaohong Wang, Jens Warfsmann, Jean Weissenbach, Doug D. White, Jim D. White, Graham B. Wiley, Patrick Wincker, Yanbo Xing, Limei Yang, Ziyun Yao, Fu Ying, Jixian Zhai, Liping Zhou, Antoine Zuber, Jean Denarie, Richard A. Dixon, Gregory D. May, David C. Schwartz, Jane Rogers, Francis Quetier, Christopher D. Town and Bruce A. Roe (2011). The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480(7378), 520-524.
  12. Xinbin Dai and Patrick X. Zhao* (2011). psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research 39(suppl 2), W155-W159.
  13. Firoz Ahmed and Patrick X. Zhao* (2011), A comprehensive analysis of isomirs and their targets using high-throughput sequencing data for Arabidopsis thaliana. Journal of Natural Science, Biology and Medicine, 2(3), 32-33.
  14. Xinbin Dai, Zhaohong Zhuang and Patrick X. Zhao* (2011). Computational analysis of miRNA targets in plants: current status and challenges. Briefings in Bioinformatics 12(2), 115-121.
  15. Firoz Ahmed, Vagner A. Benedito and Patrick X. Zhao* (2011). Mining functional elements in messenger RNAs: overview, challenges, and perspectives. Frontiers in Plant Science 2(84).

Published book chapters

  1. Firoz Ahmed, Xinbin Dai and Patrick X. Zhao*, Bioinformatics Tools for Achieving Better Gene Silencing in Plants, in Kirankumar S. Mysore and Senthil-Kumar Muthappa, Plant Gene Silencing: Methods and Protocols, Methods in Molecular Biology, 2015, vol. 1287, p. 43-60, DOI 10.1007/978-1-4939-2453-0_3, Springer, New York.
  2. Jun Li, Hairong Wei, Tingsong Liu, Xinbin Dai and Patrick X. Zhao*, LegumeIP: an integrative platform for comparative genomics and transcriptomics of model legumes, in F.J.d. Bruijn, Biological Nitrogen Fixation, 2015, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030.

Related previous publications

  1. Xinbin Dai, Guodong Wang, Dong Sik Yang, Yuhong Tang, Pierre Broun, M. David Marks, Lloyd W. Sumner, Richard A. Dixon and Patrick X. Zhao. TrichOME: A comparative omics database for plant trichomes. Plant Physiology, 2009, doi: 10.1104/pp.109.145813.
  2. Xinbin Dai and Patrick X. Zhao. pssRNAMiner: A plant short small RNA regulatory cascade analysis server. Nucleic Acids Research, 2008, doi: 10.1093/nar/gkn297.
  3. Xinbin Dai, Ji He, and Xuechun Zhao. A New Systematic Computational approach to Predict Target Genes of Transcription Factors. Nucleic Acids Research. 2007;35(13):4433-40.
   Funding by the National Science Foundation    Funding by the Oklahoma Center for the Advancement of Science & Technology    Additional funding by the Samuel Roberts Noble Foundation

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