- Li Tian , Gregory J Peel , Zhentian Lei , Naveed Aziz , Xinbin Dai , Ji He , Bonnie Watson , Patrick X. Zhao, Lloyd W Sumner and Richard A Dixon, Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots. BMC Plant Biology, 2009, 9:1, doi:10.1186/1471-2229-9-1. (Link)
- Haiquan Li, Jinyan Li and Patrick X. Zhao. Discovery of Protein Interaction Sites. In Bioinforamtics section, Encyclopedia of Data Warehousing and Mining, Second Edition, ISBN: 978-1-60566-010-3, edited by Dr. John Wang. August 2008 Published under the imprint Information Science Reference (formerly Idea Group Reference). (Link, PDF)
- Guodong Wang, Li Tian, Naveed Aziz, Pierre Broun, Xinbin Dai, Ji He, Andrew King, Patrick X. Zhao and Richard A. Dixon, Terpene biosynthesis in glandular trichomes of hop (Humulus lupulus L.), Plant Physiology, 2008, 10.1104/pp.108.125187. (Link)
- Yan Zhang, Ji He, Patrick X. Zhao, Joseph H Bouton and Maria J Monteros. Genome-wide Identification of Microsatellites in White Clover (Trifolium repens L.) using FIASCO and phpSSRMiner. Plant Methods 2008. (Link)
- 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. (Link)
- Vagner Benedito, Ivone Torez-Jerez, Jeremy Murray, Andry Andriankaja, Stacey Allen, Klementina Kakar, Maren Wandrey, Jerome Verdier, Helene Zuber, Thomas Ott, Sandra Moreau, Andreas Niebel, Tancred Frickey, Georg Weiller, Ji He, Xinbin Dai, Patrick X. Zhao, Yuhong Tang, and Michael Udvardi. A gene expression atlas of the model legume Medicago truncatula. The Plant Journal , 2008, doi:10.1111/j.1365-313X.2008.03519.x. (Link)
- Haiquan Li, Xinbin Dai and Xuechun Zhao. A Nearest Neighbor Approach for Automated Transporter Prediction and Categorization from Protein Sequences. Bioinformatics, 2008, doi:10.1093/bioinformatics/btn099. (Link)
- MA Rouf Mian, Yan Zhang, Zeng-Yu Wang, Ji-Yi Zhang, Xiaofei Cheng, Lei Chen, Konstantin Chekhovskiy, Xinbin Dai, Chunhong Mao, Foo Cheung, Xuechun Zhao, Ji He, Angela D Scott, Christopher D Town and Gregory D May. Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages. BMC Plant Biology, 2008, 8:27 doi:10.1186/1471-2229-8-27. (Link)
- Million Tadege, Jiangqi Wen, Ji He, Haidi Tu, Younsig Kwak, Alexis Eschstruth, Anne Cayrel, Gabi Endre, Patrick X. Zhao, Mireille Chabaud, Pascal Ratet and Kirankumar Mysore. Large scale insertional mutagenesis using Tnt1 retrotransposon in the model legume Medicago truncatula. The Plant Journal, 2008, 54 (2), 335-347 doi:10.1111/j.1365-313X.2008.03418.x (Link)
- Marina Naoumkina, Ivone Torres-Jerez, Stacy Allen, Ji He, Patrick X. Zhao, Richard A Dixon and Gregory D May, Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub). BMC Plant Biology, Nov. 23, 2007. 7 (1):62. (PDF)
- Asuka Itaya, Ralf Bundschuh, Anthony Archual, Je-Gun Joung, Zhangjun Fei, Xinbin Dai, Patrick X. Zhao, Yuhong Tang, Richard S. Nelson and Biao Ding, Small RNAs in Tomato Fruit and Leaf Development, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2008, 1779(2): 99-107 (Link)
- Saeed Irian, Ping Xu, Xinbin Dai, Patrick X. Zhao, and Marilyn J. Roossinck, Regulation of a Virus-Induced lethal disease in Tomato Revealed by Long SAGE analyses, Molecular Plant-Microbe Interactions, Dec. 2007, 20 (12):1477-88. (PDF)
- Ji He, Xinbin Dai, and Xuechun Zhao. Mixture Model Adaptive Neural Network for Mining Gene Functional Patterns from Heterogeneous Knowledge Domains. International Journal of Information Technology and Intelligent Computing. 2007. Accepted for publication. (PDF)
- 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. NAR Online. (PDF)
- Amanda K. Broz, Corey D. Broeckling, Ji He, Xinbin Dai, Patrick X. Zhao, and Jorge M. Vivanco. A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa. BMC Plant Biology. 7:25, 2007. (PDF)
- Ji He, Xinbin Dai, and Xuechun Zhao. 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). April 2007. p17-24. (PDF)
- Ji He, Xinbin Dai, and Xuechun Zhao. PLAN: A web platform for automating high-throughput BLAST searches and for managing and mining results. BMC Bioinformatics. 8:53, 2007. (PDF)
- Vagner A. Benedito, Xinbin Dai, Ji He, Patrick X. Zhao, and Michael K. Udvardi. Functional Genomics of Plant Transporters in Legume Nodules. Functional Plant Biology. 33(8), p731–736, 2006. (PDF)
- Ji He, Xinbin Dai, and Xuechun Zhao. A Systematic Computational Approach for Transcription Factor Target Gene Prediction. In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). September 2006. p385-391. (PDF)
- Corey D. Broeckling, Indira Reddy, Tony Duran, Xuechun Zhao, and Lloyd W. Sumner, MET-IDEA: data extraction tool for mass spectrometry-based metabolomics, Anal Chem. July 2006, 78(13):4334-41. (Link)
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