Vagner A. Benedito, Haiquan Li, Xinbin Dai, Maren Wandrey, Ji He, Rakesh Kaundal, Ivone Torres-Jerez, S. Karen Gomez, Maria J. Harrison, Yuhong Tang, Patrick X. Zhao and Michael K. Udvardi. “Genomic inventory and transcriptional analysis of Medicago truncatula transporters”. Plant Physiology. 2009. Accepted for publication.
Online Open Access | PDF (716K) | BibTEX (benedito09genomic)
Ji He, Vagner A. Benedito, Mingyi Wang, Jeremy D. Murray, Patrick X. Zhao, Yuhong Tang and Michael K. Udvardi. “The Medicago truncatula gene expression atlas web server”. BMC Bioinformatics. 2009, 10:441
BMC Open Access | PDF (1.1M) | BibTEX (he09bmcbioinfo)
Also check the MtGEA web server.
M. David Marks, Li Tian, Jonathan P. Wenger, Stephanie N. Omburo, Wilfredo Soto-Fuentes, Ji He, David R. Gang, George D. Weiblen and Richard A. Dixon. “Identification of candidate genes affecting {Delta}9-tetrahydrocannabinol biosynthesis in Cannabis sativa”. Journal of Experimental Botany. 2009. Accepted for publication. Online advance access available.
JXB Advance Access | PDF (620K) | BibTEX (marks09identification)
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. 9:1, 2009.
Mike Guether, Raffaella Balestrini, Matthew Hannah, Ji He, Michael Udvardi, and Paola Bonfante. “Genome-wide reprogramming of regulatory networks, transport, cell wall and membrane biogenesis during arbuscular mycorrhizal symbiosis in Lotus japonicus”. New Phytologist. 182(1):200 -- 212, 2009.
Guodong Wang, Li Tian, Naveed Aziz, Pierre Broun, Xinbin Dai, Ji He, Andrew King, Patrick Zhao and Richard A. Dixon. “Terpene biosynthesis in glandular trichomes of hop (Humulus lupulus L.)”. Plant Physiology. 148:1254--1266, 2008.
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. 4:19, 2008.
Ji He. “Improving Feature Representation of Natural Language Gene Functional Annotations Using Automatic Term Expansion”. In the Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2008. p173-179.
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 Zhao, Yuhong Tang, and Michael Udvardi. “A gene expression atlas of the model legume Medicago truncatula”. The Plant Journal. 55(3):504 -- 513, 2008.
Also check out the Mt Gene Expression Atlas web server.
Cover Article @ Blackwell Publishing | PDF (754K) | BibTEX (benedito08gene)
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. 8:27, 2008.
Million Tadege, Jiangqi Wen, Ji He, Haidi Tu, Younsig Kwak, Alexis Eschstruth, Anne Cayrel, Gabi Endre, Patrick Zhao, Mireille Chabaud, Pascal Ratet and Kirankumar Mysore. “Large scale insertional mutagenesis using Tnt1 retrotransposon in the model legume Medicago truncatula”. The Plant Journal. 54(2):335-347, 2008.
Marina Naoumkina, Ivone Torres-Jerez, Stacy Allen, Ji He, Patrick Zhao, Richard A. Dixon and Gregory D. May. “Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub)”. BMC Plant Biology. 7:62, 2007.
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.
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.
Xinbin Dai, Ji He, and Xuechun Zhao. “A New Systematic Computational Approach to Predicting Target Genes of Transcription Factors”. Nucleic Acids Research. 35(13):4433-4440, 2007.
Advance Access Online | PDF (253K) | BibTEX (dai07systematic)
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 the Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). April 2007. p17-24.
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.
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):731--736, 2006.
Ji He, Xinbin Dai, and Xuechun Zhao. “A Systematic Computational Approach for Transcription Factor Target Gene Prediction”. In the Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). September 2006. p385-391.
Ji He, Man Lan, Chew-Lim Tan, Sam-Yuan Sung and Hwee-Boon Low. “Initialization of Cluster Refinement Algorithms: A Review and Comparative Study”. In the Proceedings of International Joint Conference on Neural Networks (IJCNN). July 2004. p297-302. Also here: Supplementary resources of this paper.
Ji He, Chew-Lim Tan, Hwee-Boon Low, and Dan Shen. “Unsupervised Learning for Document Classification: Feasibility, Limitation, and the Bottom Line”. In the Proceedings of International Joint Conference on Natural Language Processing (IJCNLP). March 2004. p25-28.
Ji He, Ah-Hwee Tan and Chew-Lim Tan. “Modified ART 2A Growing Network Capable of Generating a Fixed Number of Nodes”. IEEE Transactions on Neural Networks. 15(3):728-737, 2004.
Ji He, Ah-Hwee Tan, and Chew-Lim Tan. “On Machine Learning Methods for Chinese Document Categorization”. Applied Intelligence 18:311-322, 2003.
Ji He, Ah-Hwee Tan and Chew-Lim Tan. “Self-organizing Neural Networks for Efficient Clustering of Gene Expression Data”. In the Proceedings of International Joint Conference on Neural Networks (IJCNN). July 2003. Portland, OR, USA. p1684-1689.
Ji He, Ah-Hwee Tan, Chew-Lim Tan, and Sam-Yuan Sung. “On quantitative evaluation of clustering systems”. In Weili Wu et al, editors, Clustering and Information Retrieval. Kluwer Academic Publishers, Boston Hardbound, ISBN 1-4020-7682-7. December 2003. pp105-133
Ji He, Ah-Hwee Tan and Chew-Lim Tan. “ART-C: A Neural Architecture for Self-Organization Under Constraints”. In the Proceedings of International Joint Conference on Neural Networks (IJCNN). May 2002. Hawaii, USA. p2550-2555.
Ji He, Ah-Hwee Tan and Chew-Lim Tan. “Machine Learning Methods for Chinese Web Page Categorization”. In the ACL’2000 2nd Workshop on Chinese Language Processing. October 2000. Hongkong, China. p93-100.
Ji He, Ah-Hwee Tan and Chew-Lim Tan. “A Comparative Study on Chinese Text Categorization Methods”. In the PRICAI’2000 International Workshop on Text and Web Mining. August 2000. Melbourne, Australia. p24-35.
