@INPROCEEDINGS{he08cibcb,
    Author         = {Ji He},
    Booktitle      = {Proceedings of IEEE Symposium on Coumputational Intelligence in Bioinformatics and Computational Biology ({CIBCB})},
    Pages          = {173--179},
    Title          = {Improving Feature Representation of Natural Language Gene Functional Annotations Using Automatic Term Expansion},
    Year           = {2008}
}

@ARTICLE{he07itic,
    Author         = {Ji He and Xinbin Dai and Xuechun Zhao},
    Journal        = {International Journal of Information Technology and Intelligent Computing},
    Note           = {Accepted for publication},
    Title          = {Mixture Model Adaptive Neural Network for Mining Gene Functional Patterns from Heterogeneous Knowledge Domains},
    Year           = {2007}
}

@ARTICLE{he07bmcbioinfo,
    Author         = {Ji He and Xinbin Dai and Xuechun Zhao},
    Journal        = {BMC Bioinformatics},
    Number         = {1},
    Pages          = {53},
    Title          = {{PLAN}: A web platform for automating high-throughput BLAST searches and for managing and mining results},
    Volume         = {8},
    Year           = {2007}
}

@INPROCEEDINGS{he07cibcb,
    Address        = {Honolulu, Hawaii, USA},
    Author         = {Ji He and Xinbin Dai and Xuechun Zhao},
    Booktitle      = {Proceedings of IEEE Symposium on Coumputational Intelligence in Bioinformatics and Computational Biology ({CIBCB})},
    Month          = {April},
    Pages          = {17--24},
    Title          = {Associative Artificial Neural Network for Discovery of Highly Correlated Gene Groups Based on Gene Ontology and Gene Expression},
    Year           = {2007}
}

@INPROCEEDINGS{he06cibcb,
    Address        = {Toronto, Ontario, Canada},
    Author         = {Ji He and Xinbin Dai and Xuechun Zhao},
    Booktitle      = {Proceedings of IEEE Symposium on Coumputational Intelligence in Bioinformatics and Computational Biology ({CIBCB})},
    Month          = {September},
    Pages          = {385--391},
    Title          = {A Systematic Computational Approach for Transcription Factor Target Gene Prediction},
    Year           = {2006}
}

@INPROCEEDINGS{he04ijcnn,
    Address        = {Budapest, Hungary},
    Author         = {Ji He and Man Lan and Chew-Lim Tan and Sam-Yuan Sung and Hwee-Boon Low},
    Booktitle      = {Proceedings of International Joint Conference on Neural Networks ({IJCNN})},
    Month          = {July},
    Pages          = {297--302},
    Title          = {Initialization of Cluster Refinement Algorithms: A Review and Comparative Study},
    Year           = {2004}
}

@INPROCEEDINGS{he04ijcnlp,
    Address        = {Sanya, Hainan, China},
    Author         = {Ji He and Chew-Lim Tan and Hwee-Boon Low and Dan Shen},
    Booktitle      = {Proceedings of International Joint Conference on Natural Language Processing ({IJCNLP}), Interactive Poster Session},
    Month          = {March},
    Pages          = {25--28},
    Title          = {Unsupervised Learning for Document Classification: Feasibility, Limitation, and the Bottom Line},
    Year           = {2004}
}

@ARTICLE{he04tnn,
    Author         = {Ji He and Ah-Hwee Tan and Chew-Lim Tan},
    Journal        = {IEEE Transactions on Neural Networks},
    Number         = {3},
    Pages          = {728--737},
    Title          = {Modified {ART 2A} Growing Network Capable of Generating a Fixed Number of Nodes},
    Volume         = {15},
    Year           = {2004}
}

@INPROCEEDINGS{he03ijcnn,
    Address        = {Portland, OR, USA},
    Author         = {Ji He and Ah-Hwee Tan and Chew-Lim Tan},
    Booktitle      = {Proceedings of International Joint Conference on Neural Networks ({IJCNN})},
    Month          = {July},
    Pages          = {1684--1689},
    Title          = {Self-organizing Neural Networks for Efficient Clustering of Gene Expression Data},
    Year           = {2003}
}

@INCOLLECTION{he03cir,
    Author         = {Ji He and Ah-Hwee Tan and Chew-Lim Tan and Sam-Yuan Sung},
    Booktitle      = {Clustering and Information Retrieval},
    Editor         = {Weili Wu and Hui Xiong and Shashi Shekhar},
    Pages          = {105--133},
    Publisher      = {Kluwer Academic Publishers},
    Title          = {On Quantitative Evaluation of Clustering Systems},
    Year           = {2003},
    ISBN           = {1-4020-7682-7}
}

@INPROCEEDINGS{he02ijcnn,
    Author         = {Ji He and Ah-Hwee Tan and Chew-Lim Tan},
    Booktitle      = {Proceedings of International Joint Conference on Neural Networks ({IJCNN})},
    Pages          = {2550--2555},
    Title          = {{ART-C}: A Neural Architecture for Self-Organization Under Constraints},
    Year           = {2002}
}

@ARTICLE{he03apin,
    Author         = {Ji He and Ah-Hwee Tan and Chew-Lim Tan},
    Journal        = {Applied Intelligence},
    Pages          = {311--322},
    Title          = {On Machine Learning Methods for Chinese Document Categorization},
    Volume         = {18},
    Year           = {2003}
}

@INPROCEEDINGS{he00acl,
    Author         = {Ji He and Ah-Hwee Tan and Chew-Lim Tan},
    Booktitle      = {2nd {ACL} Workshop on Chinese Language Processing},
    Month          = {October},
    Pages          = {93--100},
    Title          = {Machine Learning Methods for Chinese Web Page Categorization},
    Year           = {2000}
}

@INPROCEEDINGS{he00pricai,
    Author         = {Ji He and Ah-Hwee Tan and Chew-Lim Tan},
    Booktitle      = {{PRICAI} International Workshop on Text and Web Mining},
    Month          = {August},
    Pages          = {24--35},
    Title          = {A Comparative Study on Chinese Text Categorization Methods},
    Year           = {2000}
}

@ARTICLE{benedito06transporter,
    Author         = {Vagner A. Benedito and Xinbin Dai and Ji He and Patrick X. Zhao and Michael K. Udvardi  },
    Journal        = {Functional Plant Biology},
    Number         = {8},
    Pages          = {731--736},
    Title          = {Functional genomics of plant transporters in legume nodules},
    Volume         = {33},
    Year           = {2006}
}

@ARTICLE{dai07systematic,
    Author         = {Xinbin Dai and Ji He and Patrick Xuechun Zhao},
    Journal        = {Nucleic Acids Research},
    Number         = {13},
    Pages          = {4433--4440},
    Title          = {A New Systematic Computational Approach to Predicting Target Genes of Transcription Factors},
    Volume         = {35},
    Year           = {2007}
}

@ARTICLE{broz07first,
    Author         = {Amanda K. Broz and Corey D. Broeckling and Ji He and Xinbin Dai and Patrick X. Zhao and Jorge M. Vivanco},
    Journal        = {BMC Plant Biology},
    Pages          = {25},
    Title          = {A first step in understanding an invasive weed through its genes: an {EST} analysis of invasive {Centaurea} maculosa},
    Volume         = {7},
    Year           = {2007}
}

@ARTICLE{naoumkina07analysis,
    Author         = {Marina Naoumkina and Ivone Torres-Jerez and Stacy Allen and Ji He and Patrick Zhao and Richard A. Dixon and Gregory D. May},
    Journal        = {BMC Plant Biology},
    Pages          = {62},
    Title          = {Analysis of {cDNA} libraries from developing seeds of guar ({Cyamopsis tetragonoloba (L.) Taub})},
    Volume         = {7},
    Year           = {2007}
}

@ARTICLE{tadege08large,
    Author         = {Million Tadege and Jiangqi Wen and Ji He and Haidi Tu and Younsig Kwak and Alexis Eschstruth and Anne Cayrel and Gabi Endre and  Patrick Zhao and Mireille Chabaud and Pascal Ratet and Kirankumar Mysore},
    Journal        = {The Plant Journal},
    Number         = {2},
    Pages          = {335--347},
    Title          = {Large scale insertional mutagenesis using {Tnt1} retrotransposon in the model legume {Medicago} truncatula},
    Volume         = {54},
    Year           = {2008}
}

@ARTICLE{mian08analysis,
    Author         = {MA Rouf Mian and Yan Zhang and Zeng-Yu Wang and Ji-Yi Zhang and Xiaofei Cheng and Lei Chen and Konstantin Chekhovskiy and Xinbin Dai and Chunhong Mao and Foo Cheung and Xuechun Zhao and Ji He and Angela D Scott and Christopher D Town and Gregory D May},
    Journal        = {BMC Plant Biology},
    Pages          = {27},
    Title          = {Analysis of tall fescue {EST}s representing different abiotic stresses, tissue types and developmental stages },
    Volume         = {8},
    Year           = {2008}
}

@ARTICLE{benedito08gene,
    Author         = {Vagner Benedito and Ivone Torez-Jerez and Jeremy Murray and Andry Andriankaja and Stacey Allen and Klementina Kakar and Maren Wandrey and Jerome Verdier and Helene Zuber and Thomas Ott and  Sandra Moreau and Andreas Niebel and Tancred Frickey and Georg Weiller and Ji He and Xinbin Dai and Patrick Zhao and Yuhong Tang and Michael Udvardi},
    Journal        = {The Plant Journal},
    Number         = {3},
    Pages          = {504 -- 513},
    Title          = {A gene expression atlas of the model legume {Medicago truncatula}},
    Volume         = {55},
    Year           = {2008}
}

@ARTICLE{zhang08genome,
    Author         = {Yan Zhang and Ji He and Patrick X Zhao and Joseph H Bouton and Maria J Monteros},
    Journal        = {Plant Methods},
    Pages          = {19},
    Title          = {Genome-wide Identification of Microsatellites in White Clover ({Trifolium repens L.}) using {FIASCO} and {phpSSRMiner}},
    Volume         = {4},
    Year           = {2008}
}

@ARTICLE{wang08terpene,
    Author         = {Guodong Wang and Li Tian and Naveed Aziz and Pierre Broun and Xinbin Dai and Ji He and Andrew King and Patrick Zhao and Richard A. Dixon},
    Journal        = {Plant Physiology},
    Pages          = {1254--1266},
    Title          = {Terpene biosynthesis in glandular trichomes of hop ({Humulus lupulus L.})},
    Volume         = {148},
    Year           = {2008}
}

@ARTICLE{guether08genome,
    Author         = {Mike Guether and Raffaella Balestrini and Matthew Hannah and Ji He and Michael Udvardi and Paola Bonfante},
    Journal        = {New Phytologist},
    Note           = {Accepted for publication},
    Title          = {Genome-wide reprogramming of regulatory networks, transport, cell wall and membrane biogenesis during arbuscular mycorrhizal symbiosis in {Lotus japonicus}},
    Year           = {2008}
}