@Article{yu2012,
	title = {clusterProfiler: an R package for comparing biological themes among gene clusters},
	volume = {16},
	issn = {1536-2310},
	url = {},
	doi = {},
	journal = {OMICS: A Journal of Integrative Biology},
	author = {Guangchuang Yu and Le-Gen Wang and Yanyan Han and Qing-Yu He},
	year = {2012},
	note = {},
	keywords = {clusterProfiler, Gene Ontology, KEGG, Enrichment analysis, R package, Cluster comparison},
	pages = {in press}
}

@Article{yu2011,
	title = {Functional similarity analysis of human virus-encoded {miRNAs}},
	volume = {1},
	issn = {2043-9113},
	url = {http://www.jclinbioinformatics.com/content/1/1/15},
	doi = {10.1186/2043-9113-1-15},
	number = {1},
	journal = {Journal of Clinical Bioinformatics},
	author = {Yu, Guangchuang and He, {Qing-Yu}},
	month = may,
	year = {2011},
	pages = {15}
}

@Article{yu_new_2011,
	title = {A new method for measuring functional similarity of microRNAs},
	volume = {1},
	issn = {2182-0287},
	url = {http://www.jiomics.com/index.php/jio/article/view/21},
	doi = {10.5584/jiomics.v1i1.21},
	number = {1},
	journal = {Journal of Integrated {OMICS}},
	author = {Yu, Guangchuang and Xiao, {Chuan-Le} and Bo, Xiaochen and Lu, {Chun-Hua} and Qin, Yide and Zhan, Sheng and He, {Qing-Yu}},
	month = feb,
	year = {2011},
	keywords = {Clustering, Gene, {microRNA;}, Ontology;, Semantic, Similarity;},
	pages = {49--54}
}

@Article{yu2010,
	title = {GOSemSim: an R package for measuring semantic similarity among GO terms and gene products},
	volume = {26},
	issn = {1367-4803},
	url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976},
	doi = {10.1093/bioinformatics/btq064},
	journal = {Bioinformatics},
	author = {Guangchuang Yu and Fei Li and Yide Qin and Xiaochen Bo and Yibo Wu and Shengqi Wang},
	month = April,
	year = {2010},
	note = {PMID: 20179076},
	keywords = {Gene Ontology, Semantic Similarity, Bioconductor},
	pages = {976-978}
}

@Article{wang_new_2007,
	title = {A new method to measure the semantic similarity of GO terms},
	volume = {23},
	issn = {1460-2059},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17344234},
	doi = {btm087},
	journal = {Bioinformatics (Oxford, England)},
	author = {James Z Wang and Zhidian Du and Rapeeporn Payattakool and Philip S Yu and Chin-Fu Chen},
	month = may,
	year = {2007},
	note = {PMID: 17344234},
	keywords = {Algorithms,Computational Biology,Databases, Genetic,Humans,Semantics,Terminology as Topic,Vocabulary, Controlled},
	pages = {1274-81}
}

@Article{lord_semantic_2003,
	title = {Semantic similarity measures as tools for exploring the gene ontology},
	issn = {1793-5091},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12603061},
	doi = {12603061},
	journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing},
	author = {P W Lord and R D Stevens and A Brass and C A Goble},
	year = {2003},
	note = {PMID: 12603061},
	keywords = {Classification,Computational Biology,Databases, Protein,Genomics,Humans,Proteomics,Sequence Alignment},
	pages = {601-12}
}

@Article{jiang_semantic_1997,
	title = {Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy},
	url = {http://www.citebase.org/abstract?id=oai:arXiv.org:cmp-lg/9709008},
	journal={Proceedings of 10th International Conference on Research In Computational Linguistics},
	author = {Jay J. Jiang and David W. Conrath},
	year = {1997}
}

@Article{philip_semantic_1999,
	title = {Semantic Similarity in a Taxonomy: An {Information-Based} Measure and its Application to Problems of Ambiguity in Natural Language},
	volume = {11},
	url = {},
	journal = {Journal of Artificial Intelligence Research},
	author = {Resnik Philip},
	year = {1999},
	pages = {95--130}
}

@Article{lin_information-theoretic_1998,
	title = {An {Information-Theoretic} Definition of Similarity},
	url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.55.1832},
	doi = {10.1.1.55.1832},
	journal = {In Proceedings of the 15th International Conference on Machine Learning},
	author = {Dekang Lin},
	year = {1998},
	pages = {296---304}
}

@Article{schlicker_new_2006,
	title = {A new measure for functional similarity of gene products based on Gene Ontology},
	volume = {7},
	issn = {1471-2105},
	doi = {1471-2105-7-302},
	journal = {BMC Bioinformatics},
	author = {Andreas Schlicker and Francisco S Domingues and Jörg Rahnenführer and Thomas Lengauer},
	year = {2006},
	note = {PMID: 16776819},
	keywords = {{Algorithms,Artificial} {Intelligence,Databases,} {Protein,Genes,Information} Storage and {Retrieval,Multigene} {Family,Natural} Language {Processing,Proteins,Structure-Activity} {Relationship,User-Computer} {Interface,Vocabulary,} Controlled},
	pages = {302}
}

