Towards integrative gene functional similarity measurement

[1]  Xiaoyan Liu,et al.  Measuring gene functional similarity based on group-wise comparison of GO terms , 2013, Bioinform..

[2]  Xiaomei Wu,et al.  Improving the Measurement of Semantic Similarity between Gene Ontology Terms and Gene Products: Insights from an Edge- and IC-Based Hybrid Method , 2013, PloS one.

[3]  Yadong Wang,et al.  Identifying cross-category relations in gene ontology and constructing genome-specific term association networks , 2013, BMC Bioinformatics.

[4]  Igor Jurisica,et al.  Novel semantic similarity measure improves an integrative approach to predicting gene functional associations , 2013, BMC Systems Biology.

[5]  Diyuan Yang,et al.  An integration strategy to measure enzyme activities for detecting irreversible inhibitors with dimethoate on butyrylcholinesterase as a model , 2011 .

[6]  David Sánchez,et al.  An ontology-based measure to compute semantic similarity in biomedicine , 2011, J. Biomed. Informatics.

[7]  Phillip W. Lord,et al.  Semantic Similarity in Biomedical Ontologies , 2009, PLoS Comput. Biol..

[8]  K. Dolinski,et al.  Use and misuse of the gene ontology annotations , 2008, Nature Reviews Genetics.

[9]  Catia Pesquita,et al.  Metrics for GO based protein semantic similarity: a systematic evaluation , 2008, BMC Bioinformatics.

[10]  Mark Gerstein,et al.  Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications , 2007, Bioinform..

[11]  Haiyuan Yu,et al.  Developing a similarity measure in biological function space , 2007 .

[12]  Yves A. Lussier,et al.  Evaluation of high-throughput functional categorization of human disease genes , 2007, BMC Bioinformatics.

[13]  Zheng Guo,et al.  Globally predicting protein functions based on co-expressed protein-protein interaction networks and ontology taxonomy similarities. , 2007, Gene.

[14]  Philip S. Yu,et al.  A new method to measure the semantic similarity of GO terms , 2007, Bioinform..

[15]  J. J. Díaz-Mejía,et al.  A network perspective on the evolution of metabolism by gene duplication , 2007, Genome Biology.

[16]  D. Nutt,et al.  Translocator protein (18kDa): new nomenclature for the peripheral-type benzodiazepine receptor based on its structure and molecular function. , 2006, Trends in pharmacological sciences.

[17]  Thomas Lengauer,et al.  A new measure for functional similarity of gene products based on Gene Ontology , 2006, BMC Bioinformatics.

[18]  D. Allison,et al.  Microarray data analysis: from disarray to consolidation and consensus , 2006, Nature Reviews Genetics.

[19]  Angel Rubio,et al.  Correlation between gene expression and GO semantic similarity , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[20]  Frank Holstege,et al.  Predicting gene function through systematic analysis and quality assessment of high-throughput data , 2005, Bioinform..

[21]  Zhiyong Lu,et al.  GO Molecular Function Terms Are Predictive of Subcellular Localization , 2004, Pacific Symposium on Biocomputing.

[22]  Padhraic Smyth,et al.  Analysis and Visualization of Network Data using JUNG , 2005 .

[23]  P. Karp Call for an enzyme genomics initiative , 2004, Genome Biology.

[24]  Douglas P. Wiens,et al.  MATCH - A Software Package for Robust Profile Matching Using S-Plus , 2004 .

[25]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[26]  C. Burge,et al.  Prediction of Mammalian MicroRNA Targets , 2003, Cell.

[27]  C. Claudel-Renard,et al.  Enzyme-specific profiles for genome annotation: PRIAM. , 2003, Nucleic acids research.

[28]  Carole A. Goble,et al.  Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation , 2003, Bioinform..

[29]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[30]  Philip Resnik,et al.  Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language , 1999, J. Artif. Intell. Res..

[31]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[32]  Göran Goldkuhl,et al.  Method intergration: the need for a learning perspective , 1998, IEE Proc. Softw..

[33]  Dekang Lin,et al.  An Information-Theoretic Definition of Similarity , 1998, ICML.

[34]  David W. Conrath,et al.  Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy , 1997, ROCLING/IJCLCLP.

[35]  Matthew O. Ward,et al.  XmdvTool: integrating multiple methods for visualizing multivariate data , 1994, Proceedings Visualization '94.

[36]  Rupert G. Miller Simultaneous Statistical Inference , 1967 .