http://www.bibsonomy.org/burst/user/sb3000/bioinformaticsBibSonomy BuRST Feed for /user/sb3000/bioinformatics2008-07-21T01:30:20+02:00http://www.bibsonomy.org/bibtex/22226dfeef2ca4037bc100cf70ef14c08/sb3000sb30002007-06-01T17:31:49+02:00text-classification data bioinformatics <span style="color:#555555;">JP <a href="http://www.bibsonomy.org/author/Pestian">Pestian</a> and C <a href="http://www.bibsonomy.org/author/Brew">Brew</a> and P <a href="http://www.bibsonomy.org/author/Matykiewicz">Matykiewicz</a> and DJ <a href="http://www.bibsonomy.org/author/Hovermale">Hovermale</a> and N. <a href="http://www.bibsonomy.org/author/Johnson">Johnson</a> and K. <a href="http://www.bibsonomy.org/author/Bretonnel Cohen">Bretonnel Cohen</a> and W. <a href="http://www.bibsonomy.org/author/Duch">Duch</a> </span><em>Proceedings of ACL BioNLP, </em><em>Prague, </em><em>Association of Computational Linguistics, </em><em>June2007. </em>Fri Jun 01 17:31:49 CEST 2007PragueProceedings of ACL BioNLPJuneA Shared Task Involving Multi-label Classification of Clinical Free Text2007text-classification data bioinformatics http://www.bibsonomy.org/bibtex/258bbdbe65011841b5375c300f2a84b4e/sb3000sb30002006-11-03T13:31:10+01:00ontologies classification bioinformatics <span style="color:#555555;">K. <a href="http://www.bibsonomy.org/author/Wolstencroft">Wolstencroft</a> and P. <a href="http://www.bibsonomy.org/author/Lord">Lord</a> and L. <a href="http://www.bibsonomy.org/author/Tabernero">Tabernero</a> and A. <a href="http://www.bibsonomy.org/author/Brass">Brass</a> and R. <a href="http://www.bibsonomy.org/author/Stevens">Stevens</a> </span><em>Bioinformatics</em><em>July2006. </em>Fri Nov 03 13:31:10 CET 2006School of Computer Science, University of Manchester UK.BioinformaticsJuly14Protein classification using ontology classification.222006ontologies classification bioinformatics http://www.bibsonomy.org/bibtex/2f2b420d46545a608cd616dc952330b7f/sb3000sb30002006-10-05T22:54:48+02:00tree-kernels bioinformatics <span style="color:#555555;">Jean-Philippe <a href="http://www.bibsonomy.org/author/Vert">Vert</a> </span><em>Bioinformatics</em><em>18(S1):S276-284</em>(<em>2002</em>)Thu Oct 05 22:54:48 CEST 2006BioinformaticsS1S276-284{A tree kernel to analyse phylogenetic profiles}182002tree-kernels bioinformatics Motivation: The phylogenetic profile of a protein is a string that encodes the presence or absence of the protein in every fully sequenced genome. Because proteins that participate in a common structural complex or metabolic pathway are likely to evolve in a correlated fashion, the phylogenetic profiles of such proteins are often similar' or at least related' to each other. The question we address in this paper is the following: how to measure the similarity' between two profiles, in an evolutionarily relevant way, in order to develop efficient function prediction methods? Results: We show how the profiles can be mapped to a high-dimensional vector space which incorporates evolutionarily relevant information, and we provide an algorithm to compute efficiently the inner product in that space, which we call the tree kernel. The tree kernel can be used by any kernel-based analysis method for classification or data mining of phylogenetic profiles. As an application a Support Vector Machine (SVM) trained to predict the functional class of a gene from its phylogenetic profile is shown to perform better with the tree kernel than with a naive kernel that does not include any information about the phylogenetic relationships among species. Moreover a kernel principal component analysis (KPCA) of the phylogenetic profiles illustrates the sensitivity of the tree kernel to evolutionarily relevant variations. Availability: All data and software used are freely and publicly available upon request. Contact: Jean-Philippe.Vert@mines.org Keywords: phylogenetic profile; tree; kernel; support vector machine; gene function prediction. http://www.bibsonomy.org/bibtex/2c31129d87ba02e09ec59eb9c4831be63/sb3000sb30002006-09-06T13:27:13+02:00bioinformatics ontologies <span style="color:#555555;">Gene Ontology <a href="http://www.bibsonomy.org/author/Consortium}">Consortium</a> </span><em>Nucleic acids research</em><em>32(1):D258-D261</em><em>JAN2004. </em>Wed Sep 06 13:27:13 CEST 2006Nucleic acids researchJAN1D258-D261The Gene Ontology (GO) database and informatics resource.322004bioinformatics ontologies