<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fatima Al-Shahrour</style></author><author><style face="normal" font="default" size="100%">Carbonell, J.</style></author><author><style face="normal" font="default" size="100%">Minguez, P.</style></author><author><style face="normal" font="default" size="100%">Goetz, S.</style></author><author><style face="normal" font="default" size="100%">A. Conesa</style></author><author><style face="normal" font="default" size="100%">Tarraga, J.</style></author><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Alloza, E.</style></author><author><style face="normal" font="default" size="100%">Montaner, D.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">babelomics</style></keyword><keyword><style  face="normal" font="default" size="100%">funtional profiling</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://nar.oxfordjournals.org/content/36/suppl_2/W341.long</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">36</style></volume><pages><style face="normal" font="default" size="100%">W341-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;We present a new version of Babelomics, a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available. In addition to the well-known functional definitions (GO, KEGG), Babelomics includes new ones such as Biocarta pathways or text mining-derived functional terms. Regulatory modules implemented include transcriptional control (Transfac, CisRed) and other levels of regulation such as miRNA-mediated interference. Moreover, Babelomics allows for sub-selection of terms in order to test more focused hypothesis. Also gene annotation correspondence tables can be imported, which allows testing with user-defined functional modules. Finally, a tool for the ’de novo’ functional annotation of sequences has been included in the system. This allows using yet unannotated organisms in the program. Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Al-Shahrour, Fatima Carbonell, Jose Minguez, Pablo Goetz, Stefan Conesa, Ana Tarraga, Joaquin Medina, Ignacio Alloza, Eva Montaner, David Dopazo, Joaquin Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W341-6. Epub 2008 May 31.&lt;/p&gt;</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fatima Al-Shahrour</style></author><author><style face="normal" font="default" size="100%">Minguez, P.</style></author><author><style face="normal" font="default" size="100%">Tarraga, J.</style></author><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Alloza, E.</style></author><author><style face="normal" font="default" size="100%">Montaner, D.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">babelomics</style></keyword><keyword><style  face="normal" font="default" size="100%">functional enrichment analysys</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=17478504</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">Web Server issue</style></number><volume><style face="normal" font="default" size="100%">35</style></volume><pages><style face="normal" font="default" size="100%">W91-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The ultimate goal of any genome-scale experiment is to provide a functional interpretation of the data, relating the available information with the hypotheses that originated the experiment. Thus, functional profiling methods have become essential in diverse scenarios such as microarray experiments, proteomics, etc. We present the FatiGO+, a web-based tool for the functional profiling of genome-scale experiments, specially oriented to the interpretation of microarray experiments. In addition to different functional annotations (gene ontology, KEGG pathways, Interpro motifs, Swissprot keywords and text-mining based bioentities related to diseases and chemical compounds) FatiGO+ includes, as a novelty, regulatory and structural information. The regulatory information used includes predictions of targets for distinct regulatory elements (obtained from the Transfac and CisRed databases). Additionally FatiGO+ uses predictions of target motifs of miRNA to infer which of these can be activated or deactivated in the sample of genes studied. Finally, properties of gene products related to their relative location and connections in the interactome have also been used. Also, enrichment of any of these functional terms can be directly analysed on chromosomal coordinates. FatiGO+ can be found at: http://www.fatigoplus.org and within the Babelomics environment http://www.babelomics.org.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Al-Shahrour, Fatima Minguez, Pablo Tarraga, Joaquin Medina, Ignacio Alloza, Eva Montaner, David Dopazo, Joaquin Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2007 Jul;35(Web Server issue):W91-6. Epub 2007 May 3.&lt;/p&gt;</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fatima Al-Shahrour</style></author><author><style face="normal" font="default" size="100%">Arbiza, L.</style></author><author><style face="normal" font="default" size="100%">H. Dopazo</style></author><author><style face="normal" font="default" size="100%">Huerta-Cepas, J.</style></author><author><style face="normal" font="default" size="100%">Minguez, P.</style></author><author><style face="normal" font="default" size="100%">Montaner, D.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">From genes to functional classes in the study of biological systems</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Bioinformatics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Algorithms Chromosome Mapping/*methods Computer Simulation Gene Expression Profiling/methods *Models</style></keyword><keyword><style  face="normal" font="default" size="100%">babelomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Biological Multigene Family/*physiology Signal Transduction/*physiology *Software Systems Biology/*methods *User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=17407596</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">114</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;BACKGROUND: With the popularization of high-throughput techniques, the need for procedures that help in the biological interpretation of results has increased enormously. Recently, new procedures inspired in systems biology criteria have started to be developed. RESULTS: Here we present FatiScan, a web-based program which implements a threshold-independent test for the functional interpretation of large-scale experiments that does not depend on the pre-selection of genes based on the multiple application of independent tests to each gene. The test implemented aims to directly test the behaviour of blocks of functionally related genes, instead of focusing on single genes. In addition, the test does not depend on the type of the data used for obtaining significance values, and consequently different types of biologically informative terms (gene ontology, pathways, functional motifs, transcription factor binding sites or regulatory sites from CisRed) can be applied to different classes of genome-scale studies. We exemplify its application in microarray gene expression, evolution and interactomics. CONCLUSION: Methods for gene set enrichment which, in addition, are independent from the original data and experimental design constitute a promising alternative for the functional profiling of genome-scale experiments. A web server that performs the test described and other similar ones can be found at: http://www.babelomics.org.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Al-Shahrour, Fatima Arbiza, Leonardo Dopazo, Hernan Huerta-Cepas, Jaime Minguez, Pablo Montaner, David Dopazo, Joaquin Research Support, Non-U.S. Gov’t England BMC bioinformatics BMC Bioinformatics. 2007 Apr 3;8:114.&lt;/p&gt;</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">L. Conde</style></author><author><style face="normal" font="default" size="100%">Montaner, D.</style></author><author><style face="normal" font="default" size="100%">Burguet-Castell, J.</style></author><author><style face="normal" font="default" size="100%">Tarraga, J.</style></author><author><style face="normal" font="default" size="100%">Fatima Al-Shahrour</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Functional profiling and gene expression analysis of chromosomal copy number alterations</style></title><secondary-title><style face="normal" font="default" size="100%">Bioinformation</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">babelomics</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=17597935</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">10</style></number><volume><style face="normal" font="default" size="100%">1</style></volume><pages><style face="normal" font="default" size="100%">432-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Contrarily to the traditional view in which only one or a few key genes were supposed to be the causative factors of diseases, we discuss the importance of considering groups of functionally related genes in the study of pathologies characterised by chromosomal copy number alterations. Recent observations have reported the existence of regions in higher eukaryotic chromosomes (including humans) containing genes of related function that show a high degree of coregulation. Copy number alterations will consequently affect to clusters of functionally related genes, which will be the final causative agents of the diseased phenotype, in many cases. Therefore, we propose that the functional profiling of the regions affected by copy number alterations must be an important aspect to take into account in the understanding of this type of pathologies. To illustrate this, we present an integrated study of DNA copy number variations, gene expression along with the functional profiling of chromosomal regions in a case of multiple myeloma.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Conde, Lucia Montaner, David Burguet-Castell, Jordi Tarraga, Joaquin Al-Shahrour, Fatima Dopazo, Joaquin Singapore Bioinformation Bioinformation. 2007 Apr 10;1(10):432-5.&lt;/p&gt;</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Minguez, P.</style></author><author><style face="normal" font="default" size="100%">Fatima Al-Shahrour</style></author><author><style face="normal" font="default" size="100%">Montaner, D.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Functional profiling of microarray experiments using text-mining derived bioentities</style></title><secondary-title><style face="normal" font="default" size="100%">Bioinformatics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Artificial Intelligence *Databases</style></keyword><keyword><style  face="normal" font="default" size="100%">babelomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Gene Expression Profiling/*methods Information Storage and Retrieval/*methods *Natural Language Processing Proteins/*classification/*metabolism Research/*methods Systems Integration</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=17855415</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">22</style></number><volume><style face="normal" font="default" size="100%">23</style></volume><pages><style face="normal" font="default" size="100%">3098-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;MOTIVATION: The increasing use of microarray technologies brought about a parallel demand in methods for the functional interpretation of the results. Beyond the conventional functional annotations for genes, such as gene ontology, pathways, etc. other sources of information are still to be exploited. Text-mining methods allow extracting informative terms (bioentities) with different functional, chemical, clinical, etc. meanings, that can be associated to genes. We show how to use these associations within an appropriate statistical framework and how to apply them through easy-to-use, web-based environments to the functional interpretation of microarray experiments. Functional enrichment and gene set enrichment tests using bioentities are presented.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Minguez, Pablo Al-Shahrour, Fatima Montaner, David Dopazo, Joaquin Research Support, Non-U.S. Gov’t England Bioinformatics (Oxford, England) Bioinformatics. 2007 Nov 15;23(22):3098-9. Epub 2007 Sep 13.&lt;/p&gt;</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Montaner, D.</style></author><author><style face="normal" font="default" size="100%">Tarraga, J.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Prophet, a web-based tool for class prediction using microarray data</style></title><secondary-title><style face="normal" font="default" size="100%">Bioinformatics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">babelomics</style></keyword><keyword><style  face="normal" font="default" size="100%">gepas</style></keyword><keyword><style  face="normal" font="default" size="100%">predictors</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://bioinformatics.oxfordjournals.org/cgi/content/full/23/3/390?view=long&amp;pmid=17138587</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">3</style></number><volume><style face="normal" font="default" size="100%">23</style></volume><pages><style face="normal" font="default" size="100%">390-1</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Sample classification and class prediction is the aim of many gene expression studies. We present a web-based application, Prophet, which builds prediction rules and allows using them for further sample classification. Prophet automatically chooses the best classifier, along with the optimal selection of genes, using a strategy that renders unbiased cross-validated errors. Prophet is linked to different microarray data analysis modules, and includes a unique feature: the possibility of performing the functional interpretation of the molecular signature found. Availability: Prophet can be found at the URL http://prophet.bioinfo.cipf.es/ or within the GEPAS package at http://www.gepas.org/ Supplementary information: http://gepas.bioinfo.cipf.es/tutorial/prophet.html.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Medina, Ignacio Montaner, David Tarraga, Joaquin Dopazo, Joaquin Research Support, Non-U.S. Gov’t England Bioinformatics (Oxford, England) Bioinformatics. 2007 Feb 1;23(3):390-1. Epub 2006 Nov 30.&lt;/p&gt;</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fatima Al-Shahrour</style></author><author><style face="normal" font="default" size="100%">Minguez, P.</style></author><author><style face="normal" font="default" size="100%">Tarraga, J.</style></author><author><style face="normal" font="default" size="100%">Montaner, D.</style></author><author><style face="normal" font="default" size="100%">Alloza, E.</style></author><author><style face="normal" font="default" size="100%">Vaquerizas, J. M.</style></author><author><style face="normal" font="default" size="100%">L. Conde</style></author><author><style face="normal" font="default" size="100%">Blaschke, C.</style></author><author><style face="normal" font="default" size="100%">Vera, J.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">babelomics</style></keyword><keyword><style  face="normal" font="default" size="100%">functional profiling</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://nar.oxfordjournals.org/content/34/suppl_2/W472.long</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">34</style></volume><pages><style face="normal" font="default" size="100%">W472-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at http://www.babelomics.org.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Al-Shahrour, Fatima Minguez, Pablo Tarraga, Joaquin Montaner, David Alloza, Eva Vaquerizas, Juan M Conde, Lucia Blaschke, Christian Vera, Javier Dopazo, Joaquin Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W472-6.&lt;/p&gt;</style></notes></record></records></xml>