<?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%">Minguez, Pablo</style></author><author><style face="normal" font="default" size="100%">Gotz, S.</style></author><author><style face="normal" font="default" size="100%">Montaner, David</style></author><author><style face="normal" font="default" size="100%">Fatima Al-Shahrour</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks</style></title><secondary-title><style face="normal" font="default" size="100%">Nucl. Acids Res.</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">interactome</style></keyword><keyword><style  face="normal" font="default" size="100%">network</style></keyword><keyword><style  face="normal" font="default" size="100%">snow</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://nar.oxfordjournals.org/content/early/2009/05/19/nar.gkp402.full</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">37</style></volume><pages><style face="normal" font="default" size="100%">W109-114</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Understanding the structure and the dynamics of the complex intercellular network of interactions that contributes to the structure and function of a living cell is one of the main challenges of today’s biology. SNOW inputs a collection of protein (or gene) identifiers and, by using the interactome as scaffold, draws the connections among them, calculates several relevant network parameters and, as a novelty among the rest of tools of its class, it estimates their statistical significance. The parameters calculated for each node are: connectivity, betweenness and clustering coefficient. It also calculates the number of components, number of bicomponents and articulation points. An interactive network viewer is also available to explore the resulting network. SNOW is available at http://snow.bioinfo.cipf.es.&lt;/p&gt;</style></abstract></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%">A. Conesa</style></author><author><style face="normal" font="default" size="100%">Gotz, S.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Plant Genomics</style></secondary-title></titles><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://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=18483572</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">2008</style></volume><pages><style face="normal" font="default" size="100%">619832</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Functional annotation of novel sequence data is a primary requirement for the utilization of functional genomics approaches in plant research. In this paper, we describe the Blast2GO suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes function transfer from homologous sequences through an elaborate algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. The tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim. Blast2GO is a suitable tool for plant genomics research because of its versatility, easy installation, and friendly use.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Conesa, Ana Gotz, Stefan Egypt International journal of plant genomics Int J Plant Genomics. 2008;2008:619832.&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%">A. Conesa</style></author><author><style face="normal" font="default" size="100%">Bro, R.</style></author><author><style face="normal" font="default" size="100%">Garcia-Garcia, F.</style></author><author><style face="normal" font="default" size="100%">Prats, J. M.</style></author><author><style face="normal" font="default" size="100%">Gotz, S.</style></author><author><style face="normal" font="default" size="100%">Kjeldahl, K.</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%">Direct functional assessment of the composite phenotype through multivariate projection strategies</style></title><secondary-title><style face="normal" font="default" size="100%">Genomics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Breast Neoplasms/genetics Computational Biology/*methods Databases</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Female Gene Expression Profiling/*statistics &amp; numerical data Humans Mathematical Computing Multivariate Analysis Phenotype</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://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=18652888</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">6</style></number><volume><style face="normal" font="default" size="100%">92</style></volume><pages><style face="normal" font="default" size="100%">373-83</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 novel approach for the analysis of transcriptomics data that integrates functional annotation of gene sets with expression values in a multivariate fashion, and directly assesses the relation of functional features to a multivariate space of response phenotypical variables. Multivariate projection methods are used to obtain new correlated variables for a set of genes that share a given function. These new functional variables are then related to the response variables of interest. The analysis of the principal directions of the multivariate regression allows for the identification of gene function features correlated with the phenotype. Two different transcriptomics studies are used to illustrate the statistical and interpretative aspects of the methodology. We demonstrate the superiority of the proposed method over equivalent approaches.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Conesa, Ana Bro, Rasmus Garcia-Garcia, Francisco Prats, Jose Manuel Gotz, Stefan Kjeldahl, Karin Montaner, David Dopazo, Joaquin Evaluation Studies Research Support, Non-U.S. Gov’t United States Genomics Genomics. 2008 Dec;92(6):373-83. Epub 2008 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%">Terol, J.</style></author><author><style face="normal" font="default" size="100%">A. Conesa</style></author><author><style face="normal" font="default" size="100%">Colmenero, J. M.</style></author><author><style face="normal" font="default" size="100%">Cercos, M.</style></author><author><style face="normal" font="default" size="100%">Tadeo, F.</style></author><author><style face="normal" font="default" size="100%">Agusti, J.</style></author><author><style face="normal" font="default" size="100%">Alos, E.</style></author><author><style face="normal" font="default" size="100%">Andres, F.</style></author><author><style face="normal" font="default" size="100%">Soler, G.</style></author><author><style face="normal" font="default" size="100%">Brumos, J.</style></author><author><style face="normal" font="default" size="100%">Iglesias, D. J.</style></author><author><style face="normal" font="default" size="100%">Gotz, S.</style></author><author><style face="normal" font="default" size="100%">Legaz, F.</style></author><author><style face="normal" font="default" size="100%">Argout, X.</style></author><author><style face="normal" font="default" size="100%">Courtois, B.</style></author><author><style face="normal" font="default" size="100%">Ollitrault, P.</style></author><author><style face="normal" font="default" size="100%">Dossat, C.</style></author><author><style face="normal" font="default" size="100%">Wincker, P.</style></author><author><style face="normal" font="default" size="100%">Morillon, R.</style></author><author><style face="normal" font="default" size="100%">Talon, M.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Acclimatization/*genetics Amino Acid Motifs Citrus/*genetics Cluster Analysis Expressed Sequence Tags Fruit/genetics Gene Duplication *Gene Expression Regulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Gene Library Genes</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Genomics Molecular Sequence Data Multigene Family Phylogeny *Salts/adverse effects</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=17254327</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">31</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Improvement of Citrus, the most economically important fruit crop in the world, is extremely slow and inherently costly because of the long-term nature of tree breeding and an unusual combination of reproductive characteristics. Aside from disease resistance, major commercial traits in Citrus are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity. RESULTS: A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties (Citrus clementina and C. sinensis) and rootstocks (C. reshni, and C. sinenis x Poncirus trifoliata) differing in fruit quality, resistance to abscission, and tolerance to salinity. The goal of this work was to provide a large expressed sequence tag (EST) collection enriched with transcripts related to these well appreciated agronomical traits. Towards this end, more than 54000 ESTs derived from these libraries were analyzed and annotated. Assembly of 52626 useful sequences generated 15664 putative transcription units distributed in 7120 contigs, and 8544 singletons. BLAST annotation produced significant hits for more than 80% of the hypothetical transcription units and suggested that 647 of these might be Citrus specific unigenes. The unigene set, composed of  13000 putative different transcripts, including more than 5000 novel Citrus genes, was assigned with putative functions based on similarity, GO annotations and protein domains CONCLUSION: Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in Citrus and also the occurrence of both gene duplication events and increased number of genes for specific pathways. In addition, phylogenetic analysis performed on the ammonium transporter family and glycosyl transferase family 20 suggested the existence of Citrus paralogs. Analysis of the Citrus gene space showed that the most important metabolic pathways known to affect fruit quality were represented in the unigene set. Overall, the similarity analyses indicated that the sequences of the genes belonging to these varieties and rootstocks were essentially identical, suggesting that the differential behaviour of these species cannot be attributed to major sequence divergences. This Citrus EST assembly contributes both crucial information to discover genes of agronomical interest and tools for genetic and genomic analyses, such as the development of new markers and microarrays.</style></abstract><notes><style face="normal" font="default" size="100%">Terol, Javier Conesa, Ana Colmenero, Jose M Cercos, Manuel Tadeo, Francisco Agusti, Javier Alos, Enriqueta Andres, Fernando Soler, Guillermo Brumos, Javier Iglesias, Domingo J Gotz, Stefan Legaz, Francisco Argout, Xavier Courtois, Brigitte Ollitrault, Patrick Dossat, Carole Wincker, Patrick Morillon, Raphael Talon, Manuel Comparative Study Research Support, Non-U.S. Gov’t England BMC genomics BMC Genomics. 2007 Jan 25;8:31.</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%">Aparicio, G.</style></author><author><style face="normal" font="default" size="100%">Gotz, S.</style></author><author><style face="normal" font="default" size="100%">A. Conesa</style></author><author><style face="normal" font="default" size="100%">Segrelles, D.</style></author><author><style face="normal" font="default" size="100%">Blanquer, I.</style></author><author><style face="normal" font="default" size="100%">Garcia, J. M.</style></author><author><style face="normal" font="default" size="100%">Hernandez, V.</style></author><author><style face="normal" font="default" size="100%">Robles, M.</style></author><author><style face="normal" font="default" size="100%">Talon, M.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Blast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis</style></title><secondary-title><style face="normal" font="default" size="100%">Stud Health Technol Inform</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%">2006</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=16823138</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">120</style></volume><pages><style face="normal" font="default" size="100%">194-204</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 vast amount in complexity of data generated in Genomic Research implies that new dedicated and powerful computational tools need to be developed to meet their analysis requirements. Blast2GO (B2G) is a bioinformatics tool for Gene Ontology-based DNA or protein sequence annotation and function-based data mining. The application has been developed with the aim of affering an easy-to-use tool for functional genomics research. Typical B2G users are middle size genomics labs carrying out sequencing, ETS and microarray projects, handling datasets up to several thousand sequences. In the current version of B2G. The power and analytical potential of both annotation and function data-mining is somehow restricted to the computational power behind each particular installation. In order to be able to offer the possibility of an enhanced computational capacity within this bioinformatics application, a Grid component is being developed. A prototype has been conceived for the particular problem of speeding up the Blast searches to obtain fast results for large datasets. Many efforts have been done in the literature concerning the speeding up of Blast searches, but few of them deal with the use of large heterogeneous production Grid Infrastructures. These are the infrastructures that could reach the largest number of resources and the best load balancing for data access. The Grid Service under development will analyse requests based on the number of sequences, splitting them accordingly to the available resources. Lower-level computation will be performed through MPIBLAST. The software architecture is based on the WSRF standard.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Aparicio, G Gotz, S Conesa, A Segrelles, D Blanquer, I Garcia, J M Hernandez, V Robles, M Talon, M Netherlands Studies in health technology and informatics Stud Health Technol Inform. 2006;120:194-204.&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%">A. Conesa</style></author><author><style face="normal" font="default" size="100%">Gotz, S.</style></author><author><style face="normal" font="default" size="100%">Garcia-Gomez, J. M.</style></author><author><style face="normal" font="default" size="100%">Terol, J.</style></author><author><style face="normal" font="default" size="100%">Talon, M.</style></author><author><style face="normal" font="default" size="100%">Robles, M.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research</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></keywords><dates><year><style  face="normal" font="default" size="100%">2005</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=16081474</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">18</style></number><volume><style face="normal" font="default" size="100%">21</style></volume><pages><style face="normal" font="default" size="100%">3674-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;SUMMARY: We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. AVAILABILITY: Blast2GO is freely available via Java Web Start at http://www.blast2go.de. SUPPLEMENTARY MATERIAL: http://www.blast2go.de -&amp;gt; Evaluation.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Conesa, Ana Gotz, Stefan Garcia-Gomez, Juan Miguel Terol, Javier Talon, Manuel Robles, Montserrat Research Support, Non-U.S. Gov’t England Bioinformatics (Oxford, England) Bioinformatics. 2005 Sep 15;21(18):3674-6. Epub 2005 Aug 4.&lt;/p&gt;</style></notes></record></records></xml>