<?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%">Ostaszewski, Marek</style></author><author><style face="normal" font="default" size="100%">Niarakis, Anna</style></author><author><style face="normal" font="default" size="100%">Mazein, Alexander</style></author><author><style face="normal" font="default" size="100%">Kuperstein, Inna</style></author><author><style face="normal" font="default" size="100%">Phair, Robert</style></author><author><style face="normal" font="default" size="100%">Orta-Resendiz, Aurelio</style></author><author><style face="normal" font="default" size="100%">Singh, Vidisha</style></author><author><style face="normal" font="default" size="100%">Aghamiri, Sara Sadat</style></author><author><style face="normal" font="default" size="100%">Acencio, Marcio Luis</style></author><author><style face="normal" font="default" size="100%">Glaab, Enrico</style></author><author><style face="normal" font="default" size="100%">Ruepp, Andreas</style></author><author><style face="normal" font="default" size="100%">Fobo, Gisela</style></author><author><style face="normal" font="default" size="100%">Montrone, Corinna</style></author><author><style face="normal" font="default" size="100%">Brauner, Barbara</style></author><author><style face="normal" font="default" size="100%">Frishman, Goar</style></author><author><style face="normal" font="default" size="100%">Monraz Gómez, Luis Cristóbal</style></author><author><style face="normal" font="default" size="100%">Somers, Julia</style></author><author><style face="normal" font="default" size="100%">Hoch, Matti</style></author><author><style face="normal" font="default" size="100%">Kumar Gupta, Shailendra</style></author><author><style face="normal" font="default" size="100%">Scheel, Julia</style></author><author><style face="normal" font="default" size="100%">Borlinghaus, Hanna</style></author><author><style face="normal" font="default" size="100%">Czauderna, Tobias</style></author><author><style face="normal" font="default" size="100%">Schreiber, Falk</style></author><author><style face="normal" font="default" size="100%">Montagud, Arnau</style></author><author><style face="normal" font="default" size="100%">Ponce de Leon, Miguel</style></author><author><style face="normal" font="default" size="100%">Funahashi, Akira</style></author><author><style face="normal" font="default" size="100%">Hiki, Yusuke</style></author><author><style face="normal" font="default" size="100%">Hiroi, Noriko</style></author><author><style face="normal" font="default" size="100%">Yamada, Takahiro G</style></author><author><style face="normal" font="default" size="100%">Dräger, Andreas</style></author><author><style face="normal" font="default" size="100%">Renz, Alina</style></author><author><style face="normal" font="default" size="100%">Naveez, Muhammad</style></author><author><style face="normal" font="default" size="100%">Bocskei, Zsolt</style></author><author><style face="normal" font="default" size="100%">Messina, Francesco</style></author><author><style face="normal" font="default" size="100%">Börnigen, Daniela</style></author><author><style face="normal" font="default" size="100%">Fergusson, Liam</style></author><author><style face="normal" font="default" size="100%">Conti, Marta</style></author><author><style face="normal" font="default" size="100%">Rameil, Marius</style></author><author><style face="normal" font="default" size="100%">Nakonecnij, Vanessa</style></author><author><style face="normal" font="default" size="100%">Vanhoefer, Jakob</style></author><author><style face="normal" font="default" size="100%">Schmiester, Leonard</style></author><author><style face="normal" font="default" size="100%">Wang, Muying</style></author><author><style face="normal" font="default" size="100%">Ackerman, Emily E</style></author><author><style face="normal" font="default" size="100%">Shoemaker, Jason E</style></author><author><style face="normal" font="default" size="100%">Zucker, Jeremy</style></author><author><style face="normal" font="default" size="100%">Oxford, Kristie</style></author><author><style face="normal" font="default" size="100%">Teuton, Jeremy</style></author><author><style face="normal" font="default" size="100%">Kocakaya, Ebru</style></author><author><style face="normal" font="default" size="100%">Summak, Gökçe Yağmur</style></author><author><style face="normal" font="default" size="100%">Hanspers, Kristina</style></author><author><style face="normal" font="default" size="100%">Kutmon, Martina</style></author><author><style face="normal" font="default" size="100%">Coort, Susan</style></author><author><style face="normal" font="default" size="100%">Eijssen, Lars</style></author><author><style face="normal" font="default" size="100%">Ehrhart, Friederike</style></author><author><style face="normal" font="default" size="100%">Rex, Devasahayam Arokia Balaya</style></author><author><style face="normal" font="default" size="100%">Slenter, Denise</style></author><author><style face="normal" font="default" size="100%">Martens, Marvin</style></author><author><style face="normal" font="default" size="100%">Pham, Nhung</style></author><author><style face="normal" font="default" size="100%">Haw, Robin</style></author><author><style face="normal" font="default" size="100%">Jassal, Bijay</style></author><author><style face="normal" font="default" size="100%">Matthews, Lisa</style></author><author><style face="normal" font="default" size="100%">Orlic-Milacic, Marija</style></author><author><style face="normal" font="default" size="100%">Senff Ribeiro, Andrea</style></author><author><style face="normal" font="default" size="100%">Rothfels, Karen</style></author><author><style face="normal" font="default" size="100%">Shamovsky, Veronica</style></author><author><style face="normal" font="default" size="100%">Stephan, Ralf</style></author><author><style face="normal" font="default" size="100%">Sevilla, Cristoffer</style></author><author><style face="normal" font="default" size="100%">Varusai, Thawfeek</style></author><author><style face="normal" font="default" size="100%">Ravel, Jean-Marie</style></author><author><style face="normal" font="default" size="100%">Fraser, Rupsha</style></author><author><style face="normal" font="default" size="100%">Ortseifen, Vera</style></author><author><style face="normal" font="default" size="100%">Marchesi, Silvia</style></author><author><style face="normal" font="default" size="100%">Gawron, Piotr</style></author><author><style face="normal" font="default" size="100%">Smula, Ewa</style></author><author><style face="normal" font="default" size="100%">Heirendt, Laurent</style></author><author><style face="normal" font="default" size="100%">Satagopam, Venkata</style></author><author><style face="normal" font="default" size="100%">Wu, Guanming</style></author><author><style face="normal" font="default" size="100%">Riutta, Anders</style></author><author><style face="normal" font="default" size="100%">Golebiewski, Martin</style></author><author><style face="normal" font="default" size="100%">Owen, Stuart</style></author><author><style face="normal" font="default" size="100%">Goble, Carole</style></author><author><style face="normal" font="default" size="100%">Hu, Xiaoming</style></author><author><style face="normal" font="default" size="100%">Overall, Rupert W</style></author><author><style face="normal" font="default" size="100%">Maier, Dieter</style></author><author><style face="normal" font="default" size="100%">Bauch, Angela</style></author><author><style face="normal" font="default" size="100%">Gyori, Benjamin M</style></author><author><style face="normal" font="default" size="100%">Bachman, John A</style></author><author><style face="normal" font="default" size="100%">Vega, Carlos</style></author><author><style face="normal" font="default" size="100%">Grouès, Valentin</style></author><author><style face="normal" font="default" size="100%">Vazquez, Miguel</style></author><author><style face="normal" font="default" size="100%">Porras, Pablo</style></author><author><style face="normal" font="default" size="100%">Licata, Luana</style></author><author><style face="normal" font="default" size="100%">Iannuccelli, Marta</style></author><author><style face="normal" font="default" size="100%">Sacco, Francesca</style></author><author><style face="normal" font="default" size="100%">Nesterova, Anastasia</style></author><author><style face="normal" font="default" size="100%">Yuryev, Anton</style></author><author><style face="normal" font="default" size="100%">de Waard, Anita</style></author><author><style face="normal" font="default" size="100%">Turei, Denes</style></author><author><style face="normal" font="default" size="100%">Luna, Augustin</style></author><author><style face="normal" font="default" size="100%">Babur, Ozgun</style></author><author><style face="normal" font="default" size="100%">Soliman, Sylvain</style></author><author><style face="normal" font="default" size="100%">Valdeolivas, Alberto</style></author><author><style face="normal" font="default" size="100%">Esteban-Medina, Marina</style></author><author><style face="normal" font="default" size="100%">Peña-Chilet, Maria</style></author><author><style face="normal" font="default" size="100%">Rian, Kinza</style></author><author><style face="normal" font="default" size="100%">Helikar, Tomáš</style></author><author><style face="normal" font="default" size="100%">Puniya, Bhanwar Lal</style></author><author><style face="normal" font="default" size="100%">Modos, Dezso</style></author><author><style face="normal" font="default" size="100%">Treveil, Agatha</style></author><author><style face="normal" font="default" size="100%">Olbei, Marton</style></author><author><style face="normal" font="default" size="100%">De Meulder, Bertrand</style></author><author><style face="normal" font="default" size="100%">Ballereau, Stephane</style></author><author><style face="normal" font="default" size="100%">Dugourd, Aurélien</style></author><author><style face="normal" font="default" size="100%">Naldi, Aurélien</style></author><author><style face="normal" font="default" size="100%">Noël, Vincent</style></author><author><style face="normal" font="default" size="100%">Calzone, Laurence</style></author><author><style face="normal" font="default" size="100%">Sander, Chris</style></author><author><style face="normal" font="default" size="100%">Demir, Emek</style></author><author><style face="normal" font="default" size="100%">Korcsmaros, Tamas</style></author><author><style face="normal" font="default" size="100%">Freeman, Tom C</style></author><author><style face="normal" font="default" size="100%">Augé, Franck</style></author><author><style face="normal" font="default" size="100%">Beckmann, Jacques S</style></author><author><style face="normal" font="default" size="100%">Hasenauer, Jan</style></author><author><style face="normal" font="default" size="100%">Wolkenhauer, Olaf</style></author><author><style face="normal" font="default" size="100%">Wilighagen, Egon L</style></author><author><style face="normal" font="default" size="100%">Pico, Alexander R</style></author><author><style face="normal" font="default" size="100%">Evelo, Chris T</style></author><author><style face="normal" font="default" size="100%">Gillespie, Marc E</style></author><author><style face="normal" font="default" size="100%">Stein, Lincoln D</style></author><author><style face="normal" font="default" size="100%">Hermjakob, Henning</style></author><author><style face="normal" font="default" size="100%">D'Eustachio, Peter</style></author><author><style face="normal" font="default" size="100%">Saez-Rodriguez, Julio</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Valencia, Alfonso</style></author><author><style face="normal" font="default" size="100%">Kitano, Hiroaki</style></author><author><style face="normal" font="default" size="100%">Barillot, Emmanuel</style></author><author><style face="normal" font="default" size="100%">Auffray, Charles</style></author><author><style face="normal" font="default" size="100%">Balling, Rudi</style></author><author><style face="normal" font="default" size="100%">Schneider, Reinhard</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">COVID-19 Disease Map Community</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.</style></title><secondary-title><style face="normal" font="default" size="100%">Mol Syst Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Mol Syst Biol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Antiviral Agents</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Graphics</style></keyword><keyword><style  face="normal" font="default" size="100%">COVID-19</style></keyword><keyword><style  face="normal" font="default" size="100%">Cytokines</style></keyword><keyword><style  face="normal" font="default" size="100%">Data Mining</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Factual</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Host Microbial Interactions</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Immunity, Cellular</style></keyword><keyword><style  face="normal" font="default" size="100%">Immunity, Humoral</style></keyword><keyword><style  face="normal" font="default" size="100%">Immunity, Innate</style></keyword><keyword><style  face="normal" font="default" size="100%">Lymphocytes</style></keyword><keyword><style  face="normal" font="default" size="100%">Metabolic Networks and Pathways</style></keyword><keyword><style  face="normal" font="default" size="100%">Myeloid Cells</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Interaction Mapping</style></keyword><keyword><style  face="normal" font="default" size="100%">SARS-CoV-2</style></keyword><keyword><style  face="normal" font="default" size="100%">Signal Transduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">Viral Proteins</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 10</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">e10387</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 need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34664389?dopt=Abstract</style></custom1></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%">Salavert Torres, Jose</style></author><author><style face="normal" font="default" size="100%">Blanquer Espert, Ignacio</style></author><author><style face="normal" font="default" size="100%">Domínguez, Andrés Tomás</style></author><author><style face="normal" font="default" size="100%">Hernández García, Vicente</style></author><author><style face="normal" font="default" size="100%">Medina Castelló, Ignacio</style></author><author><style face="normal" font="default" size="100%">Tárraga Giménez, Joaquín</style></author><author><style face="normal" font="default" size="100%">Dopazo Blázquez, Joaquín</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Using GPUs for the exact alignment of short-read genetic sequences by means of the Burrows-Wheeler transform.</style></title><secondary-title><style face="normal" font="default" size="100%">IEEE/ACM Trans Comput Biol Bioinform</style></secondary-title><alt-title><style face="normal" font="default" size="100%">IEEE/ACM Trans Comput Biol Bioinform</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Algorithms</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Graphics</style></keyword><keyword><style  face="normal" font="default" size="100%">Data Compression</style></keyword><keyword><style  face="normal" font="default" size="100%">Drosophila melanogaster</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Insect</style></keyword><keyword><style  face="normal" font="default" size="100%">Image Processing, Computer-Assisted</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012 Jul-Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">1245-56</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;General Purpose Graphic Processing Units (GPGPUs) constitute an inexpensive resource for computing-intensive applications that could exploit an intrinsic fine-grain parallelism. This paper presents the design and implementation in GPGPUs of an exact alignment tool for nucleotide sequences based on the Burrows-Wheeler Transform. We compare this algorithm with state-of-the-art implementations of the same algorithm over standard CPUs, and considering the same conditions in terms of I/O. Excluding disk transfers, the implementation of the algorithm in GPUs shows a speedup larger than 12, when compared to CPU execution. This implementation exploits the parallelism by concurrently searching different sequences on the same reference search tree, maximizing memory locality and ensuring a symmetric access to the data. The paper describes the behavior of the algorithm in GPU, showing a good scalability in the performance, only limited by the size of the GPU inner memory.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/22450827?dopt=Abstract</style></custom1></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%">Jimenez, Rafael C</style></author><author><style face="normal" font="default" size="100%">Salazar, Gustavo A</style></author><author><style face="normal" font="default" size="100%">Gel, Bernat</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Mulder, Nicola</style></author><author><style face="normal" font="default" size="100%">Corpas, Manuel</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">myKaryoView: a light-weight client for visualization of genomic data.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS One</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS One</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computer Graphics</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Annotation</style></keyword><keyword><style  face="normal" font="default" size="100%">User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">e26345</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 Distributed Annotation System (DAS) is a protocol for easy sharing and integration of biological annotations. In order to visualize feature annotations in a genomic context a client is required. Here we present myKaryoView, a simple light-weight DAS tool for visualization of genomic annotation. myKaryoView has been specifically configured to help analyse data derived from personal genomics, although it can also be used as a generic genome browser visualization. Several well-known data sources are provided to facilitate comparison of known genes and normal variation regions. The navigation experience is enhanced by simultaneous rendering of different levels of detail across chromosomes. A simple interface is provided to allow searches for any SNP, gene or chromosomal region. User-defined DAS data sources may also be added when querying the system. We demonstrate myKaryoView capabilities for adding user-defined sources with a set of genetic profiles of family-related individuals downloaded directly from 23andMe. myKaryoView is a web tool for visualization of genomic data specifically designed for direct-to-consumer genomic data that uses publicly available data distributed throughout the Internet. It does not require data to be held locally and it is capable of rendering any feature as long as it conforms to DAS specifications. Configuration and addition of sources to myKaryoView can be done through the interface. Here we show a proof of principle of myKaryoView's ability to display personal genomics data with 23andMe genome data sources. The tool is available at: http://mykaryoview.com.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/22046276?dopt=Abstract</style></custom1></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, Pablo</style></author><author><style face="normal" font="default" size="100%">Götz, Stefan</style></author><author><style face="normal" font="default" size="100%">Montaner, David</style></author><author><style face="normal" font="default" size="100%">Al-Shahrour, Fátima</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%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computer Graphics</style></keyword><keyword><style  face="normal" font="default" size="100%">Data Interpretation, Statistical</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Protein</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Interaction Mapping</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">37</style></volume><pages><style face="normal" font="default" size="100%">W109-14</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><issue><style face="normal" font="default" size="100%">Web Server issue</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/19454602?dopt=Abstract</style></custom1></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%">Tárraga, Joaquín</style></author><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Carbonell, José</style></author><author><style face="normal" font="default" size="100%">Huerta-Cepas, Jaime</style></author><author><style face="normal" font="default" size="100%">Minguez, Pablo</style></author><author><style face="normal" font="default" size="100%">Alloza, Eva</style></author><author><style face="normal" font="default" size="100%">Al-Shahrour, Fátima</style></author><author><style face="normal" font="default" size="100%">Vegas-Azcárate, Susana</style></author><author><style face="normal" font="default" size="100%">Goetz, Stefan</style></author><author><style face="normal" font="default" size="100%">Escobar, Pablo</style></author><author><style face="normal" font="default" size="100%">Garcia-Garcia, Francisco</style></author><author><style face="normal" font="default" size="100%">Conesa, Ana</style></author><author><style face="normal" font="default" size="100%">Montaner, David</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%">GEPAS, a web-based tool for microarray data analysis and interpretation.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computer Graphics</style></keyword><keyword><style  face="normal" font="default" size="100%">Dose-Response Relationship, Drug</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jul 01</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">36</style></volume><pages><style face="normal" font="default" size="100%">W308-14</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Gene Expression Profile Analysis Suite (GEPAS) is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena. GEPAS offers diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression have been included. The new pipeliner module allows automating the execution of sequential analysis steps by means of a simple but powerful graphic interface. An extensive re-engineering of GEPAS has been carried out which 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. GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">Web Server issue</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/18508806?dopt=Abstract</style></custom1></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%">Götz, Stefan</style></author><author><style face="normal" font="default" size="100%">García-Gómez, Juan Miguel</style></author><author><style face="normal" font="default" size="100%">Terol, Javier</style></author><author><style face="normal" font="default" size="100%">Williams, Tim D</style></author><author><style face="normal" font="default" size="100%">Nagaraj, Shivashankar H</style></author><author><style face="normal" font="default" size="100%">Nueda, Maria José</style></author><author><style face="normal" font="default" size="100%">Robles, Montserrat</style></author><author><style face="normal" font="default" size="100%">Talon, Manuel</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Conesa, Ana</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">High-throughput functional annotation and data mining with the Blast2GO suite.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Graphics</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Expressed Sequence Tags</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, Protein</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Vocabulary, Controlled</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">36</style></volume><pages><style face="normal" font="default" size="100%">3420-35</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 genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/18445632?dopt=Abstract</style></custom1></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%">Conde, Lucia</style></author><author><style face="normal" font="default" size="100%">Montaner, David</style></author><author><style face="normal" font="default" size="100%">Burguet-Castell, Jordi</style></author><author><style face="normal" font="default" size="100%">Tárraga, Joaquín</style></author><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Al-Shahrour, Fátima</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%">ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Cluster Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Graphics</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Nucleic Acid Hybridization</style></keyword><keyword><style  face="normal" font="default" size="100%">Oligonucleotide Array Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Programming Languages</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Systems Integration</style></keyword><keyword><style  face="normal" font="default" size="100%">User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">35</style></volume><pages><style face="normal" font="default" size="100%">W81-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;We present the ISACGH, a web-based system that allows for the combination of genomic data with gene expression values and provides different options for functional profiling of the regions found. Several visualization options offer a convenient representation of the results. Different efficient methods for accurate estimation of genomic copy number from array-CGH hybridization data have been included in the program. Moreover, the connection to the gene expression analysis package GEPAS allows the use of different facilities for data pre-processing and analysis. A DAS server allows exporting the results to the Ensembl viewer where contextual genomic information can be obtained. The program is freely available at: http://isacgh.bioinfo.cipf.es or within http://www.gepas.org.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">Web Server issue</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/17468499?dopt=Abstract</style></custom1></record></records></xml>