<?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%">Peña-Chilet, Maria</style></author><author><style face="normal" font="default" size="100%">Roldán, Gema</style></author><author><style face="normal" font="default" size="100%">Perez-Florido, Javier</style></author><author><style face="normal" font="default" size="100%">Ortuno, Francisco M</style></author><author><style face="normal" font="default" size="100%">Carmona, Rosario</style></author><author><style face="normal" font="default" size="100%">Aquino, Virginia</style></author><author><style face="normal" font="default" size="100%">López-López, Daniel</style></author><author><style face="normal" font="default" size="100%">Loucera, Carlos</style></author><author><style face="normal" font="default" size="100%">Fernandez-Rueda, Jose L</style></author><author><style face="normal" font="default" size="100%">Gallego, Asunción</style></author><author><style face="normal" font="default" size="100%">Garcia-Garcia, Francisco</style></author><author><style face="normal" font="default" size="100%">González-Neira, Anna</style></author><author><style face="normal" font="default" size="100%">Pita, Guillermo</style></author><author><style face="normal" font="default" size="100%">Núñez-Torres, Rocío</style></author><author><style face="normal" font="default" size="100%">Santoyo-López, Javier</style></author><author><style face="normal" font="default" size="100%">Ayuso, Carmen</style></author><author><style face="normal" font="default" size="100%">Minguez, Pablo</style></author><author><style face="normal" font="default" size="100%">Avila-Fernandez, Almudena</style></author><author><style face="normal" font="default" size="100%">Corton, Marta</style></author><author><style face="normal" font="default" size="100%">Moreno-Pelayo, Miguel Ángel</style></author><author><style face="normal" font="default" size="100%">Morin, Matías</style></author><author><style face="normal" font="default" size="100%">Gallego-Martinez, Alvaro</style></author><author><style face="normal" font="default" size="100%">Lopez-Escamez, Jose A</style></author><author><style face="normal" font="default" size="100%">Borrego, Salud</style></author><author><style face="normal" font="default" size="100%">Antiňolo, Guillermo</style></author><author><style face="normal" font="default" size="100%">Amigo, Jorge</style></author><author><style face="normal" font="default" size="100%">Salgado-Garrido, Josefa</style></author><author><style face="normal" font="default" size="100%">Pasalodos-Sanchez, Sara</style></author><author><style face="normal" font="default" size="100%">Morte, Beatriz</style></author><author><style face="normal" font="default" size="100%">Carracedo, Ángel</style></author><author><style face="normal" font="default" size="100%">Alonso, Ángel</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">Spanish Exome Crowdsourcing Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">CSVS, a crowdsourcing database of the Spanish population genetic variability.</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%">Alleles</style></keyword><keyword><style  face="normal" font="default" size="100%">Chromosome Mapping</style></keyword><keyword><style  face="normal" font="default" size="100%">Crowdsourcing</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Exome</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Frequency</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Variation</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetics, Population</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Human</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</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%">Precision Medicine</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Spain</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 01 08</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">49</style></volume><pages><style face="normal" font="default" size="100%">D1130-D1137</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 knowledge of the genetic variability of the local population is of utmost importance in personalized medicine and has been revealed as a critical factor for the discovery of new disease variants. Here, we present the Collaborative Spanish Variability Server (CSVS), which currently contains more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated in a collaborative crowdsourcing effort collecting sequencing data produced by local genomic projects and for other purposes. Sequences have been grouped by ICD10 upper categories. A web interface allows querying the database removing one or more ICD10 categories. In this way, aggregated counts of allele frequencies of the pseudo-control Spanish population can be obtained for diseases belonging to the category removed. Interestingly, in addition to pseudo-control studies, some population studies can be made, as, for example, prevalence of pharmacogenomic variants, etc. In addition, this genomic data has been used to define the first Spanish Genome Reference Panel (SGRP1.0) for imputation. This is the first local repository of variability entirely produced by a crowdsourcing effort and constitutes an example for future initiatives to characterize local variability worldwide. CSVS is also part of the GA4GH Beacon network. CSVS can be accessed at: http://csvs.babelomics.org/.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">D1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/32990755?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%">Garrido-Rodriguez, Martín</style></author><author><style face="normal" font="default" size="100%">López-López, Daniel</style></author><author><style face="normal" font="default" size="100%">Ortuno, Francisco M</style></author><author><style face="normal" font="default" size="100%">Peña-Chilet, Maria</style></author><author><style face="normal" font="default" size="100%">Muñoz, Eduardo</style></author><author><style face="normal" font="default" size="100%">Calzado, Marco A</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%">A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS Comput Biol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS Comput Biol</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Algorithms</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Line, Tumor</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Factual</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">High-Throughput Nucleotide Sequencing</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Theoretical</style></keyword><keyword><style  face="normal" font="default" size="100%">mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA-seq</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%">Transcriptome</style></keyword><keyword><style  face="normal" font="default" size="100%">whole exome sequencing</style></keyword><keyword><style  face="normal" font="default" size="100%">Workflow</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 02</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">e1008748</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;MIGNON is a workflow for the analysis of RNA-Seq experiments, which not only efficiently manages the estimation of gene expression levels from raw sequencing reads, but also calls genomic variants present in the transcripts analyzed. Moreover, this is the first workflow that provides a framework for the integration of transcriptomic and genomic data based on a mechanistic model of signaling pathway activities that allows a detailed biological interpretation of the results, including a comprehensive functional profiling of cell activity. MIGNON covers the whole process, from reads to signaling circuit activity estimations, using state-of-the-art tools, it is easy to use and it is deployable in different computational environments, allowing an optimized use of the resources available.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/33571195?dopt=Abstract</style></custom1></record></records></xml>