<?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%">Martorell-Marugán, Jordi</style></author><author><style face="normal" font="default" size="100%">López-Domínguez, Raúl</style></author><author><style face="normal" font="default" size="100%">García-Moreno, Adrián</style></author><author><style face="normal" font="default" size="100%">Toro-Domínguez, Daniel</style></author><author><style face="normal" font="default" size="100%">Villatoro-García, Juan Antonio</style></author><author><style face="normal" font="default" size="100%">Barturen, Guillermo</style></author><author><style face="normal" font="default" size="100%">Martín-Gómez, Adoración</style></author><author><style face="normal" font="default" size="100%">Troule, Kevin</style></author><author><style face="normal" font="default" size="100%">Gómez-López, Gonzalo</style></author><author><style face="normal" font="default" size="100%">Al-Shahrour, Fátima</style></author><author><style face="normal" font="default" size="100%">González-Rumayor, Víctor</style></author><author><style face="normal" font="default" size="100%">Peña-Chilet, Maria</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Saez-Rodriguez, Julio</style></author><author><style face="normal" font="default" size="100%">Alarcón-Riquelme, Marta E</style></author><author><style face="normal" font="default" size="100%">Carmona-Sáez, Pedro</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A comprehensive database for integrated analysis of omics data in autoimmune diseases.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Bioinformatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Bioinformatics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Autoimmune Diseases</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%">Humans</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 Jun 24</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">22</style></volume><pages><style face="normal" font="default" size="100%">343</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;BACKGROUND: &lt;/b&gt;Autoimmune diseases are heterogeneous pathologies with difficult diagnosis and few therapeutic options. In the last decade, several omics studies have provided significant insights into the molecular mechanisms of these diseases. Nevertheless, data from different cohorts and pathologies are stored independently in public repositories and a unified resource is imperative to assist researchers in this field.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS: &lt;/b&gt;Here, we present Autoimmune Diseases Explorer ( https://adex.genyo.es ), a database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most common autoimmune diseases. The database provides, in an easy-to-use environment, advanced data analysis and statistical methods for exploring omics datasets, including meta-analysis, differential expression or pathway analysis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;CONCLUSIONS: &lt;/b&gt;This is the first omics database focused on autoimmune diseases. This resource incorporates homogeneously processed data to facilitate integrative analyses among studies.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34167460?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%">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%">Yang, Mi</style></author><author><style face="normal" font="default" size="100%">Petralia, Francesca</style></author><author><style face="normal" font="default" size="100%">Li, Zhi</style></author><author><style face="normal" font="default" size="100%">Li, Hongyang</style></author><author><style face="normal" font="default" size="100%">Ma, Weiping</style></author><author><style face="normal" font="default" size="100%">Song, Xiaoyu</style></author><author><style face="normal" font="default" size="100%">Kim, Sunkyu</style></author><author><style face="normal" font="default" size="100%">Lee, Heewon</style></author><author><style face="normal" font="default" size="100%">Yu, Han</style></author><author><style face="normal" font="default" size="100%">Lee, Bora</style></author><author><style face="normal" font="default" size="100%">Bae, Seohui</style></author><author><style face="normal" font="default" size="100%">Heo, Eunji</style></author><author><style face="normal" font="default" size="100%">Kaczmarczyk, Jan</style></author><author><style face="normal" font="default" size="100%">Stępniak, Piotr</style></author><author><style face="normal" font="default" size="100%">Warchoł, Michał</style></author><author><style face="normal" font="default" size="100%">Yu, Thomas</style></author><author><style face="normal" font="default" size="100%">Calinawan, Anna P</style></author><author><style face="normal" font="default" size="100%">Boutros, Paul C</style></author><author><style face="normal" font="default" size="100%">Payne, Samuel H</style></author><author><style face="normal" font="default" size="100%">Reva, Boris</style></author><author><style face="normal" font="default" size="100%">Boja, Emily</style></author><author><style face="normal" font="default" size="100%">Rodriguez, Henry</style></author><author><style face="normal" font="default" size="100%">Stolovitzky, Gustavo</style></author><author><style face="normal" font="default" size="100%">Guan, Yuanfang</style></author><author><style face="normal" font="default" size="100%">Kang, Jaewoo</style></author><author><style face="normal" font="default" size="100%">Wang, Pei</style></author><author><style face="normal" font="default" size="100%">Fenyö, David</style></author><author><style face="normal" font="default" size="100%">Saez-Rodriguez, Julio</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">NCI-CPTAC-DREAM Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.</style></title><secondary-title><style face="normal" font="default" size="100%">Cell Syst</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Cell Syst</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Crowdsourcing</style></keyword><keyword><style  face="normal" font="default" size="100%">Female</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%">Machine Learning</style></keyword><keyword><style  face="normal" font="default" size="100%">Male</style></keyword><keyword><style  face="normal" font="default" size="100%">Neoplasms</style></keyword><keyword><style  face="normal" font="default" size="100%">Phosphoproteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 08 26</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">186-195.e9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods to infer protein levels from other omics measurements, we leveraged crowdsourcing via the NCI-CPTAC DREAM proteogenomic challenge. We asked for methods to predict protein and phosphorylation levels from genomic and transcriptomic data in cancer patients. The best performance was achieved by an ensemble of models, including as predictors transcript level of the corresponding genes, interaction between genes, conservation across tumor types, and phosphosite proximity for phosphorylation prediction. Proteins from metabolic pathways and complexes were the best and worst predicted, respectively. The performance of even the best-performing model was modest, suggesting that many proteins are strongly regulated through translational control and degradation. Our results set a reference for the limitations of computational inference in proteogenomics. A record of this paper's transparent peer review process is included in the Supplemental Information.&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/32710834?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%">Menden, Michael P</style></author><author><style face="normal" font="default" size="100%">Wang, Dennis</style></author><author><style face="normal" font="default" size="100%">Mason, Mike J</style></author><author><style face="normal" font="default" size="100%">Szalai, Bence</style></author><author><style face="normal" font="default" size="100%">Bulusu, Krishna C</style></author><author><style face="normal" font="default" size="100%">Guan, Yuanfang</style></author><author><style face="normal" font="default" size="100%">Yu, Thomas</style></author><author><style face="normal" font="default" size="100%">Kang, Jaewoo</style></author><author><style face="normal" font="default" size="100%">Jeon, Minji</style></author><author><style face="normal" font="default" size="100%">Wolfinger, Russ</style></author><author><style face="normal" font="default" size="100%">Nguyen, Tin</style></author><author><style face="normal" font="default" size="100%">Zaslavskiy, Mikhail</style></author><author><style face="normal" font="default" size="100%">Jang, In Sock</style></author><author><style face="normal" font="default" size="100%">Ghazoui, Zara</style></author><author><style face="normal" font="default" size="100%">Ahsen, Mehmet Eren</style></author><author><style face="normal" font="default" size="100%">Vogel, Robert</style></author><author><style face="normal" font="default" size="100%">Neto, Elias Chaibub</style></author><author><style face="normal" font="default" size="100%">Norman, Thea</style></author><author><style face="normal" font="default" size="100%">Tang, Eric K Y</style></author><author><style face="normal" font="default" size="100%">Garnett, Mathew J</style></author><author><style face="normal" font="default" size="100%">Veroli, Giovanni Y Di</style></author><author><style face="normal" font="default" size="100%">Fawell, Stephen</style></author><author><style face="normal" font="default" size="100%">Stolovitzky, Gustavo</style></author><author><style face="normal" font="default" size="100%">Guinney, Justin</style></author><author><style face="normal" font="default" size="100%">Dry, Jonathan R</style></author><author><style face="normal" font="default" size="100%">Saez-Rodriguez, Julio</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">AstraZeneca-Sanger Drug Combination DREAM Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Commun</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Commun</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">ADAM17 Protein</style></keyword><keyword><style  face="normal" font="default" size="100%">Antineoplastic Combined Chemotherapy Protocols</style></keyword><keyword><style  face="normal" font="default" size="100%">Benchmarking</style></keyword><keyword><style  face="normal" font="default" size="100%">Biomarkers, Tumor</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%">Datasets as Topic</style></keyword><keyword><style  face="normal" font="default" size="100%">Drug Antagonism</style></keyword><keyword><style  face="normal" font="default" size="100%">Drug Resistance, Neoplasm</style></keyword><keyword><style  face="normal" font="default" size="100%">Drug Synergism</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%">Molecular Targeted Therapy</style></keyword><keyword><style  face="normal" font="default" size="100%">mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Neoplasms</style></keyword><keyword><style  face="normal" font="default" size="100%">pharmacogenetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Phosphatidylinositol 3-Kinases</style></keyword><keyword><style  face="normal" font="default" size="100%">Phosphoinositide-3 Kinase Inhibitors</style></keyword><keyword><style  face="normal" font="default" size="100%">Treatment Outcome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2019 06 17</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">2674</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 effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca's large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for &gt;60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31209238?dopt=Abstract</style></custom1></record></records></xml>