Enviaments recents

  • Ten steps to get started in Genome Assembly and Annotation 

    Dominguez del Angel, Victoria; Hjerde, Erik; Sterck, Lieven; Capella-Gutierrez, Salvador; Notredame, Cederic; Vinnere Pettersson, Olga; Amselem, Joelle; Bouri, Laurent; Bocs, Stephanie; Klopp, Christophe; Gibrat, Jean-Francois; Vlasova, Anna; Leskosek, Brane L.; Soler, Lucile; Binzer-Panchal, Mahesh; Lantz, Henrik (F1000Research, 2018-02-05)
    Article
    Accés obert
    As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, ...
  • Hot-spot analysis for drug discovery targeting protein-protein interactions 

    Rosell, Mireia; Fernández-Recio, Juan (Taylor & Francis, 2018-01-29)
    Article
    Accés restringit per política de l'editorial
    Introduction: Protein-protein interactions are important for biological processes and pathological situations, and are attractive targets for drug discovery. However, rational drug design targeting protein-protein interactions ...
  • LightDock: a new multi-scale approach to protein–protein docking 

    Jiménez-García, Brian; Roel-Touris, Jorge; Romero-Durana, Miguel; Vidal-Piñol, Miquel; Jiménez-González, Daniel; Fernández-Recio, Juan (Oxford University Press, 2017-09-04)
    Article
    Accés restringit per política de l'editorial
    Computational prediction of protein–protein complex structure by docking can provide structural and mechanistic insights for protein interactions of biomedical interest. However, current methods struggle with difficult ...
  • Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes 

    Bonàs-Guarch, Sílvia; Guindo-Martínez, Marta; Miguel-Escalada, Irene; Grarup, Niels; Sebastian, David; Rodriguez-Fos, Elias; Sánchez, Friman; Planas-Fèlix, Mercè; Cortes-Sánchez, Paula; González, Santi; Timshel, Pascal; Pers, Tune H.; Morgan, Claire C.; Moran, Ignasi; Atla, Goutham; González, Juan R.; Puiggros, Montserrat; Martí, Jonathan; Andersson, Ehm A.; Díaz, Carlos; Badia, Rosa M.; Udler, Miriam; Leong, Aaron; Kaur, Varindepal; Flannick, Jason; Jorgensen, Torben; Linneberg, Allan; Jorgensen, Marit E.; Witte, Daniel R.; Christensen, Cramer; Brandslund, Ivan; Appel, Emil V.; Scott, Robert A.; Luan, Jian' an; Langenberg, Claudia; Wareham, Nicholas J.; Pedersen, Oluf; Zorzano, Antonio; Florez, Jose C.; Hansen, Torben; Ferrer, Jorge; Mercader, Josep M.; Torrents, David (Nature Publishing Group, 2018-01-22)
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    Accés obert
    The reanalysis of existing GWAS data represents a powerful and cost-effective opportunity to gain insights into the genetics of complex diseases. By reanalyzing publicly available type 2 diabetes (T2D) genome-wide association ...
  • APPRIS 2017: principal isoforms for multiple gene sets 

    Rodriguez, Jose M.; Rodriguez-Rivas, Juan; di Domenico, Tomás; Vázquez, Jesús; Valencia, Alfonso; Tress, Michael L. (Oxford University Press (OUP), 2017-10-23)
    Article
    Accés obert
    The APPRIS database (http://appris-tools.org) uses protein structural and functional features and information from cross-species conservation to annotate splice isoforms in protein-coding genes. APPRIS selects a single ...
  • Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity 

    Ecker, Simone; Pancaldi, Vera; Valencia, Alfonso; Beck, Stephan; Paul, Dirk S. (Wiley, 2017-12-18)
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    Accés obert
    Epigenetic and transcriptional variability contribute to the vast diversity of cellular and organismal phenotypes and are key in human health and disease. In this review, we describe different types, sources, and determinants ...
  • Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains 

    García-Pardo, Javier; Tanco, Sebastian; Diaz, Lucia; Dasgupta, Sayani; Fernandez-Recio, Juan; Lorenzo, Julia; Aviles, Francesc X.; Fricker, Lloyd D. (Public Library of Science, 2017-11-13)
    Article
    Accés obert
    Metallocarboxypeptidase D (CPD) is a membrane-bound component of the trans-Golgi network that cycles to the cell surface through exocytic and endocytic pathways. Unlike other members of the metallocarboxypeptidase family, ...
  • Towards efficient data exchange and sharing for big-data driven materials science: metadata and data formats 

    Ghiringhelli, Luca M.; Carbogno, Christian; Levchenko, Sergey; Mohamed, Fawzi; Huhs, Georg; Lüders, Martin; Oliveira, Micael; Scheffler, Matthias (Nature Publishing Group, 2017-11-06)
    Article
    Accés obert
    With big-data driven materials research, the new paradigm of materials science, sharing and wide accessibility of data are becoming crucial aspects. Obviously, a prerequisite for data exchange and big-data analytics is ...
  • The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths 

    Gygli, Gudrun; Lucas, Maria F.; Guallar, Victor; van Berkel, Willhem J.H. (Public Library of Science, 2017-10-06)
    Article
    Accés obert
    Vanillyl alcohol oxidase (VAO) is a homo-octameric flavoenzyme belonging to the VAO/PCMH family. Each VAO subunit consists of two domains, the FAD-binding and the cap domain. VAO catalyses, among other reactions, the ...
  • Automatic identification of informative regions with epigenomic changes associated to hematopoiesis 

    Carrillo-de-Santa-Pau, Enrique; Juan, David; Pancaldi, Vera; Were, Felipe; Martin-Subero, Ignacio; Rico, Daniel; Valencia, Alfonso (Oxford University Press, 2017-09-19)
    Article
    Accés obert
    Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate ...
  • The Influence of Autumnal Eurasian Snow Cover on Climate and Its Link with Arctic Sea Ice Cover 

    Gastineau, Guillaume; García-Serrano, Javier; Frankignoul, Claude (American Meteorological Society, 2017-08)
    Article
    Accés obert
    The relationship between Eurasian snow cover extent (SCE) and Northern Hemisphere atmospheric circulation is studied in reanalysis during 1979–2014 and in CMIP5 preindustrial control runs. In observations, dipolar SCE ...
  • The Functional Impact of Alternative Splicing in Cancer 

    Climente-Gonzalez, Héctor; Porta-Pardo, Eduard; Godzik, Adam; Eyras, Eduardo (Elsevier (Cell Press), 2017-08-29)
    Article
    Accés obert
    Alternative splicing changes are frequently observed in cancer and are starting to be recognized as important signatures for tumor progression and therapy. However, their functional impact and relevance to tumorigenesis ...

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