• A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer 

    Sánchez-Valle, Jon; Tejero, Héctor; Ibáñez, Kristina; Portero, Jose L.; Krallinger, Martin; Al-Shahrour, Fátima; Tabarés-Seisdedos, Rafael; Baudot, Anaïs; Valencia, Alfonso (Nature Publishing Group, 2017-06-30)
    Artículo
    Acceso abierto
    Epidemiological studies indicate that patients suffering from Alzheimer’s disease have a lower risk of developing lung cancer, and suggest a higher risk of developing glioblastoma. Here we explore the molecular scenarios ...
  • 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)
    Artículo
    Acceso abierto
    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 ...
  • 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)
    Artículo
    Acceso abierto
    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 ...
  • ChiPPI: a novel method for mapping chimeric protein–protein interactions uncovers selection principles of protein fusion events in cancer 

    Frenkel-Morgenstern, Milana; Gorohovski, Alessandro; Tagore, Somnath; Sekar, Vaishnovi; Vazquez, Miguel; Valencia, Alfonso (Oxford University Press, 2017-05-26)
    Artículo
    Acceso abierto
    Fusion proteins, comprising peptides deriving from the translation of two parental genes, are produced in cancer by chromosomal aberrations. The expressed fusion protein incorporates domains of both parental proteins. Using ...
  • Comparison of algorithms for the detection of cancer drivers at subgene resolution 

    Porta-Pardo, Eduard; Kamburov, Atanas; Tamborero, David; Pons, Tirso; Grases, Daniela; Valencia, Alfonso; Lopez-Bigas, Nuria; Getz, Gad; Godzik, Adam (Nature Publishing Group, 2017-08)
    Artículo
    Acceso abierto
    Understanding genetic events that lead to cancer initiation and progression remains one of the biggest challenges in cancer biology. Traditionally, most algorithms for cancer-driver identification look for genes that have ...
  • Deep and cognitive learning applied to Precision Medicine: the initial experiments linking (epi)genome to phenotypes-disease characteristics 

    Cirillo, Davide; Valencia, Alfonso (Barcelona Supercomputing Center, 2017-05-04)
    Texto en actas de congreso
    Acceso abierto
    Present-day era of Big Data provides the unique opportunity to develop innovative approaches for data analysis to find new insights into specialized fields of biomedical research such as Precision Medicine [1]. Precision ...
  • Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity 

    Ecker, Simone; Pancaldi, Vera; Valencia, Alfonso; Beck, Stephan; Paul, Dirk S. (Wiley, 2017-12-18)
    Artículo
    Acceso abierto
    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 ...
  • Information Retrieval and Text Mining Technologies for Chemistry 

    Krallinger, Martin; Rabal, Obdulia; Lourenço, Anália; Oyarzabal, Julen; Valencia, Alfonso (American Chemical Society, 2017-05-05)
    Artículo
    Acceso restringido por política de la editorial
    Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval ...
  • Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking 

    Capella-Gutierrez, Salvador; de la Iglesia, Diana; Haas, Juergen; Lourenco, Analia; Fernandez, José M.; Repchevsky, Dmitry; Dessimoz, Christophe; Schwede, Torsten; Notredame, Cedric; Gelpi, Josep Ll.; Valencia, Alfonso (2017)
    Working paper
    Acceso abierto
    The dependence of life scientists on software has steadily grown in recent years. For many tasks, researchers have to decide which of the available bioinformatics software are more suitable for their specific needs. ...
  • LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes 

    Cañada, Andres; Capella-Gutierrez, Salvador; Rabal, Obdulia; Oyarzabal, Julen; Valencia, Alfonso; Krallinger, Martin (Oxford University Press, 2017-05-22)
    Artículo
    Acceso abierto
    A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in ...
  • The biomedical abbreviation recognition and resolution (BARR) track: Benchmarking, evaluation and importance of abbreviation recognition systems applied to Spanish biomedical abstracts 

    Intxaurrondo, Ander; Pérez-Pérez, Martin; Pérez-Rodríguez, Gael; López-Martín, Jose A.; Santamaria, Jesus; de la Peña, Santiago; Villegas, Marta; Akhondi, Saber A.; Valencia, Alfonso; Lourenço, Analia; Krallinger, Martin (2017-09-19)
    Acceso abierto
    Healthcare professionals are generating a substantial volume of clinical data in narrative form. As healthcare providers are confronted with serious time constraints, they frequently use telegraphic phrases, domain-specific ...