Now showing items 1-19 of 19

    • 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)
      Article
      Open Access
      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 ...
    • A multilayer network approach to elucidate severity in Congenital Myasthenic Syndromes 

      Núñez-Carpintero, Iker; Cirillo, Davide; Valencia, Alfonso (Barcelona Supercomputing Center, 2019-05-07)
      Conference report
      Open Access
    • A user guide for the online exploration and visualization of PCAWG data 

      Goldman, Mary J.; Zhang, Junjun; Fonseca, Nuno A.; Cortés-Ciriano, Isidro; Xiang, Qian; Craft, Brian; Piñeiro-Yáñez, Elena; O'connor, Brian D.; Bazant, Wojciech; Barrera, Elisabet; Muñoz-Pomer, Alfonso; Petryszak, Robert; Füllgrabe, Anja; Al-Shahrour, Fatima; Keays, Maria; Haussler, David; Weinstein, John N; Huber, Wolfgang; Park, Peter J.; Papatheodorou, Elena; Valencia, Alfonso; Zhu, Jingchun; Ferretti, Vincent; Vazquez, Miguel (Springer Nature, 2020)
      Article
      Open Access
      The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which ...
    • 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
      Open Access
      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)
      Article
      Open Access
      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)
      Article
      Open Access
      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 ...
    • Chromatin network markers of leukemia 

      Malod-Dognin, Noel; Pancaldi, Vera; Valencia, Alfonso; Pržulj, Natasa (Oxford University Press, 2020-07)
      Article
      Open Access
      Motivation The structure of chromatin impacts gene expression. Its alteration has been shown to coincide with the occurrence of cancer. A key challenge is in understanding the role of chromatin structure (CS) in cellular ...
    • 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)
      Article
      Open Access
      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)
      Conference report
      Open Access
      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)
      Article
      Open Access
      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)
      Article
      Open Access
      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 ...
    • Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships 

      Sánchez, Jon; Tejero, Héctor; Fernández, José María; Juan, David; Urda García, Beatriz; Capella Gutiérrez, Salvador; Al-Shahrour, Fátima; Tabarés Seisdedos, Rafael; Baudot, Anais; Pancaldi, Vera; Valencia, Alfonso (Springer Nature, 2020)
      Article
      Open Access
      Comorbidity is a medical condition attracting increasing attention in healthcare and biomedical research. Little is known about the involvement of potential molecular factors leading to the emergence of a specific disease ...
    • 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; Gelpí, Josep Lluís; Valencia, Alfonso (2017)
      Working paper
      Open Access
      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)
      Article
      Open Access
      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 ...
    • Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm 

      Pérez Pérez, Martín; Pérez Rodríguez, Gael; Blanco Míguez, Aitor; Fernández Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, Anália (BMC, 2019)
      Article
      Open Access
      Background Shared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such ...
    • Patient dossier: healthcare queries over distributed resources 

      Vazquez, Miguel; Valencia, Alfonso (PLOS, 2019-10-17)
      Article
      Open Access
      As with many other aspects of the modern world, in healthcare, the explosion of data and resources opens new opportunities for the development of added-value services. Still, a number of specific conditions on this domain ...
    • Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare 

      Cirillo, Davide; Catuara Solarz, Silvina; Morey, Czuee; Guney, Emre; Subirats, Laia; Mellino, Simona; Gigante, Annalisa; Valencia, Alfonso; Rementeria, María José; Santuccione Chadha, Antonella; Mavridis, Nikolaos (Springer Nature, 2020)
      Article
      Open Access
      Precision Medicine implies a deep understanding of inter-individual differences in health and disease that are due to genetic and environmental factors. To acquire such understanding there is a need for the implementation ...
    • 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)
      Open Access
      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 ...
    • Unveiling new disease, pathway, and gene associations via multi-scale neural network 

      Gaudelet, Thomas; Malod Dognin, Noël; Sánchez, Jon; Pancaldi, Vera; Valencia, Alfonso; Pržulj, Nataša (PLOS, 2020-04-06)
      Article
      Open Access
      Diseases involve complex modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, new biological knowledge about a disease can ...