Now showing items 1-20 of 45

    • A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration 

      Ehrhart, Friederike; Jacobsen, Annika; Rigau, Maria; Bosio, Mattia; Kaliyaperumal, Rajaram; Laros, Jeroen F. J.; Willighagen, Egon L.; Valencia, Alfonso; Roos, Marco; Capella Gutiérrez, Salvador; Curfs, Leopold M. G.; Evelo, Chris T. (Springer Nature, 2021)
      Article
      Open Access
      Rett syndrome (RTT) is a rare neurological disorder mostly caused by a genetic variation in MECP2. Making new MECP2 variants and the related phenotypes available provides data for better understanding of disease mechanisms ...
    • 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 ...
    • Artificial intelligence in cancer research: learning at different levels of data granularity 

      Cirillo, Davide; Nuñez Carpintero, Iker; Valencia, Alfonso (Wiley, 2021)
      Article
      Open Access
      From genome-scale experimental studies to imaging data, behavioral footprints, and longitudinal healthcare records, the convergence of big data in cancer research and the advances in Artificial Intelligence (AI) is paving ...
    • Artificial Intelligence–Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development 

      Santus, Enrico; Marino, Nicola; Cirillo, Davide; Chersoni, Emmanuele; Montagud, Arnau; Santuccione Chadha, Antonella; Valencia, Alfonso; Hughes, Kevin; Lindvall, Charlotta (JMIR Publications, 2021-03)
      Article
      Open Access
      Artificial intelligence (AI) technologies can play a key role in preventing, detecting, and monitoring epidemics. In this paper, we provide an overview of the recently published literature on the COVID-19 pandemic in four ...
    • Assessing the accuracy of contact and distance predictions in CASP14 

      Ruiz Serra, Victoria; Pontes, Camila; Milanetti, Edoardo; Kryshtafovych, Andriy; Lepore, Rosalba; Valencia, Alfonso (Wiley, 2021)
      Article
      Open Access
      We present the results of the assessment of the intramolecular residue–residue contact and distance predictions from groups participating in the 14th round of the CASP experiment. The performance of contact prediction ...
    • 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 ...
    • BioFVM-X: an MPI+OpenMP 3-D simulator for biological systems 

      Saxena, Gaurav; Ponce De Leon, Miguel; Montagud, Arnau; Vicente Dorca, David; Valencia, Alfonso (Springer, 2021)
      Conference report
      Open Access
      Multi-scale simulations require parallelization to address large-scale problems, such as real-sized tumor simulations. BioFVM is a software package that solves diffusive transport Partial Differential Equations for 3-D ...
    • 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 ...
    • COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms 

      Ostaszewski, Marek; Niarakis, Anna; Mazein, Alexander; Kuperstein, Inna; Phair, Robert; Montagud, Arnau; Ponce De Leon, Miguel; Vazquez, Miguel; Valencia, Alfonso (Wiley Open Access, 2021-10-21)
      Article
      Open Access
      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. ...
    • 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 ...
    • Detection of SARS-CoV-2 in a cat owned by a COVID-19−affected patient in Spain 

      Segalés, Joaquim; Puig, Mariona; Rodon, Jordi; Avila-Nieto, Carlos; Carrillo, Jorge; Cantero, Guillermo; Terrón, Maria Teresa; Cruz, Sílvia; Parera, Mariona; Noguera-Julián, Marc; Izquierdo-Useros, Nuria; Guallar, Victor; Vidal, Enric; Valencia, Alfonso; Blanco, Ignacio; Blanco, Julià; Clotet, Bonaventura; Vergara-Alert, Júlia (National Academy of Sciences, 2020-10)
      Article
      Open Access
      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, is considered a zoonotic pathogen mainly transmitted human to human. Few reports indicate that pets may be exposed to the ...
    • 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 ...
    • From comorbidities to gene expression fingerprints and back 

      Urda-García, Beatriz; Valencia, Alfonso (Barcelona Supercomputing Center, 2021-05)
      Conference report
      Open Access
      Epidemiological evidence shows that some diseases tend to co-occur more than expected by chance and that patientspecific trends are observed. However, the molecular processes underlying these phenomena remain unclear. Here ...
    • GOPHER, an HPC framework for large scale graph exploration and inference 

      Josep Fabregó, Marc; Teruel García, Xavier; Giménez Ábalos, Víctor; Cirilo, Davide; Garcia Gasulla, Dario; Álvarez Napagao, Sergio; Garcia Gasulla, Marta; Ayguadé Parra, Eduard; Valencia, Alfonso (Springer, 2020)
      Conference report
      Open Access
      Biological ontologies, such as the Human Phenotype Ontology (HPO) and the Gene Ontology (GO), are extensively used in biomedical research to investigate the complex relationship that exists between the phenome and the ...
    • Identification of plitidepsin as potent inhibitor of SARS-CoV-2-induced cytopathic effect after a drug repurposing screen 

      Rodon, Jordi; Muñoz-Basagoiti, Jordana; Perez, Carles; Valencia, Alfonso; Guallar, Victor (Frontiers Media, 2021)
      Article
      Open Access
      There is an urgent need to identify therapeutics for the treatment of Coronavirus disease 2019 (COVID-19). Although different antivirals are given for the clinical management of SARS-CoV-2 infection, their efficacy is still ...