Browsing by Author "Valencia, Alfonso"
Now showing items 1-20 of 25
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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 AccessRett 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 AccessEpidemiological 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 AccessThe 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 AccessThe 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 AccessHematopoiesis 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 AccessFusion 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 AccessMotivation 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 AccessUnderstanding 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 AccessPresent-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 AccessSevere 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 AccessEpigenetic 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 ... -
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 AccessBiological 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 ... -
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 AccessEfficient 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 AccessComorbidity 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 AccessThe 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 AccessA 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 AccessBackground 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 AccessAs 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 ... -
Pigs are not susceptible to SARS‐CoV‐2 infection but are a model for viral immunogenicity studies
Vergara-Alert, Júlia; Rodon, Jordi; Carrillo, Jorge; Te, Nigeer; Izquierdo‐Useros, Nuria; Rodríguez de la Concepción, María Luisa; Ávila‐Nieto, Carlos; Guallar, Victor; Valencia, Alfonso; Cantero, Guillermo; Blanco, Julià; Clotet, Bonaventura; Bensaid, Albert; Segalés, Joaquim (Wiley, 2020-10)
Article
Open AccessConventional piglets were inoculated with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) through different routes, including intranasal, intratracheal, intramuscular and intravenous ones. Although piglets ...