Browsing by Author "Valencia, Alfonso"Més informació

Now showing items 1-20 of 85

    • 3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures 

      Ruiz Serra, Victoria; Valentini, Samuel; Madroñero, Sergi; Valencia, Alfonso; Porta Pardo, Eduard (Oxford University Press [, 2024)
      Article
      Open Access
      Motivation The interpretation of genomic data is crucial to understand the molecular mechanisms of biological processes. Protein structures play a vital role in facilitating this interpretation by providing functional ...

    • A benchmark of synthetic transcriptomic cancer data reconstruction 

      Prol Castelo, Guillermo; Cirillo, Davide; Valencia, Alfonso (Barcelona Supercomputing Center, 2024-05)
      Conference report
      Open Access
      Cancer is the second most common cause of death worldwide, and its incidence is increasing [1]. Some methodologies have been developed to study cancer. For instance, PAM50, a collection of 50 genes important for cancer ...

    • 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 ...

    • An AGS cell line digital twin for studying novel treatment strategies 

      Hayoun-Mya, Othmane; Ponce De Leon, Miguel; Montagud, Arnau; Valencia, Alfonso (Barcelona Supercomputing Center, 2024-05)
      Conference report
      Open Access
      The discovery of novel therapeutic strategies against tumor systems is often focused on combinatorial approaches and in silico testing. The former is a consequence of the wellknown apparition of adaptive and acquired ...

    • 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 ...

    • Clinical course impacts early kinetics,magnitude, and amplitude of SARS-CoV-2 neutralizing antibodies beyond 1 year after infection 

      Pradenas, Edwards; Trinité, Benjamin; Urrea, Víctor; Marfil, Silvia; Tarrés Freixas, Ferran; Guallar, Victor; Valencia, Alfonso (Cell Press, 2022-02)
      Article
      Open Access
      To understand the determinants of long-term immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the concurrent impact of vaccination and emerging variants, we follow a prospective cohort ...

    • 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 ...

    • Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells 

      Mukherjee, Sumit; Detroja, Rajesh; Balamurali, Deepak; Matveishina, Elena; Medvedeva, Yulia A; Valencia, Alfonso; Gorohovski, Alessandro; Frenkel-Morgenstern, Milana (Oxford University Press, 2021-08)
      Article
      Open Access
      Many human genes are transcribed from both strands and produce sense-antisense gene pairs. Sense-antisense (SAS) chimeric transcripts are produced upon the coalescing of exons/introns from both sense and antisense transcripts ...

    • COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain 

      Ponce De Leon, Miguel; Valle, Javier del; Fernández González, Jose María; Bernardo, Marc; Cirillo, Davide; Sanchez Valle, Jon; Smith, Matthew; Capella Gutiérrez, Salvador; Gullón, Tania; Valencia, Alfonso (Nature Research, 2021)
      Article
      Open Access
      COVID-19 is an infectious disease caused by the SARS-CoV-2 virus, which has spread all over the world leading to a global pandemic. The fast progression of COVID-19 has been mainly related to the high contagion rate of the ...

    • 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. ...