Browsing by Author "Valencia, Alfonso"
Now showing items 1-20 of 73
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3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures
(Oxford University Press [, 2024)
Article
Open AccessMotivation 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 catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration
(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
(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
(Barcelona Supercomputing Center, 2019-05-07)
Conference report
Open Access -
A user guide for the online exploration and visualization of PCAWG data
(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
(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 ... -
Artificial intelligence in cancer research: learning at different levels of data granularity
(Wiley, 2021)
Article
Open AccessFrom 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
(JMIR Publications, 2021-03)
Article
Open AccessArtificial 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
(Wiley, 2021)
Article
Open AccessWe 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
(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 ... -
BioFVM-X: an MPI+OpenMP 3-D simulator for biological systems
(Springer, 2021)
Conference report
Open AccessMulti-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
(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
(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 ... -
Clinical course impacts early kinetics,magnitude, and amplitude of SARS-CoV-2 neutralizing antibodies beyond 1 year after infection
(Cell Press, 2022-02)
Article
Open AccessTo 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
(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 ... -
Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells
(Oxford University Press, 2021-08)
Article
Open AccessMany 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
(Nature Research, 2021)
Article
Open AccessCOVID-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
(Wiley Open Access, 2021-10-21)
Article
Open AccessWe 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
(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
(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 ...
