Browsing by Author "Valencia, Alfonso"
Now showing items 1-19 of 19
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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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity
(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 ... -
Information Retrieval and Text Mining Technologies for Chemistry
(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
(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
(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
(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
(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
(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 ... -
Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare
(Springer Nature, 2020)
Article
Open AccessPrecision 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
(2017-09-19)
Open AccessHealthcare 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
(PLOS, 2020-04-06)
Article
Open AccessDiseases 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 ...
