A5054199754- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Biomedical Text Mining and Ontologies
- Health, Environment, Cognitive Aging
- Tryptophan and brain disorders
- Genomics and Rare Diseases
- Stress Responses and Cortisol
- Genetics, Bioinformatics, and Biomedical Research
- Genetic Associations and Epidemiology
- Nutrition, Genetics, and Disease
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Metabolomics and Mass Spectrometry Studies
- SARS-CoV-2 and COVID-19 Research
- COVID-19 Clinical Research Studies
- Electronic Health Records Systems
- Spine and Intervertebral Disc Pathology
- Medical Imaging and Analysis
- Epigenetics and DNA Methylation
- Plant and fungal interactions
- Neurobiology and Insect Physiology Research
- COVID-19 epidemiological studies
- Topic Modeling
- Alzheimer's disease research and treatments
- Colorectal Cancer Treatments and Studies
Universitat Pompeu Fabra
2016-2025
Hospital del Mar Research Institute
2015-2025
Hospital Del Mar
2022-2025
Municipal Institute for Medical Research
2012-2024
Bioinformatics Solutions (Canada)
2024
Barcelona Biomedical Research Park
2018
Roche (Spain)
2015
Universitat Autònoma de Barcelona
2015
Parc de Salut
2015
University of Havana
2008-2011
The information about the genetic basis of human diseases lies at heart precision medicine and drug discovery. However, to realize its full potential support these goals, several problems, such as fragmentation, heterogeneity, availability different conceptualization data must be overcome. To provide community with a resource free hurdles, we have developed DisGeNET (http://www.disgenet.org), one largest available collections genes variants involved in diseases. integrates from expert...
Abstract One of the most pressing challenges in genomic medicine is to understand role played by genetic variation health and disease. Thanks exploration variants at large scale, hundreds thousands disease-associated loci have been uncovered. However, identification clinical relevance a significant challenge that requires comprehensive interrogation previous knowledge linkage new experimental results. To assist this complex task, we created DisGeNET (http://www.disgenet.org/), management...
DisGeNET is a comprehensive discovery platform designed to address variety of questions concerning the genetic underpinning human diseases. contains over 380 000 associations between >16 genes and 13 diseases, which makes it one largest repositories currently available its kind. integrates expert-curated databases with text-mined data, covers information on Mendelian complex includes data from animal disease models. It features score based supporting evidence prioritize gene-disease...
Thanks to the unbiased exploration of genomic variants at large scale, hundreds thousands disease-associated loci have been uncovered. In parallel, network-based approaches proven be essential understand molecular mechanisms underlying human diseases. The use these has boosted by abundance information about disease associated genes and variants, high quality interactomics data, emergence new types omics data. DisGeNET Cytoscape App combines capabilities with those DisGeNET, a knowledge...
Current biomedical research needs to leverage and exploit the large amount of information reported in scientific publications. Automated text mining approaches, particular those aimed at finding relationships between entities, are key for identification actionable knowledge from free repositories. We present BeFree system identifying entities with a special focus on genes their associated diseases. By exploiting morpho-syntactic text, is able identify gene-disease, drug-disease drug-target...
Abstract The current wealth of genomic variation data identified at nucleotide level presents the challenge understanding by which mechanisms amino acid affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in development disease. Physical interactions molecules are linking steps underlying most, if not all, Understanding that sequence has on a molecule’s is key step towards connecting mechanistic characterization...
Abstract Summary: PsyGeNET (Psychiatric disorders and Genes association NETwork) is a knowledge platform for the exploratory analysis of psychiatric diseases their associated genes. composed database web interface supporting data search, visualization, filtering sharing. integrates information from DisGeNET extracted literature by text mining, which has been curated domain experts. It currently contains 2642 associations between 1271 genes 37 disease concepts. In its first release, focused...
Intervertebral disc degeneration (IDD) results from an imbalance between anabolic and catabolic processes in the extracellular matrix (ECM). Due to complex biochemical interactions, a comprehensive understanding is needed. This study presents regulatory network model (RNM) for nucleus pulposus cells (NPC), representing normal intervertebral (IVD) conditions. The RNM includes 33 proteins, 153 interactions based on literature, incorporating key NPC mechanisms. A semi-quantitative approach...
Patients with chronic obstructive pulmonary disease (COPD) often suffer concomitant disorders that worsen significantly their health status and vital prognosis. The pathogenic mechanisms underlying COPD multimorbidities are not completely understood, thus the exploration of potential molecular biological linkages between associated diseases is great interest. We developed a novel, unbiased, integrative network medicine approach for analysis diseasome, interactome, pathways tobacco smoke...
Abstract Motivation: DisGeNET-RDF makes available knowledge on the genetic basis of human diseases in Semantic Web. Gene-disease associations (GDAs) and their provenance metadata are published as human-readable machine-processable web resources. The information GDAs included is interlinked to other biomedical databases support development bioinformatics approaches for translational research through evidence-based exploitation a rich fully interconnected linked open data. Availability...
Abstract Background Major depression (MD) is the most prevalent psychiatric disease in population and considered a prodromal stage of Alzheimer’s (AD). Despite both diseases having robust genetic component, common transcriptomic signature remains unknown. Methods We investigated cognitive emotional behavioural responses 3- 6-month-old APP/PSEN1-Tg mice, before β-amyloid plaques were detected. studied pathway deregulation prefrontal cortex, striatum, hippocampus amygdala mice at ages, using...
The use of molecular biomarkers to support disease diagnosis, monitor its progression, and guide drug treatment has gained traction in the last decades. While only a dozen have been approved for their exploitation clinic by FDA, many more are evaluated context translational research clinical trials. Furthermore, information on which measured, purpose, relation conditions not readily accessible: used studies available through resources such as ClinicalTrials.gov described free text, posing...
The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification drug repurposing.
The past decades have witnessed a paradigm shift from the traditional drug discovery shaped around idea of “one target, one disease” to polypharmacology (multiple targets, disease). Given lack clear-cut boundaries across disease (endo)phenotypes and genetic heterogeneity patients, natural extension current is target common biological pathways involved in diseases via endopharmacology multiple diseases). In this study, we present proximal pathway enrichment analysis (PxEA) for...
Mechanism-based risk assessment is urged to advance and fully permeate into current safety practices, possibly at early phases of drug testing. Toxicogenomics a promising source mechanisms-revealing data, but interpretative analysis tools specific for the testing systems (e.g. hepatocytes) are lacking. In this study, we present TXG-MAPr webtool (available https://txg-mapr.eu/WGCNA_PHH/TGGATEs_PHH/ ), an R-Shiny-based implementation weighted gene co-expression network (WGCNA) obtained from...
Abstract Knowledge graph embeddings (KGE) are a powerful technique used in the biomedical domain to represent biological knowledge low dimensional space. However, deep understanding of these methods is still missing, and, particular, regarding their applications prioritize genes associated with complex diseases reduced genetic information. In this contribution, we built (KG) by integrating heterogeneous data and generated KGE implementing state-of-the-art methods, two novel algorithms: Dlemb...
Abstract Characterizing the behavior of disease genes in context biological networks has potential to shed light on mechanisms, and reveal both new candidate therapeutic targets. Previous studies addressing network properties have produced contradictory results. Here we explored causes these discrepancies assessed relationship between roles their tolerance deleterious germline variants human populations leveraging on: abundance interactome resources, a comprehensive catalog exome variation...
Understanding relationships between diseases, such as comorbidities, has important socio-economic implications, ranging from clinical study design to health care planning. Most studies characterize disease comorbidity using shared genetic origins, ignoring pathway-based commonalities diseases. In this study, we define the pathways an interactome-based extension of known disease-genes and introduce several measures functional overlap. The analysis reveals 206 significant links among 94 giving...
eTRANSAFE is a research project funded within the Innovative Medicines Initiative (IMI), which aims at developing integrated databases and computational tools (the ToxHub) that support translational safety assessment of new drugs by using legacy data provided pharmaceutical companies participate in project. The objectives include development containing preclinical clinical data, systems for analysis including query, visualization, as well models to explain predict drug events.
Protein-protein interaction (PPI) networks provide a static map of functional protein interactions, which when combined with algorithms, can prioritize key candidates experimental studies cannot capture. This study, aimed to construct knowledge-based nucleus pulposus (NP)-specific PPI could be deployed investigate complex interactions in human NP cells and tissues following IL-4 IL-10 stimulation. NP-specific were developed based on mass spectrometry (MS) secretome datasets from cells. These...
Abstract Background Vascular smooth muscle cells loaded with cholesterol (foam-VSMCs) play a crucial role in the progression of human atherosclerosis. Exchange Protein Directly Activated by cAMP 1 (EPAC1) is critical protein regulation vascular tone, endothelial function, and inflammation. Our objectives were to identify proteins specifically secreted foam coronary VSMCs (foam-hcVSMC) evaluate their potential as circulating biomarkers for diagnosing artery disease (CAD), ascertain mechanisms...