A5028520416- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Genomics and Rare Diseases
- SARS-CoV-2 and COVID-19 Research
- Retinal Development and Disorders
- Genomics and Phylogenetic Studies
- COVID-19 Clinical Research Studies
- RNA and protein synthesis mechanisms
- Computational Drug Discovery Methods
- MicroRNA in disease regulation
- Microbial Metabolic Engineering and Bioproduction
- Retinal Diseases and Treatments
- Gene Regulatory Network Analysis
- Cancer-related gene regulation
- Asthma and respiratory diseases
- Ubiquitin and proteasome pathways
- Liver Disease Diagnosis and Treatment
- RNA modifications and cancer
- RNA regulation and disease
- RNA Research and Splicing
- SARS-CoV-2 detection and testing
- Molecular Biology Techniques and Applications
- interferon and immune responses
- Plant Virus Research Studies
- CRISPR and Genetic Engineering
Instituto de Salud Carlos III
2020-2025
Centre for Biomedical Network Research on Rare Diseases
2008-2025
Universidad Autónoma de Madrid
2016-2025
Hospital Universitario Fundación Jiménez Díaz
2016-2025
Centro de Investigación Biomédica en Red
2021-2025
Instituto de Investigación de Enfermedades Raras
2023-2025
Hospital Universitario Insular de Gran Canaria
2024
European Molecular Biology Laboratory
2012-2017
Centro de Investigacion Principe Felipe
2006-2014
SIB Swiss Institute of Bioinformatics
2010-2012
Complete knowledge of all direct and indirect interactions between proteins in a given cell would represent an important milestone towards comprehensive description cellular mechanisms functions. Although this goal is still elusive, considerable progress has been made—particularly for certain model organisms functional systems. Currently, protein associations are annotated at various levels detail online resources, ranging from raw data repositories to highly formalized pathway databases....
An essential prerequisite for any systems-level understanding of cellular functions is to correctly uncover and annotate all functional interactions among proteins in the cell. Toward this goal, remarkable progress has been made recent years, both terms experimental measurements computational prediction techniques. However, public efforts collect present protein interaction information have struggled keep up with pace discovery, partly because protein–protein can be error-prone require...
We present a new version of Babelomics, complete suite web tools for functional analysis genome-scale experiments, with and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An indexing has considerably speeded up several the modules. FatiScan method studying coordinate behaviour groups related genes is presented, along similar tool, Gene Set Enrichment Analysis. Babelomics now more oriented to test...
The ultimate goal of any genome-scale experiment is to provide a functional interpretation the data, relating available information with hypotheses that originated experiment. Thus, profiling methods have become essential in diverse scenarios such as microarray experiments, proteomics, etc. We present FatiGO+, web-based tool for specially oriented experiments. In addition different annotations (gene ontology, KEGG pathways, Interpro motifs, Swissprot keywords and text-mining based...
We present Babelomics, a complete suite of web tools for the functional analysis groups genes in high-throughput experiments, which includes use information on Gene Ontology terms, interpro motifs, KEGG pathways, Swiss-Prot keywords, predicted transcription factor binding sites, chromosomal positions and presence tissues with determined histological characteristics, through five integrated modules: FatiGO (fast assignment transference information), FatiWise, association test, GenomeGO mining...
OGEE is an Online GEne Essentiality database. Its main purpose to enhance our understanding of the essentiality genes. This achieved by collecting not only experimentally tested essential and non-essential genes, but also associated gene features such as expression profiles, duplication status, conservation across species, evolutionary origins involvement in embryonic development. We focus on large-scale experiments complement data with text-mining results. Genes are organized into sets...
Controlled ovarian stimulation induces morphological, biochemical, and functional genomic modifications of the human endometrium during window implantation.Our objective was to compare gene expression profile in natural vs. controlled cycles throughout early-mid secretory transition using microarray technology.Microarray data from 49 endometrial biopsies obtained LH+1 LH+9 (n=25) chorionic gonadotropin (hCG) +1 hCG+9 (n=24) were analyzed different methods, such as clustering, profiling...
Assembly of protein complexes is considered a posttranslational process involving random collision subunits. We show that within the Escherichia coli cytosol, bacterial luciferase subunits LuxA and LuxB assemble into close to site subunit synthesis. efficiency decreases markedly if are synthesized on separate messenger RNAs from genes integrated at distant chromosomal sites. Subunit assembly initiates cotranslationally nascent in vivo. The ribosome-associated chaperone trigger factor delays...
Post-translational modifications (PTMs) are involved in the regulation and structural stabilization of eukaryotic proteins. The combination individual PTM states is a key to modulate cellular functions as became evident few well-studied This combinatorial setting, dubbed code, has been proposed be extended whole proteomes eukaryotes. Although we still far from deciphering such complex language, thousands protein sites being mapped by high-throughput technologies, thus providing sufficient...
The post-translational regulation of proteins is mainly driven by two molecular events, their modification several types moieties and interaction with other proteins. These processes are interdependent together responsible for the function protein in a particular cell state. Several databases focus on prediction compilation protein–protein interactions (PPIs) no less collection analysis modifications (PTMs), however, there resources that concentrate describing regulatory role PTMs PPIs. We...
With the popularization of high-throughput techniques, need for procedures that help in biological interpretation results has increased enormously. Recently, new inspired systems biology criteria have started to be developed.Here we present FatiScan, a web-based program which implements threshold-independent test functional large-scale experiments does not depend on pre-selection genes based multiple application independent tests each gene. The implemented aims directly behaviour blocks...
The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it evolved to keep pace with the new interests and trends in still changing world of microarray data analysis. GEPAS designed provide an intuitive although powerful web-based interface that offers diverse analysis options from early step preprocessing (normalization Affymetrix two-colour experiments other options), final functional annotation experiment (using Ontology, pathways,...
Asthma is a syndrome characterized by airway inflammation and obstruction. Due to its heterogeneity, the difficulties in asthma diagnosis treatment make discovery of new biomarkers focus research. So, we determined differential miRNA expression eosinophils between healthy asthmatic patients establish differentially expressed profile detectable sera for use as biomarker.MicroRNAs from peripheral subjects were isolated analyzed next-generation sequencing confirmed quantitative PCR 29...
The mechanisms underlying early atherosclerotic plaque formation are not completely understood. Moreover, plasma biomarkers of subclinical atherosclerosis lacking. purpose this study was to analyze the temporal and topologically resolved protein changes taking place in human aortas with find new potential diagnostic and/or therapeutic targets. composition healthy (media layer) or atheroma (fatty streak fibrolipidic, media intima layers) analyzed by deep quantitative multiplexed proteomics....
Abstract Despite the improved accuracy of next-generation sequencing (NGS), it is widely accepted that variants need to be validated using Sanger before reporting. Validation all NGS considerably increases turnaround time and costs clinical diagnosis. We comprehensively assessed this in 1109 from 825 exomes, largest sample set date Illumina chemistry reported. With a concordance 100%, we conclude can very useful as an internal quality control, but not so much verification method for...
Bacterial infections may complicate the course of COVID-19 patients. The rate and predictors bacterial were examined in patients consecutively admitted with at one tertiary hospital Madrid between March 1st April 30th, 2020. Among 1594 hospitalized COVID-19, 135 (8.5%) experienced infectious events, distributed as follows: urinary tract (32.6%), bacteremia (31.9%), pneumonia (31.8%), intra-abdominal (6.7%) skin soft tissue (6.7%). Independent older age, neurological disease, prior...
There is a need for effective anti-COVID-19 treatments, mainly individuals at risk of severe disease such as the elderly and immunosuppressed. Drug repositioning has proved in identifying drugs that can find new application control coronavirus disease, particular COVID-19. The purpose present study was to synergistic antiviral combinations COVID-19 based on lethal mutagenesis.
Copy-number variants (CNVs) play a substantial role in the molecular pathogenesis of hereditary disease and cancer, as well normal human interindividual variation. However, they are still rather difficult to identify mainstream sequencing projects, especially involving exome sequencing, because often occur DNA regions that not targeted for analysis. To overcome this problem, we developed OFF-PEAK, user-friendly CNV detection tool builds on denoising approach use "off-target" reads, which...
The Gene Expression Profile Analysis Suite, GEPAS, has been running for more than three years. With >76 000 experiments analysed during the last year and a daily average of almost 300 analyses, GEPAS can be considered well-established widely used platform gene expression microarray data analysis. is oriented to analysis whole series experiments. Its design development have driven by demands biomedical community, probably most active collective in field users. Although clustering methods...
We present a new version of Babelomics, complete suite web tools for the functional profiling genome scale experiments, with and improved methods as well more types definitions.Babelomics includes different flavours conventional enrichment advanced gene set analysis that makes it unique tool among similar resources available.In addition to well-known definitions (GO, KEGG), Babelomics ones such Biocarta pathways or text mining-derived terms.Regulatory modules implemented include...
The genome of Mycobacterium tuberculosis (H37Rv) contains 4,019 protein coding genes, which more than thousand have been categorized as 'hypothetical' implying that for these not even weak functional associations could be identified so far. We here predict reliable indications half this large hypothetical orfeome: 497 genes can annotated based on orthology, and another 125 linked to interacting proteins via integrated genomic context analysis literature mining. assignments include newly...
To provide a comprehensive overview of the molecular basis autosomal dominant retinitis pigmentosa (adRP) in Spanish families. Thus, we established characterization rate, gene prevalence, and mutational spectrum largest European cohort reported to date.A total 258 unrelated families with clinical diagnosis RP suspected inheritance were included. Clinical was based on complete ophthalmologic examination family history. Retrospective prospective analysis adRP carried out using combined...
Proteomics techniques can identify thousands of phosphorylation sites in a single experiment, the majority which are new and lack precise information about function or molecular mechanism. Here we present fast method to predict potential switches by mapping protein-protein interactions known structure analysing properties protein interface. We 1024 that could potentially enable disable particular interactions. tested selection these showed phosphomimetic mutations indeed affect estimate...