A5065049632- Bioinformatics and Genomic Networks
- Genomics and Rare Diseases
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Genomic variations and chromosomal abnormalities
- Protein Kinase Regulation and GTPase Signaling
- Gene expression and cancer classification
- Pharmacogenetics and Drug Metabolism
- RNA Research and Splicing
- Gene Regulatory Network Analysis
- Genetic Associations and Epidemiology
- RNA modifications and cancer
- Viral Infections and Immunology Research
- Asthma and respiratory diseases
- Epigenetics and DNA Methylation
- Cardiomyopathy and Myosin Studies
- Cancer Genomics and Diagnostics
- Animal Disease Management and Epidemiology
- Ubiquitin and proteasome pathways
- Microtubule and mitosis dynamics
Universidad de Málaga
2016-2025
Centro de Investigación Biomédica en Red
2014-2025
Instituto de Salud Carlos III
2018-2025
Instituto de Investigación Biomédica de Málaga
2014-2025
Instituto de Investigación de Enfermedades Raras
2014-2024
Centre for Biomedical Network Research on Rare Diseases
2013-2024
Andalusian Centre for Nanomedicine and Biotechnology
2023-2024
Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas
2023
European Molecular Biology Laboratory
2015
Spanish National Cancer Research Centre
2015
We identified families of proteins characterized by the presence a domain similar to human p23 protein, which include such as Sgt1, involved in yeast kinetochore assembly; melusin, specific interactions with cytoplasmic integrin β1 domain; Rar1, related pathogenic resistance plants, and development animals; B5+B5R flavo‐hemo cytochrome NAD(P)H oxidoreductase type B humans mice; NudC, nucleus migration during mitosis. also found that HSP20/α‐crystallin family heat shock proteins, share same...
Biofilm formation is a strategy of many bacterial species to adapt variety stresses and has become part infections, contaminations, or beneficial interactions. In this study, we demonstrate that profound physiological changes permit Bacillus cereus switch from floating sessile lifestyle, undergo further maturation the biofilm differentiate into offensive defensive features. We report cells are populations metabolically, with members each subpopulation developing different branches certain...
Abstract Meniere Disease (MD) is a chronic inner ear disorder characterized by vertigo attacks, sensorineural hearing loss, tinnitus, and aural fullness. Extensive evidence supporting the inflammatory etiology of MD has been found, therefore, using transcriptome analysis, we aim to describe variants MD. We performed Bulk RNAseq on 45 patients with definite 15 healthy controls. were classified according their basal levels IL-1β into 2 groups: high low. Differentially expression analysis was...
The Ral effector protein RLIP76 (also called RIP/RalBP1) binds to Ral·GTP via a region that shares no sequence homology with the Ras-binding domains of Ser/Thr kinase c-Raf-1 and Ral-specific guanine nucleotide exchange factors. Whereas have similar ubiquitin-like structure, Ral-binding domain RLIP was predicted comprise coiled-coil region. In order obtain more information about specificity structural mode interaction between RLIP, we performed space mutational analysis. analysis...
The advent of genome-wide RNA interference (RNAi)-based screens puts us in the position to identify genes for all functions human cells carry out. However, many functions, assay complexity and cost make genome-scale knockdown experiments impossible. Methods predict required cell are therefore needed focus RNAi from whole genome on most likely candidates. Although different bioinformatics tools gene function prediction exist, they lack experimental validation rarely used by experimentalists....
Introduction Most drugs fail during development and there is a clear unmet need for approaches to better understand mechanistically how exert both their intended adverse effects. Gaining traction in this field the use of disease data linking genes with pathological phenotypes combining drugtarget interaction data. Methods We introduce methodology associate effects, adverse, using tripartite network approach that combines drug-target target-phenotype data, which targets can be represented as...
Autophagy is a fundamental cellular process that enables adaptation to metabolic stress and has emerged as critical modulator of cancer progression. However, how autophagy contributes phenotypic heterogeneity at the single-cell level remains poorly understood. Here, we leverage High-Content Screening (HCS) coupled with time-lapse imaging advanced segmentation systematically dissect autophagic dynamics in two breast models: MDA-MB-231 (triple-negative) MCF-7 (estrogen receptor-positive) under...
Protein domains mediate drug-protein interactions and this principle can guide the design of multi-target drugs i.e. polypharmacology. In study, we associate with CATH functional families through overrepresentation targets those in families. Thus, identify that are currently enriched (druggable families) use network properties these druggable protein to analyse their association drug side effects. Analysis selected families, targets, show relatives exhibit highly conserved binding sites....
PMM2-CDG (MIM # 212065), the most common congenital disorder of glycosylation, is caused by deficiency phosphomannomutase 2 (PMM2). It a multisystemic disease variable severity that particularly affects nervous system; however, its molecular pathophysiology remains poorly understood. Currently, there no effective treatment. We performed an RNA-seq based transcriptomic study using patient-derived fibroblasts to gain insight into mechanisms underlying clinical symptomatology and identify...
The recent availability of the full Saccharomyces cerevisiae genome sequence offers a first opportunity to analyze composition, function and evolution GTPases in ras‐p21 superfamily. This superfamily yeast is composed 29 proteins divided into five families: ras with four sequences implicated cell signalling; rho, six genes related shape machinery; ypt‐rab, ten different roles intracellular trafficking; arf‐sar, seven vesicular trafficking secretory pathways; ran, two acting as components...
"Phylogenetic profiling" is based on the hypothesis that during evolution functionally or physically interacting genes are likely to be inherited eliminated in a codependent manner. Creating presence-absence profiles of orthologous now common and powerful way identifying associated genes. In this approach, correctly determining orthology, as means functional equivalence between two genes, critical nontrivial step largely explains why previous work area has mainly focused using prokaryotic...
Determining the network of physical protein associations is an important first step in developing mechanistic evidence for elucidating biological pathways. Despite rapid advances field high throughput experiments to determine interactions, majority remain unknown. Here we describe computational methods significantly expanding association networks. We integrating multiple independent sources obtain higher quality predictions and compare major publicly available resources experimentalists use.
Identifying 14-3-3 isoform-specific substrates and functions may be of broad relevance to cell signaling research because the key role played by this family proteins in many vital processes. A multitude ligands have been identified, but extent which they are is a matter debate. Herein we demonstrate, both vitro vivo, specific, functionally relevant interaction human 14-3-3gamma with molecular scaffold KSR1, mediated C-terminal stretch 14-3-3gamma. Specific binding protected KSR1 from...
Protein function prediction remains a key challenge. Domain composition affects protein function. Here we present DomFun, Ruby gem that uses associations between domains and functions, calculated using multiple indices based on tripartite network analysis. These domain-function are combined at the level, to generate protein-function predictions.
An entire family of methodologies for predicting protein interactions is based on the observed fact that families interacting proteins tend to have similar phylogenetic trees due co-evolution. One application this concept prediction mapping between members two (which within one interacts with which other). The idea real would be maximizing similarity trees. Since exhaustive exploration all possible mappings not feasible large families, current approaches use heuristic techniques do ensure...
Accurate modelling of biological systems requires a deeper and more complete knowledge about the molecular components their functional associations than we currently have. Traditionally, new on protein generated by experiments has played central role in modelling, contrast to generally less trusted bio-computational predictions. However, will not achieve realistic complex if current experimental designs lead biased screenings real networks leave large, functionally important areas poorly...
Abstract Motivation: Polypharmacology (the ability of a single drug to affect multiple targets) is key feature that may explain part the decreasing success conventional discovery strategies driven by quest for drugs act selectively on target. Most targets are proteins composed domains (their structural and functional building blocks). Results: In this work, we model drug–domain networks explore role protein as polypharmacology in terms interactions between domains. We find organized around...