A5074140420- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Genomics and Rare Diseases
- Gene Regulatory Network Analysis
- RNA modifications and cancer
- SARS-CoV-2 and COVID-19 Research
- Genetics, Bioinformatics, and Biomedical Research
- Sarcoma Diagnosis and Treatment
- Congenital gastrointestinal and neural anomalies
- Machine Learning in Bioinformatics
- Genetic Associations and Epidemiology
- Animal Disease Management and Epidemiology
- Viral Infections and Immunology Research
- Cell Image Analysis Techniques
- Molecular Biology Techniques and Applications
- Genomic variations and chromosomal abnormalities
- Microbial Metabolic Engineering and Bioproduction
- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Biomedical Text Mining and Ontologies
- Bacteriophages and microbial interactions
- Cancer-related molecular mechanisms research
Fundación Progreso y Salud
2017-2025
Instituto de Biomedicina de Sevilla
2017-2025
Centre for Biomedical Network Research on Rare Diseases
2016-2025
Instituto de Salud Carlos III
2009-2025
Universidad de Sevilla
2017-2025
Centro de Investigación Biomédica en Red
2014-2025
Hospital Universitario Virgen de las Nieves
2025
Hospital Universitario Virgen del Rocío
2017-2024
Instituto de Investigación de Enfermedades Raras
2008-2024
Hospital Universitario Fundación Jiménez Díaz
2023
Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation DNA or protein sequences is a major requirement for successful application these approaches as information on gene products often key to interpretation experimental results. Therefore, there an increasing need bioinformatics resources which are able cope with large amount sequence data, produce valuable results easily accessible...
Next-generation sequencing (NGS) technologies are revolutionizing genome research, and in particular, their application to transcriptomics (RNA-seq) is increasingly being used for gene expression profiling as a replacement microarrays. However, the properties of RNA-seq data have not been yet fully established, additional research needed understanding how these respond differential analysis. In this work, we set out gain insights into characteristics analysis by studying an important...
We present a simple but powerful procedure to extract Gene Ontology (GO) terms that are significantly over- or under-represented in sets of genes within the context genome-scale experiment (DNA microarray, proteomics, etc.). Said has been implemented as web application, FatiGO, allowing for easy and interactive querying. which takes multiple-testing nature statistical contrast into account, currently includes GO associations diverse organisms (human, mouse, fly, worm yeast) TrEMBL/Swissprot...
Abstract Motivation: The sequence alignment/map (SAM) and the binary (BAM) formats have become standard method of representation nucleotide alignments for next-generation sequencing data. SAM/BAM files usually contain information from tens to hundreds millions reads. Often, technology, protocol and/or selected mapping algorithm introduce some unwanted biases in these systematic detection such is a non-trivial task that crucial drive appropriate downstream analyses. Results: We developed...
The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses 60 accessions representing diverse germ plasms, propose that diversified during late Miocene epoch through a rapid southeast Asian radiation correlates with marked weakening monsoons. A second enabled by migration across Wallace line gave rise to Australian limes in...
Monozygotic (MZ) twins are partially concordant for most complex diseases, including autoimmune disorders. Whereas phenotypic concordance can be used to study heritability, discordance suggests the role of non-genetic factors. In environmentally driven epigenetic changes thought contribute their etiology. Here we report first high-throughput and candidate sequence analyses DNA methylation investigate disease in twins. We a cohort MZ discordant three diseases whose clinical signs often...
Abstract Motivation: We describe a new approach to the analysis of gene expression data coming from DNA array experiments, using an unsupervised neural network. technologies allow monitoring thousands genes rapidly and efficiently. One interests these studies is search for correlated patterns, this usually achieved by clustering them. The Self-Organising Tree Algorithm, (SOTA) (Dopazo,J. Carazo,J.M. (1997) J. Mol. Evol. , 44, 226–233), network that grows adopting topology binary tree. result...
Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used represent the relationships among different biological entities, thus facilitating analysis and interpretation. A number of standalone programs available that focus on tree visualization or perform specific analyses them. However, such applications rarely suitable for large-scale surveys, in which a higher level automation is required. Currently, many...
We report for the first time genomics of a nuclear compartment eukaryotic cell. 454 sequencing and microarray analysis revealed pattern nucleolus-associated chromatin domains (NADs) in linear human genome identified different gene families certain satellite repeats as major building blocks NADs, which constitute about 4% genome. Bioinformatic evaluation showed that NAD-localized genes take part specific biological processes, like response to other organisms, odor perception, tissue...
Obesity-associated insulin resistance is characterized by a state of chronic, low-grade inflammation that associated with the accumulation M1 proinflammatory macrophages in adipose tissue. Although different evidence explains mechanisms linking expansion tissue and macrophage (ATM) polarization, current study we investigated concept lipid-induced toxicity as pathogenic link could explain trigger this response.
Babelomics is a response to the growing necessity of integrating and analyzing different types genomic data in an environment that allows easy functional interpretation results. includes complete suite methods for analysis gene expression include normalization (covering most commercial platforms), pre-processing, differential (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale genotyping assays (case controls TDTs, population stratification...
Abstract The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number possible combinations vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large combination dataset, consisting 11,576 experiments from 910 across 85 molecularly characterized cell lines, and results a DREAM Challenge evaluate computational strategies for...
Citrus genus includes some of the most important cultivated fruit trees worldwide. Despite being extensively studied because its commercial relevance, origin citrus species and history domestication still remain an open question. Here, we present a phylogenetic analysis chloroplast genomes 34 genotypes which constitutes comprehensive detailed study to date on evolution variability Citrus. A statistical model was used estimate divergence times between major groups. Additionally, complete map...
Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate impact PMI on expression using data from multiple donors obtained GTEx project. find that many genes change over relatively short PMIs in tissue-specific manner, but this potentially confounding effect biological analysis be minimized taking into account...
Single nucleotide variants (SNVs) are, together with copy number variation, the primary source of variation in human genome and are associated phenotypic such as altered response to drug treatment susceptibility disease. Linking structural effects non-synonymous SNVs functional outcomes is a major issue bioinformatics. The SNPeffect database (http://snpeffect.switchlab.org) uses sequence- structure-based bioinformatics tools predict effect protein-coding on phenotype proteins. It integrates...
Tumors are heterogeneous at the cellular level where ability to maintain tumor growth resides in discrete cell populations. Floating sphere-forming assays broadly used test stem activity tissues, tumors and lines. Spheroids originated from a small population of cells with features able grow suspension culture behaving as tumorigenic mice. We tested eleven common breast cancer lines representing major subtypes mammospheres, measuring viability upon serial non-adherent passage. Only MCF7,...
We have developed a web tool, PupasView, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupasView constitutes an interactive environment in which functional information and population frequency data can be used as sequential filters over linkage disequilibrium parameters to obtain final list SNPs optimal genotyping purposes. is first resource that integrates effects caused by at both translational transcriptional level. retrieves could affect...
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...