Ramona Britto
A5043724107- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Advanced Proteomics Techniques and Applications
- Glioma Diagnosis and Treatment
- Animal Genetics and Reproduction
- Data Mining Algorithms and Applications
- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- Developmental Biology and Gene Regulation
- Metal complexes synthesis and properties
- Ferrocene Chemistry and Applications
- Ubiquitin and proteasome pathways
- Gene expression and cancer classification
- Research Data Management Practices
- Natural Language Processing Techniques
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Cell death mechanisms and regulation
- Cancer-related molecular mechanisms research
- Click Chemistry and Applications
- CRISPR and Genetic Engineering
- Advanced biosensing and bioanalysis techniques
- Scientific Computing and Data Management
- Data Quality and Management
- Virus-based gene therapy research
European Bioinformatics Institute
2016-2020
Wellcome Trust
2016-2020
Institut de Recherche en Informatique et Systèmes Aléatoires
2012
Centre National de la Recherche Scientifique
2012
Institut national de recherche en informatique et en automatique
2012
Institut de Recherche en Santé, Environnement et Travail
2012
Inserm
2012
Université de Rennes
2012
Indian Institute of Science Bangalore
2004-2009
Institute of Cell Biology and Neurobiology
2008
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this article, we describe significant updates that have made over last two years resource. number in UniProtKB has risen approximately 190 million, despite continued work reduce sequence redundancy at proteome level. We adopted new methods assessing completeness quality. continue extract detailed annotations from...
Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this publication we describe enhancements made our data processing pipeline website adapt an ever-increasing information content. number in UniProtKB has risen over 227 million are working towards including reference proteome for each taxonomic group. We continue extract detailed annotations from literature...
Abstract Motivation To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities Biological Interest), to better support efforts study and predict functionally interactions between protein sequences structures small molecule ligands. Results We structured data model cognate ligand site annotations performed a complete reannotation all stable unique identifiers from...
Abstract Purpose: Current methods of classification astrocytoma based on histopathologic are often subjective and less accurate. Although patients with glioblastoma have grave prognosis, significant variability in patient outcome is observed. Therefore, the aim this study was to identify diagnostic prognostic markers through microarray analysis. Experimental Design: We carried out transcriptome analysis 25 diffusely infiltrating samples [WHO grade II—diffuse astrocytoma, III—anaplastic...
Abstract Motivation The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result genome sequencing and prediction protein-coding genes. Providing functional annotation for these proteins presents significant continuing challenge. Results In response this challenge, has developed method annotation, known UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) by members...
Advances in high-throughput sequencing have led to an unprecedented growth genome sequences being submitted biological databases. In particular, the of large numbers nearly identical bacterial genomes during infection outbreaks and for other large-scale studies has resulted a high level redundancy nucleotide databases consequently UniProt Knowledgebase (UniProtKB). Redundancy negatively impacts on database searches by causing slower searches, increase statistical bias cumbersome result...
Biological databases represent an extraordinary collective volume of work. Diligently built up over decades and comprising many millions contributions from the biomedical research community, biological provide worldwide access to a massive number records (also known as entries) [1]. Starting individual laboratories, genomes are sequenced, assembled, annotated, ultimately submitted primary nucleotide such GenBank [2], European Nucleotide Archive (ENA) [3], DNA Data Bank Japan (DDBJ) [4]...
We present gene prioritization system (GPSy), a cross-species that facilitates the arduous but critical task of prioritizing genes for follow-up functional analyses. GPSy’s modular design with regard to species, data sets and scoring strategies enables users formulate queries in highly flexible manner. Currently, encompasses 20 topics related conserved biological processes including male gamete development discussed this article. The web server-based tool is freely available at...
UniProt continues to support the ongoing process of making scientific data FAIR. Here we contribute this with a FAIRness assessment our UniProtKB dataset followed by critical reflection on challenges and future directions adoption validation FAIR principles metrics.
Activator protein 2α (AP-2α) has been shown to be lost in the advanced stages of many cancers, including gliomas. In this study, we wanted analyze expression AP-2α astrocytoma samples different grades both at RNA level, by real-time qPCR and immunohistochemistry, examine its correlation, if any, with patient outcome. Five Grade I, 14 II, 18 III, 72 IV 13 normal brain controls were included. We did not find any clear pattern regulation level tumor grade. The levels however, correlated a large...
Abstract The volume of biological database records is growing rapidly, populated by complex drawn from heterogeneous sources. A specific challenge duplication, that is, the presence redundancy (records with high similarity) or inconsistency (dissimilar correspond to same entity). characteristics (which are duplicates), impact (why duplicates significant), and solutions (how address duplication), not well understood. Studies on topic neither recent nor comprehensive. In addition, other data...