Michele Magrane
A5004635493- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Advanced Proteomics Techniques and Applications
- Gene expression and cancer classification
- Scientific Computing and Data Management
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Computational Drug Discovery Methods
- Genetics, Aging, and Longevity in Model Organisms
- Cell Image Analysis Techniques
- Genomics and Rare Diseases
- Microbial Metabolic Engineering and Bioproduction
- Research Data Management Practices
- Single-cell and spatial transcriptomics
- Microbial Natural Products and Biosynthesis
- RNA modifications and cancer
- Data Mining Algorithms and Applications
- Semantic Web and Ontologies
- Explainable Artificial Intelligence (XAI)
- Natural Language Processing Techniques
- Enzyme Structure and Function
- Data Quality and Management
- Data Management and Algorithms
European Bioinformatics Institute
2016-2025
SIB Swiss Institute of Bioinformatics
2011-2023
University at Buffalo, State University of New York
2023
University of Southern California
2023
University of Padua
2023
University College London
2023
Stanford University
2023
Phoenix Bioinformatics
2023
Wellcome Trust
2000-2020
Georgetown University
2011-2014
To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, Swiss-Prot, TrEMBL PIR database activities have united to form Universal Protein Knowledgebase (UniProt) consortium. Our mission is comprehensive, fully classified, richly accurately annotated sequence knowledgebase, extensive cross-references query interfaces. The central will two sections, corresponding familiar Swiss-Prot (fully manually curated entries)...
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...
The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing unified view sequence and functional information. Manual automatic annotation procedures are used to add data directly the database while extensive cross-referencing more than 120 external databases provides access additional relevant information in specialized collections. UniProtKB also integrates range from other resources. All is attributed its original source, allowing users trace provenance...
The primary mission of Universal Protein Resource (UniProt) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references querying interfaces freely accessible the scientific community. UniProt produced Consortium which consists groups from European Bioinformatics Institute (EBI), Swiss (SIB) Information (PIR). comprised four major components, each optimized for...
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over past year, GOC has implemented several processes to increase quantity, quality and specificity GO annotations. First, number manual, literature-based annotations grown at an increasing rate. Second, as result new 'phylogenetic annotation' process, manually reviewed, homology-based...
A major bottleneck in our understanding of the molecular underpinnings life is assignment function to proteins. While experiments provide most reliable annotation proteins, their relatively low throughput and restricted purview have led an increasing role for computational prediction. However, assessing methods protein prediction tracking progress field remain challenging.We conducted second critical assessment functional (CAFA), a timed challenge assess that automatically assign function....
The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 proteins in more than 360,000 taxa, this has increased 2-fold last 2 years benefited wealth checks improve correctness consistency as well now greater information content enabled format developments. Detailed, manual obtained...
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...
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this publication, we describe ongoing changes our production pipeline limit available in UniProtKB high-quality, non-redundant reference proteomes. We continue manually curate scientific literature add latest data use machine learning techniques. also encourage community curation...
Gene Ontology Annotation (GOA) is a project run by the European Bioinformatics Institute (EBI) that aims to provide assignments of terms from (GO) resource gene products in number its databases ( http://www.ebi.ac.uk/GOA ). In first stage this project, GO have been applied data set representing complete human proteome combination electronic mappings and manual curation. This vocabulary has also nonredundant sets for all other completely sequenced organisms as well proteins wide range where...
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. number GO annotations products has increased due to curation efforts among Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. ontologies continue expand improve as result targeted ontology development, introduction computable logical definitions...
Abstract Background The Gene Ontology Annotation (GOA) database http://www.ebi.ac.uk/GOA aims to provide high-quality supplementary GO annotation proteins in the UniProt Knowledgebase. Like many other biological databases, GOA gathers much of its content from careful manual curation literature. However, as both volume literature and requiring characterization increases, processing capability can become overloaded. Consequently, semi-automated aids are often employed expedite process....
Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene protein sets for their organisms of interest. Using the example human proteome, we will describe content a complete UniProt Knowledgebase (UniProtKB). We show how manual expert curation UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation build comprehensive, traceable...
Biological knowledgebases, such as UniProtKB/Swiss-Prot, constitute an essential component of daily scientific research by offering distilled, summarized and computable knowledge extracted from the literature expert curators. While knowledgebases play increasingly important role in community, their ability to keep up with growth biomedical is under scrutiny. Using UniProtKB/Swiss-Prot a case study, we address this concern via multiple triage approaches.With assistance PubTator text-mining...
Abstract The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. UniProt Web site receives ∼400,000 unique visitors per month the primary means to access UniProt. It provides ten searchable datasets three main tools. key are Knowledgebase (UniProtKB), Reference Clusters (UniRef), Archive (UniParc), sets completely sequenced genomes (Proteomes). Other supporting include information about proteins that present in UniProtKB entries such as...
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...
A major scientific drive is to characterize the protein-coding genome as it provides primary basis for study of human health. But fundamental question remains: what has been missed in prior genomic analyses? Over past decade, translation non-canonical open reading frames (ncORFs) observed across cell types and disease states, with implications proteomics, genomics, clinical science. However, impact ncORFs limited by absence a large-scale understanding their contribution proteome. Here, we...
A general overview of the protein sequence set for mouse transcriptome produced during FANTOM2 sequencing project is presented here. We applied different algorithms to characterize sequences derived from a nonredundant representative (RPS) and variant (VPS) transcriptome. The functional characterization assignment Gene Ontology terms was done by analysis proteome using InterPro. Superfamily database analyses gave detailed structural classification according SCOP provide additional evidence...
UniProtKB/Swiss-Prot provides expert curation with information extracted from literature and curator-evaluated computational analysis. As knowledgebases continue to play an increasingly important role in scientific research, a number of studies have evaluated their accuracy revealed various errors. While some are errors, others the result incorrect published literature. By taking example sirtuin-5, complex annotation case, we will describe procedure detail how report conflicting database. We...
Abstract The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. UniProt website receives about 800,000 unique visitors per month the primary means to access UniProt. It provides 10 searchable datasets four main tools. key are Knowledgebase (UniProtKB), Reference Clusters (UniRef), Archive (UniParc), sets completely sequenced genomes (Proteomes). Other supporting include information proteins that present in UniProtKB entries, such as...
ABSTRACT Ribosome profiling (Ribo-seq) has catalyzed a paradigm shift in our understanding of the translational ‘vocabulary’ human genome, discovering thousands translated open reading frames (ORFs) within long non-coding RNAs and presumed untranslated regions protein-coding genes. However, reference gene annotation projects have been circumspect their incorporation these ORFs due to uncertainties about experimental reproducibility physiological roles. Yet, it is indisputable that certain...