Search Results - "De Castro, Edouard"

The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection by Hulo, Chantal, Masson, Patrick, de Castro, Edouard, Auchincloss, Andrea H, Foulger, Rebecca, Poux, Sylvain, Lomax, Jane, Bougueleret, Lydie, Xenarios, Ioannis, Le Mercier, Philippe

“…Viruses are genetically diverse, infect a wide range of tissues and host cells and follow unique processes for replicating themselves. All these processes were…”
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ViralZone 2024 provides higher-resolution images and advanced virus-specific resources by De Castro, Edouard, Hulo, Chantal, Masson, Patrick, Auchincloss, Andrea, Bridge, Alan, Le Mercier, Philippe

“…Abstract ViralZone (http://viralzone.expasy.org) is a knowledge repository for viruses that links biological knowledge and databases. It contains data on…”
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Enzyme annotation in UniProtKB using Rhea by Morgat, Anne, Lombardot, Thierry, Coudert, Elisabeth, Axelsen, Kristian, Neto, Teresa Batista, Gehant, Sebastien, Bansal, Parit, Bolleman, Jerven, Gasteiger, Elisabeth, de Castro, Edouard, Baratin, Delphine, Pozzato, Monica, Xenarios, Ioannis, Poux, Sylvain, Redaschi, Nicole, Bridge, Alan

“…Abstract Motivation To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase…”
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HAMAP in 2015: updates to the protein family classification and annotation system by Pedruzzi, Ivo, Rivoire, Catherine, Auchincloss, Andrea H, Coudert, Elisabeth, Keller, Guillaume, de Castro, Edouard, Baratin, Delphine, Cuche, Béatrice A, Bougueleret, Lydie, Poux, Sylvain, Redaschi, Nicole, Xenarios, Ioannis, Bridge, Alan

“…HAMAP (High-quality Automated and Manual Annotation of Proteins--available at http://hamap.expasy.org/) is a system for the automatic classification and…”
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PROSITE, a protein domain database for functional characterization and annotation by Sigrist, Christian J.A, Cerutti, Lorenzo, de Castro, Edouard, Langendijk-Genevaux, Petra S, Bulliard, Virginie, Bairoch, Amos, Hulo, Nicolas

“…PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify…”
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EnzChemRED, a rich enzyme chemistry relation extraction dataset by Lai, Po-Ting, Coudert, Elisabeth, Aimo, Lucila, Axelsen, Kristian, Breuza, Lionel, de Castro, Edouard, Feuermann, Marc, Morgat, Anne, Pourcel, Lucille, Pedruzzi, Ivo, Poux, Sylvain, Redaschi, Nicole, Rivoire, Catherine, Sveshnikova, Anastasia, Wei, Chih-Hsuan, Leaman, Robert, Luo, Ling, Lu, Zhiyong, Bridge, Alan

“…Expert curation is essential to capture knowledge of enzyme functions from the scientific literature in FAIR open knowledgebases but cannot keep pace with the…”
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HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes by Bolleman, Jerven, de Castro, Edouard, Baratin, Delphine, Gehant, Sebastien, Cuche, Beatrice A, Auchincloss, Andrea H, Coudert, Elisabeth, Hulo, Chantal, Masson, Patrick, Pedruzzi, Ivo, Rivoire, Catherine, Xenarios, Ioannis, Redaschi, Nicole, Bridge, Alan

“…Abstract Background Genome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of…”
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An integrated ontology resource to explore and study host-virus relationships by Masson, Patrick, Hulo, Chantal, de Castro, Edouard, Foulger, Rebecca, Poux, Sylvain, Bridge, Alan, Lomax, Jane, Bougueleret, Lydie, Xenarios, Ioannis, Le Mercier, Philippe

“…Our growing knowledge of viruses reveals how these pathogens manage to evade innate host defenses. A global scheme emerges in which many viruses usurp key…”
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Isolation of long-lived mutants in Caenorhabditis elegans using selection for resistance to juglone by de Castro, Edouard, Hegi de Castro, Sarah, Johnson, Thomas E

“…The accumulation of molecular damage from attack by reactive oxygen species is one cause of aging. Therefore, some mutant organisms showing increased…”
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Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB by Feuermann, Marc, Boutet, Emmanuel, Morgat, Anne, Axelsen, Kristian B, Bansal, Parit, Bolleman, Jerven, de Castro, Edouard, Coudert, Elisabeth, Gasteiger, Elisabeth, Géhant, Sébastien, Lieberherr, Damien, Lombardot, Thierry, Neto, Teresa B, Pedruzzi, Ivo, Poux, Sylvain, Pozzato, Monica, Redaschi, Nicole, Bridge, Alan, On Behalf Of The UniProt Consortium

“…The UniProt Knowledgebase UniProtKB is a comprehensive, high-quality, and freely accessible resource of protein sequences and functional annotation that covers…”
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Ca2+ signaling via the neuronal calcium sensor-1 regulates associative learning and memory in C. elegans by Gomez, M, De Castro, E, Guarin, E, Sasakura, H, Kuhara, A, Mori, I, Bartfai, T, Bargmann, C I, Nef, P

“…On a radial temperature gradient, C. elegans worms migrate, after conditioning with food, toward their cultivation temperature and move along this isotherm…”
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Relationship between increased longevity and stress resistance as assessed through gerontogene mutations in Caenorhabditis elegans by Johnson, Thomas E., de Castro, Edouard, Hegi de Castro, Sarah, Cypser, James, Henderson, Sam, Tedesco, Pat

“…We review the status of the hypothesis that interventions that increase the resistance to stress offer the potential for effective life prolongation and…”
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ViralZone: a knowledge resource to understand virus diversity by Hulo, Chantal, de Castro, Edouard, Masson, Patrick, Bougueleret, Lydie, Bairoch, Amos, Xenarios, Ioannis, Le Mercier, Philippe

“…The molecular diversity of viruses complicates the interpretation of viral genomic and proteomic data. To make sense of viral gene functions, investigators…”
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New and continuing developments at PROSITE by Sigrist, Christian J A, de Castro, Edouard, Cerutti, Lorenzo, Cuche, Béatrice A, Hulo, Nicolas, Bridge, Alan, Bougueleret, Lydie, Xenarios, Ioannis

“…PROSITE (http://prosite.expasy.org/) consists of documentation entries describing protein domains, families and functional sites, as well as associated…”
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UniProt: the universal protein knowledgebase

“…The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of…”
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UniProt: a hub for protein information

“…UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This…”
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ExPASy: SIB bioinformatics resource portal by Artimo, Panu, Jonnalagedda, Manohar, Arnold, Konstantin, Baratin, Delphine, Csardi, Gabor, de Castro, Edouard, Duvaud, Séverine, Flegel, Volker, Fortier, Arnaud, Gasteiger, Elisabeth, Grosdidier, Aurélien, Hernandez, Céline, Ioannidis, Vassilios, Kuznetsov, Dmitry, Liechti, Robin, Moretti, Sébastien, Mostaguir, Khaled, Redaschi, Nicole, Rossier, Grégoire, Xenarios, Ioannis, Stockinger, Heinz

“…ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible…”
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Update on activities at the Universal Protein Resource (UniProt) in 2013

“…The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to support biological research by providing a freely accessible, stable,…”
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Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef) by Cannarozzi, Gina, Plaza-Wüthrich, Sonia, Esfeld, Korinna, Larti, Stéphanie, Wilson, Yi Song, Girma, Dejene, de Castro, Edouard, Chanyalew, Solomon, Blösch, Regula, Farinelli, Laurent, Lyons, Eric, Schneider, Michel, Falquet, Laurent, Kuhlemeier, Cris, Assefa, Kebebew, Tadele, Zerihun

“…Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and…”
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ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins by de Castro, Edouard, Sigrist, Christian J. A., Gattiker, Alexandre, Bulliard, Virginie, Langendijk-Genevaux, Petra S., Gasteiger, Elisabeth, Bairoch, Amos, Hulo, Nicolas

“…ScanProsite—http://www.expasy.org/tools/scanprosite/—is a new and improved version of the web-based tool for detecting PROSITE signature matches in protein…”
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