Juan Antonio Vizcaíno

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Juan A. Vizcaíno1,17, Eric W. Deutsch2,17, Rui Wang1, Attila Csordas1, Florian Reisinger1, Daniel Ríos1, José A. Dianes1, Zhi Sun2, Terry Farrah2, Nuno Bandeira3, Pierre-Alain Binz4, Ioannis Xenarios4,5,6, Martin Eisenacher7, Gerhard Mayer7, Laurent Gatto8, Alex Campos9, Robert J. Chalkley10, Hans-Joachim Kraus11, Juan Pablo Albar12, Salvador(More)
The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting(More)
The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and(More)
The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and(More)
volume 27 number 7 july 2009 nature biotechnology and spectrum annotations, (ii) automatic mapping of protein accession numbers to identifiers from all other commonly used proteomics databases using the PICR service8 and (iii) comprehensive protein list comparisons (through Venn diagrams)9. Submitting data to PRIDE could be challenging for some users,(More)
The functional genomics project “TrichoEST” was developed focused on different taxonomic groups of Trichoderma with biocontrol potential. Four cDNA libraries were constructed, using similar growth conditions, from four different Trichoderma strains: Trichoderma longibrachiatum T52, Trichoderma asperellum T53, Trichoderma virens T59, and Trichoderma sp. T78.(More)
The filamentous fungus Trichoderma harzianum is used as biological control agent of several plant-pathogenic fungi. In order to study the genome of this fungus, a functional genomics project called "TrichoEST" was developed to give insights into genes involved in biological control activities using an approach based on the generation of expressed sequence(More)
The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data. For the last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5(More)
We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software(More)
It has recently been shown that the Trichoderma fungal species used for biocontrol of plant diseases are capable of interacting with plant roots directly, behaving as symbiotic microorganisms. With a view to providing further information at transcriptomic level about the early response of Trichoderma to a host plant, we developed a high-density(More)