Publications

Found 45 results
Filters: Author is Vizcaino, J. A.  [Clear All Filters]
2013
Mayer G, Jones A.R, Binz P.A, et al. "Controlled vocabularies and ontologies in proteomics: Overview, principles and practice." Biochim Biophys Acta. 2013.
Csordas A., Wang R., Rios D, et al. "From Peptidome to PRIDE: Public proteomics data migration at a large scale." Proteomics. 2013;13:1692-5.
Perez-Riverol Y., Sanchez A, Noda J., et al. "HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions." Anal Chem. 2013;85:3515-20.
Foster J.M, Moreno P., Fabregat A, et al. "LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics." PLoS One. 2013;8:e61951.
Walzer M., Qi D., Mayer G, et al. "The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics." Mol Cell Proteomics. 2013.
Walzer M., Qi D., Mayer G, et al. "The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics." Mol Cell Proteomics. 2013;12:2332-40.
Perez-Riverol Y., Wang R., Hermjakob H, Müller M, Vesada V., Vizcaino J.A. "Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective." Biochim Biophys Acta. 2013.
Orchard S, Binz P.A, Jones A.R, Vizcaino J.A, Deutsch E.W, Hermjakob H. "Preparing to Work with Big Data in Proteomics - A Report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK." Proteomics. 2013;13:2931-7.
Griss J., Foster J.M, Hermjakob H, Vizcaino J.A. "PRIDE Cluster: building a consensus of proteomics data." Nat Methods. 2013;10:95-6.
Griss J., Foster J.M, Hermjakob H, Vizcaino J.A. "PRIDE Cluster: building the consensus of proteomics data." Nature Methods. 2013:in press.
Hulstaert N., Reisinger F, Rameseder J, Barsnes H., Vizcaino J.A, Martens L.. "Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra." J Proteomics. 2013.
Jimenez RC, Vizcaino J.A. "Proteomics data exchange and storage: the need for common standards and public repositories." Methods Mol Biol. 2013;1007:317-33.
Vizcaino J.A, Cote R.G, Csordas A., et al. "The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013." Nucleic Acids Res. 2013;41:D1063-9.
Liebisch G., Vizcaino J.A, Kofeler H., et al. "Shorthand notation for lipid structures derived from mass spectrometry." J Lipid Res. 2013;54:1523-30.
Ghali F, Krishna R, Lukasse P., et al. "Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML." Mol Cell Proteomics. 2013;12:3026-35.
2012
Orchard S, Albar J.P, Deutsch E.W, et al. "From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland." Proteomics. 2012;12:351-5.
Wein S.P, Cote R.G, Dumousseau M., Reisinger F, Hermjakob H, Vizcaino J.A. "Improvements in the Protein Identifier Cross-Reference service." Nucleic Acids Res. 2012;40:W276-80.
Perez-Riverol Y., Audain E, Millan A, et al. "Isoelectric point optimization using peptide descriptors and support vector machines." J Proteomics. 2012;75:2269-74.
Reisinger F, Krishna R, Ghali F, et al. "jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data." Proteomics. 2012;12:790-4.
Griss J., Reisinger F, Hermjakob H, Vizcaino J.A. "jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats." Proteomics. 2012;12:795-8.
Jones A.R, Eisenacher M., Mayer G, et al. "The mzIdentML data standard for mass spectrometry-based proteomics results." Mol Cell Proteomics. 2012;11:M111 014381.
Wang R., Fabregat A, Rios D, et al. "PRIDE Inspector: a tool to visualize and validate MS proteomics data." Nat Biotechnol. 2012;30:135-7.
Csordas A., Ovelleiro D., Wang R., et al. "PRIDE: quality control in a proteomics data repository." Database (Oxford). 2012;2012:bas004.
Cote R.G, Griss J., Dianes J.A, et al. "The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium." Mol Cell Proteomics. 2012;11:1682-9.
Orchard S, Binz P.A, Borchers C, et al. "Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA." Proteomics. 2012;12:2767-72.

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