Juan Antonio Vizcaíno

发表

Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins

Johannes Griss, Florian Stanek, Otto Hudecz, 2019, Journal of proteome research.

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

Juan Antonio Vizcaíno, Fawaz Ghali, Gerben Menschaert, 2017 .

PRIDE Cluster: building a consensus of proteomics data

Johannes Griss, Juan Antonio Vizcaíno, Henning Hermjakob, 2013, Nature Methods.

Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data

Johannes Griss, Juan Antonio Vizcaíno, Henning Hermjakob, 2011, Molecular & Cellular Proteomics.

Future Prospects of Spectral Clustering Approaches in Proteomics

Johannes Griss, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2018, Proteomics.

Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra".

Johannes Griss, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2018, Journal of proteome research.

Quantifying the impact of public omics data

Robert Petryszak, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2018 .

Expression Atlas: gene and protein expression across multiple studies and organisms

Nuno A. Fonseca, Wojciech Bazant, Elisabet Barrera, 2017, Nucleic Acids Res..

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats

Johannes Griss, Juan Antonio Vizcaíno, Henning Hermjakob, 2012, Proteomics.

Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets

Juan Antonio Vizcaíno, Andrew F. Jarnuczak, Andrew F Jarnuczak, 2017, Current protocols in bioinformatics.

Analyzing large-scale proteomics projects with latent semantic indexing.

Lennart Martens, Juan Antonio Vizcaíno, Rolf Apweiler, 2008, Journal of proteome research.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

Martin Eisenacher, Wout Bittremieux, Yasset Perez-Riverol, 2017, Journal of proteome research.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

Johannes Griss, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2016, Nature Methods.

Accurate and Fast feature selection workflow for high-dimensional omics data

Yasset Perez-Riverol, Juan Antonio Vizcaíno, Max Kun, 2017 .

Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra☆

Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, 2013, Journal of proteomics.

Accurate and fast feature selection workflow for high-dimensional omics data

Yasset Perez-Riverol, Juan Antonio Vizcaíno, Marc-Phillip Hitz, 2017, bioRxiv.

Submitting proteomics data to PRIDE using PRIDE Converter.

Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, 2011, Methods in molecular biology.

A Golden Age for Working with Public Proteomics Data

Lennart Martens, Juan Antonio Vizcaíno, J. Vizcaíno, 2017, Trends in biochemical sciences.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets

Martin Eisenacher, Johannes Griss, Yasset Perez-Riverol, 2015, Molecular & Cellular Proteomics.

Ten Simple Rules for Taking Advantage of Git and GitHub

Kai Blin, Juan Antonio Vizcaíno, Daniel S. Katz, 2014, bioRxiv.

Extending open proteomics data analysis pipelines in the cloud

Juan Antonio Vizcaíno, 2019 .

Omics Discovery Index - Discovering and Linking Public ‘Omics’ Datasets

Christoph Steinbeck, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2016, bioRxiv.

PRIDE: Data Submission and Analysis

Lennart Martens, Juan Antonio Vizcaíno, Florian Reisinger, 2010, Current protocols in protein science.

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics*

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2017, Molecular & Cellular Proteomics.

A five-level classification system for proteoform identifications

Leah V Schaffer, Michael R Shortreed, Lloyd M Smith, 2019, Nature Methods.

Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research

Lennart Martens, Juan Antonio Vizcaíno, Joseph M. Foster, 2010, Journal of proteomics.

Open source libraries and frameworks for biological data visualisation: A guide for developers

Yasset Perez-Riverol, Juan Antonio Vizcaíno, Henning Hermjakob, 2015, Proteomics.

Development of data representation standards by the human proteome organization proteomics standards initiative

Martin Eisenacher, Juan Antonio Vizcaíno, Juan P. Albar, 2015, J. Am. Medical Informatics Assoc..

Expanding the Use of Spectral Libraries in Proteomics.

Johannes Griss, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2018, Journal of proteome research.

jmzTab: A Java interface to the mzTab data standard

Johannes Griss, Juan Antonio Vizcaíno, Henning Hermjakob, 2014, Proteomics.

Data Standards in Proteomics

Juan Antonio Vizcaíno, J. Vizcaíno, 2014 .

Chapter 11. Data Formats of the Proteomics Standards Initiative

Juan Antonio Vizcaíno, Andrew R. Jones, Simon Perkins, 2016, Proteome Informatics.

The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium

Lennart Martens, Harald Barsnes, Johannes Griss, 2012, Molecular & Cellular Proteomics.

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

Martin Eisenacher, Johannes Griss, Juan Antonio Vizcaíno, 2012, Molecular & Cellular Proteomics.

Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities.

Juan Antonio Vizcaíno, Tobias Ternent, Andrew F. Jarnuczak, 2019, Methods in molecular biology.

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

Juan Antonio Vizcaíno, Henning Hermjakob, Andrew R Jones, 2012, Proteomics.

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

Johannes Griss, Juan Antonio Vizcaíno, Henning Hermjakob, 2012, Nucleic Acids Res..

Data Standards in Systems Modeling

Juan Antonio Vizcaíno, J. Vizcaíno, 2014 .

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective

Yasset Perez-Riverol, Juan Antonio Vizcaíno, Henning Hermjakob, 2014, Biochimica et biophysica acta.

BioContainers Registry: searching for bioinformatics tools, packages and containers

Olivier Sallou, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2020, bioRxiv.

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

Martin Eisenacher, Juan Antonio Vizcaíno, Henning Hermjakob, 2013, Database J. Biol. Databases Curation.

The Ontology Lookup Service: bigger and better

Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, 2010, Nucleic Acids Res..

Making sense of big data in health research: Towards an EU action plan

Magnus Rattray, Thomas Lengauer, Haralampos Karanikas, 2016, Genome Medicine.

Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets

Juan Antonio Vizcaíno, María J. Martín, Alejandro Barrera, 2014, PLoS Comput. Biol..

The Proteomics Identifications database: 2010 update

Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, 2009, Nucleic Acids Res..

The SysteMHC Atlas project

Roman A. Zubarev, Emanuel Schmid, Witold Wolski, 2017, Nucleic Acids Res..

PRIDE Converter: making proteomics data-sharing easy

Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, 2009, Nature Biotechnology.

A standardized framing for reporting protein identifications in mzIdentML 1.2

Martin Eisenacher, Juan Antonio Vizcaíno, Andrew R Jones, 2014, Proteomics.

From Proteomics Data Representation to Public Data Flow: A Report on the HUPO‐PSI Workshop September 2011, Geneva, Switzerland

Martin Eisenacher, Juan Antonio Vizcaíno, Henning Hermjakob, 2012, Proteomics.

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience*

Jun Fan, Christoph Steinbeck, Johannes Griss, 2014, Molecular & Cellular Proteomics.

Improvements in the protein identifier cross-reference service

Juan Antonio Vizcaíno, Henning Hermjakob, Richard G. Côté, 2012, Nucleic Acids Res..

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics

Juan Antonio Vizcaíno, Henning Hermjakob, Tobias Ternent, 2015, Bioinform..

qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments*

Lennart Martens, Wout Bittremieux, Juan Antonio Vizcaíno, 2014, Molecular & Cellular Proteomics.

Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE)

Juan Antonio Vizcaíno, Bjoern Peters, Alessandro Sette, 2018, Proteomics.

The HUPO-PSI standardized spectral library format

Wout Bittremieux, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2020 .

An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases

Lennart Martens, Juan Antonio Vizcaíno, Rolf Apweiler, 2007, German Conference on Bioinformatics.

Introducing the PRIDE Archive RESTful web services

Juan Antonio Vizcaíno, Henning Hermjakob, Tobias Ternent, 2015, Nucleic Acids Res..

Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach

Yasset Perez-Riverol, Juan Antonio Vizcaíno, Gorka Prieto, 2017, Journal of proteome research.

The PRIDE database and related tools and resources in 2019: improving support for quantification data

Martin Eisenacher, Johannes Griss, Juan Antonio Vizcaíno, 2018, Nucleic Acids Res..

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

Robert Petryszak, Juan Antonio Vizcaíno, Frank Oliver Glöckner, 2020, Bioinformatics.

A public repository for mass spectrometry imaging data

Juan Antonio Vizcaíno, Henning Hermjakob, Rui Wang, 2014, Analytical and Bioanalytical Chemistry.

High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7–9, 2007 Wellcome Trust Conference Centre, Hinxton, UK

Lennart Martens, Helmut E Meyer, Martin Eisenacher, 2007, Proteomics.

Analysing latent topics in large-scale proteomics

Lennart Martens, Juan Antonio Vizcaíno, Rolf Apweiler, 2007, LWA.

A survey of molecular descriptors used in mass spectrometry based proteomics.

Juan Antonio Vizcaíno, Yasset Perez-Riverol, Enrique Audain, 2014, Current topics in medicinal chemistry.

Controlled vocabularies and ontologies in proteomics: Overview, principles and practice

Martin Eisenacher, Christian Stephan, Juan Antonio Vizcaíno, 2014, Biochimica et biophysica acta.

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

Yasset Perez-Riverol, Juan Antonio Vizcaíno, Henning Hermjakob, 2015, Proteomics.

PRIDE and "Database on Demand" as valuable tools for computational proteomics.

Lennart Martens, Juan Antonio Vizcaíno, Florian Reisinger, 2011, Methods in molecular biology.

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets

Harald Barsnes, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2017, Proteomics.

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

Juan Antonio Vizcaíno, Henning Hermjakob, Eric W. Deutsch, 2016, Nucleic Acids Res..

EST analysis pipeline: use of distributed computing resources.

Juan Antonio Vizcaíno, Francisco Javier González, J. Vizcaíno, 2011, Methods in molecular biology.

Identifying novel biomarkers through data mining—A realistic scenario?

Johannes Griss, Juan Antonio Vizcaíno, Henning Hermjakob, 2015, Proteomics. Clinical applications.

Universal Spectrum Identifier for mass spectra

Wout Bittremieux, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2020, Nature Methods.

Quantifying the impact of public omics data

Robert Petryszak, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2018, Nature Communications.

Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics.

Juan Antonio Vizcaíno, Mathias Walzer, J. Vizcaíno, 2020, Methods in molecular biology.

The PSI formal document process and its implementation on the PSI website

Lennart Martens, Juan Antonio Vizcaíno, Henning Hermjakob, 2007, Proteomics.

The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics

Martin Eisenacher, Jun Fan, Juan Antonio Vizcaíno, 2013, Molecular & Cellular Proteomics.

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations

Juan Antonio Vizcaíno, Henning Hermjakob, Richard G. Côté, 2011, Database J. Biol. Databases Curation.

Proteomics data exchange and storage: the need for common standards and public repositories.

Juan Antonio Vizcaíno, Rafael C Jiménez, J. Vizcaíno, 2013, Methods in molecular biology.

and the mzidValidator

Juan Antonio Vizcaíno, Henning Hermjakob, Ritesh Krishna, 2013 .

How to submit MS proteomics data to ProteomeXchange via the PRIDE database

Juan Antonio Vizcaíno, Henning Hermjakob, Da Qi, 2014, Proteomics.

Proteomics Standards Initiative Extended FASTA Format (PEFF)

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2019, bioRxiv.

PRIDE: Quality control in a proteomics data repository

Rui Wang, Juan Antonio Vizcaíno, Henning Hermjakob, 2012, Database J. Biol. Databases Curation.

A toolkit for the mzIdentML standard: the ProteoIDViewer, the mzidLibrary and the mzidValidator

Juan Antonio Vizcaíno, Henning Hermjakob, Ritesh Krishna, 2013 .

A guide to the Proteomics Identifications Database proteomics data repository

Lennart Martens, Juan Antonio Vizcaíno, Henning Hermjakob, 2009, Proteomics.

Proteomics Standards Initiative Extended FASTA Format (PEFF)

Harald Barsnes, Martin Eisenacher, Yasset Perez-Riverol, 2019, bioRxiv.

Proteomics Data Visualisation

Harald Barsnes, Juan Antonio Vizcaíno, Henning Hermjakob, 2015, Proteomics.

A community proposal to integrate proteomics activities in ELIXIR

Lennart Martens, Martin Eisenacher, Wout Bittremieux, 2017, F1000Research.

Charting online OMICS resources: A navigational chart for clinical researchers

Lennart Martens, Juan Antonio Vizcaíno, Henning Hermjakob, 2009, Proteomics. Clinical applications.

Quality Control in Proteomics

Lennart Martens, Juan Antonio Vizcaíno, Roz Banks, 2011, Proteomics.

Using Deep Learning to Extrapolate Protein Expression Measurements

Edgars Celms, Juan Antonio Vizcaíno, Lelde Lace, 2020, Proteomics.

Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML

Juan Antonio Vizcaíno, Henning Hermjakob, Ritesh Krishna, 2013, Molecular & Cellular Proteomics.

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets

Johannes Griss, Juan Antonio Vizcaíno, Claire O'Donovan, 2011, Proteomics.

The functional landscape of the human phosphoproteome

Juan Antonio Vizcaíno, Andrew F. Jarnuczak, Pedro Beltrao, 2019, Nature Biotechnology.

Expression Atlas update: from tissues to single cells

Nuno A. Fonseca, Robert Petryszak, Irene Papatheodorou, 2019, Nucleic Acids Res..

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

Martin Eisenacher, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2019, Analytical chemistry.

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

Juan Antonio Vizcaíno, Andrew R Jones, Fawaz Ghali, 2017, Genome Biology.

Shorthand notation for lipid structures derived from mass spectrometry

Juan Antonio Vizcaíno, Martin Trötzmüller, Gerd Schmitz, 2013, Journal of Lipid Research.

Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413

Juan Antonio Vizcaíno, Santiago Gutiérrez, J. Vizcaíno, 2006, BMC Genomics.

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.

Juan Antonio Vizcaíno, Yassene Mohammed, Ekaterina Mostovenko, 2015, Journal of proteome research.

Erratum to: Making sense of big data in health research: towards an EU action plan

Magnus Rattray, Thomas Lengauer, Haralampos Karanikas, 2016, Genome Medicine.

Organelle proteomics experimental designs and analysis

Juan Antonio Vizcaíno, Henning Hermjakob, Wolfgang Huber, 2010, Proteomics.

Synthetic human proteomes for accelerating protein research

Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2017, Nature Methods.

HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.

Juan Antonio Vizcaíno, Henning Hermjakob, Diogo Borges, 2013, Analytical Chemistry.

PRIDE Inspector: a tool to visualize and validate MS proteomics data

Lennart Martens, Johannes Griss, Yasset Perez-Riverol, 2011, Nature Biotechnology.

Analysis of the experimental detection of central nervous system‐related genes in human brain and cerebrospinal fluid datasets

Lennart Martens, Juan Antonio Vizcaíno, Rolf Apweiler, 2008, Proteomics.

From Peptidome to PRIDE: Public proteomics data migration at a large scale

Juan Antonio Vizcaíno, Henning Hermjakob, Joseph M Foster, 2013, Proteomics.