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List of works by Juan Antonio Vizcaíno

2016 update of the PRIDE database and its related tools

scientific article

2016 update of the PRIDE database and its related tools.

scientific article published on 28 September 2016

A Golden Age for Working with Public Proteomics Data

scientific article

A community proposal to integrate proteomics activities in ELIXIR

scientific article

A comparison of the phenotypic and genetic stability of recombinant Trichoderma spp. generated by protoplast- and Agrobacterium-mediated transformation

scientific article published on 01 August 2006

A five-level classification system for proteoform identifications

scientific article published on 01 October 2019

A guide to the Proteomics Identifications Database proteomics data repository

scientific article (publication date: September 2009)

A high-stringency blueprint of the human proteome

scientific article published on 16 October 2020

A proteomics sample metadata representation for multiomics integration and big data analysis

scientific article published in 2021

A public repository for mass spectrometry imaging data

scientific article

A standardized framing for reporting protein identifications in mzIdentML 1.2

scientific article

A survey of molecular descriptors used in mass spectrometry based proteomics

scientific article

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

scientific article published on 20 December 2017

An integrated landscape of protein expression in human cancer

scientific article published on 23 April 2021

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

article

Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets

scientific article (publication date: July 2014)

Analysis of the tryptic search space in UniProt databases.

scientific article

Analyzing large-scale proteomics projects with latent semantic indexing

scientific article

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

scientific article published on 24 February 2021

Cell wall-degrading isoenzyme profiles of Trichoderma biocontrol strains show correlation with rDNA taxonomic species

article

Characterization of genes encoding novel peptidases in the biocontrol fungus Trichoderma harzianum CECT 2413 using the TrichoEST functional genomics approach.

scientific article

Charting online OMICS resources: A navigational chart for clinical researchers.

scientific article published on 20 November 2008

Cloning and characterization of the erg1 gene of Trichoderma harzianum: effect of the erg1 silencing on ergosterol biosynthesis and resistance to terbinafine.

scientific article published on 8 February 2006

Colour pigments of Trichoderma harzianum

scientific article published on 01 October 2000

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

scientific article published on 17 October 2011

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

scientific article

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

scientific article

Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future

scientific article published on 10 March 2021

Data Standards in Proteomics

Data Standards in Systems Modeling

Delicate Metabolic Control and Coordinated Stress Response Critically Determine Antifungal Tolerance of Candida albicans Biofilm Persisters.

scientific article

Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence.

scientific article published on September 2016

Detection of peptaibols and partial cloning of a putative peptaibol synthetase gene from T. harzianum CECT 2413.

scientific article

Detection of putative peptide synthetase genes in Trichoderma species: application of this method to the cloning of a gene from T. harzianum CECT 2413.

scientific article

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

scientific article

Discovering and linking public omics data sets using the Omics Discovery Index.

scientific article

EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023

scientific article published on 28 November 2023

EST analysis pipeline: use of distributed computing resources

scientific article

Embedding standards in metabolomics: the Metabolomics Society data standards task group

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany

scientific article

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

scientific article published on 29 September 2017

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

scientific article

Establishing the ELIXIR Microbiome Community

scientific article published on 8 January 2024

Expanding the use of spectral libraries in proteomics

Exploring the potential of public proteomics data

scientific article

Expression Atlas update: from tissues to single cells

scientific article published on 01 January 2020

Expression Atlas update: gene and protein expression in multiple species

scientific article published on 19 November 2021

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

scientific article

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

scientific article

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland

scientific article published on February 2012

Future Prospects of Spectral Clustering Approaches in Proteomics

scholarly article by Yasset Perez-Riverol published in July 2018

Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray.

scientific article

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

scientific article

Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol.

scientific article

Genetic diversity shown in Trichoderma biocontrol isolates

scientific article

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

scientific article published on 20 March 2013

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

scientific article published in August 2007

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

scientific article

Identifying novel biomarkers through data mining-a realistic scenario?

scientific article

Improvements in the Protein Identifier Cross-Reference service

scientific article

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

scientific article published on 17 June 2022

Introducing the PRIDE Archive RESTful web services

scientific article

Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future

scientific article published in 2022

Isoelectric point optimization using peptide descriptors and support vector machines.

scientific article

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics

scientific article published on 7 May 2013

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

scientific article

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

scientific article

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany

scientific article published on 9 October 2014

Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome

scientific article published in 2024

Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE).

scientific article published in June 2018

OLS Client and OLS Dialog: Open source tools to annotate public omics datasets.

scientific article published on 09 August 2017

Ontology Lookup Service for Controlled Vocabularies and Data Annotation

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

scientific article

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

scientific article (publication date: 2014)

Organelle proteomics experimental designs and analysis

scientific article

PRIDE Cluster: building a consensus of proteomics data

scientific article

PRIDE Converter: making proteomics data-sharing easy

scientific article published on July 2009

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

scientific article

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

scientific article (publication date: 8 February 2012)

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

scientific article published in January 2011

PRIDE: Data submission and analysis

scientific article

PRIDE: quality control in a proteomics data repository

scientific article (publication date: 2012)

Partial silencing of a hydroxy-methylglutaryl-CoA reductase-encoding gene in Trichoderma harzianum CECT 2413 results in a lower level of resistance to lovastatin and lower antifungal activity

article

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.

scientific article published in October 2013

Pride-asap: automatic fragment ion annotation of identified PRIDE spectra

scientific article

ProForma: A Standard Proteoform Notation.

scientific article published on 5 February 2018

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

scientific article (publication date: March 2014)

Proteomic temporal profile of human brain endothelium after oxidative stress

scientific article published on 16 December 2010

Proteomics Approaches to Uncover the Drug Resistance Mechanisms of Microbial Biofilms

Proteomics Data Visualisation

scientific article published on 01 April 2015

Proteomics Standards Initiative Extended FASTA Format

scientific article published on 23 May 2019

Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

scientific article published on 15 March 2022

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

scientific article

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

scientific article (publication date: 10 October 2010)

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data

scientific article (publication date: September 2011)

Quality Control in Proteomics ⬇️

scientific article published on 01 March 2011

Quantifying the impact of public omics data

Quantifying the impact of public omics data

scientific article published on 05 August 2019

Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities

scientific article published on 01 January 2019

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

scientific article published on 15 June 2015

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

scientific article

Response to “Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra”

scholarly article by Johannes Griss et al published 23 April 2018 in Journal of Proteome Research

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

scientific article published on 01 January 2020

Screening of antimicrobial activities in Trichoderma isolates representing three trichoderma sections

scientific article

Separation and Identification of Volatile Components in the Fermentation Broth of Trichoderma atroviride by Solid-Phase Extraction and Gas Chromatography--Mass Spectrometry

article

Shorthand notation for lipid structures derived from mass spectrometry.

scientific article

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

scientific article published on 22 March 2019

Submitting proteomics data to PRIDE using PRIDE Converter

scientific article

Synthetic human proteomes for accelerating protein research

scientific article published in February 2017

Ten Simple Rules for Taking Advantage of Git and GitHub

scientific article (publication date: July 2016)

Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA

scientific article (publication date: September 2012)

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

scientific article (publication date: 2013)

The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases

scientific article published on 19 November 2019

The Ontology Lookup Service: bigger and better

scientific article (publication date: July 2010)

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

scientific article

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

scientific article published on 01 January 2022

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

scientific article (publication date: December 2012)

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013

scientific article (publication date: 2013)

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

scientific article published on July 2007

The ProteomeXchange consortium at 10 years: 2023 update

scientific article published on 12 November 2022

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

scientific article

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics

scientific article published on 01 January 2020

The Proteomics Identifications database: 2010 update

scientific article (publication date: 2010)

The Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

scientific article

The SysteMHC Atlas project

scientific article published on 29 July 2017

The functional landscape of the human phosphoproteome

The functional landscape of the human phosphoproteome

scientific article published on 09 December 2019

The mzIdentML data standard for mass spectrometry-based proteomics results

scientific article (publication date: July 2012)

The mzIdentML data standard version 1.2, supporting advances in proteome informatics.

scientific article

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics

scientific article (publication date: August 2013)

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

scientific article

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

scientific article published on 31 January 2018

Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML

scientific article (publication date: November 2013)

Universal Spectrum Identifier for mass spectra

scientific article published on 28 June 2021

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

scientific article published on 13 September 2017

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows

scientific article published in December 2023

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

scientific article (publication date: March 2012)

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

scientific article

jmzTab: a java interface to the mzTab data standard

scientific article

lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation

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

scientific article

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

scientific article published on 13 February 2019

qcML: an exchange format for quality control metrics from mass spectrometry experiments

scientific article published on 23 April 2014

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