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List of works by Yasset Perez-Riverol

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 Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics

publication published on 13 May 2022

A Protein Standard That Emulates Homology for the Characterization of Protein Inference Algorithms

scientific article published on 16 April 2018

A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics

publication published on 30 March 2022

A multicenter study benchmarks software tools for label-free proteome quantification

scientific article published on 03 October 2016

A parallel systematic-Monte Carlo algorithm for exploring conformational space

scientific article published in January 2012

A protein standard that emulates homology for the characterization of protein inference algorithms

scholarly article published 19 December 2017

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

scientific article published in 2021

A survey of molecular descriptors used in mass spectrometry based proteomics

scientific article

ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data.

scientific article

Accurate And Fast Feature Selection Workflow For High-Dimensional Omics Data

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

scientific article published on 20 December 2017

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences

scientific article published on 14 November 2015

An "on-matrix" digestion procedure for AP-MS experiments dissects the interplay between complex-conserved and serotype-specific reactivities in Dengue virus-human plasma interactome

scientific article

An integrated landscape of protein expression in human cancer

scientific article published on 23 April 2021

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

scientific article published on 24 February 2021

BioContainers: An open-source and community-driven framework for software standardization

scientific article

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

scientific article

Bioinformatics tools for the functional interpretation of quantitative proteomics results

scientific article published on January 2014

Comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells

scientific article published on 24 May 2015

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.

scientific article

Computational proteomics: Integrating mass spectral data into a biological context

scientific article published in November 2015

Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.

scientific article

Deep learning embedder method and tool for spectral similarity search

scientific article published on 08 December 2020

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

Editorial: Genomics and proteomics behind drug design

scientific article published in January 2014

Effectively addressing complex proteomic search spaces with peptide spectrum matching

scientific article published on 27 February 2013

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

scientific article published on 29 September 2017

Evaluation of phenylthiocarbamoyl-derivatized peptides by electrospray ionization mass spectrometry: selective isolation and analysis of modified multiply charged peptides for liquid chromatography-tandem mass spectrometry experiments

scientific article published in October 2010

Expanding the use of spectral libraries in proteomics

Four simple recommendations to encourage best practices in research software

scientific article

Future Prospects of Spectral Clustering Approaches in Proteomics

scholarly article by Yasset Perez-Riverol published in July 2018

Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

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

Identifying novel biomarkers through data mining-a realistic scenario?

scientific article

In silico analysis of accurate proteomics, complemented by selective isolation of peptides

article

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

scientific article published on 4 August 2016

Introducing an Asp-Pro linker in the synthesis of random one-bead-one-compound hexapeptide libraries compatible with ESI-MS analysis

scientific article

Isoelectric point optimization using peptide descriptors and support vector machines.

scientific article

JBioWH: an open-source Java framework for bioinformatics data integration

scientific article (publication date: 2013)

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

scientific article

Mass spectrometry evaluation of a neuroblastoma SH-SY5Y cell culture protocol

scholarly article by Jimmy Rodriguez Murillo published in October 2018

MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets

scientific article published on 14 September 2020

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

scientific article published in 2024

Novel functional proteins coded by the human genome discovered in metastases of melanoma patients

scientific article published on 10 October 2019

Novel interactions of domain III from the envelope glycoprotein of dengue 2 virus with human plasma proteins.

scientific article published on 3 November 2015

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

scientific article published on 09 August 2017

Omics Discovery Index - Discovering and Linking Public Omics Datasets

On best practices in the development of bioinformatics software

scientific article published on 2 July 2014

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)

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface

scientific article published on 10 June 2015

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)

Peptide fractionation by acid pH SDS-free electrophoresis

article published in 2011

Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics

scientific article published on 21 June 2013

Protein Inference Using PIA Workflows and PSI Standard File Formats

scientific article published on 05 December 2018

Protein inference using PIA workflows and PSI standard file formats

scholarly article published 23 September 2018

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 based on peptide fractionation by SDS-free PAGE.

scientific article

Quantifying the impact of public omics data

Quantifying the impact of public omics data

scientific article published on 05 August 2019

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

scientific article

Recommendations for the packaging and containerizing of bioinformatics software

Recommendations for the packaging and containerizing of bioinformatics software

scientific article published on 14 June 2018

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

SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping

scientific article

Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines

scientific article published on 28 October 2019

Scalable data analysis in proteomics and metabolomics using BioContainers and workflows engines

Selective isolation of multiply charged peptides: a confident strategy for protein identification using a linear trap quadrupole mass spectrometer

scientific article published in January 2012

Selective isolation-detection of two different positively charged peptides groups by strong cation exchange chromatography and matrix-assisted laser desorption/ionization mass spectrometry: application to proteomics studies

scientific article published on January 2010

Sodium dodecyl sulfate free gel electrophoresis/electroelution sorting for peptide fractionation

scientific article published on 17 October 2019

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

scientific article published on 22 March 2019

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 Simple Rules for Taking Advantage of git and GitHub

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

scientific article (publication date: 2013)

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 Standards Initiative: Fifteen Years of Progress and Future Work.

scientific article

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

scientific article

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

scientific article

The omics discovery REST interface

scientific article published on 06 May 2020

ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

scientific article published on 06 December 2019

Universal Spectrum Identifier for mass spectra

scientific article published on 28 June 2021

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

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