Yasset Perez-Riverol

Overview

Best Publications

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

  Yasset Perez-Riverol;Attila Csordas;Jingwen Bai;Manuel Bernal-Llinares

  6891
  Citations

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

  Yasset Perez-Riverol;Jingwen Bai;Chakradhar Bandla;David García-Seisdedos

  6511
  Citations

• 2016 update of the PRIDE database and its related tools

  Juan Antonio Vizcaíno;Attila Csordas;Noemi Del-Toro;José A. Dianes

  3820
  Citations

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

  Juan Antonio Vizcaíno;Richard G. Côté;Attila Csordas;José A. Dianes

  2121
  Citations

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

  Eric W. Deutsch;Attila Csordas;Zhi Sun;Andrew Jarnuczak

  902
  Citations

• BioContainers: an open-source and community-driven framework for software standardization.

  Felipe da Veiga Leprevost;Björn A Grüning;Saulo Alves Aflitos;Hannes L Röst

  823
  Citations

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

  Eric W. Deutsch;Nuno Bandeira;Nuno Bandeira;Vagisha Sharma;Yasset Pérez-Riverol

  748
  Citations

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

  Pedro Navarro;Jörg Kuharev;Ludovic C. Gillet;Oliver M. Bernhardt

  366
  Citations

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

  Niels Hulstaert;Jim Shofstahl;Timo Sachsenberg;Mathias Walzer

  291
  Citations

• MaxDIA enables library-based and library-free data-independent acquisition proteomics

  Pavel Sinitcyn;Hamid Hamzeiy;Favio Salinas Soto;Daniel Itzhak

  256
  Citations

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

  Johannes Griss;Yasset Perez-Riverol;Steve Lewis;David L Tabb

  214
  Citations

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

  Yasset Perez-Riverol;Qing Wei Xu;Rui Wang;Julian Uszkoreit

  209
  Citations

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

  Yasset Perez-Riverol;Emanuele Alpi;Rui Wang;Henning Hermjakob

  209
  Citations

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

  Yasset Perez-Riverol;Mingze Bai;Mingze Bai;Mingze Bai;Felipe Da Veiga Leprevost;Silvano Squizzato

  197
  Citations

• Ten Simple Rules for Taking Advantage of Git and GitHub.

  Yasset Perez-Riverol;Laurent Gatto;Rui Wang;Timo Sachsenberg

  166
  Citations

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

  Johannes Griss;Johannes Griss;Andrew R. Jones;Timo Sachsenberg;Mathias Walzer

  161
  Citations

• Four simple recommendations to encourage best practices in research software

  Rafael C. Jiménez;Mateusz Kuzak;Monther Alhamdoosh;Michelle Barker

  153
  Citations

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

  Meena Choi;Jeremy Carver;Cristina Chiva;Manuel Tzouros

  133
  Citations

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

  Rui Wang;Antonio Fabregat;Daniel Ríos;David Ovelleiro

  132
  Citations

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

  Chengxin Dai;Anja Füllgrabe;Julianus Pfeuffer;Julianus Pfeuffer;Elizaveta M. Solovyeva;Elizaveta M. Solovyeva

  131
  Citations

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

  Yasset Perez-Riverol;Rui Wang;Henning Hermjakob;Markus Müller

  96
  Citations

• Universal Spectrum Identifier for mass spectra

  Eric W. Deutsch;Yasset Perez-Riverol;Jeremy Carver;Shin Kawano

  78
  Citations

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

  Julian Uszkoreit;Alexandra Maerkens;Yasset Perez-Riverol;Helmut E. Meyer

  76
  Citations

• Accurate estimation of Isoelectric Point of Protein and Peptide based on Amino Acid Sequences

  Enrique Audain;Yassel Ramos;Henning Hermjakob;Darren R. Flower

  66
  Citations

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

  Enrique Audain;Julian Uszkoreit;Timo Sachsenberg;Julianus Pfeuffer

  58
  Citations

• Expanding the Use of Spectral Libraries in Proteomics.

  Eric W. Deutsch;Yasset Perez-Riverol;Robert J. Chalkley;Mathias Wilhelm

  57
  Citations

• On best practices in the development of bioinformatics software.

  Felipe da Veiga Leprevost;Valmir C. Barbosa;Eduardo L. Francisco;Yasset Perez-Riverol

  56
  Citations

• An integrated landscape of protein expression in human cancer.

  Andrew F. Jarnuczak;Hanna Najgebauer;Mitra Barzine;Deepti J. Kundu

  55
  Citations

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

  Rui Wang;Yasset Perez-Riverol;Henning Hermjakob;Juan Antonio Vizcaíno

  42
  Citations

• Isoelectric point optimization using peptide descriptors and support vector machines.

  Yasset Perez-Riverol;Enrique Audain;Aleli Millan;Yassel Ramos

  38
  Citations

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

  Yasset Perez-Riverol;Julian Uszkoreit;Aniel Sanchez;Tobias Ternent

  31
  Citations

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

  Fredrik Edfors;Yasset Perez-Riverol;Samuel H. Payne

  26
  Citations