All Stories

  1. Meta-analysis of Human Serum DIA proteome: Combining Datasets for AI Analysis

    Article • August 2026, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  2. AI proteomics: from protein identification to virtual cells

    Article • Nature Chemical Biology, July 2026, Springer Science + Business Media

    Prof. Markus Ralser, Dr. Yasset Perez-Riverol

  3. The need for standardization and improved open (meta)data practices in metaproteomics

    Article • Microbiome, July 2026, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  4. quantmsdiann: a scalable SDRF-driven DIA-NN workflow for reanalysis of single-cell, spatial, and bulk proteomics datasets

    Article • July 2026, Springer Science + Business Media

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  5. onsite: An Integrated Framework for Phosphosite Localization and False Localization Rate Estimation

    Article • July 2026, openRxiv

    Dr. Yasset Perez-Riverol

  6. The PRIDE Affinity-Proteomics Archive (PRIDE-AP): Making Affinity Proteomics Data FAIR

    Article • July 2026, Springer Science + Business Media

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  7. Assessing the contribution of rare variants to congenital heart disease through a large-scale case-control exome study

    Article • npj Genomic Medicine, June 2026, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  8. An AI-Ready Phosphorylation Meta-Analysis for Saccharomyces cerevisiae

    Article • Journal of Proteome Research, May 2026, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  9. A Landscape Analysis of Human SUMOylation

    Article • Molecular & Cellular Proteomics, May 2026, Elsevier

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  10. Quantifying data reuse in proteomics using PRIDE downloads statistics and a semi-supervised LLM-based framework

    Article • April 2026, openRxiv

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  11. π-MSNet: A billion-scale, AI-ready living proteomics data portal

    Article • April 2026, openRxiv

    Dr. Yasset Perez-Riverol

  12. Blood proteomics: insights from public data

    Article • Genome Biology, March 2026, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  13. The 2025 Westlake Autumn Symposium for Al Proteomics and Virtual Cell

    Article • Genomics Proteomics & Bioinformatics, March 2026, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol

  14. LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients

    Article • February 2026, openRxiv

    Dr. Yasset Perez-Riverol

  15. pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics

    Article • Molecular & Cellular Proteomics, February 2026, Elsevier

    Dr. Yasset Perez-Riverol

  16. quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experiments

    Article • January 2026, openRxiv

    Dr. Yasset Perez-Riverol

  17. ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

    Article • December 2025, openRxiv

    Dr. Yasset Perez-Riverol

  18. BioSamples database: the global hub for sample metadata and multi-omics integration

    Article • Nucleic Acids Research, November 2025, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol

  19. EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2025

    Article • Nucleic Acids Research, November 2025, Oxford University Press (OUP)

    Catherine Brooksbank, Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  20. The ProteomeXchange consortium in 2026: making proteomics data FAIR

    Article • Nucleic Acids Research, November 2025, Oxford University Press (OUP)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  21. pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics

    Article • November 2025, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  22. mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format

    Article • Journal of Proteome Research, October 2025, American Chemical Society (ACS)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  23. A standardized framework for circulating blood proteomics

    Article • Nature Genetics, September 2025, Springer Science + Business Media

    Dr. Yasset Perez-Riverol, Prof. Markus Ralser

  24. Ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata

    Article • Journal of Proteomics, June 2025, Elsevier

    Dr. Yasset Perez-Riverol

  25. Open-Source and FAIR Research Software for Proteomics

    Article • Journal of Proteome Research, April 2025, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, Björn Grüning

  26. pridepy: A Python package to download and search data from PRIDE database

    Article • The Journal of Open Source Software, March 2025, The Open Journal

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  27. ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata

    Article • February 2025, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  28. Open-source and FAIR Research Software for Proteomics

    Article • December 2024, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

  29. EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2024

    Article • Nucleic Acids Research, November 2024, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol, Catherine Brooksbank, DR Juan Antonio Vizcaino

  30. The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF

    Article • Analytical Chemistry, November 2024, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  31. The PRIDE database at 20 years: 2025 update

    Article • Nucleic Acids Research, November 2024, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  32. Phosphorylation in the Plasmodium falciparum Proteome: A Meta-Analysis of Publicly Available Data Sets

    Article • Journal of Proteome Research, October 2024, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  33. Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer

    Article • September 2024, Association of Biomolecular Resource Facilities

    Dr. Yasset Perez-Riverol, Dr Magnus Palmblad

  34. The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF

    Article • August 2024, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

  35. quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data

    Article • Nature Chemical Biology, July 2024, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteome Research, May 2024, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  37. Proteogenomics analysis of human tissues using pangenomes

    Article • May 2024, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  38. Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer

    Article • April 2024, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, Dr Magnus Palmblad

  39. Open‐source large language models in action: A bioinformatics chatbot for PRIDE database

    Article • PROTEOMICS, March 2024, Wiley

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  40. Open Source Large Language Models in Action: A Bioinformatics Chatbot for PRIDE database

    Article • March 2024, Authorea, Inc.

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  41. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data

    Article • Nature Chemical Biology, February 2024, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  42. Mass spectrometry-based proteomics data from thousands of HeLa control samples

    Article • Scientific Data, January 2024, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  43. Abstracts from the 56th European Society of Human Genetics (ESHG) Conference: Oral Presentations

    Article • European Journal of Human Genetics, January 2024, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  44. Assessing the contribution of rare variants to congenital heart disease through a large-scale case-control exome study

    Article • December 2023, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

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

    Article • Nucleic Acids Research, November 2023, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol, Catherine Brooksbank, DR Juan Antonio Vizcaino

  46. Phosphorylation in thePlasmodium falciparumproteome: A meta-analysis of publicly available data sets

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  47. A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  48. Mass spectrometry-based proteomics data from thousands of HeLa control samples

    Article • November 2023, Research Square

    Dr. Yasset Perez-Riverol

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

    Article • Nature Communications, October 2023, Springer Science + Business Media

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  50. OpenMS 3 expands the frontiers of open-source computational mass spectrometry

    Article • August 2023, Research Square

    Dr. Yasset Perez-Riverol

  51. The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020)

    Article • Journal of Biomolecular Techniques, August 2023, Association of Biomolecular Resource Facilities

    Dr. Yasset Perez-Riverol

  52. Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments

    Article • PROTEOMICS, July 2023, Wiley

    Dr. Yasset Perez-Riverol

  53. Mass spectrometry-based proteomics data from thousands of HeLa control samples

    Article • June 2023, Research Square

    Dr. Yasset Perez-Riverol

  54. quantms: A cloud-based pipeline for proteomics reanalysis enables the quantification of 17521 proteins in 9,502 human samples.

    Article • June 2023, Research Square

    Dr. Yasset Perez-Riverol

  55. LFQ-Based Peptide and Protein Intensity Differential Expression Analysis

    Article • Journal of Proteome Research, May 2023, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

  56. lesSDRF Is More: Maximizing The Value Of Proteomics Data Through Streamlined Metadata Annotation

    Article • May 2023, Research Square

    Dr. Yasset Perez-Riverol

  57. Tissue-based absolute quantification using large-scale TMT and LFQ experiments

    Article • April 2023, Authorea, Inc.

    Dr. Yasset Perez-Riverol

  58. ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics

    Article • Journal of Proteome Research, January 2023, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino, Dr Magnus Palmblad

  59. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

    Article • Journal of Proteome Research, January 2023, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  60. Proteomic repository data submission, dissemination, and reuse: key messages

    Article • Expert Review of Proteomics, December 2022, Taylor & Francis

    Dr. Yasset Perez-Riverol

  61. The ProteomeXchange consortium at 10 years: 2023 update

    Article • Nucleic Acids Research, November 2022, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  62. The Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

    Article • October 2022, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

  63. LFQ-based peptide and protein intensity downstream analysis

    Article • October 2022, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

  64. Method for Independent Estimation of the False Localization Rate for Phosphoproteomics

    Article • Journal of Proteome Research, May 2022, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  65. A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics

    Article • Journal of Proteome Research, May 2022, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

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

    Article • Scientific Data, March 2022, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  67. Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

    Article • Journal of Proteome Research, March 2022, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino, Anthony J Cesnik

  68. A comprehensive evaluation of consensus spectrum generation methods in proteomics

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  69. Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides

    Article • Bioinformatics, December 2021, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol

  70. Mapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database

    Article • Cancers, December 2021, MDPI AG

    Dr. Yasset Perez-Riverol

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

    Article • November 2021, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

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

    Article • Nucleic Acids Research, November 2021, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  73. A method for independent estimation of false localisation rate for phosphoproteomics

    Article • October 2021, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

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

    Article • Nature Communications, October 2021, Springer Science + Business Media

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  75. Correction: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease

    Article • PLoS Genetics, September 2021, PLOS

    Dr. Yasset Perez-Riverol, Vidu Garg

  76. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease

    Article • PLoS Genetics, July 2021, PLOS

    Dr. Yasset Perez-Riverol, Vidu Garg

  77. MaxDIA enables library-based and library-free data-independent acquisition proteomics

    Article • Nature Biotechnology, July 2021, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  78. Universal Spectrum Identifier for mass spectra

    Article • Nature Chemical Biology, June 2021, Springer Science + Business Media

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  79. Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

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

    Article • May 2021, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  81. Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison

    Article • Journal of Proteome Research, May 2021, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

  82. An integrated landscape of protein expression in human cancer

    Article • Scientific Data, April 2021, Springer Science + Business Media

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  83. The European Bioinformatics Community for Mass Spectrometry (EuBIC‐MS): an open community for bioinformatics training and research

    Article • Rapid Communications in Mass Spectrometry, April 2021, Wiley

    Dr. Yasset Perez-Riverol

  84. User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

    Article • Nature Chemical Biology, March 2021, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteome Research, February 2021, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, Björn Grüning, DR Juan Antonio Vizcaino

  86. Deep learning embedder method and tool for mass spectra similarity search

    Article • Journal of Proteomics, February 2021, Elsevier

    Dr. Yasset Perez-Riverol

  87. Universal Spectrum Identifier for mass spectra

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  88. Proceedings of the EuBIC-MS 2020 Developers’ Meeting

    Article • EuPA Open Proteomics, December 2020, Elsevier

    Dr. Yasset Perez-Riverol

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

    Article • Nature Chemical Biology, September 2020, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  90. Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison

    Article • September 2020, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  91. Towards a sample metadata standard in public proteomics repositories

    Article • Journal of Proteome Research, August 2020, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

  92. BioContainers Registry: searching for bioinformatics tools, packages and containers

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol, Björn Grüning, DR Juan Antonio Vizcaino

  93. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease

    Article • June 2020, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol, Vidu Garg

  94. The omics discovery REST interface

    Article • Nucleic Acids Research, May 2020, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol

  95. User-friendly, scalable tools and workflows for single-cell analysis

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  96. The Omics Discovery REST interface

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  97. CHAPTER 19. Cross-platform Software Development and Distribution with Bioconda and BioContainers

    Article • January 2020, Royal Society of Chemistry

    Dr. Yasset Perez-Riverol

  98. Phoenix Enhancer: an online service/tool for proteomics data mining using clustered spectra

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  99. ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

    Article • Journal of Proteome Research, November 2019, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

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

    Article • Journal of Separation Science, November 2019, Wiley

    Dr. Yasset Perez-Riverol

  101. The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics

    Article • Nucleic Acids Research, November 2019, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

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

    Article • PROTEOMICS, October 2019, Wiley

    Dr. Yasset Perez-Riverol

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

    Article • Cell Biology and Toxicology, October 2019, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

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

    Article • F1000Research, September 2019, Faculty of 1000, Ltd.

    Dr. Yasset Perez-Riverol, Dr Kevin Bretonnel Cohen, Robert Hoehndorf, Karin M Verspoor, Yusuke Komiyama, Dr. Hidemasa Bono, Katsuhiko Murakami, Hiromasa Ono, Shin Kawano, Shuichi Kawashima, Tatsuya Kushida, Yosuke Nishimura, Kazuharu Arakawa, hongyan Wu

  105. Quantifying the impact of public omics data

    Article • Nature Communications, August 2019, Springer Science + Business Media

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  106. Correction: Ten Simple Rules for Taking Advantage of Git and GitHub

    Article • PLoS Computational Biology, June 2019, PLOS

    Dr. Yasset Perez-Riverol

  107. An integrated landscape of protein expression in human cancer

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  108. Proteomics Standards Initiative Extended FASTA Format

    Article • Journal of Proteome Research, May 2019, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

  109. Proteomics Standards Initiative Extended FASTA Format (PEFF)

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  110. ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

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

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  112. Recommendations for the packaging and containerizing of bioinformatics software

    Article • F1000Research, March 2019, Faculty of 1000, Ltd.

    Björn Grüning, Mr Rafael C Jimenez, Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteome Research, March 2019, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

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

    Article • Analytical Chemistry, February 2019, American Chemical Society (ACS)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  115. 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

    Article • Journal of Proteomics, February 2019, Elsevier

    Dr. Yasset Perez-Riverol

  116. Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  117. Protein Inference Using PIA Workflows and PSI Standard File Formats

    Article • Journal of Proteome Research, November 2018, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

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

    Article • Nucleic Acids Research, November 2018, Oxford University Press (OUP)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  119. Expanding the Use of Spectral Libraries in Proteomics

    Article • Journal of Proteome Research, October 2018, American Chemical Society (ACS)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Analytical Biochemistry, October 2018, Elsevier

    Dr. Yasset Perez-Riverol

  121. Protein inference using PIA workflows and PSI standard file formats

    Article • September 2018, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  122. Bioconda: sustainable and comprehensive software distribution for the life sciences

    Article • Nature Chemical Biology, July 2018, Springer Science + Business Media

    Dr. Yasset Perez-Riverol, Saket Choudhary

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

    Article • Journal of Biomolecular Techniques, July 2018, Association of Biomolecular Resource Facilities

    Dr. Yasset Perez-Riverol

  124. Recommendations for the packaging and containerizing of bioinformatics software

    Article • F1000Research, June 2018, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez, Björn Grüning, Susheel Varma, Pablo Moreno, Dr. Yasset Perez-Riverol

  125. Future prospects of spectral clustering approaches in proteomics

    Article • PROTEOMICS, June 2018, Wiley

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteome Research, April 2018, American Chemical Society (ACS)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteome Research, April 2018, American Chemical Society (ACS)

    Dr Magnus Palmblad, Dr. Yasset Perez-Riverol

  128. Quantifying the impact of public omics data

    Article • March 2018, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • PLOS One, December 2017, PLOS

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • December 2017, Cold Spring Harbor Laboratory Press

    Dr Magnus Palmblad, Dr. Yasset Perez-Riverol

  131. Bioconda: A sustainable and comprehensive software distribution for the life sciences

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteome Research, October 2017, American Chemical Society (ACS)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • PROTEOMICS, October 2017, Wiley

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteome Research, September 2017, American Chemical Society (ACS)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  135. Four simple recommendations to encourage best practices in research software

    Article • F1000Research, June 2017, Faculty of 1000, Ltd.

    Dr Monther Alhamdoosh, Mr Rafael C Jimenez, Mr Neil P Chue Hong, Professor Josep Ll. Gelpi, Prof Carole A Goble, Rob Hooft, Daniel S Katz, Mr Federico López Gómez, Dr Sonika Tyagi, Sonika Tyagi, Mateusz Kuzak, Allegra Via, Xiaochuan (Harry) Wang, Montserrat Gonzalez, Björn Grüning, Andrew Treloar, Nathan Watson-Haigh, Dr. Yasset Perez-Riverol

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

    Article • June 2017, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Molecular & Cellular Proteomics, May 2017, American Society for Biochemistry & Molecular Biology (ASBMB)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Nature Biotechnology, May 2017, Nature

    DR Juan Antonio Vizcaino, Mr Rafael C Jimenez, Dr. Yasset Perez-Riverol

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

    Article • Bioinformatics, March 2017, Oxford University Press (OUP)

    Björn Grüning, Mr Rafael C Jimenez, Dr. Yasset Perez-Riverol

  140. Synthetic human proteomes for accelerating protein research

    Article • Nature Chemical Biology, February 2017, Nature

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteomics, January 2017, Elsevier

    Dr. Yasset Perez-Riverol

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

    Article • Nucleic Acids Research, October 2016, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol

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

    Article • Nature Biotechnology, October 2016, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  144. 2016 update of the PRIDE database and its related tools

    Article • Nucleic Acids Research, September 2016, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol

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

    Article • PLoS Computational Biology, July 2016, PLOS

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Nature Chemical Biology, June 2016, Springer Science + Business Media

    Dr. Yasset Perez-Riverol

  147. Omics Discovery Index - Discovering and Linking Public Omics Datasets

    Article • April 2016, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol

  148. Ten Simple Rules for Taking Advantage of git and GitHub

    Article • April 2016, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteomics, January 2016, Elsevier

    Dr. Yasset Perez-Riverol

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

    Article • Molecular & Cellular Proteomics, January 2016, Elsevier

    Dr. Yasset Perez-Riverol

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

    Article • Bioinformatics, November 2015, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol

  152. 2016 update of the PRIDE database and its related tools

    Article • Nucleic Acids Research, November 2015, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol

  153. Computational proteomics: Integrating mass spectral data into a biological context

    Article • Journal of Proteomics, November 2015, Elsevier

    Dr. Yasset Perez-Riverol, Juan Calvete

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

    Article • Data in Brief, September 2015, Elsevier

    Dr. Yasset Perez-Riverol, Dr Mariela Bollati-Fogolin

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

    Article • Journal of Proteomics, August 2015, Elsevier

    Dr. Yasset Perez-Riverol, Dr Mariela Bollati-Fogolin

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

    Article • Journal of Proteome Research, June 2015, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

  157. ms-data-core-api: an open-source, metadata-oriented library for computational proteomics: Fig. 1.

    Article • Bioinformatics, April 2015, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol

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

    Article • PROTEOMICS, March 2015, Wiley

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • PROTEOMICS, February 2015, Wiley

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  160. Identifying novel biomarkers through data mining—A realistic scenario?

    Article • PROTEOMICS - CLINICAL APPLICATIONS, January 2015, Wiley

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  161. On best practices in the development of bioinformatics software

    Article • Frontiers in Genetics, July 2014, Frontiers

    Dr. Yasset Perez-Riverol

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

    Article • Molecular & Cellular Proteomics, June 2014, American Society for Biochemistry & Molecular Biology (ASBMB)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  163. Editorial (Thematic Issue: Genomics and Proteomics behind Drug Design)

    Article • Current Topics in Medicinal Chemistry, January 2014, Bentham Science Publishers

    Dr. Yasset Perez-Riverol

  164. Bioinformatics Tools for the Functional Interpretation of Quantitative Proteomics Results

    Article • Current Topics in Medicinal Chemistry, January 2014, Bentham Science Publishers

    Dr. Yasset Perez-Riverol

  165. A Survey of Molecular Descriptors Used in Mass Spectrometry Based Proteomics

    Article • Current Topics in Medicinal Chemistry, January 2014, Bentham Science Publishers

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, January 2014, Elsevier

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteomics, October 2013, Elsevier

    Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteomics, August 2013, Elsevier

    Dr. Yasset Perez-Riverol

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

    Article • Database, July 2013, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol

  170. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report

    Article • Journal of Proteomics, July 2013, Elsevier

    Lennart Martens, Dr. Yasset Perez-Riverol

  171. HI-Bone: A Scoring System for Identifying Phenylisothiocyanate-Derivatized Peptides Based on Precursor Mass and High Intensity Fragment Ions

    Article • Analytical Chemistry, April 2013, American Chemical Society (ACS)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  172. Effectively addressing complex proteomic search spaces with peptide spectrum matching

    Article • Bioinformatics, February 2013, Oxford University Press (OUP)

    Dr. Yasset Perez-Riverol, Felipe França

  173. Selective Isolation of Multiply Charged Peptides: A Confident Strategy for Protein Identification Using a Linear Trap Quadrupole Mass Spectrometer

    Article • European Journal of Mass Spectrometry, December 2012, SAGE Publications

    Dr. Yasset Perez-Riverol

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

    Article • Nucleic Acids Research, November 2012, Oxford University Press (OUP)

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

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

    Article • Molecular & Cellular Proteomics, September 2012, American Society for Biochemistry & Molecular Biology (ASBMB)

    DR Juan Antonio Vizcaino, Lennart Martens, Dr. Yasset Perez-Riverol

  176. A Parallel Systematic-Monte Carlo Algorithm for Exploring Conformational Space

    Article • Current Topics in Medicinal Chemistry, August 2012, Bentham Science Publishers

    Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteomics, April 2012, Elsevier

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

  178. Introducing an Asp-Pro Linker in the Synthesis of Random One-Bead-One-Compound Hexapeptide Libraries Compatible with ESI-MS Analysis

    Article • ACS Combinatorial Science, February 2012, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

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

    Article • Nature Biotechnology, February 2012, Nature

    DR Juan Antonio Vizcaino, Lennart Martens, Dr. Yasset Perez-Riverol

  180. Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: Evaluation in proteomic studies using peptide-centric database searches

    Article • Journal of Proteomics, September 2011, Elsevier

    Dr. Yasset Perez-Riverol

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

    Article • Journal of Proteomics, September 2011, Elsevier

    Dr. Yasset Perez-Riverol

  182. Peptide fractionation by acid pH SDS-free electrophoresis

    Article • Electrophoresis, May 2011, Wiley

    Dr. Yasset Perez-Riverol

  183. 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

    Article • Analytical Chemistry, October 2010, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol

  184. 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

    Article • European Journal of Mass Spectrometry, February 2010, SAGE Publications

    Dr. Yasset Perez-Riverol

  185. Proteomics Based on Peptide Fractionation by SDS-Free PAGE

    Article • Journal of Proteome Research, June 2008, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol