DR Juan Antonio Vizcaino

All Stories

1. 
   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

2. 
   The functional landscape of the human ubiquitinome

   Article • October 2025, Cold Spring Harbor Laboratory Press

   DR Juan Antonio Vizcaino

3. 
   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

4. 
   Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities

   Article • F1000Research, September 2025, Faculty of 1000, Ltd.

   DR Juan Antonio Vizcaino

5. 
   Establishing the ELIXIR Microbiome Community

   Article • F1000Research, September 2025, Faculty of 1000, Ltd.

   DR Juan Antonio Vizcaino

6. 
   Translon: a single term for translated regions

   Article • Nature Chemical Biology, September 2025, Springer Science + Business Media

   Dr.sc. Petar Ozretić, Jozef Nosek, DR Juan Antonio Vizcaino

7. 
   An expanded reference catalog of translated open reading frames for biomedical research

   Article • July 2025, Cold Spring Harbor Laboratory Press

   DR Juan Antonio Vizcaino

8. 
   Enabling pan-repository reanalysis for big data science of public metabolomics data

   Article • Nature Communications, May 2025, Springer Science + Business Media

   DR Juan Antonio Vizcaino

9. 
   An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources

   Article • PROTEOMICS, April 2025, Wiley

   DR Juan Antonio Vizcaino

10. 
    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

11. 
    Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment

    Article • February 2025, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino

12. 
    An approach to integrate metagenomics, metatranscriptomics and metaproteomics data in public resources

    Article • January 2025, Wiley

    DR Juan Antonio Vizcaino

13. 
    Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets

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

    DR Juan Antonio Vizcaino

14. 
    π-HuB: the proteomic navigator of the human body

    Article • Nature, December 2024, Springer Science + Business Media

    DR Juan Antonio Vizcaino

15. 
    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

16. 
    REDIportal: toward an integrated view of the A-to-I editing

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

    DR Juan Antonio Vizcaino

17. 
    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

18. 
    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

19. 
    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

20. 
    High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

    Article • September 2024, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino

21. 
    The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data

    Article • Journal of Lipid Research, September 2024, Elsevier

    DR Juan Antonio Vizcaino

22. 
    mzIdentML 1.3.0 – Essential progress on the support of crosslinking and other identifications based on multiple spectra

    Article • PROTEOMICS, July 2024, Wiley

    DR Juan Antonio Vizcaino

23. 
    Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java

    Article • Journal of the American Society for Mass Spectrometry, June 2024, American Chemical Society (ACS)

    DR Juan Antonio Vizcaino

24. 
    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

25. 
    Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues

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

    DR Juan Antonio Vizcaino

26. 
    Communicating mass spectrometry quality information in mzQC with Python, R, and Java

    Article • May 2024, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino

27. 
    Enabling pan-repository reanalysis for big data science of public metabolomics data

    Article • April 2024, American Chemical Society (ACS)

    DR Juan Antonio Vizcaino

28. 
    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

29. 
    Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation

    Article • PLoS Computational Biology, January 2024, PLOS

    DR Juan Antonio Vizcaino

30. 
    WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows

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

    DR Juan Antonio Vizcaino

31. 
    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

32. 
    Expression Atlas update: insights from sequencing data at both bulk and single cell level

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

    DR Juan Antonio Vizcaino

33. 
    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

34. 
    Integrated Proteomics analysis of baseline protein expression in pig tissues

    Article • November 2023, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino

35. 
    Foresight in clinical proteomics: current status, ethical considerations, and future perspectives

    Article • Open Research Europe, November 2023, Faculty of 1000, Ltd.

    DR Juan Antonio Vizcaino

36. 
    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

37. 
    mzIdentML 1.3.0 - Essential progress on the support of crosslinking and other identifications based on multiple spectra

    Article • October 2023, Wiley

    DR Juan Antonio Vizcaino

38. 
    TopDownApp: An open and modular platform for analysis and visualisation of top‐down proteomics data

    Article • PROTEOMICS, October 2023, Wiley

    DR Juan Antonio Vizcaino

39. 
    Foresight in clinical proteomics: current status, ethical considerations, and future perspectives

    Article • Open Research Europe, April 2023, Faculty of 1000, Ltd.

    DR Juan Antonio Vizcaino

40. 
    Toward an Integrated Machine Learning Model of a Proteomics Experiment

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

    DR Juan Antonio Vizcaino

41. 
    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

42. 
    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

43. 
    Integrated View of Baseline Protein Expression in Human Tissues

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

    DR Juan Antonio Vizcaino

44. 
    EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2022

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

    Catherine Brooksbank, DR Juan Antonio Vizcaino

45. 
    Identifying individuals using proteomics: are we there yet?

    Article • Frontiers in Molecular Biosciences, November 2022, Frontiers

    DR Juan Antonio Vizcaino

46. 
    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

47. 
    Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future

    Article • PROTEOMICS, September 2022, Wiley

    DR Juan Antonio Vizcaino

48. 
    Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

    Article • PLoS Computational Biology, June 2022, PLOS

    DR Juan Antonio Vizcaino

49. 
    Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

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

    DR Juan Antonio Vizcaino

50. 
    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

51. 
    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

52. 
    Expression Atlas update: gene and protein expression in multiple species

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

    DR Juan Antonio Vizcaino

53. 
    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

54. 
    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

55. 
    The growing need for controlled data access models in clinical proteomics and metabolomics

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

    DR Juan Antonio Vizcaino

56. 
    Universal Spectrum Identifier for mass spectra

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

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

57. 
    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

58. 
    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

59. 
    Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future

    Article • Molecular & Cellular Proteomics, January 2021, Elsevier

    DR Juan Antonio Vizcaino

60. 
    Using Deep Learning to Extrapolate Protein Expression Measurements

    Article • PROTEOMICS, October 2020, Wiley

    DR Juan Antonio Vizcaino

61. 
    A high-stringency blueprint of the human proteome

    Article • Nature Communications, October 2020, Springer Science + Business Media

    DR Juan Antonio Vizcaino

62. 
    Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry

    Article • Structure, October 2020, Elsevier

    Dr. Alexandre M.J.J. Bonvin, DR Juan Antonio Vizcaino

63. 
    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

64. 
    The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

    Article • Bioinformatics, January 2020, Oxford University Press (OUP)

    DR Juan Antonio Vizcaino

65. 
    The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases

    Article • Molecular & Cellular Proteomics, January 2020, Elsevier

    DR Juan Antonio Vizcaino

66. 
    The functional landscape of the human phosphoproteome

    Article • Nature Biotechnology, December 2019, Springer Science + Business Media

    DR Juan Antonio Vizcaino

67. 
    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

68. 
    Expression Atlas update: from tissues to single cells

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

    DR Juan Antonio Vizcaino

69. 
    Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics

    Article • September 2019, Springer Science + Business Media

    DR Juan Antonio Vizcaino

70. 
    A five-level classification system for proteoform identifications

    Article • Nature Chemical Biology, August 2019, Springer Science + Business Media

    DR Juan Antonio Vizcaino

71. 
    Quantifying the impact of public omics data

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

    Dr. Yasset Perez-Riverol, DR Juan Antonio Vizcaino

72. 
    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

73. 
    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

74. 
    The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

    Article • April 2019, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino

75. 
    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

76. 
    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

77. 
    The functional landscape of the human phosphoproteome

    Article • February 2019, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino

78. 
    Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities

    Article • January 2019, Springer Science + Business Media

    DR Juan Antonio Vizcaino

79. 
    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

80. 
    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

81. 
    Future prospects of spectral clustering approaches in proteomics

    Article • PROTEOMICS, June 2018, Wiley

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

82. 
    Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE)

    Article • PROTEOMICS, June 2018, Wiley

    DR Juan Antonio Vizcaino

83. 
    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

84. 
    Quantifying the impact of public omics data

    Article • March 2018, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

85. 
    ProForma: a Standard Proteoform Notation.

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

    DR Juan Antonio Vizcaino, Anthony J Cesnik

86. 
    The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

    Article • January 2018, Springer Science + Business Media

    DR Juan Antonio Vizcaino

87. 
    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

88. 
    Expression Atlas: gene and protein expression across multiple studies and organisms

    Article • Nucleic Acids Research, November 2017, Oxford University Press (OUP)

    DR Juan Antonio Vizcaino

89. 
    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

90. 
    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

91. 
    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

92. 
    Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets

    Article • September 2017, Wiley

    DR Juan Antonio Vizcaino

93. 
    The SysteMHC Atlas project

    Article • Nucleic Acids Research, July 2017, Oxford University Press (OUP)

    DR Juan Antonio Vizcaino

94. 
    The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.

    Article • June 2017, Cold Spring Harbor Laboratory Press

    DR Juan Antonio Vizcaino

95. 
    A community proposal to integrate proteomics activities in ELIXIR

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

    Dr Magnus Palmblad, Mr Rafael C Jimenez, DR Juan Antonio Vizcaino, Peter Horvatovich, Lennart Martens, Albert Heck

96. 
    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

97. 
    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

98. 
    Proteomics Approaches to Uncover the Drug Resistance Mechanisms of Microbial Biofilms

    Article • May 2017, Taylor & Francis

    DR Juan Antonio Vizcaino

99. 
    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

100. 
     Synthetic human proteomes for accelerating protein research

     Article • Nature Chemical Biology, February 2017, Nature

     DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

101. 
     A Golden Age for Working with Public Proteomics Data

     Article • Trends in Biochemical Sciences, January 2017, Elsevier

     DR Juan Antonio Vizcaino

102. 
     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

103. 
     Making sense of big data in health research: Towards an EU action plan

     Article • Genome Medicine, June 2016, Springer Science + Business Media

     Professor Werner Muller, DR Juan Antonio Vizcaino, Dr Christoph Bock, Dr Niklas U Blomberg

104. 
     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

105. 
     Exploring the potential of public proteomics data

     Article • PROTEOMICS, December 2015, Wiley

     DR Juan Antonio Vizcaino

106. 
     Delicate Metabolic Control and Coordinated Stress Response Critically Determine Antifungal Tolerance of Candida albicans Biofilm Persisters

     Article • Antimicrobial Agents and Chemotherapy, July 2015, ASM Journals

     DR Juan Antonio Vizcaino

107. 
     Embedding standards in metabolomics: the Metabolomics Society data standards task group

     Article • Metabolomics, June 2015, Springer Science + Business Media

     DR Juan Antonio Vizcaino

108. 
     Proteomics Data Visualisation

     Article • PROTEOMICS, April 2015, Wiley

     DR Juan Antonio Vizcaino

109. 
     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

110. 
     Development of data representation standards by the human proteome organization proteomics standards initiative

     Article • Journal of the American Medical Informatics Association, February 2015, Oxford University Press (OUP)

     DR Juan Antonio Vizcaino

111. 
     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

112. 
     Identifying novel biomarkers through data mining—A realistic scenario?

     Article • PROTEOMICS - CLINICAL APPLICATIONS, January 2015, Wiley

     DR Juan Antonio Vizcaino, Dr. Yasset Perez-Riverol

113. 
     Analysis of the tryptic search space in UniProt databases

     Article • PROTEOMICS, December 2014, Wiley

     DR Juan Antonio Vizcaino

114. 
     Meeting New Challenges: The 2014 HUPO-PSI/COSMOS Workshop

     Article • PROTEOMICS, October 2014, Wiley

     DR Juan Antonio Vizcaino

115. 
     How to submit MS proteomics data to ProteomeXchange via the PRIDE database

     Article • PROTEOMICS, August 2014, Wiley

     DR Juan Antonio Vizcaino

116. 
     Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets

     Article • PLoS Computational Biology, July 2014, PLOS

     DR Juan Antonio Vizcaino

117. 
     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

118. 
     jmzTab: A Java interface to the mzTab data standard

     Article • PROTEOMICS, April 2014, Wiley

     DR Juan Antonio Vizcaino

119. 
     qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments

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

     DR Juan Antonio Vizcaino

120. 
     ProteomeXchange provides globally coordinated proteomics data submission and dissemination

     Article • Nature Biotechnology, March 2014, Nature

     DR Juan Antonio Vizcaino

121. 
     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

122. 
     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

123. 
     Controlled vocabularies and ontologies in proteomics: Overview, principles and practice

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

     DR Juan Antonio Vizcaino

124. 
     Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra

     Article • Journal of Proteomics, December 2013, Elsevier

     DR Juan Antonio Vizcaino, Lennart Martens

125. 
     Preparing to Work with Big Data in Proteomics - A Report on the HUPO-PSI Spring Workshop

     Article • PROTEOMICS, October 2013, Wiley

     DR Juan Antonio Vizcaino

126. 
     Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML

     Article • Molecular & Cellular Proteomics, June 2013, American Society for Biochemistry & Molecular Biology (ASBMB)

     DR Juan Antonio Vizcaino

127. 
     LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics

     Article • PLOS One, May 2013, PLOS

     DR Juan Antonio Vizcaino, Pablo Moreno

128. 
     From Peptidome to PRIDE : P ublic proteomics data migration at a large scale

     Article • PROTEOMICS, April 2013, Wiley

     DR Juan Antonio Vizcaino

129. 
     The mzQuantML Data Standard for Mass Spectrometry-based Quantitative Studies in Proteomics

     Article • Molecular & Cellular Proteomics, April 2013, American Society for Biochemistry & Molecular Biology (ASBMB)

     Dr Da Qi, DR Juan Antonio Vizcaino

130. 
     Shorthand notation for lipid structures derived from mass spectrometry

     Article • Journal of Lipid Research, April 2013, American Society for Biochemistry & Molecular Biology (ASBMB)

     DR Juan Antonio Vizcaino

131. 
     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

132. 
     The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

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

     DR Juan Antonio Vizcaino

133. 
     PRIDE Cluster: building a consensus of proteomics data

     Article • Nature Chemical Biology, January 2013, Nature

     DR Juan Antonio Vizcaino

134. 
     Proteomics Data Exchange and Storage: The Need for Common Standards and Public Repositories

     Article • January 2013, Springer Science + Business Media

     DR Juan Antonio Vizcaino, Mr Rafael C Jimenez

135. 
     Ontology Lookup Service for Controlled Vocabularies and Data Annotation

     Article • January 2013, Springer Science + Business Media

     DR Juan Antonio Vizcaino

136. 
     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

137. 
     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

138. 
     Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop

     Article • PROTEOMICS, September 2012, Wiley

     DR Juan Antonio Vizcaino

139. 
     Improvements in the protein identifier cross-reference service

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

     DR Juan Antonio Vizcaino

140. 
     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

141. 
     PRIDE: Quality control in a proteomics data repository

     Article • Database, March 2012, Oxford University Press (OUP)

     DR Juan Antonio Vizcaino

142. 
     jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats

     Article • PROTEOMICS, March 2012, Wiley

     DR Juan Antonio Vizcaino

143. 
     jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

     Article • PROTEOMICS, March 2012, Wiley

     DR Juan Antonio Vizcaino

144. 
     The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

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

     DR Juan Antonio Vizcaino

145. 
     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

146. 
     From Proteomics Data Representation to Public Data Flow: A Report on the HUPO-PSI Workshop September 2011, Geneva, Switzerland

     Article • PROTEOMICS, January 2012, Wiley

     DR Juan Antonio Vizcaino

147. 
     Enabling BioSharing – a report on the Annual Spring Workshop of the HUPO‐PSI April 11–13, 2011, EMBL‐Heidelberg, Germany

     Article • PROTEOMICS, November 2011, Wiley

     DR Juan Antonio Vizcaino

148. 
     Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations

     Article • Database, October 2011, Oxford University Press (OUP)

     DR Juan Antonio Vizcaino

149. 
     Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets

     Article • PROTEOMICS, October 2011, Wiley

     DR Juan Antonio Vizcaino

150. 
     Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data

     Article • Molecular & Cellular Proteomics, June 2011, American Society for Biochemistry & Molecular Biology (ASBMB)

     DR Juan Antonio Vizcaino

151. 
     Quality Control in Proteomics

     Article • PROTEOMICS, March 2011, Wiley

     DR Juan Antonio Vizcaino, Lennart Martens

152. 
     EST Analysis Pipeline: Use of Distributed Computing Resources

     Article • January 2011, Springer Science + Business Media

     DR Juan Antonio Vizcaino

153. 
     Proteomic Temporal Profile of Human Brain Endothelium After Oxidative Stress

     Article • Stroke, December 2010, Wolters Kluwer Health

     DR Juan Antonio Vizcaino

154. 
     Submitting Proteomics Data to PRIDE Using PRIDE Converter

     Article • November 2010, Springer Science + Business Media

     DR Juan Antonio Vizcaino, Lennart Martens

155. 
     Organelle proteomics experimental designs and analysis

     Article • PROTEOMICS, November 2010, Wiley

     DR Juan Antonio Vizcaino

156. 
     PRIDE and “Database on Demand” as Valuable Tools for Computational Proteomics

     Article • October 2010, Springer Science + Business Media

     DR Juan Antonio Vizcaino, Lennart Martens

157. 
     Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research

     Article • Journal of Proteomics, October 2010, Elsevier

     DR Juan Antonio Vizcaino, Lennart Martens

158. 
     The Ontology Lookup Service: bigger and better

     Article • Nucleic Acids Research, May 2010, Oxford University Press (OUP)

     DR Juan Antonio Vizcaino, Lennart Martens

159. 
     PRIDE: Data Submission and Analysis

     Article • Current Protocols in Protein Science, April 2010, Wiley

     DR Juan Antonio Vizcaino, Lennart Martens

160. 
     The Proteomics Identifications database: 2010 update

     Article • Nucleic Acids Research, November 2009, Oxford University Press (OUP)

     DR Juan Antonio Vizcaino, Lennart Martens

161. 
     A guide to the Proteomics Identifications Database proteomics data repository

     Article • PROTEOMICS, August 2009, Wiley

     DR Juan Antonio Vizcaino, Lennart Martens

162. 
     PRIDE Converter: making proteomics data-sharing easy

     Article • Nature Biotechnology, July 2009, Nature

     DR Juan Antonio Vizcaino, Lennart Martens

163. 
     A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

     Article • Nature Chemical Biology, May 2009, Nature

     DR Juan Antonio Vizcaino, Lennart Martens

164. 
     Present and future of proteomics data curation at the PRIDE database

     Article • Nature Reports Climate Change, May 2009, Nature

     DR Juan Antonio Vizcaino

165. 
     Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray

     Article • BMC Microbiology, January 2009, Springer Science + Business Media

     DR Juan Antonio Vizcaino

166. 
     Charting online OMICS resources: A navigational chart for clinical researchers

     Article • PROTEOMICS - CLINICAL APPLICATIONS, November 2008, Wiley

     DR Juan Antonio Vizcaino, Lennart Martens

167. 
     Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets

     Article • PROTEOMICS, March 2008, Wiley

     DR Juan Antonio Vizcaino, Lennart Martens

168. 
     Analyzing Large-Scale Proteomics Projects with Latent Semantic Indexing

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

     DR Juan Antonio Vizcaino, Lennart Martens

169. 
     High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7–9, 2007 Wellcome Trust Conference Centre, Hinxton, UK

     Article • PROTEOMICS, August 2007, Wiley

     DR Juan Antonio Vizcaino, Lennart Martens

170. 
     The PSI formal document process and its implementation on the PSI website

     Article • PROTEOMICS, July 2007, Wiley

     DR Juan Antonio Vizcaino, Lennart Martens

171. 
     Characterization of genes encoding novel peptidases in the biocontrol fungus Trichoderma harzianum CECT 2413 using the TrichoEST functional genomics approach

     Article • Current Genetics, April 2007, Springer Science + Business Media

     DR Juan Antonio Vizcaino

172. 
     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 • Fungal Genetics and Biology, April 2007, Elsevier

     Dr Santiago Gutierrez, DR Juan Antonio Vizcaino

173. 
     Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol

     Article • Applied Microbiology and Biotechnology, March 2007, Springer Science + Business Media

     DR Juan Antonio Vizcaino

174. 
     ThPTR2, a di/tri-peptide transporter gene from Trichoderma harzianum

     Article • Fungal Genetics and Biology, April 2006, Elsevier

     Dr Santiago Gutierrez, DR Juan Antonio Vizcaino

175. 
     Detection of peptaibols and partial cloning of a putative peptaibol synthetase gene fromT. harzianum CECT 2413

     Article • Folia Microbiologica, March 2006, Springer Science + Business Media

     Dr Santiago Gutierrez, DR Juan Antonio Vizcaino

176. 
     Cloning and characterization of the erg1 gene of Trichoderma harzianum: Effect of the erg1 silencing on ergosterol biosynthesis and resistance to terbinafine

     Article • Fungal Genetics and Biology, March 2006, Elsevier

     Dr Santiago Gutierrez, DR Juan Antonio Vizcaino

177. 
     Article • BMC Genomics, January 2006, Springer Science + Business Media

     DR Juan Antonio Vizcaino, Dr Santiago Gutierrez

178. 
     Screening of antimicrobial activities in Trichoderma isolates representing three Trichoderma sections

     Article • Mycological Research, December 2005, Elsevier

     Dr Santiago Gutierrez, DR Juan Antonio Vizcaino

179. 
     Detection of putative peptide synthetase genes in Trichoderma species: Application of this method to the cloning of a gene from T. harzianum CECT 2413

     Article • FEMS Microbiology Letters, March 2005, Oxford University Press (OUP)

     DR Juan Antonio Vizcaino, Dr Santiago Gutierrez

180. 
     Data Standards in Systems Modeling

     Article • October 2004, Wiley

     DR Juan Antonio Vizcaino

181. 
     Data Standards in Proteomics

     Article • October 2004, Wiley

     DR Juan Antonio Vizcaino

182. 
     Cell wall-degrading isoenzyme profiles of Trichoderma biocontrol strains show correlation with rDNA taxonomic species

     Article • Current Genetics, October 2004, Springer Science + Business Media

     DR Juan Antonio Vizcaino

183. 
     Separation and Identification of Volatile Components in the Fermentation Broth of Trichoderma atroviride by Solid-Phase Extraction and Gas Chromatography--Mass Spectrometry

     Article • Journal of Chromatographic Science, October 2000, Oxford University Press (OUP)

     DR Juan Antonio Vizcaino

184. 
     Colour pigments of Trichoderma harzianum

     Article • Journal of Chromatography A, October 2000, Elsevier

     DR Juan Antonio Vizcaino

185. 
     ProteomeXchange submissions via PRIDE

     Article • EMBL-EBI

     DR Juan Antonio Vizcaino

186. 
     PRIDE: Quick tour

     Article • EMBL-EBI

     DR Juan Antonio Vizcaino

187. 
     PRIDE and ProteomeXchange: webinar

     Article • EMBL-EBI

     DR Juan Antonio Vizcaino

188. 
     Proteomics bioinformatics: Course materials

     Article • EMBL-EBI

     DR Juan Antonio Vizcaino

189. 
     The PRIDE database: storing, disseminating and integrating proteomics data in the public domain

     Article • EMBL-EBI

     DR Juan Antonio Vizcaino