Articles with public access mandates - Yasset Perez-RiverolLearn more
Available somewhere: 87
The PRIDE database and related tools and resources in 2019: improving support for quantification data
Y Perez-Riverol, A Csordas, J Bai, M Bernal-Llinares, S Hewapathirana, ...
Nucleic acids research 47 (D1), D442-D450, 2019
Mandates: US National Institutes of Health, UK Biotechnology and Biological Sciences …
2016 update of the PRIDE database and its related tools
JA Vizcaíno, A Csordas, N Del-Toro, JA Dianes, J Griss, I Lavidas, ...
Nucleic acids research 44 (D1), D447-D456, 2016
Mandates: UK Biotechnology and Biological Sciences Research Council, Wellcome Trust …
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
Y Perez-Riverol, J Bai, C Bandla, D García-Seisdedos, S Hewapathirana, ...
Nucleic acids research 50 (D1), D543-D552, 2022
Mandates: US National Institutes of Health, UK Biotechnology and Biological Sciences …
Bioconda: sustainable and comprehensive software distribution for the life sciences
B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ...
Nature methods 15 (7), 475-476, 2018
Mandates: US National Institutes of Health, German Research Foundation, Netherlands …
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
EW Deutsch, A Csordas, Z Sun, A Jarnuczak, Y Perez-Riverol, T Ternent, ...
Nucleic acids research, gkw936, 2016
Mandates: US National Institutes of Health, UK Biotechnology and Biological Sciences …
The ProteomeXchange consortium in 2020: enabling ‘big data’approaches in proteomics
EW Deutsch, N Bandeira, V Sharma, Y Perez-Riverol, JJ Carver, ...
Nucleic acids research 48 (D1), D1145-D1152, 2020
Mandates: US National Science Foundation, US National Institutes of Health, UK …
BioContainers: An open-source and community-driven framework for software standardization
FV Leprevost, BA Grüning, S Alves Aflitos, HL Röst, J Uszkoreit, ...
Bioinformatics, 2017
Mandates: Swiss National Science Foundation, US National Institutes of Health, UK …
A multicenter study benchmarks software tools for label-free proteome quantification
P Navarro, J Kuharev, LC Gillet, OM Bernhardt, B MacLean, HL Röst, ...
Nature biotechnology 34 (11), 1130-1136, 2016
Mandates: Swiss National Science Foundation, US National Institutes of Health, German …
The ProteomeXchange consortium at 10 years: 2023 update
EW Deutsch, N Bandeira, Y Perez-Riverol, V Sharma, JJ Carver, ...
Nucleic acids research 51 (D1), D1539-D1548, 2023
Mandates: US National Science Foundation, US National Institutes of Health, National …
Making proteomics data accessible and reusable: current state of proteomics databases and repositories
Y Perez‐Riverol, E Alpi, R Wang, H Hermjakob, JA Vizcaíno
Proteomics 15 (5-6), 930-950, 2015
Mandates: UK Biotechnology and Biological Sciences Research Council, Wellcome Trust
Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets
J Griss, Y Perez-Riverol, S Lewis, DL Tabb, JA Dianes, N Del-Toro, ...
Nature methods 13 (8), 651-656, 2016
Mandates: German Research Foundation, UK Biotechnology and Biological Sciences …
Discovering and linking public omics data sets using the Omics Discovery Index
Y Perez-Riverol, M Bai, F da Veiga Leprevost, S Squizzato, YM Park, ...
Nature biotechnology 35 (5), 406-409, 2017
Mandates: US National Institutes of Health, National Natural Science Foundation of …
ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion
N Hulstaert, J Shofstahl, T Sachsenberg, M Walzer, H Barsnes, L Martens, ...
Journal of proteome research 19 (1), 537-542, 2019
Mandates: Research Foundation (Flanders), UK Biotechnology and Biological Sciences …
PRIDE inspector toolsuite: moving toward a universal visualization tool for proteomics data standard formats and quality assessment of ProteomeXchange datasets
Y Perez-Riverol, QW Xu, R Wang, J Uszkoreit, J Griss, A Sanchez, ...
Molecular & Cellular Proteomics 15 (1), 305-317, 2016
Mandates: National Natural Science Foundation of China, UK Biotechnology and …
Ten simple rules for taking advantage of Git and GitHub
Y Perez-Riverol, L Gatto, R Wang, T Sachsenberg, J Uszkoreit, ...
PLoS computational biology 12 (7), e1004947, 2016
Mandates: US National Science Foundation, US National Institutes of Health, UK …
MaxDIA enables library-based and library-free data-independent acquisition proteomics
P Sinitcyn, H Hamzeiy, F Salinas Soto, D Itzhak, F McCarthy, C Wichmann, ...
Nature biotechnology 39 (12), 1563-1573, 2021
Mandates: German Research Foundation, UK Biotechnology and Biological Sciences …
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience
J Griss, AR Jones, T Sachsenberg, M Walzer, L Gatto, J Hartler, ...
Molecular & Cellular Proteomics 13 (10), 2765-2775, 2014
Mandates: US National Institutes of Health, German Research Foundation, UK …
Four simple recommendations to encourage best practices in research software
RC Jiménez, M Kuzak, M Alhamdoosh, M Barker, B Batut, M Borg, ...
F1000Research 6, 2017
Mandates: UK Biotechnology and Biological Sciences Research Council, UK Engineering …
PRIDE Inspector: a tool to visualize and validate MS proteomics data
R Wang, A Fabregat, D Ríos, D Ovelleiro, JM Foster, RG Côté, J Griss, ...
Nature biotechnology 30 (2), 135-137, 2012
Mandates: Government of Spain
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium
RG Côté, J Griss, JA Dianes, R Wang, JC Wright, HWP van den Toorn, ...
Molecular & Cellular Proteomics 11 (12), 1682-1689, 2012
Mandates: US National Institutes of Health
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