| The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013 JA Vizcaíno, RG Côté, A Csordas, JA Dianes, A Fabregat, JM Foster, ... Nucleic acids research 41 (D1), D1063-D1069, 2012 | 1129 | 2012 |
| 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, 2015 | 526 | 2015 |
| 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 | 96 | 2012 |
| 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 | 72 | 2012 |
| 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 | 63 | 2015 |
| 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 | 51 | 2014 |
| Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective Y Perez-Riverol, R Wang, H Hermjakob, M Müller, V Vesada, JA Vizcaíno Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1844 (1), 63-76, 2014 | 45 | 2014 |
| In silico analysis of accurate proteomics, complemented by selective isolation of peptides Y Perez-Riverol, A Sánchez, Y Ramos, A Schmidt, M Müller, L Betancourt, ... Journal of proteomics 74 (10), 2071-2082, 2011 | 26 | 2011 |
| 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 | 22 | 2016 |
| PIA: An intuitive protein inference engine with a web-based user interface J Uszkoreit, A Maerkens, Y Perez-Riverol, HE Meyer, K Marcus, ... Journal of proteome research 14 (7), 2988-2997, 2015 | 20 | 2015 |
| Isoelectric point optimization using peptide descriptors and support vector machines Y Perez-Riverol, E Audain, A Millan, Y Ramos, A Sanchez, JA Vizcaíno, ... Journal of proteomics 75 (7), 2269-2274, 2012 | 18 | 2012 |
| Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report Y Perez-Riverol, H Hermjakob, O Kohlbacher, L Martens, D Creasy, J Cox, ... Journal of proteomics 87, 134-138, 2013 | 17 | 2013 |
| On best practices in the development of bioinformatics software F da Veiga Leprevost, VC Barbosa, EL Francisco, Y Perez-Riverol, ... Frontiers in genetics 5, 2014 | 16 | 2014 |
| SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping LH Betancourt, PJ De Bock, A Staes, E Timmerman, Y Perez-Riverol, ... Journal of proteomics 91, 164-171, 2013 | 15 | 2013 |
| Proteomics based on peptide fractionation by SDS-free PAGE Y Ramos, E Gutierrez, Y Machado, A Sánchez, L Castellanos-Serra, ... Journal of proteome research 7 (6), 2427-2434, 2008 | 15 | 2008 |
| 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 | 14 | 2016 |
| 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, 2016 | 13 | 2016 |
| Open source libraries and frameworks for biological data visualisation: A guide for developers R Wang, Y Perez‐Riverol, H Hermjakob, JA Vizcaíno Proteomics 15 (8), 1356-1374, 2015 | 12 | 2015 |
| Effectively addressing complex proteomic search spaces with peptide spectrum matching D Borges, Y Perez-Riverol, FCS Nogueira, GB Domont, J Noda, ... Bioinformatics 29 (10), 1343-1344, 2013 | 12 | 2013 |
| Bioinformatics tools for the functional interpretation of quantitative proteomics results T Nunez Villavicencio-Diaz, A Rodríguez-Ulloa, O Guirola-Cruz, ... Current topics in medicinal chemistry 14 (3), 435-449, 2014 | 10 | 2014 |