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ORCIDJuan Antonio Vizcaíno
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- affiliation: European Bioinformatics Institute, Cambridge, UK
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Journal Articles
- 2025
[j27]Selvakumar Kamatchinathan, Suresh Hewapathirana
, Chakradhar Bandla, Santiago Insua, Juan Antonio Vizcaíno, Yasset Pérez-Riverol:
pridepy: A Python package to download and search data from PRIDE database. J. Open Source Softw. 10(109): 7563 (2025)- 2024
- [j26]Javier Robles, Ananth Prakash, Juan Antonio Vizcaíno, J. Ignacio Casal:
Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation. PLoS Comput. Biol. 20(1) (2024) - 2023
- [j25]Matthew Thakur, Alex Bateman, Cath Brooksbank, Mallory Ann Freeberg, Melissa Harrison, Matthew Hartley, Thomas M. Keane, Gerard J. Kleywegt, Andrew Leach, Maria Levchenko, Sarah L. Morgan, Ellen M. McDonagh, Sandra E. Orchard, Irene Papatheodorou, Sameer Velankar, Juan Antonio Vizcaíno, Rick Witham, Barbara Zdrazil, Johanna R. McEntyre:
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022. Nucleic Acids Res. 51(D1): 9-17 (2023) - [j24]Eric W. Deutsch, Nuno Bandeira, Yasset Pérez-Riverol, Vagisha Sharma, Jeremy Carver, Luis Mendoza, Deepti Jaiswal Kundu, Shengbo Wang, Chakradhar Bandla, Selvakumar Kamatchinathan, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama, Juan Antonio Vizcaíno:
The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res. 51(D1): 1539-1548 (2023) - 2022
- [j23]Pablo A. Moreno, Silvie Fexova, Nancy George, Jonathan R. Manning, Zhichao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer Fuentes, Anja Füllgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham, Andrey Solovyev, Lingyun Zhao, Ananth Prakash, David García-Seisdedos, Deepti Jaiswal Kundu, Shengbo Wang, Mathias Walzer, Laura Clarke, David Osumi-Sutherland, Marcela Karey Tello-Ruiz, Sunita Kumari, Doreen Ware, Jana Eliasova, Mark J. Arends, Martijn C. Nawijn, Kerstin B. Meyer, Tony Burdett, John C. Marioni, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma, Irene Papatheodorou:
Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Res. 50(D1): 129-140 (2022) - [j22]Yasset Pérez-Riverol, Jingwen Bai, Chakradhar Bandla, David García-Seisdedos, Suresh Hewapathirana, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Ananth Prakash, Anika Frericks-Zipper, Martin Eisenacher, Mathias Walzer, Shengbo Wang, Alvis Brazma, Juan Antonio Vizcaíno:
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50(D1): 543-552 (2022) - [j21]Shengbo Wang, David García-Seisdedos, Ananth Prakash, Deepti Jaiswal Kundu, Andrew Collins, Nancy George, Silvie Fexova, Pablo A. Moreno, Irene Papatheodorou, Andrew R. Jones, Juan Antonio Vizcaíno:
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues. PLoS Comput. Biol. 18(6) (2022) - 2020
- [j20]Rachel Drysdale, Charles E. Cook, Robert Petryszak, Vivienne Baillie Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl, Jürgen Haas, Jerry Lanfear, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Alex Bateman, Alan J. Bridge, Guy Cochrane, Robert D. Finn, Frank Oliver Glöckner, Marc Hanauer, Thomas M. Keane, Andrew Leach, Luana Licata, Per Oksvold, Sandra E. Orchard, Christine A. Orengo, Helen E. Parkinson, Bengt Persson, Pablo Porras, Jordi Rambla, Ana Rath, Charlotte Rodwell, Ugis Sarkans, Dietmar Schomburg, Ian Sillitoe, J. Dylan Spalding, Mathias Uhlén, Sameer Velankar, Juan Antonio Vizcaíno, Kalle von Feilitzen, Christian von Mering, Andrew D. Yates, Niklas Blomberg, Christine Durinx, Johanna R. McEntyre:
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinform. 36(8): 2636-2642 (2020) - [j19]Eric W. Deutsch, Nuno Bandeira, Vagisha Sharma, Yasset Pérez-Riverol, Jeremy Carver, Deepti Jaiswal Kundu, David García-Seisdedos, Andrew F. Jarnuczak, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Henning Hermjakob, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama, Juan Antonio Vizcaíno:
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. Nucleic Acids Res. 48(Database-Issue): D1145-D1152 (2020) - [j18]Irene Papatheodorou, Pablo A. Moreno, Jonathan R. Manning, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova, Nuno A. Fonseca, Anja Füllgrabe, Matthew Green, Ni Huang, Laura Huerta, Haider Iqbal, Monica Jianu, Suhaib Mohammed, Lingyun Zhao, Andrew F. Jarnuczak, Simon Jupp, John C. Marioni, Kerstin B. Meyer, Robert Petryszak, Cesar Augusto Prada Medina, Carlos Talavera-López, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma:
Expression Atlas update: from tissues to single cells. Nucleic Acids Res. 48(Database-Issue): D77-D83 (2020) - 2019
- [j17]Yasset Pérez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal Llinares, Suresh Hewapathirana, Deepti Jaiswal Kundu, Avinash Inuganti, Johannes Griss, Gerhard Mayer, Martin Eisenacher, Enrique Pérez, Julian Uszkoreit, Julianus Pfeuffer, Timo Sachsenberg, Sule Yilmaz, Shivani Tiwary, Jürgen Cox, Enrique Audain, Mathias Walzer, Andrew F. Jarnuczak, Tobias Ternent, Alvis Brazma, Juan Antonio Vizcaíno:
The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47(Database-Issue): D442-D450 (2019) - 2018
- [j16]Wenguang Shao, Patrick G. A. Pedrioli, Witold Wolski, Christian Scurtescu, Emanuel Schmid, Juan Antonio Vizcaíno, Mathieu Courcelles, Heiko Schuster, Daniel Kowalewski, Fabio Marino, Cecilia S. Lindestam Arlehamn, Kerrie Vaughan, Bjoern Peters, Alessandro Sette, Tom H. M. Ottenhoff, Krista E. Meijgaarden, Natalie Nieuwenhuizen, Stefan H. E. Kaufmann, Ralph Schlapbach, John C. Castle, Alexey I. Nesvizhskii, Morten Nielsen, Eric W. Deutsch, David S. Campbell, Robert L. Moritz, Roman A. Zubarev, Anders Jimmy Ytterberg, Anthony W. Purcell, Miguel Marcilla, Alberto Paradela, Qi Wang, Catherine E. Costello, Nicola Ternette, Peter A. van Veelen, Cécile A. C. M. van Els, Albert J. R. Heck, Gustavo A. de Souza, Ludvig Magne Sollid, Arie Admon, Stefan Stevanovic, Hans-Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron:
The SysteMHC Atlas project. Nucleic Acids Res. 46(Database-Issue): D1237-D1247 (2018) - [j15]Irene Papatheodorou, Nuno A. Fonseca, Maria Keays, Y. Amy Tang, Elisabet Barrera, Wojciech Bazant, Melissa L. Burke, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Nancy George, Laura Huerta, Satu Koskinen, Suhaib Mohammed, Matthew J. Geniza, Justin Preece, Pankaj Jaiswal, Andrew F. Jarnuczak, Wolfgang Huber, Oliver Stegle, Juan Antonio Vizcaíno, Alvis Brazma, Robert Petryszak:
Expression Atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Res. 46(Database-Issue): D246-D251 (2018) - 2017
- [j14]Eric W. Deutsch, Attila Csordas, Zhi Sun, Andrew F. Jarnuczak, Yasset Pérez-Riverol, Tobias Ternent, David S. Campbell, Manuel Bernal Llinares, Shujiro Okuda, Shin Kawano, Robert L. Moritz, Jeremy Carver, Mingxun Wang, Yasushi Ishihama, Nuno Bandeira, Henning Hermjakob, Juan Antonio Vizcaíno:
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. 45(Database-Issue): D1100-D1106 (2017) - 2016
- [j13]Juan Antonio Vizcaíno, Attila Csordas, Noemi del-Toro, José A. Dianes, Johannes Griss, Ilias Lavidas, Gerhard Mayer, Yasset Pérez-Riverol, Florian Reisinger, Tobias Ternent, Qing-Wei Xu, Rui Wang, Henning Hermjakob:
2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 44(Database-Issue): 447-456 (2016) - [j12]Yasset Pérez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, Tom J. Pollard, Alexander Konovalov, Robert M. Flight, Kai Blin, Juan Antonio Vizcaíno:
Ten Simple Rules for Taking Advantage of Git and GitHub. PLoS Comput. Biol. 12(7) (2016) - 2015
- [j11]Yasset Pérez-Riverol, Julian Uszkoreit, Aniel Sánchez, Tobias Ternent, Noemi del-Toro, Henning Hermjakob, Juan Antonio Vizcaíno, Rui Wang:
ms-data-core-api: an open-source, metadata-oriented library for computational proteomics. Bioinform. 31(17): 2903-2905 (2015) - [j10]Eric W. Deutsch, Juan P. Albar, Pierre-Alain Binz, Martin Eisenacher, Andrew R. Jones, Gerhard Mayer, Gilbert S. Omenn, Sandra E. Orchard, Juan Antonio Vizcaíno, Henning Hermjakob:
Development of data representation standards by the human proteome organization proteomics standards initiative. J. Am. Medical Informatics Assoc. 22(3): 495-506 (2015) - [j9]Florian Reisinger, Noemi del-Toro, Tobias Ternent, Henning Hermjakob, Juan Antonio Vizcaíno:
Introducing the PRIDE Archive RESTful web services. Nucleic Acids Res. 43(Webserver-Issue): W599-W604 (2015) - 2014
- [j8]Alejandro Barrera, Ana Alastruey-Izquierdo, María J. Martín, Isabel Cuesta, Juan Antonio Vizcaíno:
Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets. PLoS Comput. Biol. 10(7) (2014) - 2013
- [j7]Gerhard Mayer, Luisa Montecchi-Palazzi, David Ovelleiro, Andrew R. Jones, Pierre-Alain Binz, Eric W. Deutsch, Matthew Chambers, Marius Kallhardt, Fredrik Levander, James Shofstahl, Sandra E. Orchard, Juan Antonio Vizcaíno, Henning Hermjakob, Christian Stephan, Helmut E. Meyer, Martin Eisenacher:
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database J. Biol. Databases Curation 2013 (2013) - [j6]Juan Antonio Vizcaíno, Richard G. Côté, Attila Csordas, José A. Dianes, Antonio Fabregat, Joseph M. Foster, Johannes Griss, Emanuele Alpi, Melih Birim, Javier Contell, Gavin O'Kelly, Andreas Schoenegger, David Ovelleiro, Yasset Pérez-Riverol, Florian Reisinger, Daniel Rios, Rui Wang, Henning Hermjakob:
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41(Database-Issue): 1063-1069 (2013) - 2012
- [j5]Attila Csordas, David Ovelleiro, Rui Wang, Joseph M. Foster, Daniel Rios, Juan Antonio Vizcaíno, Henning Hermjakob:
PRIDE: Quality control in a proteomics data repository. Database J. Biol. Databases Curation 2012 (2012) - [j4]Samuel P. Wein, Richard G. Côté, Marine Dumousseau, Florian Reisinger, Henning Hermjakob, Juan Antonio Vizcaíno:
Improvements in the protein identifier cross-reference service. Nucleic Acids Res. 40(Web-Server-Issue): 276-280 (2012) - 2011
- [j3]Nelson Ndegwa, Richard G. Côté, David Ovelleiro, Peter D'Eustachio, Henning Hermjakob, Juan Antonio Vizcaíno, David Croft:
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. Database J. Biol. Databases Curation 2011 (2011) - 2010
- [j2]Juan Antonio Vizcaíno, Richard G. Côté, Florian Reisinger, Harald Barsnes, Joseph M. Foster, Jonathan Rameseder, Henning Hermjakob, Lennart Martens:
The Proteomics Identifications database: 2010 update. Nucleic Acids Res. 38(Database-Issue): 736-742 (2010) - [j1]Richard G. Côté, Florian Reisinger, Lennart Martens, Harald Barsnes, Juan Antonio Vizcaíno, Henning Hermjakob:
The Ontology Lookup Service: bigger and better. Nucleic Acids Res. 38(Web-Server-Issue): 155-160 (2010)
Conference and Workshop Papers
- 2007
- [c2]Sebastian Klie, Lennart Martens, Juan Antonio Vizcaíno, Richard G. Côté, Philip Jones, Rolf Apweiler, Alexander Hinneburg, Henning Hermjakob:
An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases. German Conference on Bioinformatics 2007: 174-184 - [c1]Sebastian Klie, Alexander Hinneburg, Lennart Martens, Juan Antonio Vizcaíno, Richard G. Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob:
Analysing latent topics in large-scale proteomics. LWA 2007: 73-80
Parts in Books or Collections
- 2016
- [p1]Juan Antonio Vizcaíno, Simon Perkins, Andrew R. Jones, Eric W. Deutsch:
Chapter 11. Data Formats of the Proteomics Standards Initiative. Proteome Informatics 2016: 229-258
Informal and Other Publications
- 2025
- [i1]Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Pérez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R. Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann, Bing Zhang, Tiannan Guo:
Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. CoRR abs/2502.15867 (2025)
Coauthor Index
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