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Yasset Pérez-Riverol
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2020 – today
- 2023
- [j15]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
- [j14]Husen M. Umer, Enrique Audain, Yafeng Zhu, Julianus Pfeuffer, Timo Sachsenberg, Janne Lehtiö, Rui Mamede Branca, Yasset Pérez-Riverol:
Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides. Bioinform. 38(5): 1470-1472 (2022) - [j13]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) - 2020
- [j12]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) - [j11]Gaurhari Dass, Manh-Tu Vu, Pan Xu, Enrique Audain, Marc-Phillip Hitz, Björn A. Grüning, Henning Hermjakob, Yasset Pérez-Riverol:
The omics discovery REST interface. Nucleic Acids Res. 48(Webserver-Issue): W380-W384 (2020) - [i5]Yasset Pérez-Riverol:
Trends in Cuban research output: publications and patents. CoRR abs/2007.09638 (2020)
2010 – 2019
- 2019
- [j10]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) - [i4]Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi:
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research 8: 1677 (2019) - 2018
- [i3]Björn A. Grüning, Olivier Sallou, Pablo A. Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel J. Blankenberg, Rafael C. Jiménez, Daniel Blankenberg, Yasset Pérez-Riverol:
Recommendations for the packaging and containerizing of bioinformatics software. F1000Research 7: 742 (2018) - 2017
- [j9]Felipe da Veiga Leprevost, Björn A. Grüning, Saulo Aflitos, Hannes L. Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo A. Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C. Jiménez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I. Nesvizhskii, Yasset Pérez-Riverol:
BioContainers: an open-source and community-driven framework for software standardization. Bioinform. 33(16): 2580-2582 (2017) - [j8]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) - [i2]Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutiérrez, Neil P. Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla J. García, Josep Lluis Gelpí, Simon L. Gladman, Carole A. Goble, Montserrat González Ferreiro, Alejandra N. González-Beltrán, Philippa C. Griffin, Björn A. Grüning, Jonas Hagberg, Petr Holub, Rob W. W. Hooft, Jon C. Ison, Daniel S. Katz, Brane Leskosek, Federico López-Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola J. Mulder, Yasset Pérez-Riverol, Robert Pergl, Horst Pichler, Bernard J. Pope, Ferran Sanz, Maria Victoria Schneider, Victoria Stodden, Radoslaw Suchecki, Radka Svobodová Vareková, Harry-Anton Talvik, Ilian T. Todorov, Andrew E. Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch:
Four simple recommendations to encourage best practices in research software. F1000Research 6: 876- (2017) - 2016
- [j7]Enrique Audain, Yassel Ramos, Henning Hermjakob, Darren R. Flower, Yasset Pérez-Riverol:
Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences. Bioinform. 32(6): 821-827 (2016) - [j6]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) - [j5]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
- [j4]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) - 2013
- [j3]Roberto Vera, Yasset Pérez-Riverol, Sonia Pérez, Balázs Ligeti, Attila Kertész-Farkas, Sándor Pongor:
JBioWH: an open-source Java framework for bioinformatics data integration. Database J. Biol. Databases Curation 2013 (2013) - [j2]Diogo B. Lima, Yasset Pérez-Riverol, Fabio C. S. Nogueira, Gilberto B. Domont, Jesus Noda, Felipe da Veiga Leprevost, Vladimir Besada, Felipe M. G. França, Valmir Carneiro Barbosa, Aniel Sánchez, Paulo C. Carvalho:
Effectively addressing complex proteomic search spaces with peptide spectrum matching. Bioinform. 29(10): 1343-1344 (2013) - [j1]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) - [i1]Yasset Pérez-Riverol, Roberto Vera Alvarez:
A UML-based Approach to Design Parallel and Distributed Applications. CoRR abs/1311.7011 (2013)
Coauthor Index
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