Open source libraries and frameworks for biological data visualisation: A guide for developers

by Wang, Rui, Perez-Riverol, Yasset, Hermjakob, Henning, Vizcaíno, Juan Antonio
Published 2015

Identifying novel biomarkers through data mining—A realistic scenario?

by Griss, Johannes, Perez‐Riverol, Yasset, Hermjakob, Henning, Vizcaíno, Juan Antonio
Published 2015

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

by Perez-Riverol, Yasset, Wang, Rui, Hermjakob, Henning, Müller, Markus, Vesada, Vladimir, Vizcaíno, Juan Antonio
Published 2014

On best practices in the development of bioinformatics software

by Leprevost, Felipe da Veiga, Barbosa, Valmir C., Francisco, Eduardo L., Perez-Riverol, Yasset, Carvalho, Paulo C.
Published 2014

JBioWH: an open-source Java framework for bioinformatics data integration

by Vera, Roberto, Perez-Riverol, Yasset, Perez, Sonia, Ligeti, Balázs, Kertész-Farkas, Attila, Pongor, Sándor
Published 2013

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

by Perez-Riverol, Yasset, Alpi, Emanuele, Wang, Rui, Hermjakob, Henning, Vizcaíno, Juan Antonio
Published 2015

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics

by Perez-Riverol, Yasset, Uszkoreit, Julian, Sanchez, Aniel, Ternent, Tobias, del Toro, Noemi, Hermjakob, Henning, Vizcaíno, Juan Antonio, Wang, Rui
Published 2015

PRIDE Inspector: a tool to visualize and validate MS proteomics data

by Wang, Rui, Fabregat, Antonio, Ríos, Daniel, Ovelleiro, David, Foster, Joseph M., Côté, Richard G., Griss, Johannes, Csordas, Attila, Perez-Riverol, Yasset, Reisinger, Florian, Hermjakob, Henning, Martens, Lennart, Vizcaíno, Juan Antonio
Published 2012

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

by Griss, Johannes, Perez-Riverol, Yasset, Lewis, Steve, Tabb, David L., Dianes, José A., del-Toro, Noemi, Rurik, Marc, Walzer, Mathias W., Kohlbacher, Oliver, Hermjakob, Henning, Wang, Rui, Vizcaíno, Juan Antonio
Published 2016

A multi-center study benchmarks software tools for label-free proteome quantification

by Navarro, Pedro, Kuharev, Jörg, Gillet, Ludovic C, Bernhardt, Oliver M., MacLean, Brendan, Röst, Hannes L., Tate, Stephen A., Tsou, Chih-Chiang, Reiter, Lukas, Distler, Ute, Rosenberger, George, Perez-Riverol, Yasset, Nesvizhskii, Alexey I., Aebersold, Ruedi, Tenzer, Stefan
Published 2016

2016 update of the PRIDE database and its related tools

by Vizcaíno, Juan Antonio, Csordas, Attila, del-Toro, Noemi, Dianes, José A., Griss, Johannes, Lavidas, Ilias, Mayer, Gerhard, Perez-Riverol, Yasset, Reisinger, Florian, Ternent, Tobias, Xu, Qing-Wei, Wang, Rui, Hermjakob, Henning
Published 2016

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets*

by Perez-Riverol, Yasset, Xu, Qing-Wei, Wang, Rui, Uszkoreit, Julian, Griss, Johannes, Sanchez, Aniel, Reisinger, Florian, Csordas, Attila, Ternent, Tobias, del-Toro, Noemi, Dianes, Jose A., Eisenacher, Martin, Hermjakob, Henning, Vizcaíno, Juan Antonio
Published 2016

2016 update of the PRIDE database and its related tools

by Vizcaíno, Juan Antonio, Csordas, Attila, del-Toro, Noemi, Dianes, José A., Griss, Johannes, Lavidas, Ilias, Mayer, Gerhard, Perez-Riverol, Yasset, Reisinger, Florian, Ternent, Tobias, Xu, Qing-Wei, Wang, Rui, Hermjakob, Henning
Published 2016

Ten Simple Rules for Taking Advantage of Git and GitHub

by Perez-Riverol, Yasset, Gatto, Laurent, Wang, Rui, Sachsenberg, Timo, Uszkoreit, Julian, Leprevost, Felipe da Veiga, Fufezan, Christian, Ternent, Tobias, Eglen, Stephen J., Katz, Daniel S., Pollard, Tom J., Konovalov, Alexander, Flight, Robert M., Blin, Kai, Vizcaíno, Juan Antonio
Published 2016

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

by Vizcaíno, Juan Antonio, Côté, Richard G., Csordas, Attila, Dianes, José A., Fabregat, Antonio, Foster, Joseph M., Griss, Johannes, Alpi, Emanuele, Birim, Melih, Contell, Javier, O’Kelly, Gavin, Schoenegger, Andreas, Ovelleiro, David, Pérez-Riverol, Yasset, Reisinger, Florian, Ríos, Daniel, Wang, Rui, Hermjakob, Henning
Published 2013

Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells

by Núñez de Villavicencio-Díaz, Teresa, Ramos Gómez, Yassel, Oliva Argüelles, Brizaida, Fernández Masso, Julio R., Rodríguez-Ulloa, Arielis, Cruz García, Yiliam, Guirola-Cruz, Osmany, Perez-Riverol, Yasset, Javier González, Luis, Tiscornia, Inés, Victoria, Sabina, Bollati-Fogolín, Mariela, Besada Pérez, Vladimir, Guerra Vallespi, Maribel
Published 2015

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience*

by Griss, Johannes, Jones, Andrew R., Sachsenberg, Timo, Walzer, Mathias, Gatto, Laurent, Hartler, Jürgen, Thallinger, Gerhard G., Salek, Reza M., Steinbeck, Christoph, Neuhauser, Nadin, Cox, Jürgen, Neumann, Steffen, Fan, Jun, Reisinger, Florian, Xu, Qing-Wei, del Toro, Noemi, Pérez-Riverol, Yasset, Ghali, Fawaz, Bandeira, Nuno, Xenarios, Ioannis, Kohlbacher, Oliver, Vizcaíno, Juan Antonio, Hermjakob, Henning
Published 2014