Publications

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2021

DOME: recommendations for supervised machine learning validation in biology

Nature Methods

I. Walsh, D. Fishman, D. Garcia-Gasulla, T. Titma, G. Pollastri, E. Capriotti, R. Casadio, S. Capella-Gutierrez, D. Cirillo, A. Del Conte, A. C. Dimopoulos, V. Dominguez Del Angel, J. Dopazo, P. Fariselli, J. Maria Fernández, F. Huber, A. Kreshuk, T. Lenaerts, P. Luigi Martelli, A. Navarro, P. Ó. Broin, J. Piñero, D. Piovesan, M. Reczko, F. Ronzano, V. Satagopam, C. Savojardo, V. Spiwok, M. Antonio Tangaro, G. Tartari, D. Salgado, A. Valencia, F. Zambelli, J. Harrow, F. E. Psomopoulos, and S. C. E. Tosatto
The Biomaterials Annotator: a system for ontology-based concept annotation of biomaterials text

Proceedings of the Second Workshop on Scholarly Document Processing

J. Corvi, C. Fuenteslópez, J. Fernández, J. Gelpí, M-P. Ginebra, S. Capella-Gutierrez, and O. Hakimi
The eTRANSAFE Project on Translational Safety Assessment through Integrative Knowledge Management: Achievements and Perspectives

Pharmaceuticals

F. Pognan, T. Steger-Hartmann, C. Díaz, N. Blomberg, F. Bringezu, K. Briggs, G. Callegaro, S. Capella-Gutierrez, E. Centeno, J. Corvi, P. Drew, W. C. Drewe, J. M. Fernández, L. I. Furlong, E. Guney, J. A. Kors, M. Angel Mayer, M. Pastor, J. Piñero, J. Manuel Ramírez-Anguita, F. Ronzano, P. Rowell, J. Saüch-Pitarch, A. Valencia, B. van de Water, J. van der Lei, E. van Mulligen, and F. Sanz

2020

The Quest for Orthologs benchmark service and consensus calls in 2020Abstract

Nucleic Acids Research

A. M. Altenhoff, J. Garrayo-Ventas, S. Cosentino, D. Emms, N. M. Glover, A. Hernández-Plaza, Y. Nevers, V. Sundesha, D. Szklarczyk, J. M. Fernández, L. Codó, the. Quest for Consortium, J. Ll Gelpi, J. Huerta-Cepas, W. Iwasaki, S. Kelly, O. Lecompte, M. Muffato, M. J. Martin, S. Capella-Gutierrez, P. D. Thomas, E. Sonnhammer, and C. Dessimoz
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships

Nature Communications

J. Sánchez-Valle, H. Tejero, J. María Fernández, D. Juan, B. Urda-García, S. Capella-Gutierrez, F. Al-Shahrour, R. Tabarés-Seisdedos, A. Baudot, V. Pancaldi, and A. Valencia

2019

Leveraging European infrastructures to access 1 million human genomes by 2022

Nature Reviews Genetics

G. Saunders, M. Baudis, R. Becker, S. Beltran, C. Béroud, E. Birney, C. Brooksbank, S. Brunak, M. Van den Bulcke, R. Drysdale, S. Capella-Gutierrez, P. Flicek, F. Florindi, P. Goodhand, I. Gut, J. Heringa, P. Holub, J. Hooyberghs, N. Juty, T. M. Keane, J. O. Korbel, I. Lappalainen, B. Leskošek, G. Matthijs, M. Th. Mayrhofer, A. Metspalu, A. Navarro, S. Newhouse, T. Nyrönen, A. Page, B. Persson, A. Palotie, H. Parkinson, J. Rambla, D. Salgado, E. Steinfelder, M. A. Swertz, A. Valencia, S. Varma, N. Blomberg, and S. Scollen
An intrinsically disordered proteins community for ELIXIR

F1000Research

N. E. Davey, M. M. Babu, M. Blackledge, A. Bridge, S. Capella-Gutierrez, Z. Dosztanyi, R. Drysdale, R. J. Edwards, A. Elofsson, I. C. Felli, T. J. Gibson, A. Gutmanas, J. M. Hancock, J. Harrow, D. Higgins, C. M. Jeffries, P. Le Mercier, B. Mészáros, M. Necci, C. Notredame, S. Orchard, C. A. Ouzounis, R. Pancsa, E. Papaleo, R. Pierattelli, D. Piovesan, V. J. Promponas, P. Ruch, G. Rustici, P. Romero, S. Sarntivijai, G. Saunders, B. Schuler, M. Sharan, D. C. Shields, J. L. Sussman, J. A. Tedds, P. Tompa, M. Turewicz, J. Vondrášek, W. F. Vranken, B. Ann Wallace, K. Wichapong, and S. C. E. Tosatto

2018

Ten steps to get started in Genome Assembly and Annotation

F1000Research

V. DominguezDel Angel, E. Hjerde, L. Sterck, S. Capella-Gutierrez, C. Notredame, O. Vinnere Pettersson, J. Amselem, L. Bouri, S. Bocs, C. Klopp, J-F. Gibrat, A. Vlasova, B. L. Leskosek, L. Soler, M. Binzer-Panchal, and H. Lantz

2017

Four simple recommendations to encourage best practices in research software

F1000Research

R. C. Jiménez, M. Kuzak, M. Alhamdoosh, M. Barker, B. Batut, M. Borg, S. Capella-Gutierrez, N. Chue Hong, M. Cook, M. Corpas, M. Flannery, L. Garcia, J L. Gelpí, S. Gladman, C. Goble, M. González Ferreiro, A. Gonzalez-Beltran, P. C. Griffin, B. Grüning, J. Hagberg, P. Holub, R. Hooft, J. Ison, D. S. Katz, B. Leskošek, F. López Gómez, L. J. Oliveira, D. Mellor, R. Mosbergen, N. Mulder, Y. Perez-Riverol, R. Pergl, H. Pichler, B. Pope, F. Sanz, M. V. Schneider, V. Stodden, R. Suchecki, R. Svobodová Vařeková, H-A. Talvik, I. Todorov, A. Treloar, S. Tyagi, M. van Gompel, D. Vaughan, A. Via, X. Wang, N. S. Watson-Haigh, and S. Crouch
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

Nucleic Acids Research

A. Cañada, S. Capella-Gutierrez, O. Rabal, J. Oyarzabal, A. Valencia, and M. Krallinger

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