Publications

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2021

Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems

Current Opinion in Systems Biology

A. Montagud, M. Ponce-de-Leon, and A. Valencia
BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems

Lecture Notes in Computer Science

G. Saxena, M. Ponce-de-Leon, A. Montagud, D. Vicente Dorca, and A. Valencia
COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain

Scientific Data

M. Ponce De Leon, J. del Valle, J. Maria Fernández, M. Bernardo, D. Cirillo, J. Sánchez-Valle, M. Smith, S. Capella-Gutierrez, T. Gullón, and A. Valencia
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
MAX mutant small-cell lung cancers exhibit impaired activities of MGA-dependent noncanonical polycomb repressive complex

Proceedings of the National Academy of Sciences

P. Llabata, M. Torres-Diz, A. Gomez, L. Tomas-Daza, O. A. Romero, J. Grego-Bessa, P. Llinas-Arias, A. Valencia, M. Esteller, B. M. Javierre, X. Zhang, and M. Sanchez-Cespedes
Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas

Leukemia

D. Hübschmann, K. Kleinheinz, R. Wagener, S. H. Bernhart, C. López, U. H. Toprak, S. Sungalee, N. Ishaque, H. Kretzmer, M. Kreuz, S. M. Waszak, N. Paramasivam, O. Ammerpohl, S. M. Aukema, R. Beekman, A. K. Bergmann, M. Bieg, H. Binder, A. Borkhardt, C. Borst, B. Brors, P. Bruns, E. Carrillo d Pau, A. Claviez, G. Doose, A. Haake, D. Karsch, S. Haas, M-L. Hansmann, J. I. Hoell, V. Hovestadt, B. Huang, M. Hummel, C. Jäger-Schmidt, J. N. A. Kerssemakers, J. O. Korbel, D. Kube, C. Lawerenz, D. Lenze, J. H. A. Martens, G. Ott, B. Radlwimmer, E. Reisinger, J. Richter, D. Rico, P. Rosenstiel, A. Rosenwald, M. Schillhabel, S. Stilgenbauer, P. F. Stadler, J. I. Martin-Subero, M. Szczepanowski, G. Warsow, M. A. Weniger, M. Zapatka, A. Valencia, H. G. Stunnenberg, P. Lichter, P. Möller, M. Loeffler, R. Eils, W. Klapper, S. Hoffmann, L. Trümper, R. Küppers, M. Schlesner, and R. Siebert
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
The multilayer community structure of medulloblastoma

iScience

I. Núñez-Carpintero, M. Petrizzelli, A. Zinovyev, D. Cirillo, and A. Valencia
Artificial Intelligence–Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development

Journal of Medical Internet Research

E. Santus, N. Marino, D. Cirillo, E. Chersoni, A. Montagud, A. Santuccion Chadha, A. Valencia, K. Hughes, and C. Lindvall
Artificial intelligence in cancer research: learning at different levels of data granularity

Molecular Oncology

D. Cirillo, I. Núñez-Carpintero, and A. Valencia

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