Publications

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2024

Lung Tissue Multilayer Network Analysis Uncovers the Molecular Heterogeneity of Chronic Obstructive Pulmonary Disease

American Journal of Respiratory and Critical Care Medicine

N. Olvera, J. Sánchez-Valle, I. Núñez-Carpintero, J. Rojas-Quintero, G. Noell, S. Casas-Recasens, A. Faiz, P. Hansbro, A. Guirao, R. Lepore, D. Cirillo, A. Agustí, F. Polverino, A. Valencia, and R. Faner
Immune digital twins for complex human pathologies: applications, limitations, and challenges

npj Systems Biology and Applications

A. Niarakis, R. Laubenbacher, G. An, Y. Ilan, J. Fisher, Å. Flobak, K. Reiche, M. Rodríguez Martínez, L. Geris, L. Ladeira, L. Veschini, M. L. Blinov, F. Messina, L. L. Fonseca, S. Ferreira, A. Montagud, V. Noël, M. Marku, E. Tsirvouli, M. M. Torres, L. A. Harris, T.. J. Sego, C. Cockrell, A. E. Shick, H. Balci, A. Salazar, K. Rian, A. Abdelmonem Hemedan, M. Esteban-Medina, B. Staumont, E. Hernandez-Vargas, S. Martis B, A. Madrid-Valiente, P. Karampelesis, L. Sordo Vieira, P. Harlapur, A. Kulesza, N. Nikaein, W. Garira, R. S. Malik Sheriff, J. Thakar, V. Du T. Tran, J. Carbonell-Caballero, S. Safaei, A. Valencia, A. Zinovyev, and J. A. Glazier
Analyzing sex imbalance in EGA and dbGaP biological databases: Recommendations for better practices

iScience

V. Ruiz-Serra, N. Buslón, O. R. Philippe, D. Saby, M. Morales, C. Pontes, A. Muñoz Andirkó, G. L. Holliday, A. Jené, M. Moldes, J. Ramblas, A. Valencia, M. José Rementeria, A. Cortés, and D. Cirillo
Analyzing sex imbalance in EGA and dbGaP biological databases: Recommendations for better practices

iScience

V. Ruiz-Serra, N. Buslón, O. R. Philippe, D. Saby, M. Morales, C. Pontes, A. Muñoz Andirkó, G. L. Holliday, A. Jené, M. Moldes, J. Rambla, A. Valencia, M. José Rementeria, A. Cortés, and D. Cirillo
Risk of cancer development associated with disease-modifying therapies for multiple sclerosis: study protocol for a systematic review and meta-analysis of randomised and non-randomised studies

Systematic Reviews

F. Catalá-López, L. Tejedor-Romero, J. A. Driver, B. Hutton, J. Vicent Sánchez-Ortí, M. Ridao, A. Alonso-Arroyo, P. Correa-Ghisays, J. Forés-Martos, V. Balanzá-Martínez, A. Valencia, I. Cobos, and R. Tabarés-Seisdedos
Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes

Nature Communications

I. Núñez-Carpintero, M. Rigau, M. Bosio, E. O’Connor, S. Spendiff, Y. Azuma, A. Topf, R. Thompson, P. A. C. ’t Hoen, T. Chamova, I. Tournev, V. Guergueltcheva, S. Laurie, S. Beltran, S. Capella-Gutierrez, D. Cirillo, H. Lochmüller, and A. Valencia
The 1+Million Genomes Minimal Dataset for Cancer

Nature Genetics

M. Riba, C. Sala, A. C. Culhane, Å. Flobak, A. Patocs, K. Boye, K. Plevova, Š. Pospíšilová, G. Gandolfi, M. J. Morelli, G. Bucci, A. Edsjö, U. Lassen, F. Al-Shahrour, N. López-Bigas, R. Hovland, E. Cuppen, A. Valencia, H. A. Poirel, R. Rosenquist, S. Scollen, J. Arenas Marquez, J. Belien, A. De Nicolo, R. De Maria, D. Torrents, and G. Tonon
p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response

Nature Communications

F. Serra, A. Nieto-Aliseda, L. Fanlo-Escudero, L. Rovirosa, M. Cabrera-Pasadas, A. Lazarenkov, B. Urmeneta, A. Alcalde-Merino, E. M. Nola, A. L. Okorokov, P. Fraser, M. Graupera, S. D. Castillo, J. L. Sardina, A. Valencia, and B. M. Javierre
3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures

Bioinformatics

V. Ruiz-Serra, S. Valentini, S. Madroñero, A. Valencia, and E. Porta-Pardo
3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures

Bioinformatics

V. Ruiz-Serra, S. Valentini, S. Madroñero, A. Valencia, and E. Porta-Pardo

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