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2024

Lung Tissue Multi-Layer Network Analysis Uncovers the Molecular Heterogeneity of COPD

Am J Respir Crit Care Med .

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
Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein familiesAbstract

Nucleic Acids Research

G. R. Parra, M. I. Freiberger, M. Poley-Gil, M. Fernandez-Martin, L. G. Radusky, V. Ruiz-Serra, P. G. Wolynes, D. U. Ferreiro, and A. Valencia
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, T. Chamova, I. Tournev, V. Guergueltcheva, S. Laurie, S. Beltran, S. Capella-Gutierrez, D. Cirillo, H. Lochmüller, and A. Valencia

2023

Local energetic frustration conservation in protein families and superfamilies

Nature Communications

M. I. Freiberger, V. Ruiz-Serra, C. Pontes, M. Romero-Durana, P. Galaz-Davison, C. A. Ramírez-Sarmiento, C. D. Schuster, M. A. Marti, P. G. Wolynes, D. U. Ferreiro, G. R. Parra, and A. Valencia
Novel Spike-stabilized trimers with improved production protect K18-hACE2 mice and golden Syrian hamsters from the highly pathogenic SARS-CoV-2 Beta variant

Frontiers in Immunology

C. Ávila-Nieto, J. Vergara-Alert, P. Amengual-Rigo, E. Ainsua-Enrich, M. Brustolin, M. Luisa Rodr de la Concepción, N. Pedreño-Lopez, J. Rodon, V. Urrea, E. Pradenas, S. Marfil, E. Ballana, E. Riveira-Muñoz, M. Pérez, N. Roca, F. Tarrés-Freixas, J. Carabelli, G. Cantero, A. Pons-Grífols, C. Rovirosa, C. Aguilar-Gurrieri, R. Ortiz, A. Barajas, B. Trinité, R. Lepore, J. Muñoz-Basagoiti, D. Perez-Zsolt, N. Izquierdo-Useros, A. Valencia, J. Blanco, B. Clotet, V. Guallar, J. Segalés, and J. Carrillo
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations

Database

A. Miranda-Escalada, F. Mehryary, J. Luoma, D. Estrada-Zavala, L. Gasco, S. Pyysalo, A. Valencia, and M. Krallinger
The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer

Nature Communications

A. Armaos, F. Serra, I. Núñez-Carpintero, J-H. Seo, S. C. Baca, S. Gustincich, A. Valencia, M. L. Freedman, D. Cirillo, C. Giambartolomei, and G. Gaetano Tartaglia
PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks

npj Syst Biol Appl

M. Ponce-de-Leon, A. Montagud, V. Noël, A. Meert, G. Pradas, E. Barillot, L. Calzone, and A. Valencia
An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Journal of Visualized Experiments

L. Rovirosa, L. Tomas-Daza, B. Urmeneta, A. Valencia, and B. M. Javierre
Engaging European society at the forefront of cancer research and care

Molecular Oncology

M. Baumann, J. Celis, U. Ringborg, M. Heitor, A. Berns, T. Albreht, J. Arabadjiev, M. Boutros, M. Brandenburg, H. Canhao, F. Carneiro, C. Chomienne, F. De Lorenzo, A. M. M. Eggermont, A. Font, E. Garralda, M. Goulart, R. Henrique, M. Lawler, L. Maier‐Hein, F. Meunier, S. Oberst, P. Oliveira, M. Papatriantafyllou, J. Schüz, E. Solary, A. Valencia, R. Vargas, E. Weiderpass, and N. Wilking

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