Alfonso Valencia

2024

• 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
• Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation

  PASC '23: Platform for Advanced Scientific Computing ConferenceProceedings of the Platform for Advanced Scientific Computing Conference

  A. Huebl, C. Silvano, T. Robinson, M. Clascà, M. Garcia-Gasulla, A. Montagud, J. Carbonell Caballero, and A. Valencia