Alfonso Valencia

2023

• 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
• eTRANSAFE: data science to empower translational safety assessment

  Nature Reviews Drug Discovery

  F. Sanz, F. Pognan, T. Steger-Hartmann, C. Díaz, S. Asakura, A. Amberg, N. Bécourt-Lhote, N. Blomberg, N. Bosc, K. Briggs, F. Bringezu, C. Brulle-Wohlhueter, S. Brunak, R. Bueters, G. Callegaro, S. Capella-Gutierrez, E. Centeno, J. Corvi, M. T. D. Cronin, P. Drew, G. Duchateau-Nguyen, G. F. Ecker, S. Escher, E. Felix, M. Ferreiro, M. Frericks, L. I. Furlong, R. Geiger, C. George, M. Grandits, D. Ivanov-Draganov, J. Kilgour-Christie, T. Kiziloren, J. A. Kors, N. Koyama, A. Kreuchwig, A. R. Leach, M-A. Mayer, P. Monecke, W. Muster, C. Miyamoto Nakazawa, G. Nicholson, R. Parry, M. Pastor, J. Piñero, N. Oberhauser, J. Manuel Ramírez-Anguita, A. Rodrigo, A. Smajic, M. Schaefer, S. Schieferdecker, I. Soininen, E. Terricabras, P. Trairatphisan, S. C. Turner, A. Valencia, B. van de Water, J. L. van der Lei, E. M. van Mulligen, E. Vock, and D. Wilkinson
• Molecular bases of comorbidities: present and future perspectives

  Trends in Genetics

  J. Sánchez-Valle, and A. Valencia
• Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution

  Nature Communications

  L. Tomas-Daza, L. Rovirosa, P. López-Martí, A. Nieto-Aliseda, F. Serra, A. Planas-Riverola, O. Molina, R. McDonald, C. Ghevaert, E. Cuatrecasas, D. Costa, M. Camós, C. Bueno, P. Menéndez, A. Valencia, and B. M. Javierre
• Predicting the evolution of COVID-19 mortality risk: A recurrent neural network approach

  Computer Methods and Programs in Biomedicine Update

  M. Villegas, A. Gonzalez-Agirre, A. Gutiérrez-Fandiño, J. Armengol-Estapé, C. Pio Carrino, D. Pérez-Fernández, F. Soares, P. Serrano, M. Pedrera, N. García, and A. Valencia