Computational Biology

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2024

Germline NPAT inactivating variants as cause of hereditary colorectal cancer

European Journal of Human Genetics

M. Terradas, S. A. Schubert, J. Viana-Errasti, D. Ruano, G. Aiza, M. Nielsen, P. Marciel, C. M. Tops, G. Parra, H. Morreau, D. Torrents, M. E. van Leerdam, G. Capellá, N. F. C. C. de Miranda, L. Valle, and T. van Wezel
A contact‐based analysis of local energetic frustration dynamics identifies key residues enabling

Protein Science

J. González‐Higueras, M. Inés Freiberger, P. Galaz‐Davison, G. R. Parra, and C. A. Ramírez‐Sarmiento
Modulating the immune response to SARS-CoV-2 by different nanocarriers delivering an mRNA expressing trimeric RBD of the spike protein: COVARNA Consortium

npj Vaccines

L. Marcos-Villar, B. Perdiguero, S. Anthiya, M. L. Borrajo, G. Lou, L. Franceschini, I. Esteban, P. J. Sánchez-Cordón, C. Zamora, C. Óscar S. Sorzano, L. Jordá, L. Codó, J. L. Gelpí, M. Sisteré-Oró, A. Meyerhans, K. Thielemans, F. Martínez-Jiménez, N. López-Bigas, F. García, M. J. Alonso, M. Plana, M. Esteban, and C. Elena Gómez
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. 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
Multi-omic and single-cell profiling of chromothriptic medulloblastoma reveals genomic and transcriptomic consequences of genome instabilityAbstract

Nature Communications

P. Smirnov, M. J. Przybilla, M. Simovic-Lorenz, G. R. Parra, H. Susak, M. Ratnaparkhe, J. K. L. Wong, V. Körber, J-P. Mallm, G. Philippos, M. Sill, T. Kolb, R. Kumar, N. Casiraghi, K. Okonechnikov, D. R. Ghasemi, K. Korinna Maaß, K. W. Pajtler, A. Jauch, A. Korshunov, T. Höfer, M. Zapatka, S. M. Pfister, W. Huber, O. Stegle, and A. Ernst
A contact‐based analysis of local energetic frustration dynamics identifies key residues enabling Abstract

Protein Science

J. González‐Higueras, M. Inés Freiberger, P. Galaz‐Davison, G. R. Parra, and C. A. Ramírez‐Sarmiento
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
Immunization with V987H-stabilized Spike glycoprotein protects K18-hACE2 mice and golden Syrian hamsters upon SARS-CoV-2 infection

Nature Communications

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, 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, V. Guallar, B. Clotet, J. Segalés, and J. Carrillo
Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Frontiers in Immunology

A. Niarakis, M. Ostaszewski, A. Mazein, I. Kuperstein, M. Kutmon, M. E. Gillespie, A. Funahashi, M. Luis Acencio, A. Hemedan, M. Aichem, K. Klein, T. Czauderna, F. Burtscher, T. G. Yamada, Y. Hiki, N. F. Hiroi, F. Hu, N. Pham, F. Ehrhart, E. L. Willighagen, A. Valdeolivas, A. Dugourd, F. Messina, M. Esteban-Medina, M. Peña-Chilet, K. Rian, S. Soliman, S. Sadat Aghamiri, B. Lal Puniya, A. Naldi, T. Helikar, V. Singh, M. Fariñas Fernández, V. Bermudez, E. Tsirvouli, A. Montagud, V. Noël, M. Ponce-de-Leon, D. Maier, A. Bauch, B. M. Gyori, J. A. Bachman, A. Luna, J. Piñero, L. I. Furlong, I. Balaur, A. Rougny, Y. Jarosz, R. W. Overall, R. Phair, L. Perfetto, L. Matthews, D. Arokia Bal Rex, M. Orlic-Milacic, L. Cristobal Gomez, B. De Meulder, J. Marie Ravel, B. Jassal, V. Satagopam, G. Wu, M. Golebiewski, P. Gawron, L. Calzone, J. S. Beckmann, C. T. Evelo, P. D’Eustachio, F. Schreiber, J. Saez-Rodriguez, J. Dopazo, M. Kuiper, A. Valencia, O. Wolkenhauer, H. Kitano, E. Barillot, C. Auffray, R. Balling, and R. Schneider
Roadmap for a European cancer data management and precision medicine infrastructure

Nature Cancer

M. Nikolski, E. Hovig, F. Al-Shahrour, N. Blomberg, S. Scollen, A. Valencia, and G. Saunders
UNCAN.eu: Toward a European Federated Cancer Research Data Hub

Cancer Discovery

M. Boutros, M. Baumann, A. Bigas, L. Chaabane, J. Guérin, J. K. Habermann, A. Jobard, P G. Pelicci, O. Stegle, G. Tonon, A. Valencia, E. C. Winkler, P. Blanc, R. De Maria, R. H. Medema, P. Nagy, J. Tabernero, and E. Solary
Virus-like particle-mediated delivery of structure-selected neoantigens demonstrates immunogenicity and antitumoral activity in mice

Journal of Translational Medicine

A. Barajas, P. Amengual-Rigo, A. Pons-Grífols, R. Ortiz, O. Gracia Carmona, V. Urrea, N. de la Iglesia, J. Blanco-Heredia, C. Anjos-Souza, I. Varela, B. Trinité, F. Tarrés-Freixas, C. Rovirosa, R. Lepore, M. Vazquez, L. De Mattos-Arruda, A. Valencia, B. Clotet, C. Aguilar-Gurrieri, V. Guallar, J. Carrillo, and J. Blanco
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
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

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