Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Computational team

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2025

Empowering cancer research in Europe: the EUCAIM cancer imaging infrastructure

Insights into Imaging

L. Marti-Bonmati, I. Blanquer, M. Tsiknakis, G. Tsakou, R. Martinez, S. Capella-Gutierrez, S. Zullino, J. Meszaros, E. E. Bron, J. Lluis Gelpí, K. Riklund, L. Chaabane, H-P. Schlemmer, M. Aznar, P. Serrano Candelas, P. Gordebeke, M. Hierath, H. Leisz, N. D’Ascenzo, M. Castelo-Branco, I. Chouvarda, L. Fournier, S. Figueiras Gómez, A. Navarro, N. Papanikolaou, L. Barbieri, J-P. Beregi, G. Langs, D. Rodríguez González, E. Sala, Y. Roussakis, G. Di Leo, A. López-Rueda, S. Pedraza, J. Blázquez, C. Luis Parra Calderón, S. Marsoni, D. Sáez-Domingo, M. Aiello, F. Strand, M-C. Jaulent, J. Hedlund, L. Saint-Aubert, C. Catalano, R. Beets-Tan, H. Heese, A. Alberich-Bayarri, B. van Ginneken, M. Van den Bulcke, D. Rückert, E. Neri, P. Lambin, G. Marx, B. Persson, W. Vos, C. Sousa Pinto, P. Fuhrmann, M. Bobowicz, C. Hernández-Ferrer, O. Humbert, J. Miguel Ros Tejada, M. França, P. Holub, Z. Dudova, I. Huys, M. Pallocca, J. Haybaeck, P. Gazinska, A. Seebohm, T. Penzkofer, N. Sandberg, O. Gil García, F. Martin-Sanchez, and S. Scollen
The need to implement FAIR principles in biomolecular simulations

Nature Methods

R. E. Amaro, J. Åqvist, I. Bahar, F. Battistini, A. Bellaiche, D. Beltrán, P. C. Biggin, M. Bonomi, G. R. Bowman, R. A. Bryce, et al.

2024

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows

PLOS Computational Biology

G. Bayarri, P. Andrio, J. Lluis Gelpí, A. Hospital, and M. Orozco
FAIRsoft—a practical implementation of FAIR principles for research software

Bioinformatics

E. Martíndel Pico, J. Lluis Gelpí, and S. Capella-Gutierrez
Heterologous mRNA/MVA delivering trimeric-RBD as effective vaccination regimen against SARS-CoV-2: COVARNA Consortium

Emerging Microbes & Infections

L. Marcos-Villar, B. Perdiguero, M. López-Bravo, C. Zamora, L. Sin, E. Álvarez, C. Óscar S. Sorzano, P. J. Sánchez-Cordón, J. M. Casasnovas, D. Astorgano, J. García-Arriaza, S. Anthiya, M. L. Borrajo, G. Lou, B. Cuesta, L. Franceschini, J. Ll. Gelpi, K. Thielemans, M. Sisteré-Oró, A. Meyerhans, F. García, I. Esteban, N. López-Bigas, M. Plana, M. J. Alonso, M. Esteban, and C. Elena Gómez
Assessment of Human SARS CoV-2-Specific T-Cell Responses Elicited In Vitro by New Computationally Designed mRNA Immunogens (COVARNA)

Vaccines

I. Esteban, C. Pastor-Quiñones, L. Usero, E. Aurrecoechea, L. Franceschini, A. Esprit, J. Lluis Gelpí, F. Martínez-Jiménez, N. López-Bigas, K. Breckpot, K. Thielemans, L. Leal, C. Elena Gómez, M. Sisteré-Oró, A. Meyerhans, M. Esteban, M. José Alonso, F. García, and M. Plana

2023

Cohort Profile: The Cardiovascular Research Data Catalogue

International Journal of Epidemiology

J. Reinikainen, T. Palosaari, A. J. Canosa-Valls, C. O. Schmidt, R. Wissa, S. Chadalavada, L. Codó, J. Lluis Gelpí, B. Joseph, A. van der Lugt, E. Pacella, S. E. Petersen, E. Ruiz Pujadas, L. Szabo, T. Zeller, T. Niiranen, K. Lekadir, and K. Kuulasmaa
Data infrastructures for AI in medical imaging: a report on the experiences of five EU projects

European Radiology Experimental

H. Kondylakis, V. Kalokyri, S. Sfakianakis, K. Marias, M. Tsiknakis, A. Jimenez-Pastor, E. Camacho-Ramos, I. Blanquer, D. J. Segrelles, S. López-Huguet, C. Barelle, M. Kogut-Czarkowska, G. Tsakou, N. Siopis, Z. Sakellariou, P. Bizopoulos, V. Drossou, A. Lalas, K. Votis, P. Mallol, L. Marti-Bonmati, L. Cerdá Alberich, K. Seymour, S. Boucher, E. Ciarrocchi, L. Fromont, J. Rambla, A. Harms, A. Gutierrez, M. P. A. Starmans, F. Prior, J. Ll. Gelpi, and K. Lekadir
RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12

Nucleic Acids Research

H. Salgado, S. Gama-Castro, P. Lara, C. Mejia-Almonte, G. Alarcón-Carranza, A. G. López-Almazo, F. Betancourt-Figueroa, P. Peña-Loredo, S. Alquicira-Hernández, D. Ledezma-Tejeida, L. Arizmendi-Zagal, F. Mendez-Hernandez, A. K. Diaz-Gomez, E. Ochoa-Praxedis, L. J. Muñiz-Rascado, J. S. García-Sotelo, F. A. Flores-Gallegos, L. Gómez, C. Bonavides-Martínez, V. M. del Moral-Chávez, A. J. Hernández-Alvarez, A. Santos-Zavaleta, S. Capella-Gutierrez, J. Lluis Gelpí, and J. Collado-Vides
A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort

Nucleic Acids Research

D. Beltrán, A. Hospital, J. Lluis Gelpí, and M. Orozco
DEBBIE: The Open Access Database of Experimental Scaffolds and Biomaterials Built Using an Automated Text Mining Pipeline

Advanced Healthcare Materials

J. O. Corvi, A. McKitrick, J. M. Fernández, C. V. Fuenteslópez, J. L. Gelpí, M‐P. Ginebra, S. Capella‐Gutierrez, and O. Hakimi
High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic

Journal of Chemical Information and Modeling

A. Suriñach, A. Hospital, Y. Westermaier, L. Jordá, S. Orozco-Ruiz, D. Beltrán, F. Colizzi, P. Andrio, R. Soliva, M. Municoy, J. Lluis Gelpí, and M. Orozco

2022

Signatures of TOP1 transcription-associated mutagenesis in cancer and germlineAbstract

Nature

M. A. M. Reijns, D. A. Parry, T. C. Williams, F. Nadeu, R. L. Hindshaw, D. O. Rios Szwed, M. D. Nicholson, P. Carroll, S. Boyle, R. Royo, A. J. Cornish, H. Xiang, K. Ridout, J. C. Ambrose, P. Arumugam, R. Bevers, M. Bleda, F. Boardman-Pretty, C. R. Boustred, H. Brittain, M. J. Caulfield, G. C. Chan, G. Elgar, T. Fowler, A. Giess, A. Hamblin, S. Henderson, T. J. P. Hubbard, R. Jackson, L. J. Jones, D. Kasperaviciute, M. Kayikci, A. Kousathanas, L. Lahnstein, S. E. A. Leigh, I. U. S. Leong, J. F. Lopez, F. Maleady-Crowe, M. McEntagart, F. Minneci, L. Moutsianas, M. Mueller, N. Murugaesu, A. C. Need, P. O’Donovan, C. A. Odhams, C. Patch, M. Buongermin Pereira, D. Perez-Gil, J. Pullinger, T. Rahim, A. Rendon, T. Rogers, K. Savage, K. Sawant, R. H. Scott, A. Siddiq, A. Sieghart, S. C. Smith, A. Sosinsky, A. Stuckey, M. Tanguy, A. Lisa Taylo Tavares, E. R. A. Thomas, S. R. Thompson, A. Tucci, M. J. Welland, E. Williams, K. Witkowska, S. M. Wood, D. Chubb, A. Cornish, B. Kinnersley, R. Houlston, D. Wedge, A. Gruber, A. Frangou, W. Cross, T. Graham, A. Sottoriva, G. Caravagna, N. López-Bigas, C. Arnedo-Pac, D. Church, R. Culliford, S. Thorn, P. Quirke, H. Wood, I. Tomlinson, B. Noyvert, A. Schuh, K. Aden, C. Palles, E. Campo, T. Stankovic, M. S. Taylor, and A. P. Jackson
Detection of early seeding of Richter transformation in chronic lymphocytic leukemia

Nature Medicine

F. Nadeu, R. Royo, R. Massoni-Badosa, H. Playa-Albinyana, B. Garcia-Torre, M. Duran-Ferrer, K. J. Dawson, M. Kulis, A. Diaz-Navarro, N. Villamor, J. L. Melero, V. Chapaprieta, A. Dueso-Barroso, J. Delgado, R. Moia, S. Ruiz-Gil, D. Marchese, A. Giró, N. Verdaguer-Dot, M. Romo, G. Clot, M. Rozman, G. Frigola, A. Rivas-Delgado, T. Baumann, M. Alcoceba, M. González, F. Climent, P. Abrisqueta, J. Castellví, F. Bosch, M. Aymerich, A. Enjuanes, S. Ruiz-Gaspà, A. López-Guillermo, P. Jares, S. Beà, S. Capella-Gutierrez, J. Ll. Gelpi, N. López-Bigas, D. Torrents, P. J. Campbell, I. Gut, D. Rossi, G. Gaidano, X. S. Puente, P. M. Garcia-Roves, D. Colomer, H. Heyn, F. Maura, J. I. Martin-Subero, and E. Campo
Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case

WIREs Computational Molecular Science

M. Wieczór, V. Genna, J. Aranda, R. M. Badia, J. Lluis Gelpí, V. Gapsys, B. L. de Groot, E. Lindahl, M. Municoy, A. Hospital, and M. Orozco
ATM germline variants in a young adult with chronic lymphocytic leukemia: 8 years of genomic evolution

Blood Cancer Journal

R. Royo, L. Magnano, J. Delgado, S. Ruiz-Gil, J. Ll. Gelpi, H. Heyn, M. A. Taylor, T. Stankovic, X. S. Puente, F. Nadeu, and E. Campo
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations

Nucleic Acids Research

G. Bayarri, P. Andrio, A. Hospital, M. Orozco, and J. Lluis Gelpí
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation

Bioinformatics

G. Bayarri, P. Andrio, A. Hospital, M. Orozco, and J. Lluis Gelpí

2021

TIGER: The gene expression regulatory variation landscape of human pancreatic islets

Cell Reports

L. Alonso, A. Piron, I. Moran, M. Guindo-Martínez, S. Bonàs-Guarch, G. Atla, I. Miguel-Escalada, R. Royo, M. Puiggròs, X. Garcia-Hurtado, M. Suleiman, L. Marselli, J. L. S. Esguerra, J-V. Turatsinze, J. M. Torres, V. Nylander, J. Chen, L. Eliasson, M. Defrance, R. Amela, H. Mulder, A. L. Gloyn, L. Groop, P. Marchetti, D. L. Eizirik, J. Ferrer, J. M. Mercader, M. Cnop, and D. Torrents
An agenda-setting paper on data sharing platforms: euCanSHare workshop

Open Research Europe

T. Devriendt, C. Ammann, F. W. Asselbergs, A. Bernier, R. Costas, M. G. Friedrich, J. L. Gelpí, M-R. Jarvelin, K. Kuulasmaa, K. Lekadir, M. Th. Mayrhofer, V. Papez, G. Pasterkamp, S. E. Petersen, C. Oliver Schmidt, J. Schulz-Menger, S. Söderberg, M. Shabani, G. Veronesi, D. Steven Viezzer, and P. Borry
Identifying causative mechanisms linking early-life stress to psycho-cardio-metabolic multi-morbidity: The EarlyCause project

PLOS ONE

N. Mariani, A. Borsini, C. A. M. Cecil, J. F. Felix, S. Sebert, A. Cattaneo, E. Walton, Y. Milaneschi, G. Cochrane, C. Amid, J. Rajan, J. Giacobbe, Y. Sanz, A. Agustí, T. Sorg, Y. Herault, J. Miettunen, P. Parmar, N. Cattane, V. Jaddoe, J. Lötjönen, C. Buisan, M. A. Gonzál Ballester, G. Piella, J. L. Gelpí, F. Lamers, B. W. J. H. Penninx, H. Tiemeier, M. von Tottleben, R. Thiel, K. F. Heil, M-R. Jarvelin, C. Pariante, I. M. Mansuy, and K. Lekadir

2020

The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome

Nature Cancer

M. Duran-Ferrer, G. Clot, F. Nadeu, R. Beekman, T. Baumann, J. Nordlund, Y. Marincevic-Zuniga, G. Lönnerholm, A. Rivas-Delgado, S. Martín, R. Ordoñez, G. Castellano, M. Kulis, A. C. Queirós, S-T. Lee, J. Wiemels, R. Royo, M. Puiggròs, J. Lu, E. Giné, S. Beà, P. Jares, X. Agirre, F. Prosper, C. López-Otín, X. S. Puente, C. C. Oakes, T. Zenz, J. Delgado, A. López-Guillermo, E. Campo, and J. Ignacio Martín-Subero
Butler enables rapid cloud-based analysis of thousands of human genomesAbstract

Nature Biotechnology

S. Yakneen, S. M. Waszak, M. Gertz, and J. O. Korbel
4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

Molecular Cell

S. Sati, B. Bonev, Q. Szabo, D. Jost, P. Bensadoun, F. Serra, V. Loubiere, G. Lucio Papadopoulos, J-C. Rivera-Mulia, L. Fritsch, P. Bouret, D. Castillo, J. Ll. Gelpi, M. Orozco, C. Vaillant, F. Pellestor, F. Bantignies, M. A. Martí-Renom, D. M. Gilbert, J-M. Lemaitre, and G. Cavalli
The Quest for Orthologs benchmark service and consensus calls in 2020Abstract

Nucleic Acids Research

A. M. Altenhoff, J. Garrayo-Ventas, S. Cosentino, D. Emms, N. M. Glover, A. Hernández-Plaza, Y. Nevers, V. Sundesha, D. Szklarczyk, J. M. Fernández, L. Codó, the. Quest for Consortium, J. Ll Gelpi, J. Huerta-Cepas, W. Iwasaki, S. Kelly, O. Lecompte, M. Muffato, M. J. Martin, S. Capella-Gutierrez, P. D. Thomas, E. Sonnhammer, and C. Dessimoz
Bioactive Conformational Ensemble Server and Database. A Public Framework to Speed Up In Silico Drug DiscoveryBioactive Conformational Ensemble Server and Database. A Public Framework to Speed Up In Silico Drug Discovery

Journal of Chemical Theory and Computation

S. Zivanovic, G. Bayarri, F. Colizzi, D. Moreno, J. Lluis Gelpí, R. Soliva, A. Hospital, and M. Orozco
Sex differences in oncogenic mutational processes

Nature Communications

C. H. Li, S. D. Prokopec, R. X. Sun, F. Yousif, N. Schmitz, P. C. Boutros, and
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nature Communications

M. H. Bailey, W. U. Meyerson, L. Jonathan Dursi, L-B. Wang, G. Dong, W-W. Liang, A. Weerasinghe, S. Li, Y. Li, S. Kelso, G. Saksena, K. Ellrott, M. C. Wendl, D. A. Wheeler, G. Getz, J. T. Simpson, M. B. Gerstein, and L. Ding
Time to kick-start text mining for biomaterials

Nature Reviews Materials

O. Hakimi, M. Krallinger, and M-P. Ginebra
Pan-cancer analysis of whole genomes

Nature

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