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PhD Thesis - Structural Bioinformatics

Meseguer A. Methods to model and assess protein-DNA and protein-protein interactions in the context of gene regulation.  Universitat Pompeu Fabra. July, 2nd 2021. Thesis Director: Oliva B.

2021

PhD Thesis - Structural Bioinformatics

Aguirre J. ​In silico tools to study diseases and polypharmacology through the lens of network medicine.  Universitat Pompeu Fabra. July, 14th 2021. Thesis Director: Oliva B.

2021

Original articles in indexed journals - Integrative Biomedical Informatics - Structural Bioinformatics

Aguirre-Plans J, Piñero J, Souza T, Callegaro G, Kunnen SJ, Sanz F, Fernandez-Fuentes N, Furlong LI, Guney E, Oliva B. An ensemble learning approach for modeling the systems biology of drug-induced injury. Biol Direct, 2021; 16(1):5. PMID: 33435983 . DOI: 10.1186/s13062-020-00288-x.

2021

Original articles in indexed journals - Structural Bioinformatics

Aguirre-Plans J, Meseguer A, Molina-Fernandez R, Marín-López MA, Jumde G, Casanova K, Bonet J, Fornes O, Fernandez-Fuentes N, Oliva B. SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions. BMC Bioinformatics, 2021; 22(1):4. PMID: 33407073 . DOI: 10.1186/s12859-020-03770-5.

2021

Original articles in indexed journals - Structural Bioinformatics

Walsh S, Izquierdo-Serra M, Acosta S, Edo A, Lloret M, Moret R, Bosch E, Oliva B, Bertranpetit J, Fernández-Fernández JM. Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population. Sci Rep, 2020; 10(1): 20999. PMID: 33268808 . DOI: 10.1038/s41598-020-78081-z.

2020

Original articles in indexed journals - Structural Bioinformatics

Artigas L, Coma M, Matos-Filipe P, Aguirre-Plans J, Farrés J, Valls R, Fernandez-Fuentes N, de la Haba-Rodriguez J, Olvera A, Barbera J, Morales R, Oliva B, Mas JM. In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm. PLoS One, 2020; 15(10): e02401495. PMID: 33006999 . DOI: 10.1371/journal.pone.0240149.

2020

Original articles in indexed journals - Structural Bioinformatics

Meseguer A, Dominguez L, Bota PM, Aguirre-Plans J, Bonet J, Fernandez-Fuentes N, Oliva B. Using collections of structural models to predict changes of binding affinity caused by mutations in protein-protein interactions. Protein Sci, 2020; 29(10): 2112-2130. PMID: 32797645 . DOI: 10.1002/pro.3930.

2020

Original articles in indexed journals - Structural Bioinformatics

Mirela-Bota P, Aguirre-Plans J, Meseguer A, Galletti C, Segura J, Planas-Iglesias J, Garcia-Garcia J, Guney E, Oliva B, Fernandez-Fuentes N. Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data. J Mol Biol, 2020: 166656. PMID: 32976910 . DOI: 10.1016/j.jmb.2020.09.015.

2020

Other - Structural Bioinformatics

Meseguer A, Arman F, Fornes O, Molina-Fernández R, Bonet J, Fernandez-Fuentes N, Oliva B. On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF. NAR Genom Bioinform, 2020; 2(3): lqaa046. PMID: 33575598 . DOI: 10.1093/nargab/lqaa046.

2020

Original articles in indexed journals - Structural Bioinformatics

Jorba G, Aguirre-Plans J, Junet V, Segú-Vergés C, Ruiz JL, Pujol A, Fernández-Fuentes N, Mas JM, Oliva B. In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan. PLoS One, 2020; 15 (2): e0228926  . PMID: 32053711 . DOI: 10.1371/journal.pone.0228926. eCollection 2020..

2020



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