Browsing by Author "Oliva Miguel, Baldomero"

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  • A collection of designed peptides to target SARS-CoV-2 spike RBD-ACE2 interaction
    Fernández Fuentes, Narcís; Molina, Ruben; Oliva Miguel, Baldomero (MDPI, 2021)
    The angiotensin-converting enzyme 2 (ACE2) is the receptor used by SARS-CoV and SARS-CoV-2 coronaviruses to attach to cells via the receptor-binding domain (RBD) of their viral spike protein. Since the start of the COVID-19 ...
  • A decision support system based on artificial intelligence and systems biology for the simulation of pancreatic cancer patient status
    Junet, Valentin; Matos Filipe, Pedro; García-Illarramendi, Juan Manuel; Ramírez, Esther; Oliva Miguel, Baldomero; Farrés, Judith; Daura, Xavier; Mas, José Manuel; Morales-Barrera, Rafael (Wiley, 2023)
    Oncology treatments require continuous individual adjustment based on the measurement of multiple clinical parameters. Prediction tools exploiting the patterns present in the clinical data could be used to assist decision ...
  • A genome-wide functional screen identifies enhancer and protective genes for amyloid beta-peptide toxicity
    Picón-Pagès, Pol; Bosch Morató, Mònica, 1986-; Subirana, Laia; Rubio-Moscardó, Francisca; Guivernau Almazán, Biuse, 1988-; Fanlo-Ucar, Hugo; Zeylan, Melisa Ece; Senyuz, Simge; Herrera-Fernández, Víctor; Vicente García, Rubén, 1978-; Fernández-Fernández, José Manuel, 1967-; García Ojalvo, Jordi; Gursoy, Attila; Keskin, Ozlem; Oliva Miguel, Baldomero; Posas Garriga, Francesc; Nadal Clanchet, Eulàlia de; Muñoz López, Francisco José, 1964- (MDPI, 2023)
    Alzheimer's disease (AD) is known to be caused by amyloid β-peptide (Aβ) misfolded into β-sheets, but this knowledge has not yet led to treatments to prevent AD. To identify novel molecular players in Aβ toxicity, we carried ...
  • A quantitative systems pharmacology model for certolizumab pegol treatment in moderate-to-severe psoriasis
    Coto-Segura, Pablo; Segú-Vergés, Cristina; Martorell, Antonio; Moreno-Ramírez, David; Jorba Argemí, Guillem; Junet, Valentin; Guerri, Filippo; Daura, Xavier; Oliva Miguel, Baldomero; Cara, Carlos; Suárez-Magdalena, Olaya; Abraham, Sonya; Mas, José Manuel (Frontiers, 2023)
    Background: Psoriasis is a chronic immune-mediated inflammatory systemic disease with skin manifestations characterized by erythematous, scaly, itchy and/or painful plaques resulting from hyperproliferation of keratinocytes. ...
  • Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population
    Walsh Capdevila, Sandra, 1991-; Izquierdo Serra, Mercè; Acosta, Sandra; Edo, Albert; Lloret, María; Moret, Roser; Bosch Fusté, Elena; Oliva Miguel, Baldomero; Bertranpetit, Jaume, 1952-; Fernández-Fernández, José Manuel, 1967- (Nature Research, 2020)
    TRPP3 (also called PKD2L1) is a nonselective, cation-permeable channel activated by multiple stimuli, including extracellular pH changes. TRPP3 had been considered a candidate for sour sensor in humans, due to its high ...
  • Al modelling of real-world patients: applications in prostate cancer
    Matos-Filipe, Pedro (Universitat Pompeu Fabra, 2024-11-08)
    This thesis investigates the integration and analysis of OMICs data to enhance in silico modelling of real-world patients, with a special focus on prostate cancer. By leveraging publicly available transcriptomics data, ...
  • Amyloid β-peptide causes the permanent activation of CaMKIIα through its oxidation
    Picón-Pagès, Pol; Fanlo-Ucar, Hugo; Herrera-Fernández, Víctor; Ausellé Bosch, Sira; Galera López, Lorena, 1993-; Gutiérrez, Daniela A.; Ozaita Mintegui, Andrés, 1969-; Álvarez, Alejandra R.; Oliva Miguel, Baldomero; Muñoz López, Francisco José, 1964- (MDPI, 2022)
    Alzheimer's disease (AD) is characterised by the presence of extracellular amyloid plaques in the brain. They are composed of aggregated amyloid beta-peptide (Aβ) misfolded into beta-sheets which are the cause of the AD ...
  • Amyloid-β peptide nitrotyrosination stabilizes oligomers and enhances NMDAR-mediated toxicity
    Guivernau Almazán, Biuse, 1988-; Bonet Martínez, Jaume, 1982-; Valls Comamala, Victòria, 1987-; Bosch Morató, Mònica, 1986-; Godoy Zeballos, Juan Alejandro, 1959-; Inestrosa, Nibaldo C.; Perálvarez Marín, Alex; Fernández-Busquets, Xavier; Andreu Martínez, David; Oliva Miguel, Baldomero; Muñoz López, Francisco José, 1964- (Society for Neuroscience, 2016)
    Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the pathological aggregation of the amyloid-β peptide (Aβ). Monomeric soluble Aβ can switch from helicoidal to β-sheet conformation, promoting its ...
  • An ensemble learning approach for modeling the systems biology of drug-induced injury
    Aguirre Plans, Joaquim, 1993-; Piñero González, Janet, 1977-; Souza, Terezinha; Callegaro, Giulia; Kunnen, Steven J.; Sanz, Ferran; Fernández Fuentes, Narcís; Furlong, Laura I., 1971-; Guney, Emre; Oliva Miguel, Baldomero (BioMed Central, 2021)
    Background: Drug-induced liver injury (DILI) is an adverse reaction caused by the intake of drugs of common use that produces liver damage. The impact of DILI is estimated to affect around 20 in 100,000 inhabitants worldwide ...
  • An in silico clinical trial platform based on systems biology approaches
    Jorba Argemí, Guillem (Universitat Pompeu Fabra, 2023-04-27)
    El procés de descobriment i desenvolupament de fàrmacs (DDD) és costós tant econòmic com temporalment, i el qual resulta en nivells d'èxit molt reduïts. Una gran quantitat de compostos son analitzats i molts descartats en ...
  • An inhibitor of interaction between the transcription factor NRF2 and the E3 ubiquitin ligase adapter β-TrCP delivers anti-inflammatory responses in mouse liver
    Fernández-Ginés, Raquel; Encinar, José Antonio; Hayes, John D.; Oliva Miguel, Baldomero; Rodríguez-Franco, Maria Isabel; Rojo, Ana I.; Cuadrado, Antonio (Elsevier, 2022)
    It is widely accepted that activating the transcription factor NRF2 will blast the physiological anti-inflammatory mechanisms, which will help combat pathologic inflammation. Much effort is being put in inhibiting the main ...
  • Analysis of the robustness of network-based disease-gene prioritization methods reveals redundancy in the human interactome and functional diversity of disease-genes
    Güney, Emre, 1983-; Oliva Miguel, Baldomero (Public Library of Science (PLoS), 2014)
    Complex biological systems usually pose a trade-off between robustness and fragility where a small number of perturbations can substantially disrupt the system. Although biological systems are robust against changes in ...
  • ArchDB 2014: structural classification of loops in proteins
    Bonet Martínez, Jaume, 1982-; Planas Iglesias, Joan, 1980-; García-García, Javier, 1982-; Marín López, Manuel Alejandro, 1987-; Fernández Fuentes, Narcís; Oliva Miguel, Baldomero (Oxford University Press, 2014)
    The function of a protein is determined by its three-dimensional structure, which is formed by regular (i.e. β-strands and α-helices) and non-periodic structural units such as loops. Compared to regular structural elements, ...
  • Backup in gene regulatory networks explains differences between binding and/nknockout results
    Gitter, Anthony; Siegfried, Zehava; Klutstein, Michael; Fornés Crespo, Oriol, 1983-; Oliva Miguel, Baldomero; Simon, Itamar; Bar-Joseph, Ziv (EMBO Press, 2009)
    The complementarity of gene expression and protein-DNA interaction data led to several successful models of biological systems. However, recent studies in multiple species raise doubts about the relationship between these ...
  • Biana: a software framework for compiling biological interactions and analyzing networks
    García-García, Javier, 1982-; Güney, Emre, 1983-; Aragüés Peleato, Ramón; Planas Iglesias, Joan, 1980-; Oliva Miguel, Baldomero (BioMed Central, 2010)
    Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, ...
  • BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference
    García-García, Javier, 1982-; Schleker, Sylvia; Klein-Seetharaman, Judith; Oliva Miguel, Baldomero (Oxford University Press, 2012)
    Protein-protein interactions (PPIs) play a crucial role in biology, and high-throughput experiments have greatly increased the coverage of known interactions. Still, identification of complete inter- and intraspecies ...
  • CACNA1A mutations causing early onset ataxia: profiling clinical, dysmorphic and structural-functional findings
    Martínez Monseny, Antonio Federico; Edo, Albert; Casas Alba, Dídac; Izquierdo Serra, Mercè; Bolasell, Mercè; Conejo, David; Martorell, Loreto; Muchart, Jordi; Carrera, Laura; Ortez, Carlos; Nascimento, Andrés; Oliva Miguel, Baldomero; Fernández-Fernández, José Manuel, 1967-; Serrano Masip, Mercedes (MDPI, 2021)
    The CACNA1A gene encodes the pore-forming α1A subunit of the voltage-gated CaV2.1 Ca2+ channel, essential in neurotransmission, especially in Purkinje cells. Mutations in CACNA1A result in great clinical heterogeneity with ...
  • CAPS-DB: A structural classification of helix-capping motifs
    Segura, Joan; Oliva Miguel, Baldomero; Fernández Fuentes, Narcís (Oxford University Press, 2012)
    The regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen ...
  • CDK2-dependent activation of PARP-1 is required for hormonal gene regulation in breast cancer cells
    Wright, Roni H.G.; Castellano, Giancarlo; Bonet Martínez, Jaume, 1982-; Le Dily, François; Font Mateu, Jofre, 1977-; Ballaré, Cecilia Julia; Nacht, A. Silvina; Soronellas, Daniel; Oliva Miguel, Baldomero; Beato, Miguel (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Eukaryotic gene regulation implies that transcription factors gain access to genomic information via poorly understood processes involving activation and targeting of kinases, histone-modifying enzymes, and chromatin ...
  • Characterization of novel pathogenic variants leading to caspase-8 cleavage-resistant RIPK1-induced autoinflammatory syndrome
    Tapiz I Reula, Alfonso José; Cochino, Alexis-Virgil; Martins, Andreia L.; Angosto-Bazarra, Diego; Ortiz de Landazuri, Iñaki; Mensa Vilaró, Anna; Cabral, Marta; Baroja-Mazo, Alberto; Baños, María C.; Lobato-Salinas, Zulema; Fabregat, Virginia; Plaza, Susana; Yagüe, Jordi L.; Casals López, Ferran; Oliva Miguel, Baldomero; Figueiredo, Antonio E.; Pelegrín, Pablo; Aróstegui Gorospe, Juan Ignacio (SpringerOpen, 2022)
    Pathogenic RIPK1 variants have been described as the cause of two different inborn errors of immunity. Biallelic loss-of-function variants cause the recessively inherited RIPK1 deficiency, while monoallelic variants impairing ...

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