Browsing by Author "Carbonell-Caballero, Jose"

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  • Amadoz, Alicia; Hidalgo, Marta R.; Çubut, Cankut; Carbonell-Caballero, Jose; Dopazo, Joaquín (Oxford University Press, 2019)
    Understanding the aspects of cell functionality that account for disease mechanisms or drug modes of action is a main challenge for precision medicine. Classical gene-based approaches ignore the modular nature of most human ...
  • Nacht, A. Silvina; Ferrari, Roberto; Zaurín Quer, Roser; Scabia, Valentina; Carbonell-Caballero, Jose; Le Dily, François; Quilez Oliete, Javier; Leopoldi, Alexandra; Brisken, Cathrin; Beato, Miguel; Vicent, Guillermo Pablo (EMBO Press, 2019)
    Steroid hormones are key gene regulators in breast cancer cells. While estrogens stimulate cell proliferation, progestins activate a single cell cycle followed by proliferation arrest. Here, we use biochemical and genome-wide ...
  • Çubut, Cankut; Hidalgo, Marta R.; Amadoz, Alicia; Rian, Kinza; Salavert, Francisco; Pujana, Miguel Angel; Mateo, Francesca; Herranz Ors, Carmen, 1992-; Carbonell-Caballero, Jose; Dopazo, Joaquín (Nature Research, 2019)
    In spite of the increasing availability of genomic and transcriptomic data, there is still a gap between the detection of perturbations in gene expression and the understanding of their contribution to the molecular ...
  • Pickup, Katherine E.; Pardow, Felicitas; Carbonell-Caballero, Jose; Lioutas, Antonio, 1980-; Villanueva Cañas, José Luis, 1984-; Wright, Roni H.G.; Beato, Miguel (MDPI, 2019)
    The growth of cancer cells as oncospheres in three-dimensional (3D) culture provides a robust cell model for understanding cancer progression, as well as for early drug discovery and validation. We have previously described ...
  • Le Dily, François; Vidal, Enrique; Cuartero, Yasmina; Quilez Oliete, Javier; Nacht, A. Silvina; Vicent, Guillermo Pablo; Carbonell-Caballero, Jose; Sharma, Priyanka; Villanueva Cañas, José Luis, 1984-; Ferrari, Roberto; De Llobet, Lara Isabel; Verde, Gaetano; Wright, Roni H.G.; Beato, Miguel (Cold Spring Harbor Laboratory Press (CSHL Press), 2019)
    In breast cancer cells, some topologically associating domains (TADs) behave as hormonal gene regulation units, within which gene transcription is coordinately regulated in response to steroid hormones. Here we further ...
  • Hidalgo, Marta R.; Amadoz, Alicia; Çubut, Cankut; Carbonell-Caballero, Jose; Dopazo, Joaquín (BioMed Central, 2018)
    Background: Despite the progress in neuroblastoma therapies the mortality of high-risk patients is still high (40–50%) and the molecular basis of the disease remains poorly known. Recently, a mathematical model was used ...
  • Ferreira, Pedro G.; Muñoz-Aguirre, Manuel; Reverter, Ferran; Godinho, Caio P. Sá; Sousa, Abel; Amadoz, Alicia; Sodaei, Reza; Hidalgo, Marta R.; Pervouchine, Dmitri D.; Carbonell-Caballero, Jose; Nurtdinov, Ramil; Breschi, Alessandra, 1988-; Amador, Raziel; Oliveira, Patrícia; Çubut, Cankut; Curado, Joao; Aguet, François; Oliveira, Carla; Dopazo, Joaquín; Sammeth, Michael; Ardlie, Kristin G.; Guigó Serra, Roderic (Nature Publishing Group, 2018)
    Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA ...