Listar por autoría "Carbonell-Caballero, Jose"

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  • A comparison of mechanistic signaling pathway activity analysis methods
    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 ...
  • A set of accessible enhancers enables the initial response of breast cancer cells to physiological progestin concentrations
    Zaurín Quer, Roser; Ferrari, Roberto; Nacht, A. Silvina; Carbonell-Caballero, Jose; Le Dily, François; Font Mateu, Jofre, 1977-; De Llobet, Lara Isabel; Vidal Ocabo, Enrique; Lioutas, Antonio, 1980-; Beato, Miguel; Vincent, Guillermo P. (Oxford University Press, 2021)
    Here, we report that in T47D breast cancer cells 50 pM progestin is sufficient to activate cell cycle entry and the progesterone gene expression program. At this concentration, equivalent to the progesterone blood levels ...
  • C/EBPα mediates the growth inhibitory effect of progestins on breast cancer cells
    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 ...
  • Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models
    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 ...
  • Expression of oncogenic drivers in 3D cell culture depends on nuclear ATP synthesis by NUDT5
    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 ...
  • Global signalling network analysis of luminal T47D breast cancer cells in response to progesterone
    Wright, Roni H.G.; Vastolo, Viviana; Quilez Oliete, Javier; Carbonell-Caballero, Jose; Beato, Miguel (Frontiers, 2022)
    Background: Breast cancer cells enter into the cell cycle following progestin exposure by the activation of signalling cascades involving a plethora of enzymes, transcription factors and co-factors that transmit the external ...
  • Hormone-control regions mediate steroid receptor-dependent genome organization
    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 ...
  • Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome
    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 ...
  • The effects of death and post-mortem cold ischemia on human tissue transcriptomes
    Ferreira, Pedro G.; Muñoz-Aguirre, Manuel; Reverter, Ferran; Godinho, Caio P. Sá; Sousa, Abel; Amadoz, Alicia; Sodaei, Reza, 1988-; 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 ...

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