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Research interests

In recent years it has become clear that cancer cells use multiple mechanisms to up-regulate oncogenes and down-regulate tumor suppressor genes. Much of the focus of this research has been on modulators of transcription; however we now estimate that transcriptional control only explains 30% to 40% of protein level variation. One of the major reasons for this discrepancy is thought to be differences in RNA translation, and this is the focus of study in our lab.

We are particularly interested in the ribosome. Recent work has shown that there is far more variation to the ribosome than previously appreciated, and we are now trying to understand whether this heterogeneity results in specialized functions. This work has led us to study immune responses, as well as various cancer models. In all, we hope to gain a much more thorough understanding of the role that ribosome specialization plays in both normal and disease biology, while at the same time identifying many new, exciting therapeutic targets.

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  • Detecting ribosome collisions with differential rRNA fragment analysis in ribosome profiling data

    Kyei-Baffour, E. S., Bak, J., Silva, J., Faller, W. J. & Alkan, F., 1 Jun 2025, In: NAR Genomics and Bioinformatics. 7, 2, 11 p., lqaf045.

    Research output: Contribution to journalArticle (Academic Journal)peer-review

    Open Access
  • NAC regulates metabolism and cell fate in intestinal stem cells

    Ramalho, S., Alkan, F., Prekovic, S., Jastrzebski, K., Barberà, E. P., Hoekman, L., Altelaar, M., de Heus, C., Liv, N., Rodríguez-Colman, M. J., Yilmaz, M., van der Kammen, R., Fedry, J., de Gooijer, M. C., Suijkerbuijk, S. J. E., Faller, W. J. & Silva, J., 10 Jan 2025, In: Science Advances. 11, 2, 14 p., eadn9750.

    Research output: Contribution to journalArticle (Academic Journal)peer-review

    Open Access
    4 Citations (Scopus)
  • P-stalk ribosomes act as master regulators of cytokine-mediated processes

    Dopler, A., Alkan, F., Malka, Y., van der Kammen, R., Hoefakker, K., Taranto, D., Kocabay, N., Mimpen, I., Ramirez, C., Malzer, E., Isaeva, O. I., Kerkhoff, M., Gangaev, A., Silva, J., Ramalho, S., Hoekman, L., Altelaar, M., Beijersbergen, R., Akkari, L. & Yewdell, J. W. & 2 others, Kvistborg, P. & Faller, W. J., 27 Nov 2024, In: Cell. 187, 24, p. 6981-6993.e23 37 p.

    Research output: Contribution to journalArticle (Academic Journal)peer-review

    Open Access
    21 Citations (Scopus)