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Results: 8
Number of items: 8
  • Open Access
    Mondeel, T. D. G. A. (2022). Waves, ChIPs, GEMMs, gears, markers and maps: Computational systems biology from cell cycle oscillations to metabolic fluxes. [Thesis, fully internal, Universiteit van Amsterdam].
  • Open Access
    Weglarz-Tomczak, E., Mondeel, T. D. G. A., Piebes, D. G. E., & Westerhoff, H. V. (2021). Simultaneous integration of gene expression and nutrient availability for studying the metabolism of hepatocellular carcinoma cell lines. BIOMOLECULES, 11(4), Article 490. https://doi.org/10.3390/biom11040490
  • Open Access
    Mondeel, T. D. G. A., Ivanov, O., Westerhoff, H. V., Liebermeister, W., & Barberis, M. (2020). Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs. Npj Systems Biology and Applications, 6, Article 8. https://doi.org/10.1038/s41540-020-0125-0
  • Open Access
    Kolodkin, A. N., Sharma, R. P., Colangelo, A. M., Ignatenko, A., Martorana, F., Jennen, D., Briedé, J. J., Brady, N., Barberis, M., Mondeel, T. D. G. A., Papa, M., Kumar, V., Peters, B., Skupin, A., Alberghina, L., Balling, R., & Westerhoff, H. V. (2020). ROS networks: Designs, aging, Parkinson's disease and precision therapies. Npj Systems Biology and Applications, 6, Article 34. https://doi.org/10.1038/s41540-020-00150-w
  • Open Access
    Mondeel, D. G. A., Holland, P., Nielsen, J., & Barberis, M. (2019). ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast. Nucleic Acids Research, 47(15), 7825–7841. https://doi.org/10.1093/nar/gkz603
  • Open Access
    Mondeel, D. G. A., Cremazy, F. G. E., & Barberis, M. (2018). GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae. Bioinformatics, 34(12), 2147–2149. https://doi.org/10.1093/bioinformatics/bty052
  • Abudukelimu, A., Mondeel, T. D. G. A., Barberis, M., & Westerhoff, H. V. (2017). Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters. Biochemical Society Transactions, 45(3), 635-652. https://doi.org/10.1042/BST20160281
  • Westerhoff, H. V., Nakayama, S., Mondeel, T. D. G. A., & Barberis, M. (2015). Systems Pharmacology: An opinion on how to turn the impossible into grand challenges. Drug Discovery Today. Technologies, 15, 23-31. https://doi.org/10.1016/j.ddtec.2015.06.006
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