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Results: 31
Number of items: 31
  • Open Access
    Verstegen, N. J. M., Ubels, V., Westerhoff, H. V., van Ham, S. M., & Barberis, M. (2021). System-Level Scenarios for the Elucidation of T Cell-Mediated Germinal Center B Cell Differentiation. Frontiers in Immunology, 12, Article 734282. https://doi.org/10.3389/fimmu.2021.734282
  • Open Access
    Barberis, M. (2021). Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast. Npj Systems Biology and Applications, 7(1), Article 48. https://doi.org/10.1038/s41540-021-00201-w
  • Open Access
    Abudukelimu, A., Barberis, M., Redegeld, F., Sahin, N., Sharma, R. P., & Westerhoff, H. V. (2020). Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity. Frontiers in Immunology, 10, Article 3091. https://doi.org/10.3389/fimmu.2019.03091
  • 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
  • van der Zee, L., & Barberis, M. (2019). Advanced Modeling of Cellular Proliferation: Toward a Multi-scale Framework Coupling Cell Cycle to Metabolism by Integrating Logical and Constraint-Based Models. In S. G. Oliver, & J. I. Castrillo (Eds.), Yeast Systems Biology : Methods and Protocols (2nd ed., pp. 365–385). (Methods in Molecular Biology; Vol. 2049). Humana Press. https://doi.org/10.1007/978-1-4939-9736-7_21
  • 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
    Puniya, B. L., Todd, R. G., Mohammed, A., Brown, D., Barberis, M., & Helikar, T. (2018). A Mechanistic Computational Model Reveals That Plasticity of CD4+ T Cell Differentiation Is a Function of Cytokine Composition and Dosage. Frontiers in Physiology, 9, Article 878. https://doi.org/10.3389/fphys.2018.00878
  • Open Access
    Barberis, M., Helikar, T., & Verbruggen, P. (2018). Simulation of Stimulation: Cytokine Dosage and Cell Cycle Crosstalk Driving Timing-Dependent T Cell Differentiation. Frontiers in Physiology, 9, Article 879. https://doi.org/10.3389/fphys.2018.00879
  • 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
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