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Dr. M. (Matteo) Barberis

Faculty of Science
Swammerdam Institute for Life Sciences
Photographer: Barberis

Visiting address
  • Science Park 904
Postal address
  • Postbus 1212
    1000 BE Amsterdam
  • Publications


    • Barberis, M. (2021). A multi-approach and multi-scale platform to model CD4+ T cells responding to infections. Npj Systems Biology and Applications.
    • Barberis, M. (2021). Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders. Npj Systems Biology and Applications.
    • Barberis, M. (2021). Quantitative model of eukaryotic Cdk control through the Forkhead CONTROLLER. Npj Systems Biology and Applications.
    • Barberis, M. (2021). SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics.
    • Maissan, P., Mooij, E. J., & Barberis, M. (2021). Sirtuins-Mediated System-Level Regulation of Mammalian Tissues at the Interface between Metabolism and Cell Cycle: A Systematic Review. Biology (Basel), 10(3), [194]. [details]
    • Verstegen, N. J. M. C., 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.


    • 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, [3091]. [details]
    • Barberis, M. (2020). Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. Frontiers in Bioengineering and Biotechnology.
    • Barberis, M. (2020). Synthetic designs regulating cellular transitions: Fine-tuning of switches and oscillators. Current Opinion in Systems Biology.
    • 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, [34]. [details]
    • 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, [8]. [details]


    • Barberis, M., & Mondeel, D. G. A. (2019). ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast. Nucleic Acids Research.
    • Barberis, M., & van der Zee, L. (2019). Advanced Modeling of Cellular Proliferation: Toward a Multi-scale Framework Coupling Cell Cycle to Metabolism by Integrating Logical and Constraint-Based Models. Methods in Molecular Biology.


    • Abudukelimu, A., Barberis, M., Redegeld, F. A., Sahin, N., & Westerhoff, H. V. (2018). Predictable Irreversible Switching Between Acute and Chronic Inflammation. Frontiers in Immunology, 9, [1596]. [details]
    • Barberis, M. (2018). A Mechanistic Computational Model Reveals That Plasticity of CD4+ T Cell Differentiation Is a Function of Cytokine Composition and Dosage. Frontiers in Physiology.
    • Barberis, M. (2018). Simulation of Stimulation: Cytokine Dosage and Cell Cycle Crosstalk Driving Timing-Dependent T Cell Differentiation. Frontiers in Physiology.
    • Barberis, M., & Mondeel, D. G. A. (2018). GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae. Bioinformatics.



    • 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. [details]



    • Naldi, A., Monteiro, P. T., Müssel, C., the Consortium for Logical Models and Tools, Kestler, H. A., Thieffry, D., Xenarios, I., Saez-Rodriguez, J., Helikar, T., Chaouiya, C., Albert, R., Barberis, M., Calzone, L., Chasapi, A., Cokelaer, T., Crespo, I., Dorier, J., Dräger, A., Hernandez, C., ... Zañudo, J. G. T. (2015). Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics, 31(7), 1154-1159. [details]
    This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list.
  • Ancillary activities
    No ancillary activities