Dr. M. (Matteo) Barberis
Faculty of Science
Swammerdam Institute for Life Sciences
Visiting address
- Science Park 904
Postal address
- Postbus 1212
1000 BE Amsterdam
Contact details
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Publications
2020
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]. https://doi.org/10.3389/fimmu.2019.03091 [details]- 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]. https://doi.org/10.1038/s41540-020-00150-w [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]. https://doi.org/10.1038/s41540-020-0125-0 [details]
2018
- 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]. https://doi.org/10.3389/fimmu.2018.01596 [details]
2017
- 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 [details]
- Barberis, M., & Verbruggen, P. (2017). Quantitative Systems Biology to decipher design principles of a dynamic cell cycle network: the "Maximum Allowable mammalian Trade-Off-Weight" (MAmTOW). Npj Systems Biology and Applications, 3, [26]. https://doi.org/10.1038/s41540-017-0028-x [details]
- Barberis, M., Todd, R. G., & van der Zee, L. (2017). Advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models. FEMS Yeast Research, 17(1), [fow103]. https://doi.org/10.1093/femsyr/fow103 [details]
- Linke, C., Chasapi, A., González-Novo, A., Al Sawad, I., Tognetti, S., Klipp, E., ... Barberis, M. (2017). A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle. Npj Systems Biology and Applications, 3, [7]. https://doi.org/10.1038/s41540-017-0008-1 [details]
- Ostrow, A. Z., Kalhor, R., Gan, Y., Villwock, S. K., Linke, C., Barberis, M., ... Aparicio, O. M. (2017). Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae. Proceedings of the National Academy of Sciences of the United States of America, 114(12), E2411-E2419. https://doi.org/10.1073/pnas.1612422114 [details]
- Zhang, Y., Kouril, T., Snoep, J. L., Siebers, B., Barberis, M., & Westerhoff, H. V. (2017). The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico. International Journal of Molecular Sciences, 18(4), [876]. https://doi.org/10.3390/ijms18040876 [details]
2015
- 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 [details]
2013
- Linke, C., Klipp, E., Lehrach, H., Barberis, M., & Krobitsch, S. (2013). Fkh1 and Fkh2 associate with Sir2 to control CLB2 transcription under normal and oxidative stress conditions. Frontiers in Physiology, 4, [173]. https://doi.org/10.3389/fphys.2013.00173 [details]
- Supady, A., Klipp, E., & Barberis, M. (2013). A variable fork rate affects timing of origin firing and S phase dynamics in Saccharomyces cerevisiae. Journal of Biotechnology, 168(2), 174-184. https://doi.org/10.1016/j.jbiotec.2013.06.022 [details]
2015
- 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. https://doi.org/10.1093/bioinformatics/btv013 [details]
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Ancillary activities
No known ancillary activities
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].