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Items where Author is "Barberis, M"

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Mondeel, Thierry D.G.A, Ivanov, Oleksandr, Westerhoff, Hans V., Liebermeister, Wolfram and Barberis, Matteo (2020) Clb3-centered regulations are recurrent across distinctparameter regions in minimal autonomous cell cycle oscillatordesigns NPJ Systems Biology and Applications, 6 (1), 8.

Abudukelimu, Abulikemu, Barberis, Matteo, Redegeld, Frank, Sahin, Nilgun, Sharma, Raju P. and Westerhoff, Hans 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.

van der Zee, Lucas and Barberis, Matteo (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, 2049. pp. 365-385.

Mondeel, Thierry D G A, Holland, Petter, Nielsen, Jens and Barberis, Matteo (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). pp. 7825-7841.

Abudukelimu, A., Barberis, Matteo, Redegeld, F.A., Sahin, N. and Westerhoff, H.V. (2018) Predictable irreversible switching between acute and chronic inflammation Frontiers in Immunology, 9, 1596. pp. 1-16.

Barberis, Matteo, Helikar, T. and Verbruggen, P. (2018) Simulation of stimulation: Cytokine dosage and cell cycle crosstalk driving timing-dependent T cell differentiation Frontiers in Physiology, 9. pp. 879-896.

Puniya, B.L., Todd, R.G., Mohammed, A., Brown, D.M., Barberis, Matteo and 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, 878. pp. 1-18.

Mondeel, Thierry D G A, Crémazy, Frédéric and Barberis, Matteo (2018) GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae Bioinformatics, 34 (12). pp. 2147-2149.

Barberis, Matteo and Verbruggen, Paul (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 (1), 26. pp. 1-14.

Abudukelimu, A., Mondeel, T.D.G.A., Barberis, Matteo and 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). pp. 635-652.

Zhang, Y., Kouril, T., Snoep, J.L., Siebers, B., Barberis, Matteo and 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).

Ostrow, A. Zachary, Kalhor, Reza, Gan, Yan, Villwock, Sandra K., Linke, Christian, Barberis, Matteo, Chen, Lin and Aparicio, Oscar M. (2017) Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes inS. cerevisiae PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114 (12). E2411-E2419.

Linke, C., Chasapi, A., González-Novo, A., Al Sawad, I., Tognetti, S., Klipp, E., Loog, M., Krobitsch, S., Posas, F., Xenarios, I. and Barberis, Matteo (2017) A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle npj Systems Biology and Applications, 3 (1).

Barberis, Matteo, Todd, R.G. and 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.

Mondeel, T.D.G.A., Rehman, S., Zhang, Y., Verma, M., Dürre, P., Barberis, Matteo and Westerhoff, H.V. (2016) Maps for when the living gets tough: Maneuvering through a hostile energy landscape IFAC-PapersOnLine, 49 (26). pp. 364-370.

Westerhoff, H.V., Nakayama, S., Mondeel, T.D.G.A. and Barberis, Matteo (2015) Systems Pharmacology: An opinion on how to turn the impossible into grand challenges Drug Discovery Today: Technologies, 15. pp. 23-31.

Naldi, A., Monteiro, P.T., Müssel, C., 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., Hucka, M., De Jong, H., Keating, S.M., Klamt, S., Klarner, H., Laubenbacher, R., Le Novère, N., Niknejad, A., Rodriguez, N., Siebert, H., Stoll, G. and Zañudo, J.G.T. (2015) Cooperative development of logical modelling standards and tools with CoLoMoTo Bioinformatics, 31 (7). pp. 1154-1159.

Supady, A., Klipp, E. and Barberis, Matteo (2013) A variable fork rate affects timing of origin firing and S phase dynamics in Saccharomyces cerevisiae Journal of Biotechnology, 168 (2). pp. 174-184.

Linke, C., Klipp, E., Lehrach, H., Barberis, Matteo and Krobitsch, S. (2013) Fkh1 and Fkh2 associate with Sir2 to control CLB2 transcription under normal and oxidative stress conditions Frontiers in Physiology, 4, 173.

Barberis, Matteo (2012) Sic1 as a timer of Clb cyclin waves in the yeast cell cycle - Design principle of not just an inhibitor FEBS Journal, 279 (18). pp. 3386-3410.

Schreiber, G., Barberis, Matteo, Scolari, S., Klaus, C., Herrmann, A. and Klipp, E. (2012) Unraveling interactions of cell cycle-regulating proteins Sic1 and B-type cyclins in living yeast cells: A FLIM-FRET approach FASEB Journal, 26 (2). pp. 546-554.

Barberis, Matteo, Linke, C., Adrover, M.T., González-Novo, A., Lehrach, H., Krobitsch, S., Posas, F. and Klipp, E. (2011) Sic1 plays a role in timing and oscillatory behaviour of B-type cyclins Biotechnology Advances, 30 (1). pp. 108-130.

Barberis, Matteo, Beck, C., Amoussouvi, A., Schreiber, G., Diener, C., Herrmann, A. and Klipp, E. (2011) A low number of SIC1 mRNA molecules ensures a low noise level in cell cycle progression of budding yeast Molecular BioSystems, 7 (10). pp. 2804-2812.

Spiesser, T.W., Diener, C., Barberis, Matteo and Klipp, E. (2010) What influences DNA replication rate in budding yeast? PLoS ONE, 5 (4), e10203. pp. 1-9.

Barberis, Matteo, Spiesser, T.W. and Klipp, E. (2010) Replication origins and timing of temporal replication in budding yeast: How to solve the conundrum? Current Genomics, 11 (3). pp. 199-211.

Spiesser, T.W., Klipp, E. and Barberis, Matteo (2009) A model for the spatiotemporal organization of DNA replication in Saccharomyces cerevisiae Molecular Genetics and Genomics, 282 (1). pp. 25-35.

Alfieri, R., Barberis, Matteo, Chiaradonna, F., Gaglio, D., Milanesi, L., Vanoni, M., Klipp, E. and Alberghina, L. (2009) Towards a systems biology approach to mammalian cell cycle: Modeling the entrance into S phase of quiescent fibroblasts after serum stimulation BMC Bioinformatics, 10 (sup.12).

Barberis, Matteo, Klipp, E., Vanoni, M. and Alberghina, L. (2007) Cell size at S phase initiation: An emergent property of the G1/S network PLoS Computational Biology, 3 (4). pp. 649-666.

Barberis, Matteo, Pagano, M.A., De Gioia, L., Marin, O., Vanoni, M., Pinna, L.A. and Alberghina, L. (2005) CK2 regulates in vitro the activity of the yeast cyclin-dependent kinase inhibitor Sic1 Biochemical and Biophysical Research Communications, 336 (4). pp. 1040-1048.

Barberis, Matteo, De Gioia, L., Ruzzene, M., Sarno, S., Coccetti, P., Fantucci, P., Vanoni, M. and Alberghina, L. (2005) The yeast cyclin-dependent kinase inhibitor Sic1 and mammalian p27Kip1 are functional homologues with a structurally conserved inhibitory domain Biochemical Journal, 387 (3). pp. 639-647.

Book Section

Westerhoff, H.V., He, F., Murabito, E., Crémazy, F. and Barberis, Matteo (2014) Understanding Principles of the Dynamic Biochemical Networks of Life Through Systems Biology In: Computational Systems Biology: From Molecular Mechanisms to Disease: Second Edition. Academic Press, pp. 21-44. ISBN 978-0-12-405926-9

Barberis, Matteo (2012) Molecular systems biology of sic1 in yeast cell cycle regulation through multiscale modeling In: Advances in Systems Biology. Advances in Experimental Medicine and Biology, 736 (736). Springer, New York, NY, pp. 135-167. ISBN 00652598 (ISSN); 978-1-4419-7209-5 (ISBN)

Barberis, Matteo, Spiesser, T.W. and Klipp, E. (2010) Kinetic modelling of DNA replication initiation in budding yeast. In: Genome Informatics 2010 (Proceedings of the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010), Kyoto University, Japan, 26 – 28 July 2010). Genome Informatics Series (Vol.24). Imperial College Press, London, pp. 1-20. ISBN 978-1-84816-657-8

Barberis, Matteo and Klipp, E. (2007) Insights into the network controlling the G1/S transition in budding yeast. In: Genome Informatics 2007. Genome Informatics Series, 18 (18). Japanese Society for Bioinformatics, pp. 85-99.

Conference or Workshop Item

Marangoni, F., Barberis, Matteo and Botta, M. (2003) Large scale prediction of protein interactions by a SVM-based method In: Neural Nets: 14th Italian Workshop on Neural Nets, WIRN VIETRI 2003, 04-07 Jun 2003, Vietri sul Mare, Italy.

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