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Mourragui, S.M.C. (author)Extensive efforts in cancer research over the past decades have markedly improved diagnosis and treatments, leading to better outcomes for cancer patients. Paradoxically, however, these discoveries have begun to shed light on a level of complexity that rules out the emergence of a universal cancer treatment. As any tumor is now known to be...doctoral thesis 2023
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Wehrens, Martijn (author), Krah, Laurens H.J. (author), Towbin, Benjamin D. (author), Hermsen, Rutger (author), Tans, S.J. (author)The inherent stochasticity of metabolism raises a critical question for understanding homeostasis: are cellular processes regulated in response to internal fluctuations? Here, we show that, in E. coli cells under constant external conditions, catabolic enzyme expression continuously responds to metabolic fluctuations. The underlying...journal article 2023
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Wang, Gangqi (author), Heijs, Bram (author), Kostidis, Sarantos (author), Rietjens, Rosalie G.J. (author), Mahfouz, A.M.E.T.A. (author), Chuva de Sousa Lopes, Susana M. (author), van den Berg, Cathelijne W. (author), van den Berg, Bernard M. (author), Rabelink, Ton J. (author)Accumulating evidence demonstrates important roles for metabolism in cell fate determination. However, it is a challenge to assess metabolism at a spatial resolution that acknowledges both heterogeneity and cellular dynamics in its tissue microenvironment. Using a multi-omics platform to study cell-type-specific dynamics in metabolism in...journal article 2022
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Khatri, I. (author), Diks, Annieck M. (author), van den Akker, E.B. (author), Oosten, Liesbeth E. M. (author), Zwaginga, Jaap Jan (author), Reinders, M.J.T. (author), van Dongen, Jacques J. M. (author), Berkowska, Magdalena A. (author)To mount an adequate immune response against pathogens, stepwise mutation and selection processes are crucial functions of the adaptive immune system. To better characterize a successful vaccination response, we performed longitudinal (days 0, 5, 7, 10, and 14 after Boostrix vaccination) analysis of the single-cell transcriptome as well as the B...journal article 2021
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Douwenga, Sieze (author), van Tatenhove-Pel, R.J. (author), Zwering, Emile (author), Bachmann, Herwig (author)During storage and ripening of fermented foods, Lactococcus cremoris is predominantly in a non-growing state. L. cremoris can become stationary due to starvation or acidification, and its metabolism in these non-growing states affects the fermented product. Available studies on the response of L. cremoris to acid and starvation stress are...journal article 2021
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Abdelaal, T.R.M. (author), van Unen, Vincent (author), Höllt, T. (author), Koning, Frits (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Mass cytometry by time-of-flight (CyTOF) is a valuable technology for high-dimensional analysis at the single cell level. Identification of different cell populations is an important task during the data analysis. Many clustering tools can perform this task, which is essential to identify “new” cell populations in explorative experiments....journal article 2019
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Van Leest, M.M. (author)In monitoring the quality of drinking water with respect to the presence of hazardous bacteria, there is a strong need for in-line sensors that allow quick identification of bacterium species at low cost. Raman spectroscopy is a very promising label-free optical technique capable of discriminating bacteria species based on their molecular...doctoral thesis 2014