Lab News

SBML Level 3: the standard for encoding models of biological processes

Brett and Bas are co-authors on a new paper in Molecular Systems Biology describing the latest developments in model encoding in systems biology. Bas enthusiastically supports the use of standards in systems biology while Brett has been active in the SBML field for 15 years as a community member, specification writer, package coordinator (FBC), libSBML

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Zoom Celebration

Zoom Celebration at SysBioLab.  Rinke has a tenure track position in Delft, Bas got a new project granted, and Frank published a massive paper in Current Biology together with Johan, all on the same (Mon)day. With such good news it is time to celebrate! Lets open the bottle (that will be delivered to you today)

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Paper by Niclas, Johan and Frank

Biphasic Cell-Size and Growth-Rate Homeostasis by Single Bacillus subtilis Cells Abstract The growth rate of single bacterial cells is continuously disturbed by random fluctuations in biosynthesis rates and by deterministic cell-cycle events, such as division, genome duplication, and septum formation. It is not understood whether, and how, bacteria reject these growth-rate disturbances. Here, we quantified

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What makes steady-state population growth possible? – a new paper by us in Current Biology

Growing cells in constant conditions at a fixed exponential growth rate in a shake flask — balanced growth — is arguably the most basic experiment in microbiology. We are so used to it that we sometimes forget to realise that this is not at all so obvious. Not only the average growth rate remains fixed,

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An integrative view on how metabolic fluxes sustain growth of liver cancer cells

Jurgen Haanstra and Bas Teusink collaborated with several research groups on interdisciplinary research combining wetlab experiments with computational models. Haanstra and Teusink collaborated with research groups in Gothenburg (Sweden), Groningen and Heidelberg (Germany). Their work on a quantitative analysis of amino acid metabolism in liver cancer, with Jurgen as co-first author, was just published in

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Standardising the quality of genome scale models

Moritz Bieber, Christian Lieven (Biosustain, DTU), Brett Olivier and Bas Teusink (AIMMS, VU Amsterdam) and a worldwide community of scientists developed quality control tools for systems biology models in Nature Biotechnology Mathematical models are key tool to understand complex biological systems. In particular, constraint-based, genome scale, models (GSM’s) can relate the physiological property of a

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Herwig and Chrats gave a science talk in a bar

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Photo competition 2019

The winning photograph and his creator.

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Fifteen different models of overflow metabolism convey a single message: overflow metabolism is caused by two growth-limiting constraints.

We recently published an article in which we reviewed the different approaches that describe a puzzling metabolic phenomenon called overflow metabolism: (https://doi.org/10.1007/s00018-019-03380-2). Many different organisms secrete ‘overflow products’ in conditions where they grow and reproduce fast. For example, many yeasts produce ethanol, Escherichia coli produces acetate, and cancer cells produce lactate. This behaviour seems counter-intuitive

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Change of the section Name

The System Bioinformatics section has a new name and from now on will be known as: Systems Biology Lab

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