Lab News

In press: Sebastián’s meticulous comparison of genome-scale metabolic reconstruction tools is published!

A genome-scale metabolic reconstruction is a network of all biochemical reactions that can occur in a cell. These reconstructions have proven to be very useful because they can be used to make phenotypic predictions. Many computational tools to create these reconstructions have been created (or updated) recently, making these genome-scale reconstructions available for everyone. However,

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Daan and NWA-Ideeëngenerator

Systeembioinformaticus Daan de Groot met Self-organising adaptation: a universal mechanism for microbial protein expression regulation Cellen kunnen zich aanpassen aan, en groeien in, een verbluffende hoeveelheid omgevingen. Dit lijkt, gezien de eenvoud van individuele cellen, een onmogelijke prestatie. Maar hoe zit dit als een populatie cellen gaat samenwerken? De onderzoekers stellen een universeel mechanisme voor

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Chrats published 2 papers

Two papers were recently published by Chrats about microbial communities. In the first paper, the authors show how microbial communities change during wine fermentations, what are the differences in microbial composition between vineyards and which ones are the species that are present during problematic fermentations. In the second paper, which is a first-authorship for Chrats,

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Paul published a review

JBAH-Vol.9 No.10 2019.pdf Journal of Biology, Agriculture and Healthcare www.iiste.org Vol.9, No.10, 2019 From Functional Potential of Soil Bacterial Communities Towards Petroleum Hydrocarbons Bioremediation Abstract Molecular ecology researches are rapidly advancing the knowledge of microorganisms associated with petroleum hydrocarbon degradation, one of the major large-scale pollutants in terrestrial ecosystems. The design and monitoring of bioremediation

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Coco and Rinke presented at NWO-Life 2019

We were represented well at the first edition of the multidisciplinary congress for life scientists: NWO Life 2019. Coco presented the three different methods that she developed to measure bacterial responses to antibiotics. Checkerboards, fermentors and droplets: Coco uses all of them to distinguish who invades, who resides, and who persists. Given that similar bacteria

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Daan, European Champignon Duathlon 2019

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In press: Rate maximisation makes the most complex microbes behave simple!

Our theoretical work on rate maximisation in metabolism has been published in Plos Computational Biology. In this work, we took a very general approach to ask a very specific question: we included genome-scale metabolic networks, complicated enzyme kinetics, and arbitrary constraints on enzyme expression, and then asked what metabolism looks like for a microorganism that

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In press: Dennis’ extensive characterisation of Fluorescent protein behaviour in yeast is published!

Dennis’ work on the behaviour of fluorescent proteins (FPs) in baker’s yeast has been published! With the help of Daan de Groot and Phillipp Schmidt, a variety of fluorescent proteins were characterised for various properties, including brightness, photobleaching, photochromism, day-to-day variation and monomerism. Many FPs showed different performance in yeast compared to previous characterisations done

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Ever thought about the semantic annotation of computational models?

Some of us in the COMBINE community did and this paper is the result: Harmonizing semantic annotations for computational models in biology – Briefings in Bioinformatics – 21 November 2018.

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Julia wins photo competition at the End-of-Summer drinks.

Although the weather still gives the idea that summer didn’t end yet, we had end-of-summer drinks last week. It was a nice get-together and many people joined for a drink and a chat.. The drinks were accompanied by a photo competition with 21 entries. During the drinks the photos were hanging on the wall for

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