Lab News

A new thesis from our lab by Susanne Roth

Susanne will defend her thesis on May 24 and today we received copies of it! This work is a successful collaboration with the Joachim Goedhart and Dorus Gadella, both from the University of Amsterdam.

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A new review by us is published

You can find it here: Our new Current Opinion in Microbiology Review It discusses how different cultivation methods can be used to select mutant bacteria with improved macroscopic growth parameters and our current understanding of whether such parameters trade off.

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This week we moved to our new building!

For more information see: O2 building information

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We have a vacancy for a PhD position

The Systems Bioinformatics section of the VU University in Amsterdam (NL) is offering a 3-year position for a PhD student to study How a single cell integrates multiple signals via one of its G-protein coupled receptors We are looking for a master student with a degree in systems biology, biophysics, or molecular biology who is

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Johan van Heerden got his PhD

On January 11th Johan van Heerden defended his PhD entitled: “Dynamic regulation of yeast glycolysis through trehalose cycling:  a probabilistic view of metabolic transitions”, of which Bas was the promoter. The committee comprised of prof Stefan Hohmann, prof Hans Westerhoff, prof Barbara Bakker, prof Frank Bruggeman and Dr Aljoscha Wahl. Previous group members, Jan Berkhout and Filipe Santos were the

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Modelling, standards – another day in the life …

Modelling standards and systems biology, you hear a lot of talk about both these topics. But what would it mean if modellers and software engineers actually started using them. In the latest special issue of ERCIM news dealing with “Big Data” Brett and Bas take a look at an idealized day in the life of

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New book chapter on simulation tools and Systems Medicine

A new book on Systems Medicine has recently been published and includes a contribution on Modeling and Simulation Tools: From Systems Biology to Systems Medicine co-authored by ex-VU colleagues Martijn Mone, Maciej Swat and Brett Olivier. We explore how software and standards need to evolve when considering Systems Medicine as compared to Systems Biology and

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Dan Fraenkel and Jens Nielsen have written an in-depth review of our Science paper

Dan Fraenkel and Jens Nielsen recently undertook an in-depth review and extended analysis of our Science paper (van Heerden et al., 2014), and we are excited to see that their story has been published! Fraenkel and Nielsen, 2016. Trehalose-6-phosphate synthase and stabilization of yeast glycolysis

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Timo Maarleveld got his PhD

On December 17th Timo Maarleveld defended his PhD entitled: “Fluxes and Fluctuations in Biochemical Models”. The committee comprised of prof Klaas Hellingwerf, prof Vitor Martins dos Santos, prof Pieter-Rein Tenwolde, prof Jaap Heringa and prof David Fell. Bas and Frank were promoter, Brett was co-promoter, his first time!

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Standardizing constraint-based models: FBC version 1 published

Constraint-based modelling is a popular methodology used in systems biology whose stock in trade is the genome-scale model. However an ongoing problem in this field is that no formal standard exists for encoding such models. Brett Olivier together with Frank Bergmann have led the development of an extension to the Systems Biology Markup Language (SBML),

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