Lab News

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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We organised an introductory systems biology course

As part of the BioSB Research School, which brings together bioinformaticians and systems biologists, we organised an introductory systems-biology course. In this course, we focussed on the basics of mathematical modelling of molecular circuits and the emergent properties of those circuits, such as their (in)stability, robustness and (in)sensitivity properties. We will organise a similar course next

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Our time-lapse segmentation and tracking algorithm can now also track growing S. pombe

We have been hard at work developing an automated segmentation and tracking tool to analyse microscopic time-lapse movies of growing bacteria. After a few minor adjustments and additions we can now also segment and track fission yeast (Schizosaccharomyces pombe) growing on an agarose pad. Our algorithm is now in its final stages of development and testing, and

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Sam Seaver from Argonne National Laboratory visited the lab

Dr. Sam Seaver is bioinformatician at Argonne National Laboratory known from e.g. modelSEED and works on (automation of) metabolic reconstructions. He discussed with lab members and presented a seminar. Sam was on a tour through Europe  and we were privileged enough to be on his tour list!

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Rick joined the group with distinction

Rick who started his PhD 1st of November got his diploma yesterday “with distinction“. Well done Rick!

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Incredibly sad news: lab member Wilfred Roling passed away

With shock and disbelieve we learned that our colleague, collaborator and supervisor dr Wilfred Roling, associated professor from our department, died on Friday the 25th of September, at the age of 48 years. Wilfred was passionate about science, our expert in microbial ecology, and a quiet rock in the often dynamic organisation of the department.

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Iraes Rabbers got her first 1st author paper

Iraes wrote a very concise and clear review on Metabolism at Evolutionary Optimal States Abstract Metabolism is generally required for cellular maintenance and for the generation of offspring under conditions that support growth. The rates, yields (efficiencies), adaptation time and robustness of metabolism are therefore key determinants of cellular fitness. For biotechnological applications and our

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