Bye bye Twitter!

Until this autumn I used to spend time on Twitter. I found many an interesting article casually browsing tweets and occasionally I would find a reason to write a tweet myself. Well, that’s history now. I may join a Mastodon server at some point, but for the moment I am going to enjoy the silence. … [Read more…]

Evolution of evolution

A couple of years ago I learned that Guillaume Beslon and Paulien Hogeweg were collaborating under the umbrella of the EvoEvo project (link). Naturally, that caught my attention. Now the project is finished and I have selected some juicy bits. Enjoy the long version or skip to the take-home messages. The central idea of EvoEvo … [Read more…]

What do we learn from evolutionary simulations?

Digital experiments of how the process of evolution works—also known as in silico (experimental) evolution or simply evolutionary simulations—have been explored and studied since the early days of computing. Nowadays, while using the computer to simulate evolution is a well-accepted approach, not everyone is clear about what it teaches us. As I use such simulations … [Read more…]

Ancient code on GitHub

Long overdue, but I’ve finally published some code of my PhD. There are two repositories on GitHub for anyone interested in my work on the evolution of evolvability [1, 2]. Here you can find them: Genomes, transposable elements, and rearrangements Evolving Boolean gene networks Happy 2017! References: [1] Mol Biol Evol 24(5), 1130–39 (2007) [2] … [Read more…]

I’ve started at Collège de France

This June I started my own team at the Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, Paris. Exciting times are ahead! If you want to do a Master’s project, a PhD, or a postdoc, you’re interested in evolution, and you like to use computers, maths & bioinformatics to pursue your research questions, … [Read more…]

The real challenge for biology

Some notes: There are some great videos on swarming behaviour of animals. Here are just two quick examples: a starling murmuration and a school of tuna. Segmentation stripes are formed in the first hours of a fly’s development. They are the molecular markers that give rise to the actual body segments of a fly. More … [Read more…]

Useful links

Below some useful websites, software and other links with a short description (work in progress). I am updating this post over time. Science: Inria’s Team Beagle Bioinformatic Processes (Utrecht course) Dutch Society of Theoretical Biology Dutch Society for Evolutionary Biology Grant writing: Proposal writing advice OPIDoR, French data-management-plan generator Text Editors: Vim Vim Plugin Repository … [Read more…]