Last week, Dr. Lisa Chabrier successfully defended her PhD work on calculating SHAP values and using them to do differential network analysis. Whilst SHAP values are a popular framework for local explanations of machine learning predictions, they come with a serious computational cost. Lisa developed an approximation algorithm to avoid calculating lots of SHAP values … [Read more…]
Great news! Sara’s work on characterizing the neurons involved in odor interpretation has been published in Nature Neuroscience (see here, or check the BiorXiv version). It took a serious amount of effort over several years, which makes me very proud of Sara’s accomplishments and of the contributions by all the co-authors. This study was really … [Read more…]
It has been… a few years actually, and I finally have some ideas to share on my blog. Indeed, I will make an effort to put out content on a more regular basis than once every few years. The reason is simple: with family life taking priority, I travel a lot less these days and … [Read more…]
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…]
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…]
After a year-and-a-half at Collège de France in Paris, I have started my permanent position at Inria in Lyon/Villeurbanne. Fyi, Inria is the French national organisation for computational research. I must admit, to not hurry from one short-term job to the next and to have an extended period of time to think is a wonderful … [Read more…]
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…]
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…]
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…]
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…]