Lisa defended her PhD

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…]

Our work published in Nature Neuroscience

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…]

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…]

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…]