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Bioinformatics engineer in integrative and systems biology.
chernand [at]

My main projects in the CSB group focus on immunology related to cancer. In melanoma for instance, cancer cells have a specificity allowing them to inactivate some members of the immune system coming in their proximity. They thus evade the immune response that could destroy them. More specifically, they express ligands at their surface that are able to stimulate inhibitory receptors and signalling cascades inside immune cells. Very promising therapies are now able to re-activate these inhibited cells, allowing our own defence system in our body to fight cancers. You can find a very nice introduction to this system on the 2018 Nobel Prize in Physiology and Medicine web page (

The focus of my work is mainly CD4+ T cells, their CTLA4 and PD-1 co-inhibitory receptors and the downstream concurrent intracellular processes. In this context, I use various approaches linked to dynamical modelling whether logic-based (GINsim) or rule-based (Kappa). I am also particularly interested in applying techniques inherited from software development to model definition and parametrisation.

Our goal is to understand what is happening inside the T cells when they are inhibited through their co-inhibitory receptors, and provide a rationale for designing and evaluating new anti-cancer therapies.

In parallel to my research activities, I have a special interest in developing and spreading good practices in bioinformatics, especially aspects related to reproducible research :
- code versioning,
- software encapsulation in virtual machines and containers,
- automation of data analyses through workflows development,
- literate computing through the usage of notebooks.