Passionate about gene expression regulation, I performed my PhD in epigenetics at Institut Pasteur. During my PhD, I contributed to the discovery of a new mechanism of alternative splicing regulation, involving histone protein post-translational modifications (Lavigne et al., PLoS Genetics 2009; Saint-André et al., Nature Structural and Molecular Biology 2011).
After that, I added to my experience of experimental molecular biology, an experience in computational biology, through working for 3 years as a post-doctoral associate of the Whitehead Institute for Biomedical Research of MIT. There, I contributed to the study of “super-enhancers”, and developed a method and a bioinformatic tool to predict the transcription factors at the core of each cell type or cell state’s gene expression program (Hnisz, Abraham and Lee et al., Cell 2013; Tan et al., Molecular Cell 2016; Saint-André et al., Genome Research 2016; Saint-André et al., US Patent 2022).
I then performed a 2-year post-doc at the Curie Institute, where I could identify a long non-coding RNA signature that separates sub-populations of immune cells upon diversification and contributed to evidence upstream control of this regulation by a TNF communication loop (Alculumbre et al., Nature Immunology 2018).
In 2018, I joined the Bioinformatics and Biostatistics HUB, where I am detached to work on the “Milieu Intérieur” project with the Translational Immunology Unit. Our aim is to better understand human immune response determinants and participate to precision medicine development. I yet contributed to multiple works on “Milieu Intérieur” data (Possémé et al., Cell Reports 2022 ; Delavy et al., Gut Microbes 2023), and studies related to tuberculosis (Libre et al., Frontiers in Immunology 2022), HIV (Lista et al., Retrovirology 2023) and Covid-19 (Smith, Possémé, Bondet et al., Nature communications 2022). In parallel, I pursue my interest in the development of bioinformatic methods to study transcriptional regulatory networks (Saint-André et al., Computational and Structural Biotechnology Journal 2021), that we are now applying to “Milieu Intérieur” transcriptomic data.
In parallel of my research work, I have set up or contribute to the following courses:
– “ChIP-seq data analysis” (1 day per session), in “Bioinformatics program for PhD students”, Institut Pasteur, Paris, since 2019
– “Multivariate Data Analysis” (2 days per session, in french or english), in “R Programming and Statistics”, Institut Pasteur, Paris, since 2018
– “IA et Santé” course (one-week), Centrale-Supelec, Paris, since 2019
– Invited lectures, Ecole Centrale de Nantes, since 2019
I am also regularly training students and participated in the following conference organization or evaluation committees:
– Member of the organization committee of JOBIM, Paris 2021
– Invited member for oral and poster evaluation at the YRLS conference, Paris 2019 and 2023
– Jury member for Societé Française de Bioinformatique (SFBI) poster price, JOBIM 2019