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About

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

Courses

Bioinformatics program for PhD students 2023 2024

This training program in statistics, bioinformatics and image analysis, financed by INCEPTION program, begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, […]

2023-10-23 09:30:00 2024-06-28 17:00:00 Europe/Paris Bioinformatics program for PhD students 2023 2024 This training program in statistics, bioinformatics and image analysis, financed by INCEPTION program, begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, […] 25-28 Rue du Docteur Roux, Paris, France

6ème école de bioinformatique AVIESAN-IFB

Objectifs La formation s’adresse à des chercheurs et ingénieurs directement impliqués dans des projets “Next Generation Sequencing” (NGS). Cette édition de l’école s’adresse aux nouveaux enjeux technologiques: elle inclura notamment une ouverture aux technologies […]

2017-11-12 18:00:00 2017-11-17 15:00:00 Europe/Paris 6ème école de bioinformatique AVIESAN-IFB Objectifs La formation s’adresse à des chercheurs et ingénieurs directement impliqués dans des projets “Next Generation Sequencing” (NGS). Cette édition de l’école s’adresse aux nouveaux enjeux technologiques: elle inclura notamment une ouverture aux technologies […] Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France

Projects

CV

EXPERIENCE:
2016 – 2018: Postdoctoral research fellow – Institut Curie – CNRS UMR3244/UPMC
2013 – 2016: Postdoctoral research associate – Whitehead Institute/MIT  – Pr. Richard Young Lab

EDUCATION:
M.Sc. in Bioinformatics, Université Paris VII, 2012
Ph.D in Molecular Biology, Genetics, Université  Paris VI, 2010

Publications

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