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About

I obtained a PhD in phylogeny in 2008 at the Muséum National d’Histoire Naturelle in Paris, then worked as a post-doc in Torino (Italy, 2009 – 2011) and Faro (Portugal, 2011 – 2013) where I worked on methodological aspects of phylogeny, applied to mongoose, fish or cyanobacteria. This was the opportunity to acquire and improve skills in data analysis and practical computing.

In 2013, I was hired as research engineer in bioinformatics at the Institut de Génétique Humaine in Montpellier where I was involved in various system administration, programming, and data analysis tasks. I mainly wrote tools to analyze high-throughput sequencing data, especially small RNA-seq.

This is also the kind of job I did when joining Institut Pasteur in 2016, in Germano Cecere’s team, where C. elegans is used as a model organism to study the role of Argonaute proteins and their associated small RNAs in development and epigenetics.

Example "rulegraph".
Graph showing dependencies between data processing steps in an automated workflow assembled using Snakemake.

I’m now part of the bioinformatics service platform (the Bioinformatics and Biostatistics Hub), where I contribute to various projects (mainly involving automation of bioinformatics workflows and development of custom exploratory data analysis tools and visualization), as well as to teaching activities (mainly aimed at PhD students).

I enjoy programming in Python, I’m interested in evolutionary biology, and I find teaching the UNIX command-line and other practical computer skills a rewarding activity. I’m also particularly involved in a course introducing PhD students (and sometimes other staff at Institut Pasteur) to R programming and basic descriptive statistics (although I wouldn’t consider myself proficient in R nor in statistics). The course support is available on-line and can hopefully be studied autonomously: https://hub-courses.pages.pasteur.fr/R_pasteur_phd/First_steps_RStudio.html

I like learning new languages (for human communication or programming), but rarely reach a working proficiency level due to lack of opportunities to practice. I’m at my third (or maybe more) attempt to learn Haskell, a fascinating programming language, and I particularly recommend this free book: http://learnyouahaskell.com/

My published work is available here: http://www.normalesup.org/~bli/useful.html

The code I develop at Institut Pasteur is mostly hosted here: https://gitlab.pasteur.fr/users/bli/projects (some access restriction may apply).

I’m the main contributor of the following online course supports:

See also my page at the bioinformatics and biostatistics hub.

Courses

Introduction to R and statistics – RS 1

virtual session (on Teams) in English. The course material for this module is available on-line permanently and is hopefully detailed enough to be studied in a self-learning mode: https://hub-courses.pages.pasteur.fr/R_pasteur_phd/First_steps_RStudio.html Part of PhD course R […]

2021-04-06 09:00:00 2021-04-09 00:30:00 Europe/Paris Introduction to R and statistics – RS 1 virtual session (on Teams) in English. The course material for this module is available on-line permanently and is hopefully detailed enough to be studied in a self-learning mode: https://hub-courses.pages.pasteur.fr/R_pasteur_phd/First_steps_RStudio.html Part of PhD course R […]

Introduction to R and statistics – RS1

virtual session (on Teams) in French. The course material for this module is available on-line permanently and is hopefully detailed enough to be studied in a self-learning mode: https://hub-courses.pages.pasteur.fr/R_pasteur_phd/First_steps_RStudio.html Part of PhD course R […]

2021-11-02 09:00:00 2021-11-05 00:30:00 Europe/Paris Introduction to R and statistics – RS1 virtual session (on Teams) in French. The course material for this module is available on-line permanently and is hopefully detailed enough to be studied in a self-learning mode: https://hub-courses.pages.pasteur.fr/R_pasteur_phd/First_steps_RStudio.html Part of PhD course R […]

Introduction to R and statistics – RS1

Part of the PhD course “R and statistics”. The course material for this module is available on-line permanently and is hopefully detailed enough to be studied in a self-learning mode: https://hub-courses.pages.pasteur.fr/R_pasteur_phd/First_steps_RStudio.html More info on […]

2022-04-04 09:30:00 2022-04-06 17:00:00 Europe/Paris Introduction to R and statistics – RS1 Part of the PhD course “R and statistics”. The course material for this module is available on-line permanently and is hopefully detailed enough to be studied in a self-learning mode: https://hub-courses.pages.pasteur.fr/R_pasteur_phd/First_steps_RStudio.html More info on […] Institut Pasteur, Rue du Docteur Roux, Paris, France

Software Carpentry

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including […]

2018-03-28 09:00:00 2018-03-29 17:00:00 Europe/Paris Software Carpentry Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including […] Pasteur, Paris, France

Projects

CV

  • 2016 – present:  Ingénieur de recherche, Institut Pasteur (Paris)
  • 2013 – 2016: Ingénieur de recherche, Institut de Génétique Humaine (CNRS, Montpellier)
  • 2011 – 2013: Bolsista de pós-doutorado, Centro de Ciências do Mar (Universidade do Algarve, Portugal)
  • 2009 – 2011: Assegnista di ricerca, Dipartimento di Fisica (Politecnico di Torino, Italie)
  • 2007 – 2008: Middle-school biology teacher (Issy-les-Moulineaux)
  • 2004 – 2007: Allocataire de recherche (Université Paris VI) Moniteur (Université Versailles – St-Quentin)
  • 2000 – 2004: Civil-servant student, ENS (Paris)

Publications

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