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Assistant professor

An associate professor position opens at the Université de Lille in computer science to work on digital health. Please contact me if you're interested.


Head of the 1st year Msc in bioinformatics in Lille
Skeptical thinking
Third year bachelor – Computer science 2014 →
Journalism - joint degree between Sciences Po Lille and the ESJ Lille 2022 →
Second year master – Journalist and scientist 2013–2022
Algorithms and data structures
Second year bachelor – Computer science 2020 →
Information theory
Second year bachelor – Computer science 2020 →
Introduction to programming
Third year bachelor – Biology of organisms and populations (BOP) 2021 →
Third year bachelor – Computer science 2020 →
Bioinformatics methods for sequence analysis
First year master – Bioinformatics 2020 →
First year master – Bioinformatics 2022 →


I am the head of the Bonsai research group.

Research interests

I'm mainly interested in the following topics in sequence bioinformatics: sequence indexing and alignment-free comparisons.

Sequence indexing

The volume of sequencing data available makes indexing data necessary, whether at the level of a genome, of a sequencing set or of collections of sequencing sets. These different facets of indexation aim for one common goal: to access and query the data as efficiently as possible. Several PhD students or post-doctoral fellows that I have co-supervised have addressed these aspects:

  • Monotigs

    Indexing collection of high-throughput sequencing datasets (post-docs of C. Marchet and F. Ingels)

  • VDJ recombination

    Indexing V(D)J recombinations (T. Rocher's PhD thesis)

  • Tige boucle

    Genome indexing for querying short sequences with high error rates (applicable to micro RNA target search, C. Vroland's PhD thesis)

Alignment-free comparison

Alignment-free comparisons compare data without aligning through dynamic programming. These approaches have the advantage of being much more frugal without necessarily losing in quality (contrary to what might be feared).

  • A duplication in the DNA

    Identifying tandem duplications in known genes (with applications to the characterization of FLT3-ITDs in acute myeloid leukemia)

  • Red and white blood cells

    Characterizing populations of white blood cells from their V(D)J recombinations (with applications to marker identification in leukemias)

  • CRAC k-mer mapping

    RNA-seq data analysis (splice, fusion detections, and more)

I'm also co-supervising T. Baudeau's PhD thesis on viral Nanopore sequence analysis.


Tandem duplication detection in genes of interest. The software was initially developped for the idenitifcation and quantification of FLT3-ITD in high-throughput sequencing data but could be applied to other cases.
A platform for the analysis of lymphocyte populations based on their V(D)J recombination in high-throughput sequencing data. That platform is especially used in leukemia follow-up by several hospitals around the world. The software is now being transferred through the not-for-profit VidjilNet consortium.
A RNA-seq read analysis tool: for detecting splicing junctions (either alternative or not), fusion gene or transcripts, point mutations (substitutions, insertions, deletions).
A C++ library for indexing reads produced by high-throughput sequencers
A dynamic and compressed full-text index implementation


Talks given

Conflicts of interest

I own the minimal number of shares of my cooperative bank. My research are exclusively funded by public funds. Within the Vidjil project, I have worked in 2015–2016 with an engineer funded by the fondation EDF. I have signed a non-paid speaker contract with Novartis for a 2-day workshop in 2016 on onco-hematology with medical doctors from hospitals in the north of France. Novartis paid for a hotel room (one night) and for the meals (three). In January 2020 I've been invited by the SeqOne company in Montpellier. The company funded the transport and some meals. During the spring 2020 I temporarily brought my expertise for SeqOne. My university received funds for that expertise, those funds have be used to fund an internship, a publication and a team lunch.


Université de Lille – CRIStAL
Bâtiment M3 – Cité scientifique
59655 Villeneuve d'Ascq Cedex - France

+33 3 28 77 84 65

Credits: picture for indexing collection of high-throughput sequencing datasets by Camille Marchet, picture of the stem-loop CC BY SA Sakurambo.

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