Positions

Teaching

Head of the 1st year Msc in bioinformatics in Lille
Skeptical thinking
Third year bachelor – Computer science 2014 →
Second year master – Journalist and scientist Since 2013
Algorithms and data structures
Second year bachelor – Computer science 2020 →
Information theory
Second year bachelor – Computer science 2020 →
Bioinformatics methods for sequence analysis
First year master – Bioinformatics 2020 →
Data structures
First year master – Bioinformatics 2020 →
Life sciences (algorithms for bioinformatics)
Second year master – Complex models, algorithms and data 2015 →

Research

Research interests

My research interests are mainly (but not restricted to) the following ones
Bioinformatics
Algorithms for processing read sequences from high-throughput sequencing technologies. More specifically, algorithms for RNA-Seq data, or for the analysis of lymphocyte clonality.
Searching microRNA targets (microRNAs are small non-protein coding RNAs, that have a regulatory role).
Stringology
Dynamic compressed text indexes (suffix tree, suffix array, Burrows-Wheeler transform)
Range minimum query

Publications

Talks given

Software

Vidjil
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.
CRAC
A RNA-seq read analysis tool: for detecting splicing junctions (either alternative or not), fusion gene or transcripts, point mutations (substitutions, insertions, deletions).
GkArrays
A C++ library for indexing reads produced by high-throughput sequencers
DFMI
A dynamic and compressed full-text index implementation

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 will be used for my research.

Contact

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

+33 3 28 77 84 65

  1. 1 If you don't understand that gibberish, do not worry! It is only there not to upset my research group parent organisms.