Positions

Teaching

Skeptical thinking
Third year bachelor – Computer science Since 2014
Second year master – Journalist and scientist Since 2013
Coding and information theory
Second year bachelor – Computer science Since 2010
Supervised project on plagiarism detection
First year master – Computer science Since 2017
Life sciences (algorithms for bioinformatics)
Second year master – Complex models, algorithms and data Since 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).

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.