- Mikaël Salson
- Associate professor of computer science
- mikael.salson@univ-lille.fr
- +33 3 28 77 85 54
Positions
- Since September 2010, I am part of the bioinformatics research group Bonsai (CRIStAL laboratory – Université de Lille and CNRS 1). You could find me wandering around office 204 in the M3 extension building.
- I prepared my PhD thesis at the university of Rouen in the TIBS group of the LITIS laboratory. I defended late 2009. I had the chance to be advised by Laurent Mouchard and Martine Léonard, and under Thierry Lecroq's supervision.
Teaching
- Skeptical thinking
- Third year bachelor – Computer science 2014→
- Second year master – Journalist and scientist 2013→
- Coding and information theory
- Second year bachelor – Computer science 2010→
- Automata and languages
- Third year bachelor – Computer science 2015→
- Bioinformatics
- First year master – Biology and biotechnology 2011→
- CS1
- First year bachelor – Hard sciences 2014→2015
- C programming
- Second year bachelor – Computer science 2013→2015
- Third year bachelor – Computer science 2010→2013
- Introduction to programming
- First year bachelor 2010→2014
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
See my publication list
Talks given
See the list of my talks
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.
- 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 also work 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 85 54
