- Mikaël Salson
- Associate professor of computer science
- mikael.salson@univ-lille.fr
- +33 3 28 77 84 65
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 close to the office S3.57 in the ESPRIT building, or to the office 216 in the M3 extension building or in-between them or possibly in any other place.
- I prepared my PhD thesis at the university of Rouen in the TIBS group of the LITIS laboratory.
Teaching
- 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
- 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
