Jean-Stéphane Varré
professor
Research interests
I am a member of the bioinformatics BONSAI research team (CRIStAL - MSV group and INRIA Lille - Nord Europe). My research interests are
  • transcription prediction : splicing orthology
  • assembly with 3rd generation sequencing technologies
  • genomic rearrangements : scenarios with duplicated markers, evolution of plant mitochondrial genomes, analysis of breakpoont regions
  • massively parallel algorithms for bioinformatics : data structures on GPUs, string matching
  • pattern matching with position weight matrices (PWM/PSSM)
  • sequence comparison with similar factors (PhD thesis work)

Have a look at our group's software server to use the methods we develop in our team.

Publications

PhD Students

I'm the co-supervisor together with Rayan Chikhi of the PhD Thesis of Pierre Marijon. He work on assembly graph analysis (see ).

I was the co-supervisor together with Aïda Ouangraoua of the PhD Thesis of Antoine Thomas. He worked on genomic rearrangements with duplicates.

I was the co-supervisor together with Mathieu Giraud of the PhD thesis of Tuan Tu Tran (2009-2012). We worked on data structures and algorithms for manycores architectures.

I was the co-supervisor together with Pascal Touzet of the PhD thesis of Aude Darracq (2006-2010). We worked on the study of the rerrangement history of plant mitochondrial genomes at the intra-specific level. Aude is currently at SESVANDERHAVE, Belgium.

I was the co-supervisor together with Hélène Touzet of the PhD thesis of Aude Liefooghe (2004-2008). The aim of the work was to design algorithms for locating efficiently transcription factor binding sites modelled with position weight matrices.

I was the co-supervisor together with Jean-Paul Delahaye of the PhD thesis of Martin Figeac (2002-2005). We studied how to compute genomic rearrangement scenarii introducing constraints on the reversals allowed. Martin is currently the head of the genomics platform at the cancer institute of Lille.

Teaching

I'm part of the computer science department at University of Lille. Courses in computer science (mainly algorithms and programming). See this page (all documents in french).

Currently Algorithms and Data Structures (2nd year), Programming with Java (2nd year), Systems (3rd year) and master project on plagiarism tools (1st year).

I'm in charge of the B. Sc. in computer science since 2015.

I was in charge of the MOCAD master's degree in computer science (Complex models, Algorithms and Data) from 2010 to 2015.

Contact
CRIStAL
Faculté des Sciences et Technologies de Lille
Bât M3 - Room 207
59655 Villeneuve d'Ascq Cedex - France
Tel: +33 3 28 77 85 57
Fax: +33 3 28 77 85 37
E-Mail: jean-stephane.varre (AT) univ-lille (DOT) fr
13/2/2018 Jean-Stéphane Varré