Jean Stephane Varre

professeur des universités
CNU : SECTION 27 - INFORMATIQUE

Jean Stephane Varre

professeur des universités

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.

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 https://gitlab.inria.fr/pmarijon/assembly_report).

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.