Jean Stephane Varre
professeur des universitésCNU : SECTION 27 - INFORMATIQUE
+33 3 28 77 85 57
- 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.
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 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.