Leave me a message
Tel/Fax: +33 (0) 4 72 72 88 23/ 80 80
mail: Laboratoire Joliot-Curie, Ecole Normale Supérieure,
46 Allée d'Italie, F-69364 Lyon Cedex 7, France
Browse the HTML version
or download the PDF file.
Consult my publication list.
En français :
Naviguez sur la version HTML
ou téléchargez le fichier PDF.
Consultez ma liste de publications.
Genome structure and evolution
We study genome evolution and chromosome organisation in terms of gene
localisation and orientation.
This research is supported by the European Union through a Marie Curie Fellowship awarded
for the project "Global measures for genome structure and evolution"
We analysed the localisation of strain-specific genes of
Helicobacter pylori and we have shown that there exist a common pattern
for the genome dynamics of the two completely sequenced H. pylori strains,
suggestive of certain spatial constraints that may act as control mechanisms of gene
Also, we revisited the issue of gene position and orientation using 89 complete
eubacterial and archaeal chromosomes.
This study brings to light a new universal, scale-invariant organisation of microbial
genome organisation (Abstract:
Long-range correlations in genomic DNA
This topic of research is related to the hierarchical nature of DNA sequences
first described in the early 90's
(see Wentian Li comprehensive bibliography on
Features, Patterns, Correlations in DNA and Protein Texts).
During my PhD thesis
we performed a statistical characterisation of the nature of the long-range
correlations using the wavelet transform
(go to Pollux software home page).
We demonstrated that for human sequences the hierarchical nature of DNA depends on its
G+C content suggesting some link with the isochore structure of warm blooded vertebrate
Also, we showed that, universally across the three domains of life, there exists
a characteristic scale around 200nt that separates two scale-invariant regimes that
we interpreted in relation to the hierarchical nature of chromatine and in
particular to the nucleosomal structure (regime between 10 and 200nt)
More recently, we analysed the influence of the sequence on the on elastic properties of DNA
Protein sequences and homology based annotations
Over the years, the Computational Genomics Group built a strong expertise in
protein sequence analysis and in particular in automated sequence annotation
e.g. the GeneQuiz system
that provides online automated annotation
and also maintain the annotation of complete genome
(Genequiz Home Page,
In collaboration with the Medical Research Council Biostatistics Unit, Cambridge,
we developed a dynamical probabilistic model of the homology based
annotation process within a database of protein sequences.
In particular, we show that the propagation of erroneous annotations
leads to a systematic deterioration of database quality
Faculty of 1000,
Computational Genomics Group home page
European Bioinformatics Institute home page
Wellcome Trust Sanger Institute home page
National Center for Biotechnology Information home page
Complete Genome Tracking Database COGENT
GeneQuiz home page
Complete genome server at EBI
Sequence Retrieval System SRS
Long-range correlation analysis of DNA sequences
The signal processing command language
An automatic graph layout algorithm for similarity visualization
Compositional Bias Detection Algorithm
Features, Patterns, Correlations in DNA and Protein Texts