Benjamin Audit

Chargé de Recherche - CNRS

Chromatin & Genome Group

Laboratoire Joliot-Curie & Laboratoire de Physique
UMR 5672 CNRS - Ecole Normale Supérieure de Lyon

Contact information
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

Curriculum Vitae
In English:
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.

Research Interests
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" (PDF).
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 flux (Abstract).
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: HTML, PDF).

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 ( resume, résumé), 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 (Abstract, PDF). 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) (Abstract 1, Abstract 2). More recently, we analysed the influence of the sequence on the on elastic properties of DNA (Abstract, PDF, VJBIO)

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 (Abstract) that provides online automated annotation (GeneQuiz Server) and also maintain the annotation of complete genome (Genequiz Home Page, Abstract, PDF).
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 (Abstract, Faculty of 1000, PDF).

Useful Links
Computational Genomics Group home page
European Bioinformatics Institute home page
Wellcome Trust Sanger Institute home page and library
National Center for Biotechnology Information home page

Complete Genome Tracking Database COGENT
GeneQuiz home page and Server
Complete genome server at EBI or NCBI.

Search engines
Sequence Retrieval System SRS

Pollux: Long-range correlation analysis of DNA sequences
LastWave: The signal processing command language
BioLayout: An automatic graph layout algorithm for similarity visualization
CAST: Compositional Bias Detection Algorithm
BLAST, FASTA : Sequence alignment

Bibliography: Features, Patterns, Correlations in DNA and Protein Texts