Odile Lecompte

Professor at the Ecole Supérieure de Biotechnologie de Strasbourg (ESBS) within the University of Strasbourg
Team : CSTB (Complex Systems and translational Bioinformatics) of ICUBE (UMR 7357)

Research

My research activities, at IGBMC and at ICUBE since 2013, combine tool developments to analyse omics data and their application to the study of biological systems. These approaches are largely based on the exploitation of the evolutionary message provided by comparative genomic and can be can classified into three topics:

• Annotation and massive exploitation of "omics" data (annotation and comparison of prokaryotic genomes, development of proteogenomics approach, analysis of transcriptomes from Metazoa)
• Targeted studies of gene and protein networks (protein complexes involved in membrane trafficking, translation, transcription and regulatory networks) through comparative and integrative approaches,
• Study of genotypes/phenotypes relationships, in particular in rare genetic diseases.

My main current projects are related to the emergent domains of personal genomics and translational bioinformatics.

• OrthoInspector
  

We developed an original algorithm for rapid detection of orthology and inparalogy relationships between genes which are central in comparative and evolutionary genomics. Compared to existing methods, OrthoInspector improves detection sensitivity, with a minimum loss of specificity. The software is suitable for the treatment of thousands of proteomes. The package includes visualization tools to facilitate comparative analysis of genomes or protein family. Databases of precalculated orthology relationships are also available. The software and databases are accessible on the OrthoInspector website.

• MyGeneFriends
  

To facilitate big data exploitation by biomedical researchers and clinicians, we created MyGeneFriends, a social network for three types of agents: genes, human and genetic diseases. Leveraging social networks like Facebook conventions, MyGeneFriends enables simple and intuitive interaction with data through appropriate visualization tools and evaluation of the degree of relationship ("friendship") between agents. MyGeneFriends suggests new friends and relevant publications, allows agents to monitor the activity of their friends, and dynamically personalizes the information according to user's interests. The network is available at: lbgi.fr/mygenefriends.

• CilioCode
  

The project aims at developing an innovative 'omics' profiling methodology for the 20000 human genes in order to characterize genotypes/phenotypes relationships in the context of ciliopathies. The ciliopathies cover many diseases involving a dysgenesis or dysfunction of cilia, organelles essential for many cellular processes (division, signaling, environmental detection...). Symptoms can be observed in tissues/organs closely dependant of cilia (retina, kidney ...) or can be more general (obesity, diabetes). The wide range of symptoms (over a dozen) and the phenotypic differences observed between ciliopathies make these rare genetic diseases a valuable model to study the link between genes and phenotypes.
Thesis in progress: Y. Nevers From « Big data » to genotype/phenotype relationship. Application to ciliopathies.

Student supervision

• PhD supervisor
  

2006-2009 N. Gagnière (co-supervisor: O. Poch, IGBMC) Développement d’une suite logicielle pour l’analyse et l’annotation intégrative automatiques de transcrits et de protéines. Application aux banques d’ADNc de l’annélide polychète Alvinella pompejana. (pdf)
2007-2010 Y.N. Anno (co-supervisor: P. Carbon, IBMC) Establishment of a biostatistics-based bioinformatics platform for integration and analysis of genomic, epigenetic and phylogenetic data - Application to hSTAF/ZNF143 transcription factor binding sites. (pdf)
2012-2015 A. Allot (co-supervisor: O. Poch, ICUBE) MyGeneFriends: towards a new relationship between researchers and BigData (pdf)
2015- Y. Nevers From « Big data » to genotype/phenotype relationship. Application to ciliopathies.
2017- A. Defosset Systemic and evolutionary study of multiciliation genes in Vertebrates.

• Encadrement de stage de Master M2S4
  

E. Perrodou (2004), N. Gagnière (2006), Y.N. Anno (2007), B. Linard (2009) A. Allot (2012), A. Nicol (2013), Y. Nevers (2015), A. Defosset (2017)

Teaching

• ESBS and Ecole Européenne de Chimie, Polymères et Matériaux (ECPM)
  

Bioinformatics (L3) - Engineering Students in Biotechnology and in Chembiotech
Genomics (M1) - Engineering Students in Biotechnology
UE Comparative and integrative genomics (M2) – Engineering Students in Biotechnology and M2 students from Faculty of Life Sciences

• Master Biologie Structurale, Bioinformatique, Biotechnologies (ESBS/Fac. Sciences de la Vie)
  

UE Macromolecular sequence analysis(M1)
UE Structure and analysis of genomes and epigenomes (M1)
UE Transcriptomes and Protéomes (M2)

• Other formations
  

Doctoral school of Life Sciences and Health: Practical courses in Bioinformatics (summer school)
Double Cursus Medecine-Sciences: Introduction to Bioinformatics (L2, Faculty of Medecine)
Continuing education: "From «big data» to a target gene validation"

Other professional duties

• Elected member of the ESBS Council
• Elected member of UDS Expert committee (section 64)
• Responsible of the third year of ESBS
• Responsible of 6 teaching units
• Responsible of the summer chool « Practical courses in Bioinformatics » of the Doctoral school of Life Sciences and Health (UDS)
• Responsible of the continuing educationdu course « From «big data» to a target gene validation – Practical initiation to translational bioinformatics»
• Editorial board member for three international journals

Publications

My full publication list in international pee-reviewed journals is available on PubMed. My publications since 2011 are available on the laboratoire site.

Contact

Odile Lecompte
CSTB - ICUBE UMR7357
Faculté de Médecine 
Bâtiment 3, 5ème étage
11 rue Humann
67085 Strasbourg
Tél : +33 (0)3 68 85 32 96
odile.lecompte@unistra.fr