Date : 23/01/2012

Laboratory
I2D3 - Integrative Immunology: Differentiation, Diversity, Dynamics
UMR7211, "I3" Université Pierre et Marie Curie - Paris 6 & CNRS
Bâtiment CERVI, Sce Biothérapies (Pr. Klatzmann)
83 bd de l'Hôpital
75013 Paris
Website: www.i3-immuno.fr ; www.immunocomplexit.net
Main discipline : Systems Biology
Lab director : David Klatzmann

PhD Supervisor
Adrien SIX
email : This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
phone: +33 1 42 17 65 11

Subjects
1.: Integrative immunology
2.: T-cell differentiation & cell dynamics
3.: Cell population & Repertoire diversity

Tools and Methodologies
1.: Integrative immunology
2.: T-cell differentiation & cell dynamics
3.: Cell population & Repertoire diversity

Summary of lab's interests
Our aim is to design an "immuno-physiome" of the immune system considered as a complex system. The team is involved in the global analysis of the immune system, from the integration of multi-scale and multi-level data (flow cytometry, transcriptome, repertoire) to the modelling of dynamics and in the analysis of transcriptome and diversity repertoire of lymphocytes. Our integrated "immunomics" perspective is designed to describe, predict and explain the puzzling complex T cells dynamics and immunological perturbations through ageing or diseases, associated molecular and cellular alterations, and T cell repertoire diversity alterations.

Summary of project
The PhD project will be to assist in the development of an international ComplexiT project. This project aims to develop a more thorough understanding of T-cell differentiation & dynamics by complementing lab-based immunological methods with statistical discovery and analysis, computational modelling of structural relationships and mathematical modelling of dynamics. We propose an innovative hybridisation of graphical modelling languages directly executable by immunologists, to support interdisciplinary research in systems immunology to allow interoperabilty and implementation. The project uses UML as a lingua franca for encoding and sharing knowledge between sub-groups, which are individually focused on knowledge-management, computer simulation and analysis. The candidate will be joining the project at a key point in its development. Initial work to develop the necessary framework to obtain experimental immunological data and describe current knowledge will be complete. At this point, the project's focus will move to deconstructing this traditional picture based on a mixture of finer-grained data analysis, ontological reorganisation and more sophisticated computer simulations to develop a visual and semantic interoperable computational approach towards a better understanding of the complexity of the immuno-physiome.

Interdisciplinarity of the project
The immune system complexity precludes individual work from a single frame of reference. The I2D3 team has expertise in differentiation & dynamics of lymphocytes, mathematical, statistical modelling & computer simulation and thus assembles experts in immunology, statistics and bioinformatics. This interdisciplinary research requires specific tools, developed in close association with the immunologists who will use them and regarding the research questions to provide a multiscale & multiparametric database description and computer modelling of T lymphocytes dynamics and repertoire selection processes. This systems-biology approach favours global rather than reductionist approach and requires interdisciplinary knowledge to develop simultaneously strategic tools to favour data storage, analysis and modelling and sharing and understanding of the immune systems behaviour.