Available a PhD position for a computer scientist at the Institute of Complex Systems in Paris Île-de-France

Proposed project: Computer modelling of immune system complexity and lymphocyte dynamics

General research aim: Global analysis and computer modelling of the immune system as a complex multi-scale heterogeneous adaptive, biological system.

Project: This interdisciplinary project aims to develop a more thorough understanding of the complexity of the immune system that behaves like a micro-ecological system by rapid adaptation to a changing environment by cell differentiation, cell death, cell selection, molecular and cell interaction, migration and complex dynamics regulations, by processes involving multi-scale biological levels from molecules to organism. Computational modelling of structural relationships and mathematical modelling of lymphocyte dynamics are required for a better understanding and simulations of the complex immune system behaviour in to understand the resilience and robustness in health but alterations in aging and diseases.

The PhD project aim is to develop a multi-scale computer model platform of lymphocytes dynamics. Our systems-biology approach favours global rather than reductionist approach and aims to develop simultaneously strategic tools to favour data storage, analysis, modelling and sharing in the team and with collaborators. The project uses UML as a lingua franca for encoding and sharing knowledge between research sub-groups, which are individually focused on knowledge-management, 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 describe current biological knowledge will be complete. The aim of the PhD project will be to develop the computer platform allowing for population or agent based models and simulations, integration of ontologies to design a platform using graphical and standardized languages, with an interface designed to help biologist to program and run their model and fit on experimental data to validate them. Indeed, originally applied to mice, the modelling tools will be extended for modelling the immune system behaviour of patients in the context of TransImmunom LabEx and as underlined in the Virtual Physiological Human VPH conference. This model could be in turn applied to other population-/agent-based models such as social or ecological systems.

Candidates should have solid computational (UML, java, xml, ontologies, standard languages), mathematical and statistical experience with a strong motivation for biological modelling, and interest in complex systems behaviour to test robustness and resilience of the system. Background in Immunology is welcome.

Bibliographical references related to the project

See publication here:  http://www.immunocomplexit.net/

Related team publications

• Thomas-Vaslin, V., Altes, H. K., de Boer, R. J., and Klatzmann, D. (2008). Comprehensive assessment and mathematical modeling of T cell population dynamics and homeostasis. J Immunol 180, 2240-2250.
  
• Lavelle, C., H. Berry, G. Beslon, F. Ginelli, J. Giavitto, Z. Kapoula, A. Le Bivic, N. Peyrieras, O. Radulescu, A. Six, V. Thomas-Vaslin and P. Bourgine (2008). "From molecules to organisms: towards multiscale integrated models of biological systems."Theoretical Biology Insights1: 13-22.
  
• C. H. McEwan, H. Bersini, D. Klatzmann, V. Thomas-Vaslin, A. Six. A computational technique to scale mathematical models towards complex heterogeneous systems(2011), COSMOS 2011 Conference Proceeding of the 2011 workshop on complex systems modeling and simulation Luniver press. IBSN 978-1-905986-32-3
  
• Thomas-Vaslin, V., A. Six, H. P. Pham, C. Dansokho, W. Chaara, B. Gouritin, B. Bellier and D. Klatzmann (2012). Immunodepression & Immunosuppression in aging mice "Immunosuppression" InTech - Open
  
• Bersini, H., D. Klatzmann, A. Six and V. Thomas-Vaslin (2012). "State-Transition Diagrams for Biologists." PloS one 7 (7), e41165
  
• Thomas-Vaslin, V., A. Six, B. Bellier and D. Klatzmann (2013). Lymphocytes dynamics repertoires, modeling. Encyclopedia of Systems Biology. W. O. Dubitzky W, Springer, Heidelberg NewYork. http://link.springer.com/referenceworkentry/10.1007/978-1-4419-9863-7_96
• Thomas-Vaslin, V., A. Six, J. G. Ganascia and H. Bersini (2013). "Dynamical and mechanistic reconstructive approaches of T lymphocyte dynamics: Using visual modelling languages to bridge the gap between immunologists, theoreticians and programmers." Frontiers in Immunology 01 October 2013 | doi: 10.3389/fimmu.2013.00300  http://www.frontiersin.org/Journal/Abstract.aspx?s=1177&name=t_cell_biology&ART_DOI=10.3389/fimmu.2013.00300
• Thomas-Vaslin, V. (2014). "A complex immunological idiotypic network for maintenance of tolerance." Front Immunol 5: 369. http://www.ncbi.nlm.nih.gov/pubmed/25132837
  

Dr Véronique THOMAS-VASLIN/ Prof. Adrien SIX

Phone: +33 01 42 17 74 66 
Email: veronique.thomas-vaslin@upmc.fr /adrien.six@upmc.fr
Institution: UPMC, INSERM, CNRS
Unit Director: Prof. David KLATZMANN,
Immunology, Immunopathology, Immunotherapy
CNRS FRE3632, UPMC INSERM UMRS959
83 Boulevard de l’Hôpital, 75013 Paris
http://www.i3-immuno.fr/

Additional information can be found at: http://www.iscpif.fr/tiki-index.php?page=aap15_doc