Structural and parametric identification of bacterial regulatory networks
Ph.D. position, 3 years, Grenoble, 1900-2000 euros

re-posted from, 17.05.2010

Qualifications and experience

Candidates should have a background in mathematics, computer science or physics, preferably with a specialization in system identification or control theory. Programming skills are necessary and knowledge of scientific software (Matlab, Scilab, Maple, Mathematica,...) is desirable. A strong interest for biological applications is essential. Successful candidates will be working in an international and multidisciplinary environment.


A Ph.D. position opens within the team IBIS at the Grenoble - Rhone-Alpes Research Unit of INRIA (French National Institute for Research in Computer Science and Control) , located near Grenoble and Lyon.
The project concerns the identification of dynamical models of biochemical regulatory networks in bacteria. Recent advances in molecular biology and in biophysics have led to new technologies for measuring cellular processes at the molecular level and in real time, including fluorescence and luminescence microscopy, microfluidics and mass-spectrometry measurement of metabolites. The objective of the thesis is the development of methods for the structural and parametric identification of bacterial regulatory network models that fully exploit the data provided by the new techniques mentioned above. Depending on the interests of the candidate and on the priorities encountered, the project will focus on several among the following methodological issues:
   The choice of appropriate modeling formalisms.
A special attention will be devoted to models combining discrete properties (Boolean functions) and continuous dynamics (ordinary and piecewise linear differential equations, stochastic differential equations, ...) ;
   The study of model identifiability in the presence of noisy data, different time scales and hidden variables ;
   The design of maximally informative experiments for identification, for instance by the use of information-theoretic approaches ;
   The development of effective algorithms for the parametric and structural identification of the system, based on the chosen modelling formalism.
The project will take advantage of experimental data and modelling expertise available within IBIS or via the participation of IBIS to national and international projects. Focus will be placed on the regulatory mechanisms underlying the adaptation of enterobacterium Escherichia coli to changes in the environmental carbon sources, investigated by the team in collaboration with J.Geiselmann (member of IBIS) at the Microorganism Pathogeny and Adaptation Laboratory of the Universite Joseph Fourier.

Monthly salary will be around 1900-2000 euros (gross).
Interested candidates may visit IBIS position for additional details and should apply for the position by contacting Eugenio Cinquemani and/or Hidde de Jong .