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Drulhe, Samuel
Allocataire de recherche (Ministère de la Recherche), Moniteur (Rectorat)
 

INRIA Rhône-Alpes / Project HELIX

655 avenue de l'Europe, Montbonnot
38334 Saint Ismier cedex
France

Professional phone number : +33 4 76 61 53 24
Fax machine number :  +33 4 76 61 54 08

Office Manager : Françoise de Coninck
Tel. +33 4 76 61 53 63

Samuel.Drulhe*inrialpes.fr

Portrait of Samuel Drulhe

 

Résumé in brief

Samuel Drulhe obtained a M.Sc. in electrical engineering in 2000 as a student of the Université Paris XI - Orsay, the scientific university of south Paris, and of Ecole Normale Supérieure, a selective school dedicated to high level research and teaching in Cachan. He also passed an "agrégation" in applied physics in 2002, which is a highly competitive degree entitling the holder to teach in the French educational state system.

In the meantime, he was welcomed at the Robotics Institute of the Carnegie Mellon University by Martial Hebert (Pittsburgh, PA, 2001) and the Centre for Imaging Science of the Johns Hopkins University by Donald Geman and Laurent Younès (Baltimore, MD, 2004).

After he had passed a "Diplôme d'Etudes Approfondies" dealing with mathematics, computer vision and machine learning at the CMLA (CNRS, ENS Cachan), he started in 2004 a PhD in computer science at the Institut National de Recherche en Informatique et en Automatique, in the Helix research group of bioinformatics, headed by Alain Viari. His work is supervised by Hidde de Jong and Giancarlo Ferrari-Trecate. He is a student of the Université Joseph Fourier where he also teaches as a "moniteur" CIES.

 

Printable CV

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Systems biology (PhD subject)


Context :

It is now commonly accepted that most interesting properties of an organism emerge from the interactions between its genes, proteins, metabolites, and other constituents. This implies that, in order to understand the functioning of an organism, we need to elucidate the networks of interactions involved in gene regulation, metabolism, signal transduction, and other cellular and intercellular processes.

Genetic regulatory networks control the spatiotemporal expression of genes in an organism, and thus underlie complex processes like cell differentiation and development. Genetic regulatory networks consist of genes, proteins, metabolites, and other small molecules, as well as their mutual interactions. Their study has taken a qualitative leap through the use of modern genomic techniques that allow simultaneous measurement of the expression of all genes of an organism.

In addition to experimental tools, mathematical methods supported by computer tools are indispensable for the analysis of genetic regulatory networks. As most networks of interest involve many genes connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is difficult to obtain and may lead to erroneous conclusions. Modeling and simulation tools allow the behaviour of large and complex systems to be predicted in a systematic way.

A variety of methods for the modeling and simulation of genetic regulatory networks have been proposed, such as approaches based on differential equation models and stochastic models. These models provide detailed descriptions of genetic regulatory networks, down to the molecular level. In addition, they can be used to make precise, numerical predictions of the behaviour of regulatory systems. Many excellent examples of the application of these methods to prokaryote and eukaryote networks can be found in the literature.

In many situations of biological interest, however, the application of differential equations and stochastic models is seriously hampered. In the first place, the biochemical reaction mechanisms underlying regulatory interactions are usually not or incompletely known. In the second place, quantitative information on kinetic parameters and molecular concentrations is only seldom available, even in the case of well-studied model systems.

Our research follows the development of methods for the modeling and simulation of genetic regulatory networks that are capable of dealing with the current lack of detailed, quantitative data. In particular, our team have developed a method for the qualitative simulation of genetic regulatory networks that has been implemented in the computer tool Genetic Network Analyzer (GNA). The method and the tool have been applied to the analysis of prokaryote regulatory networks in collaboration with experimental biologists at the Université Joseph Fourier (Grenoble) and the Ecole Normale Supérieure (Paris).

The choice of well-studied piecewise-linear models are proved to be relevant considering the trade-off between complexity of the model and preservation of the dynamical properties (attractors): graphs of reachable states are builded that correspond to a certain interval of tolerance in the choice of the parameters. The qualitative behavior of the network is then simulated.

PhD subject :

Hidde de Jong (INRIA Rhônes-Alpes - HELIX) and Giancarlo Ferrari-Trecate (INRIA Rocquencourt - SOSSO and Universita` degli Studi di Pavia) are supervising this research.

An other major aspect of the exploration of genetic regulatory networks is the inference of the parameters from a chosen model based on the collection of biological observations (measures of expression levels and protein concentrations).

Precise time dependant acquisitions are presently available.

In piecewise linear systems, different domains of a closed convex space are defined to partition it, in which the dynamic of the network can be described through well-known linear differential equations. The "frontiers" as well as the dynamical parameters in each domain are to be estimated from the data.

Our research aims at adapting powerful system identification tools to piecewise affine models in order to infer model parameters from measures of protein concentrations. Piecewise affine systems are a special case of hybrid systems; the major difficulty comes from the context where few information is available (a small amount of trajectories are measured), and this information is very degraded (noisy). More than an inference problem, the hyperplane frontiers are to be estimated simultaneously with the local parameters. Furthermore, piecewise affine models of genetic regulatory networks confine the frontier geometry and constrain the parameters related to "neighbor regions" to be strongly dependent.

 

Grenoble

Learning management systems (information technologies for education)

The potential applications number of Information and Communication Technologies (ICT) in education is presently booming: many innovative tools have been developed for many years and are now in a process of being fully integrated in national educational systems. If it first allowed elaborating new ways of communicating and data exchanging, we are now exploring Learning Management Systems (LMS) that aim at helping students in their learning practice. Such an approach might modify the present education strategies. It then becomes critical to examine the integration of these technologies in the current teaching practices. We set up a teaching platform based on Moodle software, and we evaluated its use in the context of our courses. We tried different pedagogical experiments and we are now evaluating (through a quantitative inquiry) the effect of using such sysems in a mixed context (as an add-on to the usual academic manners of teaching in presence of the students).

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Courses

-> Moniteur (teaching assistant) at Université Jospeh Fourier (Grenoble, FR) since 2004.

-> Founder of Campus Numérque des Alpes with Sébastien Laborie, a teaching platform that is to be evaluated in term of its ability to improve some pedagogical aspects.

Campus Numérique des Alpes
Year 2006/2007:
Level: Bac+1 , L1 UJF Valence
Title: Introduction to computer science
Head teacher: Philippe Morat
Description: Object oriented languages, Java
Level: Bac+1, option Passeport pour l'Ingénieur, Polytech'Grenoble
Title: Scientific communication
Head teacher: myself
Description: Office suites, HTML

Year 2005/2006:

Level: Bac+3 , filière TIS Polytech'Grenoble, 1ère année
Title: Information retrieval
Head teacher: Catherine Berrut
Description: use of search engines, IR evaluation
Level: Bac+4, filière RICM Polytech'Grenoble, 2ème année
Title: Data bases and information systems
Head teacher: Marie-Christine Fauvet
Description: relational algebra, SQL, functional dependancies, UML

Level: Bac+4 info (ecole info IUP2 Miage)
Title: Data bases and information systems
Head teacher: Marie-Christine Fauvet
Description: relational algebra, SQL, functional dependancies, UML

Year 2004/2005:
Level: Bac+3 , filière TIS Polytech'Grenoble, 1ère année
Title: Information retrieval
Head teacher: Catherine Berrut
Description: acces to information, use of search engine
Level: Bac+4 info (ecole info IUP2 Miage)
Title: Data bases and information systems
Head teacher: Catherine Berrut
Description: relational algebra, SQL, functional dependancies, UML

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Selected publications and talks in - Systems Biology, Hybrid Systems -

Paper

S. Drulhe, G. Ferrari-Trecate, H. de Jong, The switching threshold reconstruction problem for piecewise affine models of genetic regulatory networks, IEEE Transactions on Circuits and Systems I, special issue on systems biology (in press)

Conference

S. Drulhe, G. Ferrari-Trecate, H. de Jong, A. Viari (2006), Reconstruction of switching thresholds in piecewise-affine models of genetic regulatory networks , J.P. Hespanha, A. Tiwari (eds), Hybrid Systems: Computation and Control, HSCC 2006, Lecture Notes in Computer Science, Springer-Verlag, Berlin. Link

Conference posters

S. Drulhe, R. Porreca, G. Ferrari-Trecate, and H. de Jong. An identification procedure for piecewise-affine models of genetic regulatory networks. The Eight International Conference on Systems Biology (ICSB2007), Long Beach, CA, USA, 2007.

S. Drulhe, R. Porreca, G. Ferrari-Trecate, and H. de Jong. An identification procedure for piecewise-affine models of genetic regulatory networks. Toward systems biology, Grenoble, France, 2007.

Technical Report

S. Drulhe, G. Ferrari-Trecate, H. de Jong, A. Viari (2006), Reconstruction of switching thresholds in piecewise-affine models of genetic regulatory networks, Technical report INRIA RT-0322, INRIA, March 2006. Link

Talks

Identification Procedure for PWA Models of Genetic Regulatory Networks, Journée satellite modélisation dynamique et simulation des réseaux biologiques, JOBIM 2007 (*), Marseille, Juillet 2007. Link

Reconstruction des seuils de transition dans le cadre de modèles affines par morceaux de réseaux de régulation génique, projects "GDyn - Gene networks DYNamics"(*) and "BacAttract - Theoretical and Experimental Analysis of Attractors of Genetic Regulatory Networks"(*), Ecole Normale Supérieure, Paris, December 2005.

 

Selected publications and talks in - Learning Management Systems -

Conference

S. Drulhe, Moodle permet-il de faire un enseignement vraiment différent ?, in Conférence Francophone Moodle Moot (*), Castres, 2007. Link

Research Report

M. Coquerelle, S. Drulhe, S. Laborie, Y. Lambert, Étude et expérimentation d'un nouveau support d'échange et de suivi pédagogique, in Annales des ateliers du CIES de l'Académie de Grenoble, 2007. Link

Talks

S. Abry, S. Drulhe, S. Laborie, Moodle en cinq minutes, Séminaire LMS (dédié aux cellules TICE des universités et IUT de Grenoble), mars 2007.Link

S. Abry, M. Coquerelle, S. Drulhe, S. Laborie, Y. Lambert, Étude et expérimentation d'un nouveau support d'échange et de suivi pédagogique, Journée de présentation des ateliers du CIES de l'Académie de Grenoble, mars 2007.Link

S. Drulhe, S. Laborie, Université virtuelle : des innovations pour l'enseignement, Journée d'accueil des moniteurs du CIES de l'Académie de Grenoble, octobre 2006.Link

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Organizational and other activities

Samuel Drulhe has been elected in March 2005 to represent people without INRIA open-ended contract at the advisory board called Comité d'Unité de Recherche.
Standing by FOURMI with others PhD students of the Doctorate School in Computer Science, Applied and Pure Mathematics of Joseph Fourier University, Samuel has been elected in June 2006 to take part of the school body.

By the way, I recommend the "Guide du Doctorant MSTII" (in French) written by Alexandre Donze which is an excellent travel book concerning the administrative labyrinth that any PhD student has to face : it is focused on the Graduate school of Mathematics and Computer Science of Joseph Fourier University, and being precise, it is precious.

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Présentation CIES 1A (PDF; 183.8 ko)
Présentation CIES 3A (PDF; 4.7 Mo)
Séminaire LMS (PDF; 692.1 ko)
Annales du CIES (PDF; 1 Mo)
Moodle Moot 2007 (PDF; 215.6 ko)
Jobim 2007 (PDF; 1.6 Mo)
CV - Résumé (PDF; 353 ko)
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