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Boyer, Frédéric
INRIA / Aventis Pasteur

Frédéric Boyer

INRIA Rhône-Alpes
655 avenue de l'Europe, Montbonnot
38334 Saint Ismier CEDEX
Tel. +33 4 76 61 53 40
Fax +33 4 76 61 54 08

Secretary (Françoise de Coninck)
Tel. +33 4 76 61 53 63

-  Short CV
-  Post-Doc subject
-  PhD abstract
-  Teaching


Short CV

-  since 2004 : Post-doctoral position - BBE, Universite Claude Bernard, Lyon, France

-  2003-2004 : ATER - IUT 2 - Université Pierre Mendès France, Grenoble, France

-  2000-2004 : PhD student - Helix team, INRIA Rhône-Alpes, Grenoble, France

-  2000 : Master degree in computer science - IMAG, Grenoble, France

-  1999 : Engineer degree in computer science - Université de Technologie de Belfort-Montbéliard, Belfort, France

-  ...

-  1976 : Born in Chambéry, capital of Savoie, France

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Post-Doc subject

Comparative reannotation of Neisseria species.

This work is done under the supervision of Marie-France Sagot.


PhD abstract

Reconstructing the metabolic pathways of fully sequenced organisms is becoming a task of major importance and several approaches have already been proposed in order to help biologists in identifying and analysing the metabolic pathways of a newly sequenced organism.

A first approach relies on a database of already characterised metabolic pathways and the problem is then to find if each pathway of the database is present or not in the organism under study. This approach is clearly unable to predict unknown or alternative pathways and more exploratory approaches are needed.

What is called ab initio metabolic pathway reconstruction is the problem of finding a metabolic pathway connecting two or more compounds relying only on a database of feasible reactions. We propose a new formulation for the problem of the ab initio metabolic pathway reconstruction. Given a set of biochemical reactions together with their substrates and products, we consider the reactions as transfers of atoms between the chemical compounds and we look for sequences of reactions transferring a maximal (or preset) number of atoms between a given source and the sink compound. We state this problem as the one of finding a composition of partial injections that maximises the image size. The theoretical complexity of this problem has been studied and a practical algorithm to solve it is presented.

-  Publication : ab initio reconstruction of metabolic pathways
-  PhD manuscript (in french) :
Reconstruction ab initio de voies métaboliques - Formalisation et approches combinatoires  - 4.5 Mo
Reconstruction ab initio de voies métaboliques - Formalisation et approches combinatoires
(PDF, 4.5 Mo)

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-  2003-2004 : Initiation to Internet (e-mail, web & HTML programming)
-  2001-2003 : Initiation to computer science (Scheme programming)
-  2001-2002 : LISP programming
-  2001-2002 : UML modelling
-  2000-2001 : ADA programming
-  2000-2001, 2003-2004 : Initiation to Windows

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