Jean-François Tomb

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Sequence assembly is an essential requirement for determining the complete sequence of long DNA. However, sequence assembly programs often generate misassembled contigs by either joining diierent repeat copies, resulting in joining non contiguous DNA regions (inverted or swapped) or by including many fragments from diierent repeat copies resulting in errors(More)
Elementary flux modes (EFMs) have been claimed as one of the most promising approaches for pathway analysis. These are a set of vectors that emerge from the stoichiometric matrix of a biochemical network through the use of convex analysis. The computation of all EFMs of a given network is an NP-hard problem and existing algorithms do not scale well.(More)
Flux analysis methods lie at the core of Metabolic Engineering (ME), providing methods for phenotype simulation that allow the determination of flux distributions under different conditions. Although many constraint-based modeling software tools have been developed and published, none provides a free user-friendly application that makes available the full(More)
Elementary Flux Modes (EFMs) have been claimed as one of the most promising approaches for pathway analysis. These are a set of vectors that emerge from the stoichiometric matrix of a biochemical network through the use of convex analysis. The computation of all EFMs of a given network is an NP-hard problem and existing algorithms do not scale well.(More)
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