Isabelle Dutour

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The combination of sequencing and post-sequencing experimental approaches produces huge collections of data that are highly heterogeneous both in structure and in semantics. We propose a new strategy for the integration of such data. This strategy uses structured sets of sequences as a unified representation of biological information and defines a(More)
BACKGROUND The search for enriched features has become widely used to characterize a set of genes or proteins. A key aspect of this technique is its ability to identify correlations amongst heterogeneous data such as Gene Ontology annotations, gene expression data and genome location of genes. Despite the rapid growth of available data, very little has been(More)
We present a new computer algebra package which permits to count and to generate combinatorial structures of various types, provided that these structures can be described by a speciication, as deened in 7]. R esum e Nous pr esentons un nouveau module de calcul formel d edi e au d enombrement et a la g en eration al eatoire uniforme de structures(More)
The central dogma in molecular biology postulated that `DNA makes RNA makes protein', however this dogma has been recently extended to integrate new biological activities involving small bacterial noncoding RNAs, called sRNAs. Accordingly, increasing attention has been given to these molecules over the last decade and related experimental works have shown a(More)
The revolution in high-throughput sequencing technologies has enabled the acquisition of gigabytes of RNA sequences in many different conditions and has highlighted an unexpected number of small RNAs (sRNAs) in bacteria. Ongoing exploitation of these data enables numerous applications for investigating bacterial transacting sRNA-mediated regulation(More)
Trypanosoma brucei is a protozoan parasite of major of interest in discovering new genes for drug targets. This parasite alternates its life cycle between the mammal host(s) (bloodstream form) and the insect vector (procyclic form), with two divergent glucose metabolism amenable to in vitro culture. While the metabolic network of the bloodstream forms has(More)
Photochemistry of giant planets and their satellites is characterized by numerous reactions involving a lot of chemical species. In the present paper, chemical systems are modeled by signal flow graphs. Such a technique evaluates the transmission of any input into the system (solar flux, electrons ... ) and gives access to the identification of the most(More)
The BlastSets strategy uses a probabilistic model to compare a query set to target sets of proteins. Target sets are neighborhoods that group proteins sharing some biological properties. Target sets are generated from a compact internal representation, BlastSets Classifications, constructed by the interpretation of results taken from the literature. We face(More)
The central dogma in molecular biology postulated that 'DNA makes RNA makes protein', however this dogma has been recently extended to integrate new biological activities involving small non-coding RNAs, called sRNAs. In particular, it has been shown that sRNAs regulate the production of proteins by interacting on mRNAs to regulate positively or negatively(More)
Photochemistry of giant planets and their satellites is characterized by numerous reactions involving many chemical species. In the present paper, chemical systems are modeled by signal flow graphs. Such a technique evaluates the transmission of any input into the system (solar flux, electrons...) and gives access to the identification of the most(More)