Isabelle Dutour

Université Bordeaux 1 · UMR LaBRI - Laboratoire Bordelais de Recherche en Informatique

Background Bacterial sRNA-mediated regulatory networks has been introduced as a powerful way to analyze the fast rewiring capabilities of a bacteria in response to changing environmental conditions. The identification of mRNA targets of bacterial sRNAs is essential to investigate their functional activities. However, this step remains challenging w...

Life sciences are currently going through a great number of transformations raised by the in-going revolution in high-throughput technologies for the acquisition of data. The integration of their high dimensionality, ranging from omics to clinical data, is becoming one of the most challenging stages. It involves inter-disciplinary developments with...

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...

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 hav...

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 fo...

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...

We propose a new approach to study the chemical complexity of Titan's atmosphere. We have developed an evolutionary algorithm-based model that simulates the evolution of interacting elements with different valences. This abstract model mimics a C–H–O–N system that might get an insight into the general properties of the chemistry of Titan's atmosphe...

We suggest that the study of the general behavior of a chemical system in planetary atmospheres might be equivalent to the study of the evolution of connected components in a random graphs model. The main result of our model is that interacting elements in a system self-organize in such a way that the distribution in size of the created compounds f...

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...

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 specification, as defined in [7].

A new systematic approach for the speciøcation of bijections between sets of combinatorial objects is presented. It is based on the notion of object grammars. Object grammmars are recursive descriptions of objects which generalize context free grammars. The study of a particular substitution in these object grammars conørms once more the key role o...

We propose a simple algorithm based on a Markov chain for generating acyclic digraphs with a given number of vertices uniformly at random. In addition, standard combinatorial techniques allow us to describe the overall shape and average edge density of an acyclic digraph. As an application, we were able to estimate the density function of classical...

The Graph Drawing community uses test suites for comparing layout quality and efficiency. Those suites often claim to collect randomly generated graphs, although in most cases randomness is a loosely defined notion. Wepropose a simple algorithm for generating acyclic digraphs with a given number of vertices uniformly at random. Applying standard co...

International audience This paper presents a new systematic approach for the uniform random generation of combinatorial objects. The method is based on the notion of object grammars which give recursive descriptions of objects and generalize context-freegrammars. The application of particular valuations to these grammars leads to enumeration and ra...

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 specification, as defined 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 structur...

Nous étudions une quantité liée aux chemins constitués de pas Nord et Est restant sous la droite de pente d partant de l'origine. Nous donnons une estimation asymptotique de cette quantité en fonction de la largeur n de ces chemins et de la pente d, répondant ainsi à une question posée par Bernard Mourrain.

This article presents a new systematic approach for the uniform random generation of combinatorial objects. The method is based on the notion of object grammars which are recursive descriptions of objects generalizing context-free grammars. The application of particular valuations to these grammars allows to reach to enumeration and random generati...

We give an enumerating formula for convex directed polyominoes according to their width, height, area and number of corners. Hence, we propose a unifying formula for a set of sub-families of convex directed polyominoes (Ferrers diagrams, stack, parallelogram and convex directed polyominoes). Most of the known results on each of these sub-families m...

this article, we refine the result by Delest and F'edou, introducing the parameter corner. In fact, the properties of the last paragraph were studied before obtaining Theorem 2.3 which seems more general. 2. A new generating function for parallelogram polyominoes

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...

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...

The BlastSets strategy uses a probabilistic model to compare a query set to target sets of pro-teins. 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 interpreta-tion of results taken from the literatu...