PASQUIER , Claude

GENMINER is a smart adaptation of closed itemsets based association rules extraction to genomic data. It takes advantage of the novel NORDI discretization method and of the JCLOSE algorithm to efficiently generate minimal non-redundant association rules. GENMINER facilitates the integration of numerous sources of biological information such as...

During the last decade, several clustering and association rule mining techniques have been applied to identify groups of co-regulated genes in gene expression data. Nowadays, integrating biological knowledge and gene expression data into a single framework has become a major challenge to improve the relevance of mined patterns and simplify...

Biology has become an enormously data-rich subject. Data is generated in many flavors and follows particularities of the omics perspective adopted along experimental studies. For instance, genomics is the field of study dealing with genomes and it is mostly associated with the static view (the genes and where they are placed along the genome)....

During the last decade, several clustering and association rule mining techniques have been applied to highlight groups of co-regulated genes in gene expression data. Nowadays, integrating these data and biological knowledge into a single framework has become a ma- jor challenge to improve the relevance of mined patterns and simplify their...

During the last decade, several clustering and association rule mining techniques have been applied to highlight groups of co-regulated genes in gene expression data. Nowadays, integrating these data and biological knowledge into a single framework has become a ma- jor challenge to improve the relevance of mined patterns and simplify their...

GENMINER is a smart adaptation of closed itemsets based association rules extraction to genomic data. It takes advantage of the novel NORDI discretization method and of the CLOSE algorithm to efficiently generate minimal non-redundant association rules. GENMINER facilitates the integration of numerous sources of biological information such as...

GenMiner is an implementation of association rule discovery dedicated to the analysis of genomic data. It allows the analysis of datasets integrating multiple sources of biological data represented as both discrete values, such as gene annotations, and continuous values, such as gene expression measures. GenMiner implements the new NorDi...

Using several analyse techniques for the hierarchical clustering of a SAGE expression dataset of 822 tags from 74 tissue samples (normal and cancer) we show that cleaning the dataset (tags and experiments) is critical and that attribution of a tag to a gene is not easy. Comparison of cancers from various tissues is a difficult task as tissue...

Biology is now an information-intensive science and various research areas, like molecular biology, evolutionary biology or environmental biology, heavily depend on the availability and the efficient use of information. Data mining, that regroups several techniques for analyzing very large datasets, is used to solve problems in an increasing...

La technologie des biopuces permet de mesurer les niveaux d'expression de milliers de gènes dans différentes conditions biologiques générant ainsi des masses de données à analyser. De nos jours, l'interprétation de ces volumineux jeux de donnés à la lumière des différentes sources d'informations est l'un des principaux défis dans la...

Using several analyse techniques for the hierarchical clustering of a SAGE expression dataset of 822 tags from 74 tissue samples (normal and cancer) we show that cleaning the dataset (tags and experiments) is critical and that attribution of a tag to a gene is not easy. Comparison of cancers from various tissues is a difficult task as tissue...

J'ai effectué un DEA puis une thèse dans le domaine du génie logiciel sous la supervision de Paul Franchi-Zannettacci, professeur à l'Université de Nice - Sophia Antipolis. Mes travaux portaient sur la modélisation et la manipulation de documents structurés. Ils visaient à généraliser les techniques du génie logiciel au domaine de la gestion...

This paper describes the design of a system for extracting keyphrases from a single document The principle of the algorithm is to cluster sentences of the documents in order to highlight parts of text that are semantically related. The clusters of sentences, that reflect the themes of the document, are then analyzed to find the main topics of...

Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common framework allowing data to be shared and reused between applications, can be applied to the management of...

Implementation of the method MIRAI described in:Pasquier, C., & Gardès, J. (2016). Prediction of miRNA-disease associations with a vector space model.Scientific reports, 6(1), 27036.The method allows the prediction of the associations between miRNAs and diseases. The basic approach is to represent distributional information on miRNAs and...

Implementation of the attributed graph mining method described in the manuscript:Pasquier, C., Flouvat, F., Sanhes, J., & Selmaoui-Folcher, N. (2017). Attributed graph mining in the presence of automorphism.Knowledge and Information Systems, 50, 569-584.

International standards for the representation of structured documents like ODA [1S08613 89] or SGML [ISO8679 86] are well adapted for the design and the generation of long and sophisticated documents like books or technical documentation. But, in the tertiary industry, most documents are intended for clients. Their constitution depends on the...

Documents, like computer programs have a logical structure defined by syntaxical and semantical rules. This fact allowed the use of software engineering knowledge to define the foundations for representation and handling of structured documents. However, documents and programs are different in many aspects. In this thesis, we consider two...

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International standards for the representation of structured documents like ODA [1S08613 89] or SGML [ISO8679 86] are well adapted for the design and the generation of long and sophisticated documents like books or technical documentation. But, in the tertiary industry, most documents are intended for clients. Their constitution depends on the...

Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common framework allowing data to be shared and reused between applications, can be applied to the management of...

Microarray technology produces vast amounts of data by measuring simultaneously the expression levels of thousands of genes under hundreds of biological conditions. Nowadays, one of the principal challenges in bioinformatics is the interpretation of huge data using different sources of information. We propose a novel data analysis method named...

Microarray technology produces vast amounts of data by measuring simultaneously the expression levels of thousands of genes under hundreds of biological conditions. Nowadays, one of the principal challenges in bioinformatics is the interpretation of this large amount of data using different sources of information. We have developed a novel data...

La technologie des biopuces permet de mesurer les niveaux d'expression de milliers de gènes dans différentes conditions biologiques générant ainsi des masses de données à analyser. De nos jours, l'interprétation de ces volumineux jeux de donnés à la lumière des différentes sources d'informations est l'un des principaux défis dans la...