Claude Pasquier

French National Centre for Scientific Research | CNRS · Laboratoire d'Informatique, Signaux et Systèmes de Sophia-Antipolis (I3S) - UMR7271

Simple Summary Glioblastomas, primitive infiltrating brain tumors, are a real public health problem because of their dismal prognosis. The persistence of aggressive tumor stem cells after conventional cytotoxic treatment is one of the major causes of therapeutic failure. The identification of targets involved in the molecular mechanisms repressing...

The identification of condition-specific gene sets from transcriptomic experiments is important to reveal regulatory and signaling mechanisms associated with a given cellular response. Statistical methods of differential expression analysis, designed to assess individual gene variations, have trouble highlighting modules of small varying genes whos...

The phosphorylation of proteins affects their functions in extensively documented circumstances. However, the role of phosphorylation in many interactive networks of proteins remains very elusive due to the experimental limits of exploring the transient interaction in a large complex of assembled proteins induced by stimulation. Previous studies ha...

Despite the development of new therapeutic strategies, cancer remains one of the leading causes of mortality worldwide. One of the current major challenges is the resistance of cancers to chemotherapy treatments inducing metastases and relapse of the tumor. The Hedgehog receptor Patched (Ptch1) is overexpressed in many types of cancers. We showed t...

In this study, we reanalyzed available datasets of gene expression changes in female Drosophila head induced by mating. Mated females present metabolic phenotypic changes and display behavioral characteristics that are not observed in virgin females, such as repulsion to male sexual aggressiveness, fidelity to food spots selected for oviposition, a...

Recent evidence suggests that the chimeric protein SETMAR is a factor of interest in cancer, especially in glioblastoma. However, little is known about the expression of this protein in glioblastoma tissues, and no study has been done to assess if SETMAR could be a prognostic and/or diagnostic marker of glioblastoma. We analyzed protein extracts of...

The identification of condition-specific gene sets from transcriptomic experiments is important to reveal regulatory and signaling mechanisms associated with a given cellular response. Statistical approaches using only expression data allow the identification of genes whose expression is most altered between different conditions. However, a phenoty...

The role of the RNAi/Dicer/Ago system in degrading RNA viruses has been elusive in mammals in the past, which has prompted authors to think that interferon (IFN) synthesis is essential in this clade, relegating the RNAi defense strategy against viral infection as an accessory function. However, recent publications highlight the existence of abundan...

Directed acyclic graphs (DAGs) are used in many domains ranging from computer science to bioinformatics, including industry and geoscience. They enable to model complex evolutions where spatial objects (e.g., soil erosion) may move, (dis)appear, merge or split. We study a new graph-based representation, called attributed DAG (a-DAG). It enables to...

Perfect annealing between microRNAs (miRNAs) and messenger RNAs (mRNAs) was computationally searched at a broad scale in the human genome to determine whether theoretical pairing is restrictively represented in functional subnetworks or is randomly distributed. Massive RNA interference (RNAi) pairing motifs in genes constitute a remarkable subnetwo...

The role of the RNAi/Dicer/Ago system to degrade RNA viruses has been elusive, which prompt authors to think that interferon (IFN) synthesis is essential, relegating the dsRNAs as accessory function. We investigate SARS-CoV-2 genome responsible of the new deadly COVID-19 pandemic for the theoretical possibilities to engage intra pairing within the...

RNA interference (RNAi) refers to a conserved posttranscriptional mechanism for the degradation of RNA by short dsRNAs. A genome-wide analysis of mRNAs that are complementary to RNAs of variable length that are transcribed from the full transcriptome and susceptible to being loaded onto Argonaute type 2 was performed through computational searches...

MicroRNAs, small non-coding elements implied in gene regulation, are very interesting biomarkers for various diseases such as cancers. They represent potential prodigious biotechnologies for early diagnosis and gene therapies. However, experimental verification of microRNA-disease associations are time-consuming and costly, so that computational mo...

Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson-Crick duplex. The "triplex-forming oligonucleotide" (TFO) can be a short sequence of RNA that binds to th...

Attributed directed graphs are directed graphs in which nodes are associ- ated with sets of attributes. Many data from the real world can be naturally represented by this type of structure, but few algorithms are able to directly handle these complex graphs. Mining attributed graphs is a di�cult task because it requires combining the exploration 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 this large amount of data using different sources of information. We have developed a novel data ana...

MicroRNAs play critical roles in many physiological processes. Their dysregulations are also closely related to the development and progression of various human diseases, including cancer. Therefore, identifying new microRNAs that are associated with diseases contributes to a better understanding of pathogenicity mechanisms. MicroRNAs also represen...

Frequent pattern mining is an important data mining task with a broad range of applications. Initially focused on the discovery of frequent itemsets, studies were extended to mine structural forms like sequences, trees or graphs. In this paper, we introduce a new domain of patterns, attributed trees (atrees), and a method to extract these patterns...

Heritability of acquired phenotypic traits is an adaptive evolutionary process that appears more complex than the basic allele selection guided by environmental pressure. In insects, the trans-generational transmission of epigenetic marks in clonal and/or sexual species is poorly documented. Aphids were used as a model to explore this feature becau...

To support knowledge discovery from data, many pattern mining techniques have been proposed. One of the bottlenecks for their dissemination is the number of computed patterns that appear to be either trivial or uninteresting with respect to available knowledge. Integration of domain knowledge in constraint-based data mining is limited. Relevant pat...

Directed acyclic graphs can be used across many application domains. In this paper, we study a new pattern domain for supporting their analysis. Therefore, we propose the pattern language of weighted paths, primitive constraints that enable to specify their relevancy (e.g., frequency and compactness constraints), and algorithms that can compute the...

Frequent pattern mining is an important data mining task with a broad range of applications. Initially focused on the discovery of frequent itemsets, studies were extended to mine structural forms like sequences, trees or graphs. In this paper, we introduce a new data mining method that consists in mining new kind of patterns in a collection of att...

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. SemanticWeb technologies, which provide a common framework allowing data to be shared and reused between applications, can be applied to the management of disse...

This paper describes the design of a sys-tem for extracting keyphrases from a sin-gle document The principle of the algo-rithm is to cluster sentences of the doc-uments 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 t...

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 their i...

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 interpre...

XML is based on two essential aspects: the modelization of data in a tree like structure and the separation between the information itself and the way it is displayed. XML structures are easily serializable. The separation between an abstract representation and one or several views on it allows the elaboration of specialized interfaces to visualize...

Summary : FT is a tool written in C++, which implements the Fourier analysis method to locate periodicities in aminoacid or DNA sequences. It is provided for free public use on a WWW server with a Java interface. Availability : The server address is http://o2.db.uoa.gr/FT Contact : shamodr@atlas.uoa.gr

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 number...

Unlabelled: 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 Nor...

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 diss...

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 bio-informatiqu...

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 [27] algorithm to efficiently generate min- imal non-redundant association rules. GENMINER facili- tates the integration of numerous sources of biological in- formation su...

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 CGGA...

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 sample...

Motivation: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In addition, a performance evaluation of automated systems that attempt to tackle sequence analyses rapidly and reproducibly is generally missing. In orde...

SmartTools is a semantic framework generator, based on XML and object technologies. Thanks to a process of automatic generation from specifications, SmartTools makes it possible to quickly develop environments dedicated to domain-specific and programming languages. Some of these specifications (XML, DTD, Schemas, XSLT) are issued from the W3C which...

SmartTools is a semantic framework generator, based on XML and object technologies. Thanks to a process of automatic generation from specications, SmartTools makes it possible to quickly develop environments dedicated to domain-specic and programming languages. Some of these specications (XML, DTD, Schemas, XSLT) are issued from the W3C which is an...

A cascading system of hierarchical, artificial neural networks (named PRED-CLASS) is presented for the generalized classification of proteins into four distinct classes-transmembrane, fibrous, globular, and mixed-from information solely encoded in their amino acid sequences. The architecture of the individual component networks is kept very simple,...

OrienTM is a computer software that utilizes an initial definition of transmembrane segments to predict the topology of transmembrane proteins from their sequence. It uses position-specific statistical information for amino acid residues which belong to putative non-transmembrane segments derived from statistical analysis of non-transmembrane regio...

SmartTools is a development environment generator that provides a structure editor and semantic tools as main features. The well-known visitor pattern technique is commonly used for designing semantic analysis, it has been automated and extended. SmartTools is easy to use thanks to its graphical user interface designed with the Java Swing APIs. It...

SmartTools is a development environment generator that provides a structure editor and semantic tools as main features. SmartTools is easy to use, thanks to its graphical user interface. Being based on Java and XML technologies offers all the features of SmartTools to any defined language. The main goal of this tool is to provide help and support f...

SmartTools is a development environment generator that provides a structure editor and semantic tools as main features. The well-known visitor pattern technique is commonly used for designing semantic analysis, it has been automated and extended. SmartTools is easy to use thanks to its graphical user interface designed with the Java Swing APIs. It...

Computational analysis of protein sequences with statistical models, machine learning techniques or empirical rules leads to prediction of structural and functional features of the corresponding molecules. Taking into account the recent explosion of biological information in terms of complete genome sequences the use of computational tools of analy...

This work presents a simple artificial neural network which classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment and analysis of open reading frames (ORF's) identified in complete genomes and, especially, those ORF's that co...

This work presents a simple artificial neural network which classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment and analysis of open reading frames (ORF's) identified in complete genomes and, especially, those ORF's that co...

We present a novel method that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The PRED-TMR algorithm described, refines a standard hydrophobicity analysis with a detection of potential termini (`edges', starts and ends) of transmembrane regions. This allows one both to discard highly hydrophobi...

CoPreTHi is a Java based web application, which combines the results of methods that predict the location of transmembrane segments in protein sequences into a joint prediction histogram. Clearly, the joint prediction algorithm, produces superior quality results than individual prediction schemes. The program is available at http://o2.db.uoa.gr/CoP...

FT is a tool written in C++, which implements the Fourier analysis method to locate periodicities in aminoacid or DNA sequences. It is provided for free public use on a WWW server with a Java interface. Availability : The server address is http://o2.db.uoa.gr/FT Contact : shamodr@atlas.uoa.gr

ion (du monde r#el) [11]. Cette approche permet de proposer une architecture originale dans des mondes homog#nes o# tout composant peut #tre d#crit par des d#pendances ou en mondes h#t#rog#nes o# l'int#gration d'un gestionnaire de dialogue devient n#cessaire. Ces travaux ont donn# lieu # plusieurs pr#sentations dans le cadre des GDR et # un d#but d...