BARBRY , Pascal

Mediante is a MIAME-compliant microarray data manager that links together annotations and experimental data. Developed as a J2EE three-tier application, Mediante integrates a management system for production of long oligonucleotide microarrays, an experimental data repository suitable for home made or commercial microarrays, and a user...

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This report focuses on text mining in the biomedical domain for the generation of semantic annotations based on a formal model which is ontology. We start by exposing the generic methodology for the generation of annotations from texts. Then, we present a state of the art on different knowledge extraction techniques used on biomedical texts. We...

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Living in the age of the digital media explosion the urge for finding new efficient methods of data storage increases significantly. Existing storage devices such as hard disks, flash, tape or even optical storage have limited durability in the range of 5 to 20 years. Recent studies have proven that the method of DNA data storage introduces a...

Living in the age of data explosion, the research of solutions for efficient long term storage of the infrequently used "cold" data is becoming of great interest. However, even if existing storage systems suggest efficiency in capacity, they are lacking in durability. Hard disks, flash, tape or even optical storage have limited lifespan in the...

Living in the age of the digital media explosion, the amount of data that is being stored increases dramatically. However, even if existing storage systems suggest efficiency incapacity, they are lacking in durability. Hard disks, flash, tape or even optical storage have limited lifespan in the range of 5 to 20 years. Interestingly, recent...

Droplet-based high throughput single cell sequencing techniques tremendously advanced our insight into cell-to-cell heterogeneity. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing. In consequence, information on splicing and sequence heterogeneity is lost. To overcome this limitation,...

C. burnetii is a Gram-negative intracellular Y-proteobacteria that causes the zoonotic disease Q fever. Q fever can manifest as an acute or chronic illness. Different typing methods have been previously developed to classify C. burnetii isolates to explore its pathogenicity. Here, we report a comprehensive genomotyping method based on the...

The exponential increase of digital data that is being generated every year along with the capacity and durability limits of conventional storage devices are raising one of the greatest challenges for the field of data storage. The use of DNA for digital data archiving is a very promising alternative as the biological properties of...

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This paper addresses the problem of the integration of expert knowledge in a data mining process. We present the KTA ( integrating expert Knowledge in Transcriptome analysis) framework which allows the mining process to be driven by prior knowledge on the application domain. KTA is embedded in the MEDIANTE project for evaluating and using DNA...

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OBJECTIVES AND METHODS: Tropheryma whipplei is a poorly studied bacterium responsible for Whipple's disease. In this study, its susceptibility to doxycycline was investigated at a transcriptional level using a whole-genome DNA microarray. RESULTS: Exposure of T. whipplei to the MIC of doxycycline (0.5 mg/L) induced antibiotic-specific primary...

Osteosarcoma is the most common primary tumor of bone. The rapid development of metastatic lesions and resistance to chemotherapy remain major mechanisms responsible for the failure of treatments and the poor survival rate for patients. We showed previously that the HMGCoA (3-hydroxy-3-methylglutaryl-coenzyme A) reductase inhibitor statin...

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Pathological remodeling of the airway epithelium is commonly observed in cystic fibrosis (CF). Thus, tissue repair is critical to restore integrity and maintenance of the epithelial barrier function. Epithelial repair is a multi-step process initiated by progenitor cell migration into the injured area, proliferation, and re-differentiation into...

Multiciliated cells lining the surface of some vertebrate epithelia are essential for various physiological processes, such as airway cleansing. Their apical surface is constituted by hundreds of motile cilia, which beat in a coordinated manner to generate directional fluid flow. We recently reported the identification of microRNAs of the...

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