Sylvain Lespinats

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Horizontal DNA transfer is an important factor of evolution and participates in biological diversity. Unfortunately, the location and length of horizontal transfers (HTs) are known for very few species. The usage of short oligonucleotides in a sequence (the so-called genomic signature) has been shown to be species-specific even in DNA fragments as short as(More)
Mapping high-dimensional data in a low-dimensional space, for example, for visualization, is a problem of increasingly major concern in data analysis. This paper presents data-driven high-dimensional scaling (DD-HDS), a nonlinear mapping method that follows the line of multidimensional scaling (MDS) approach, based on the preservation of distances between(More)
Although polymicrobial infections, caused by combinations of viruses, bacteria, fungi and parasites, are being recognised with increasing frequency, little is known about the occurrence of within-species diversity in bacterial infections and the molecular and evolutionary bases of this diversity. We used multiple approaches to study the genomic and(More)
Comparative genomic analysis of the malaria causative agent, Plasmodium falciparum, with other eukaryotes for which the complete genome is available, revealed that the genome from P. falciparum was more similar to the genome of a plant, Arabidopsis thaliana, than to other non-apicomplexan taxa. Plant-like sequences are thought to result from horizontal gene(More)
Multidimensional scaling is a must-have tool for visual data miners, projecting multidimensional data onto a two-dimensional plane. However, what we see is not necessarily what we think about. In many cases, end-users do not take care of scaling the projection space with respect to the multidimensional space. Anyway, when using nonlinear mappings, scaling(More)
GENSTYLE (http://Genstyle.imed.jussieu.fr) is a workspace designed for the characterization and classification of nucleotide sequences. Based on the genomic signature paradigm, GENSTYLE focuses on oligonucleotide frequencies in DNA sequences. Users can select sequences of interest in the GENSTYLE companion database, where the whole set of GenBank sequences(More)
BACKGROUND According to recent reports, herpes simplex virus type 1 (HSV-1) induces bronchopneumonitis (BPn) in immunocompetent patients undergoing prolonged mechanical ventilation (MV), whose respiratory functions deteriorate with a poor outcome. HSV-1 BPn is associated with HSV symptomatic or symptomless reactivation in the oropharynx. OBJECTIVES We(More)
Tears and false neighborhoods are the defaults that may occur when a mapping is set up. Three recent articles discuss about these risks and proposed various means to detect and avoid such penalizing situations. In the present paper we link these methods and suggest a new strategy to visualize tears and false neighborhoods on a mapping by adapting well-tried(More)
Whatever the phylogenetic method, genetic sequences are often described as strings of characters, thus molecular sequences can be viewed as elements of a multi-dimensional space. As a consequence, studying motion in this space (ie, the evolutionary process) must deal with the amazing features of high-dimensional spaces like concentration of measured(More)