Alexandre Masselot

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We discuss the cellular automata approach and its extensions, the lattice Boltzmann and multiparticle methods. The potential of these techniques is demonstrated in the case of modeling complex systems. In particular, we consider applications taken from various fields of physics, such as reaction-diffusion systems, pattern formation phenomena, fluid flows,(More)
Mass spectrometry combined with database searching has become the preferred method for identifying proteins in proteomics projects. Proteins are digested by one or several enzymes to obtain peptides, which are analyzed by mass spectrometry. We introduce a new family of scoring schemes, named OLAV, aimed at identifying peptides in a database from their(More)
In a previous paper we introduced a novel model-based approach (OLAV) to the problem of identifying peptides via tandem mass spectrometry, for which early implementations showed promising performance. We recently further improved this performance to a remarkable level (1-2% false positive rate at 95% true positive rate) and characterized key properties of(More)
Cellular automata (CA) and lattice Boltzmann LB approaches are computational methods that ooer exibility, eeciency and outstanding amenability to parallelism when modeling complex phenomena. In this paper, the CA and LB approach are combined in the same model, in order to describe a system where point-particles are transported in a uid ow. This model is(More)
neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase(More)
We consider a simple lattice gas model to simulate erosion, deposition and particle transport in a streaming fluid. In our approach, the fluid is described by a standard lattice Boltzmann model and the granular suspension by a multiparticle cellular automata. A good agreement is obtained between the predictions of the model and field measurements, as(More)
The diversity of experimental workflows involving LC-MS/MS and the extended range of mass spectrometers tend to produce extremely variable spectra. Variability reduces the accuracy of compound identification produced by commonly available software for a spectral library search. We introduce here a new algorithm that successfully matches MS/MS spectra(More)
De novo peptide sequencing algorithms are often tested on relatively small data sets made of excellent spectra. Since there are always more and more tandem mass spectra available, we have assembled six large, reliable, and diverse (three mass spectrometer types) data sets intended for such tests and we make them accessible via a web server. To exemplify(More)
Numerous oncogenic mutations occur within the BRAF kinase domain (BRAF(KD)). Here we show that stable BRAF-MEK1 complexes are enriched in BRAF(WT) and KRAS mutant (MT) cells but not in BRAF(MT) cells. The crystal structure of the BRAF(KD) in a complex with MEK1 reveals a face-to-face dimer sensitive to MEK1 phosphorylation but insensitive to BRAF(More)