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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 elds of physics, such as reaction-diiusion systems, pattern formation phenomena, uid ows,(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)
BACKGROUND To unravel molecular targets involved in glycopeptide resistance, three isogenic strains of Staphylococcus aureus with different susceptibility levels to vancomycin or teicoplanin were subjected to whole-genome microarray-based transcription and quantitative proteomic profiling. Quantitative proteomics performed on membrane extracts showed(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)
Tandem mass spectrometry has become central in proteo-mics projects. In particular, it is of prime importance to design sensitive and selective score functions to reliably identify peptides in databases. By using a huge collection of 140 000+ peptide MS/MS spectra, we systematically study the importance of many characteristics of a match (peptide(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)
Mass spectrometry is a powerful alternative to antibody-based methods for the analysis of histone post-translational modifications (marks). A key development in this approach was the deliberate propionylation of histones to improve sequence coverage across the lysine-rich and hydrophilic tails that bear most modifications. Several marks continue to be(More)
UNLABELLED pViz.js is a visualization library for displaying protein sequence features in a Web browser. By simply providing a sequence and the locations of its features, this lightweight, yet versatile, JavaScript library renders an interactive view of the protein features. Interactive exploration of protein sequence features over the Web is a common need(More)
The identification and characterization of peptides from tandem mass spectrometry (MS/MS) data represents a critical aspect of proteomics. Today, tandem MS analysis is often performed by only using a single identification program achieving identification rates between 10-50% (Elias and Gygi, 2007). Beside the development of new analysis tools, recent(More)
Ubiquitination is a process that involves the covalent attachment of the 76-residue ubiquitin protein through its C-terminal di-glycine (GG) to lysine (K) residues on substrate proteins. This post-translational modification elicits a wide range of functional consequences including targeting proteins for proteasomal degradation, altering subcellular(More)