Jean-Marc Steyaert

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Transmembrane beta-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. The cellular location and functional diversity of beta-barrel outer membrane proteins (omps) makes them an important protein class. At the present time, very few nonhomologous TMB structures have been determined by X-ray(More)
Any tree can be represented in a max/ma//y compact form as a directed acyclic graph where common subtrees are factored and shared, being represented only once. Such a compaction can be effected in linear time. It is used to save storage in implementations of functional programming languages, as well as in symbolic manipulation and computer a/gebra systems.(More)
In this paper we present a more efficient algorithm for comparison of minisatellites which has complexity O(n′ + m′ + mn′ + nm′ +mn) where n and m are the lengths of the maps and n′ and m′ are the sizes of run-length encoded maps. We show that this algorithm makes a significant improvement for the real biological data, dividing the computing time by a(More)
Subsequent duplication events are responsible for the evolution of the minisatellite maps. Alignment of two minisatellite maps should therefore take these duplication events into account, in addition to the well-known edit operations. All algorithms for computing an optimal alignment of two maps, including the one presented here, first deduce the costs of(More)
Transmembrane beta-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts. The cellular location and functional diversity of beta-barrel outer membrane proteins makes them an important protein class. At the present time, very few non-homologous TMB structures have been determined by X-ray(More)
This paper presents general results on the probabilities of occurrences of patterns in trees, which serve to analyze a commonly used pattern matching algorithm on trees. It appears that for a wide class of statistics on trees, pattern-matching has a linear expected time complexity (in contrast to a quadratic worst-case behaviour). The methods used are both(More)
Modeling and predicting the structure of proteins is one of the most important challenges of computational biology. Exact physical models are too complex to provide feasible prediction tools and other ab-initio methods only use local and probabilistic information to fold a given sequence. We show in this paper that all-α transmembrane protein secondary and(More)
We consider a generic protocell model consisting of any conservative chemical reaction network embedded within a membrane. The membrane results from the self-assembly of a membrane precursor and is semi-permeable to some nutrients. Nutrients are metabolized into all other species including the membrane precursor, and the membrane grows in area and the(More)