The success of ligand docking calculations typically depends on the quality of the receptor structure. Given improvements in protein structure prediction approaches, approximate protein models now can be routinely obtained for the majority of gene products in a given proteome. Structure-based virtual screening of large combinatorial libraries of lead candidates against theoretically modeled rec...

MOTIVATION Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation. RESULTS We present a new homology search algorithm '...

A topos theoretic generalisation of the category of sets allows for modelling spaces which vary according to time intervals. Persistent homology, or more generally persistence, is a central tool in topological data analysis, which examines the structure of data through topology. The basic techniques have been extended in several different directions, encoding topological features by so called b...

As discussed in Chapter 2, we have complete topological information about 2-manifolds. How about higher dimensional manifolds? It turns out that recognizing whether two triangulations of 4-manifolds (and above) are homeomorphic or not are undecidable. 3-dimensional case is still open. On the other hand, testing homotopy equivalence is also hard beyond 2-dimensions and some specific cases. In th...

The PB2 protein of influenza A viruses has been shown as host range determinant. In this study PB2gene of five H9N2 isolates from Tehran province during the period of 1998-2001 were partially amplifiedand sequenced to do phylogenetic study. Iranian isolates could be classified in Eurasian lineage according totheir PB2 gene sequences. The PB2 genes of these isolates are different from those of M...

We show that on any closed contact manifold of dimension greater than 1 a contact structure with vanishing contact homology can be constructed. The basic idea for the construction comes from Giroux. We use a special open book decomposition for spheres. The page is the cotangent bundle of a sphere and the monodromy is given by a left-handed Dehn twist. In the resulting contact manifold we exhibi...