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The number of completely sequenced bacterial genomes has been growing fast. There are computer methods available for finding genes but yet there is a need for more accurate algorithms. The GeneMark. hmm algorithm presented here was designed to improve the gene prediction quality in terms of finding exact gene boundaries. The idea was to embed the GeneMark(More)
A major challenge of current neuroscience is to elucidate the brain mechanisms that underlie cognitive function. There is no doubt that cognitive processing in the brain engages large populations of cells. This article explores the logic of investigating these problems by combining psychological studies in human subjects and neurophysiological studies of(More)
MOTIVATION Cluster analysis of genome-wide expression data from DNA microarray hybridization studies has proved to be a useful tool for identifying biologically relevant groupings of genes and samples. In the present paper, we focus on several important issues related to clustering algorithms that have not yet been fully studied. RESULTS We describe a(More)
We analyzed whether interferon-alpha 2b (IFN-alpha 2b) and IFN-beta 1a engage their common receptor to generate activated receptor complexes possessing distinct signaling properties. Human vascular endothelial cells (HUVEC) are 100-1000-fold more sensitive to IFN-beta 1a than to IFN-alpha 2b in in vitro assays. An nonarray-based expression profiling(More)
The effect of superhelicity on the base-pair opening probability and on the probability of occurrence of cruciform states in palindromic regions is theoretically treated. The calculations show that below the superhelix density value of -sigma=0.05 superhelicity does not appreciably affect the characteristics of DNA secondary structure fluctuations. In the(More)
The distribution of closed unknotted polymer chains over the writhing number is calculated by the Monte-Carlo method. For circular duplex DNA the variance of the distribution equals approximately half the observed variance of equilibrium distribution over the linking number. The balance which arises from fluctuations in DNA twisting makes it possible to(More)
We have developed a model that simulates possible mechanisms by which supraspinal neuronal signals coding forces could converge in the spinal cord and provide an ongoing integrated signal to the motoneuronal pools whose activation results in the exertion of force. The model consists of a three-layered neural network connected to a two-joint-six-muscle model(More)
We consider the problem of the mean field (Poisson-Boltzmann) calculation of the electrostatic free energy for a strongly charged polyelectrolyte such as DNA in a salt solution. We compare two approaches to calculate the free energy: (i) direct one starting from the statistical-mechanical expression for the electrostatic free energy and (ii) the polyion(More)
In order to allow for real dielectric properties of a solvent in calculating of electrostatic characteristics of strongly charged polyions such as DNA in salt solution we consider a simple model of linear dielectric response of a medium. The interactions between charged particles are treated in the framework of self-consistent-field approximation. The basic(More)