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The main aim of this paper is to present a simple probabilistic model for the early stage of neuron growth: the specification on an axon out of several initially similar neurites. The model is a Markov process with competition between the growing neurites, wherein longer objects have more chances to grow, and parameter alpha determines the intensity of the(More)
MOTIVATION Despite theoretical arguments that so-called 'loop designs' for two-channel DNA microarray experiments are more efficient, biologists continue to use 'reference designs'. We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammalian cells and Streptomyces coelicolor). In each case, both a(More)
OBJECTIVE MicroRNAs (miRNAs) are small noncoding RNAs that have the capacity to control protein production through binding "seed" sequences within a target mRNA. Each miRNA is capable of potentially controlling hundreds of genes. The regulation of miRNAs in the lung during the development of pulmonary arterial hypertension (PAH) is unknown. METHODS AND(More)
The concept of scale-free network has emerged as a powerful unifying paradigm in the study of complex systems in biology and in physical and social studies. Metabolic, protein, and gene interaction networks have been reported to exhibit scale-free behavior based on the analysis of the distribution of the number of connections of the network nodes. Here we(More)
BACKGROUND In many approaches to the inference and modeling of regulatory interactions using microarray data, the expression of the gene coding for the transcription factor is considered to be an accurate surrogate for the true activity of the protein it produces. There are many instances where this is inaccurate due to post-translational modifications of(More)
In the present work we show that diffusion cannot provide the observed fast discharge of neurotransmitter from a synaptic vesicle during neurotransmitter release, mainly because it is not sufficiently rapid nor is it sufficiently temperature-dependent. Modeling the discharge from the vesicle into the cleft as a continuous point source, we have determined(More)
MicroRNAs (miRNAs) have recently emerged as a new complex layer of gene regulation. MiRNAs act post-transcriptionally, influencing the stability, compartmentalization, and translation of their target mRNAs. Computational efforts to understand the post-transcriptional gene regulation by miRNAs have been focused on the target prediction tools, while(More)
Owing to the dynamic nature of the transcriptome, gene expression profiling is a promising tool for discovery of disease-related genes and biological pathways. In the present study, we examined gene expression in whole blood of 12 patients with CAD (coronary artery disease) and 12 healthy control subjects. Furthermore, ten patients with CAD underwent(More)
Gene transcription models must take account of intrinsic stochasticity. The Chemical Master Equation framework is based on modelling assumptions that are highly appropriate for this context, and the Stochastic Simulation Algorithm (also known as Gillespie's algorithm) allows for practical simulations to be performed. However, for large networks and/or fast(More)
BACKGROUND The mutually exclusive pattern of the major driver oncogenes in lung cancer suggests that other mutually exclusive oncogenes exist. We conducted a systematic search for tyrosine kinase fusions by screening all tyrosine kinases for aberrantly high RNA expression levels of the 3' kinase domain (KD) exons relative to more 5' exons. METHODS We(More)