Prediction of protein secondary structure (alpha-helix, beta-sheet, coil) from primary sequence of amino acids is a very challenging and difficult task, and the problem has been approached from several angles. A protein is a sequence of amino acid residues and can thus be considered as a one dimensional chain of ‘beads’ where each bead correspond to one of the 20 different amino acid residues k...

Protein function prediction is a complex multiclass multilabel classification problem, characterized by multiple issues such as the incompleteness of the available annotations, the integration of multiple sources of high dimensional biomolecular data, the unbalance of several functional classes, and the difficulty of univocally determining negative examples. Moreover, the hierarchical relations...

The fact that a large majority of mammalian genes are subject to alternative splicing indicates that this phenomenon represents a major mechanism for increasing proteome complexity. Here, we provide an overview of current methods for the computational prediction of alternative splicing based on the alignment of genome and transcript sequences. Specific features and limitations of different appr...

The higher-order structure of genes and other features of biological sequences can be described by means of formal grammars. These grammars can then be used by general-purpose parsers to detect and to assemble such structures by means of syntactic pattern recognition. We describe a grammar and parser for eukaryotic protein-encoding genes, which by some measures is as effective as current connec...

The coarse grid of numerical weather prediction and climate models requires parametrization models to resolve atmospheric processes that are smaller than the grid size. For parametrization development, these processes are simulated by a high resolution model. At the Royal Netherlands Meteorological Institute, the Dutch Atmospheric Large-Eddy Simulation (DALES) is used [15]. This three-dimension...

MicroRNAs (miRNAs) are important players in gene regulation. The final and maybe the most important step in their regulatory pathway is the targeting. Targeting is the binding of the miRNA to the mature RNA via the RNA-induced silencing complex. Expression patterns of miRNAs are highly specific in respect to external stimuli, developmental stage, or tissue. This is used to diagnose diseases suc...

The problem presented in this thesis is to specify and implement a solution which could be used to automatically classify previously completed calls to a call routing service, and furthermore, to specify and implement a solution which could be used to automatically predict the outcome of calls to this service “on-line”, i.e. as they happen. The specific service on which to investigate this prob...

Epileptic seizures occur due to disorder in brain functionality which can affect patient's health. Prediction of epileptic seizures before the beginning of the onset is quite useful for preventing the seizure by medication. Machine learning techniques and computational methods are used for predicting epileptic seizures from Electroencephalograms (EEG) signals. However, preprocessing of EEG sign...

In this paper we analyze briefly the use of two classical perturbation methods vs. the formulation using cartesian coordinates in the numerical integration of satellite orbits. In particular, we compare with the variation-of-parameters (VOP) and Encke’s methods. The numerical tests performed with a realistic Earth potential model and using a well-recognized numerical ODE integrator (dop853) per...