Markku Siermala

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Polyproline type II stretches are somewhat rare on proteins. The backbone of this secondary structural element folds to a triangular form instead of the normal alpha-helix with 3.6 residues per turn. It is a very challenging task to try to detect them computationally from protein sequence. Here, we have studied the preprocessing phase in particular, which(More)
Freshwater areas are an evanescent resource in the globe and, hence, the water quality assessment and examination of human induced changes on aquatic ecosystems are important. Benthic macroinvertebrates are excellent indicators of the state of freshwater area due to their intermediate life cycle and their ability to react changes in an aquatic ecosystem.(More)
It is frequently useful and advantageous to investigate not only the classification efficacy of neural networks, but also the reasons for misclassification and relations between input variables and output classes. We have developed novel techniques to disentangle these dilemmas: a network structure and learning strategy for biased output class(More)
Cells react to changing intra- and extracellular signals by dynamically modulating complex biochemical networks. Cellular responses to extracellular signals lead to changes in gene and protein expression. Since the majority of genes encode proteins, we investigated possible correlations between protein parameters and gene expression patterns to identify(More)
Many genes and proteins are required to carry out the processes of innate and adaptive immunity. For many studies, including systems biology, it is necessary to have a clear and comprehensive definition of the immune system, including the genes and proteins that take part in immunological processes. We have identified and cataloged a large portion of the(More)
BACKGROUND The immune system, which is a complex machinery, is based on the highly coordinated expression of a wide array of genes and proteins. The evolutionary history of the human immune system is not well characterised. Although several studies related to the development and evolution of immunological processes have been published, a full-scale(More)
This study considers detection of polyproline type II secondary structures from protein sequences. This difficult problem was handled with multilayer perceptron neural networks, which were found to be useful for such bioinformatics studies. Polyproline II secondary structures have not previously been tried to be predicted from sequences.
In our previous studies, we predicted protein secondary structures of polyproline type II by applying feedforward perceptron neural networks with the backpropagation learning algorithm. With a uniformly distributed test set, prediction succeeded in approximately 74% of cases, which is indeed a highvalue for a prediction problem in bioinformatics. To enable(More)