The key problem of bioinformatics is the prediction of properties, such as structure or function, based on similarity This chapter reviews the concepts and tools of similarity analysis used in various fields of bioinformatics.

This review provides an overview of the ways in which techniques from artificial intelligence (AI) can be usefully employed in bioinformatics, both for modelling biological data and for making new discoveries. The paper covers three techniques: symbolic machine learning approaches (nearest neighbour and identification tree techniques), artificial neural networks and genetic algorithms. Each tec...

Bacterial small RNAs (sRNAs) are an emerging class of regulatory RNAs of about 40-500 nucleotides in length and, by binding to their target mRNAs or proteins, get involved in many biological processes such as sensing environmental changes and regulating gene expression. Thus, identification of bacterial sRNAs and their targets has become an important part of sRNA biology. Current strategies for...

A standing question in the field of Intelligent Tutoring Systems and User Modeling in general is what is the appropriate level of model granularity (how many skills to model) and how is that granularity derived? In this paper we will explore varying levels of skill generality within 8 grade mathematics using models containing 1, 5, 39 and 106 skills. We will measure the accuracy of these models...

The combination of distinct algorithms expertise to improve prediction accuracy, inspired by the theory of wisdom of crowds, has been increasingly discussed in literature. However, its application to bioinformatics-related tasks is still in its infancy. This thesis aims at investigating the potential and limitations of ensemble-based solutions for two bioinformatics prediction tasks, namely inf...

MOTIVATION The automated functional annotation of biological macromolecules is a problem of computational assignment of biological concepts or ontological terms to genes and gene products. A number of methods have been developed to computationally annotate genes using standardized nomenclature such as Gene Ontology (GO). However, questions remain about the possibility for development of accurat...

Self-avoiding walks (SAW) are the source of very difficult problems in probabilities and enumerative combinatorics. They are also of great interest as they are, for instance, the basis of protein structure prediction in bioinformatics. Authors of this article have previously shown that, depending on the prediction algorithm, the sets of obtained conformations differ: all the self-avoiding walks...

brucellosis, produced by brucella species, is a disease that causes severe economic losses for livestock farms worldwide due to serious economic and medical consequences of this disease, many efforts have been made to prevent the infection through the use of recombinant vaccines based on brucella outer membrane protein (omp) antigens. in the present study, a wide range of on-line prediction sof...

This April, in Cambridge (UK), principal investigators from the Mathematical Biology Group of the Medical Research Council's National Institute of Medical Research organized a workshop in structural bioinformatics at the Centre for Mathematical Sciences. Bioinformatics researchers of several nationalities from labs around the country presented and discussed their computational work in biomolecu...