Proč má DNA tři terminační triplety a jen jeden iniciační?
Reversal distance for strings with duplicates: linear time approximation using hitting set.
Self-replication processes in nanosystems of informatics
Recent research on the nanotechnological processes of molecular products and object synthesis as well as research on the nanosystems of informatics, stimulates the development of technical systems of informatics. Until now, they have been used mainly for computational tasks when, similarly to biological organisms, they allowed the development of self-replicating products and complete objects. One can focus here on the model of a circulation of materials, information and energy in a biological cell,...
Significance tests to identify regulated proteins based on a large number of small samples
Modern biology is interested in better understanding mechanisms within cells. For this purpose, products of cells like metabolites, peptides, proteins or mRNA are measured and compared under different conditions, for instance healthy cells vs. infected cells. Such experiments usually yield regulation or expression values – the abundance or absence of a cell product in one condition compared to another one – for a large number of cell products, but with only a few replicates. In order to distinguish...
The common ancestor process for a Wright-Fisher diffusion.
The tree of life and other affine buildings.
The Uniform Minimum-Ones 2SAT Problem and its Application to Haplotype Classification
Analyzing genomic data for finding those gene variations which are responsible for hereditary diseases is one of the great challenges in modern bioinformatics. In many living beings (including the human), every gene is present in two copies, inherited from the two parents, the so-called haplotypes. In this paper, we propose a simple combinatorial model for classifying the set of haplotypes in a population according to their responsibility for a certain genetic disease. This model is based...
Two algorithms based on Markov chains and their application to recognition of protein coding genes in prokaryotic genomes
Methods based on the theory of Markov chains are most commonly used in the recognition of protein coding sequences. However, they require big learning sets to fill up all elements in transition probability matrices describing dependence between nucleotides in the analyzed sequences. Moreover, gene prediction is strongly influenced by the nucleotide bias measured by e.g. G+C content. In this paper we compare two methods: (i) the classical GeneMark algorithm, which uses a three-periodic non-homogeneous...