Vladimir Rogojin

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4 Acknowledgments I am very proud of natural computing community, especially, of P-friends community, for their achievements and for the scientific framework in which I was privileged to work during elaborating this thesis. My heartfelt thanks to my supervisors Dr. Gheorghe P˘ aun and Prof. Dr. Mario de J. Pérez-Jiménez for their fundamental encouragement(More)
The adverse effects of alcohol consumption during pregnancy are known, but the molecular events that lead to the phenotypic characteristics are unclear. To unravel the molecular mechanisms, we have used a mouse model of gestational ethanol exposure, which is based on maternal ad libitum ingestion of 10% (v/v) ethanol for the first 8 days of gestation (GD(More)
The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organism. Three molecular operations (ld, hi, and dlad) have been postulated for the gene assembly process, [3], [1]. We propose in this paper a mathematical model for contextual variants of ld and dlad on strings:(More)
The intramolecular model for gene assembly in ciliates considers three operations, ld, hi, and dlad that can assemble any gene pattern through folding and recombination: the molecule is folded so that two occurrences of a pointer (short nucleotide sequence) get aligned and then the sequence is rearranged through recombination of pointers. In general, the(More)
We survey in this paper the main differences among three variants of an intramolecular model for gene assembly: the general, the simple, and the elementary models. We present all of them in terms of sorting signed permutations and compare their behavior with respect to: (i) completeness, (ii) confluence (with the notion defined in three different setups),(More)
In computational processes based on backwards chaining, a rule of the type A ← B1, . . . , Bn is seen as a procedure which points that the problem A can be split into the problems B1, . . . , Bn. In classical devices, the subproblems B1, . . . , Bn are solved sequentially. In this paper we present some questions that circulated during the Second(More)