Konstantin Yu Gorbunov

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A model and algorithm are proposed to infer evolution of a gene family, given the gene tree, with respect to species evolution, given the species tree. The model describes such evolution using the "nested tree" concept. Performance of the algorithm is verified on several orthologous protein groups. The evolutionary events inferred are: speciation, gene(More)
A long recognized problem is the inference of the supertree S that amalgamates a given set {G j } of trees G j , with leaves in each G j being assigned homologous elements. We ground on an approach to find the tree S by minimizing the total cost of mappings α j of individual gene trees G j into S. Traditionally, this cost is defined basically as a sum of(More)
We suggest a new algorithm to search a given set of the RNA sequences for conserved secondary structures. The algorithm is based on alignment of the sequences for potential helical strands. This procedure can be used to search for new structured RNAs and new regulatory elements. It is efficient for the genome-scale analysis. The results of various tests run(More)
Important desired properties of an algorithm to construct a supertree (species tree) by reconciling input trees are its low complexity and applicability to large biological data. In its common statement the problem is proved to be NP-hard, i.e. to have an exponential complexity in practice. We propose a reformulation of the supertree building problem that(More)
A model of evolution of a regulatory signal along the phylogenetic tree of species taking into account the secondary RNA structure is suggested. Based on this model, an algorithm is presented. It inputs the extant primary structure of a signal for the leaves of the phylogenetic tree and computes the primary and secondary structures of all the nodes. Another(More)
The article introduces two novel approaches to detect potential incongruence between the protein family tree and the species tree. The first approach implements substitution of a known mapping of gene tree G into species tree S with somewhat analogous multivalued G-into-S "mapping". The second approach is based on elementary concepts from the fuzzy-set(More)
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