“Search for Alternative RNA Secondary Structures Regulating Expression of Bacterial Genes” Molecular biology, V. 37, No 5, 2003, p. 707–715. PMID 14593920

DNA: from molecules toward genomes, from biochemical breakthroughs toward algorithmic analysis. Proceedings of the RAS (Vestnik RAN), No 11, 2003, p. 963-970. [in Russian]

“Computer-Assisted Analysis of Regulation of the Glycerol-3-Phosphate Metabolism in Genomes of Proteobacteria” Molecular Biology, V. 37, No 5, 2003, сс. 716–722. PMID 14593921

“Identification of Horizontal Gene Transfer from Phylogenetic Gene Trees” Molecular biology, V. 37, No 4, 2003, p. 571-584. PMID 12942641
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“An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation” In Silico Biology, V. 3, No 1,2, 2003, pp. 33–47. PMID 12762844
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“Tree Reconciliation: Reconstruction of Species Phylogeny by Phylogenetic Gene Trees” Molecular biology, 2002, V. 36, No 5, p. 650-658. PMID 12391844
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“Algorithm of Regulatory Signal Recognition in DNA Sequences” Molecular Biology, V. 35, No 6, 2001, p. 841-848. PMID 11771146

An approach to infer evolutionary species tree from multiple gene data. Information processes, V. 1, No 1, 2001, p. 64-77. [in Russian]

An algorithm to detect regulatory signals in DNA sequence data (1). Information processes, V. 1, No 1, 2001, p. 56-63. [in Russian]