Horizontal gene transfer and genome evolution in Methanosarcina, BMC Evolutionary Biology, 15(1):102,2015.

Sequence-derived structural features driving proteolytic processing, Proteomics, 14(1), pp. 42-50, 2014.

ANA HEp-2 cells image classification using number, size, shape and localization of targeted cell regions, Pattern Recognition, 47(7), pp. 2360-2366, 2014.

Evaluation and Comparison of Current Fetal Ultrasound Image Segmentation Methods for Biometric Measurements: A Grand Challenge, IEEE Transactions on Medical Imaging, 33(4), pp.797-813, 2014.

Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica, J Bacteriol. 2013 Jun;195(12):2786-92.

Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res. 2012 Dec 2.
Go to publication

Evolution of transcriptional regulation in closely related bacteria. BMC Evol Biol. 2012 Oct 6;12:200.
Go to publication

Glutamine versus ammonia utilization in the NAD synthetase family
Go to publication

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics. 2011 Jun 15;12 Suppl 1:S3.
Go to publication

Complete genome and proteome of Acholeplasma laidlawii. Journal of Bacteriology 2011 Sep;193(18):4943-4953.
Go to publication

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010,
Go to publication Download (474.3 KB)

“Evolution of regulatory motifs of bacterial transcription factors” In Silico Biology, 2010, 10, 0012.
Go to publication Download (381.9 KB)

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics. 2009, 10: 78.
Go to publication

Modulation of alternative splicing by long-range RNA structures in Drosophila. Nucleic Acids Res. 2009, 37(14):4533-44 .
Go to publication

Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res. 2009, 37: 2493-503.
Go to publication Download (2.6 MB)

Evolution of Regulatory Systems in Bacteria. Lecture Notes in Bioinformatics. 2009; 5542 (ISBRA 2009): 1-4.

Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs. BMC Evol Biol. 2009, 9: 142.
Go to publication

Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure. 2009, 17: 939-51.
Go to publication Download (2.1 MB)

Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics. 2009, 10: 174.

Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics. 2008, 9(1): 13.
Go to publication

“Comparative genomic analysis of T-box regulatory systems in bacteria” Ribonucleic acids molecular biology (RNA), V. 14, No. 4, April 2008, pp. 717-735. PMID: 18359782
Go to publication

Abundance and functional diversity of riboswitches in microbial communities. BMC Genomics. 2007 Oct 1;8:347.
Go to publication

“Analysis of evolution of T-box regulatory elements prediction of amino acid transporters and other amino acid related genes” Proceedings of the international scientific conference “Computational Phylogenetics and Molecular Systematics, CPMS’2007”, November 16–19 2007, KMK Scientific Press, Moscow, pp. 30–37.

“Function and evolutionary analysis of the T-box regulon in bacteria” Proceedings of International Moscow Conference on Computational Molecular Biology: МССМВ’07, November 2007, pp. 309–310.

“Reconstruction of ancestral regulatory signal along a phylogeny” Proceedings of International Moscow Conference on Computational Molecular Biology: МССМВ’07, 2007, pp. 111–113.

“Evolutional and Functional Analysis of T-box Regulon in Bacteria: Identification of new Genes Involved in Amino Acid Metabolism” Proceedings of The Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS’2006), Novosibirsk, July 16–22 2006, V. 3, pp. 236–240.
Go to publication

"Comparative genomics of regulation of heavy metal resistance in Eubacteria." BMC Microbiol., 2006, 6:49.
Go to publication

Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter. Journal of Bioinformatics and Computational Biology 4(5):981–998.
Download (1 MB)

“Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria” BMC Microbiology, 2005, 5:54. PMID: 16202131
Go to publication

“Bioinformatics of Bacteria: central issues and model types” International conference “Issues of control and modeling in complex systems”, June 14–17 2004, RAS, pp. 5–11. [in Russian]

“Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis” FEMS Microbiological Letters, 2004, 234(2), pp. 357–370. PMID: 15135544
Go to publication

“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