Group of Bioinformatics and Functional Genomics

A.E. Vinogradov (Ph.D., Sci.D.), O.V. Anatskaya (Ph.D.)

Initially the main direction of our work was the study of functional significance of general genomic structure. The latter includes such parameters as quantity, intragenomic distribution and characteristics of noncoding DNA sequence, GC content and physical properties of DNA, size and structure of genes, gene and genome duplications, genome evolution. Another long-tem direction is devoted to ontogenetic programming of disease triggers. In the last time we are also engaged in functional analysis of transcriptomes, gene (protein) modules and networks, their evolution and tissue-specificity.

The main publications after 2000:

Vinogradov A.E., Anatskaya O.V. 2019. Gene Golden Age paradox and its partial solution. Genomics (in press).

Anatskaya O.V., Erenpreisa J.A., Salmina K.A., Vazquez-Martin A., Huna A., Nikolsky N.N., Vinogradov A.E. 2018. Polyploidy activates biological pathways related to morphogenesis in mammalian tissues. MOJ Immunol. 6: 90-93.

Shilina M.A, Grinchuk T.M, Anatskaya O.V., Vinogradov A.E., Alekseenko L.L., Elmuratov A.U., Nikolsky N.N. 2018. Cytogenetic and transcriptomic analysis of human endometrial MSC retaining proliferative activity after sublethal heat shock. Cells 7: E184.

Filatova N.A., Knyazev N.A., Skarlato S.O., Anatskaya O.V., Vinogradov A.E. 2018. Natural killer cell activity irreversibly decreases after Cryptosporidium gastroenteritis in neonatal mice. Parasite Immunol. 40: e12524.

Alekseenko L.L., Shilina M.A., Lyublinskaya O.G., Kornienko J.S., Anatskaya O.V., Vinogradov A.E., Grinchuk T.M., Fridlyanskaya I.I., Nikolsky N.N. 2018. Quiescent human mesenchymal stem cells are more resistant to heat stress than cycling cells. Stem Cells Int. 2018: 3753547.

Vinogradov A.E., Anatskaya O.V. 2017. DNA helix: the importance of being AT-rich. Mamm. Genome 28: 455-464.

Vinogradov A.E., Shilina M.A., Anatskaya O.V., Alekseenko L.L., Fridlyanskaya I.I., Krasnenko A., Kim A., Korostin D., Ilynsky V., Elmuratov A., Tsyganov O., Grinchuk T.M., Nikolsky N.N. 2017. Molecular genetic analysis of human endometrial mesenchymal stem cells that survived sublethal heat shock. Stem Cells Int. 2017: 2362630.

Vazquez-Martin A., Anatskaya O.V., Giuliani A., Erenpreisa J., Huang S., Salmina K., Inashkina I., Huna A., Nikolsky N.N., Vinogradov A.E. 2016. Somatic polyploidy is associated with the upregulation of c-MYC interacting genes and EMT-like signature. Oncotarget 7: 75235-75260.

Anatskaya O.V., Erenpreisa J.A., Nikolsky N.N., Vinogradov A.E. 2016. Pairwise comparison of mammalian transcriptomes associated with the effect of polyploidy on the expression activity of developmental gene modules. Cell Tiss. Biol. 10: 122-132.

Vinogradov A.E. 2015. Accelerated pathway evolution in mouse-like rodents involves cell cycle control. Mamm. Genome 26: 609-618.

Vinogradov A.E. 2015. Consolidation of slow or fast but not moderately evolving genes at the level of pathways and processes. Gene 561: 30-34.

Anatskaya O.V., Matveev I.V., Sidorenko N.V., Kharchenko M.V., Kropotov A.V., Vinogradov A.E. 2013. Changes in the heart of neonatal rats after cryptosporidial gastroenteritis of different degrees of severity. J. Evol. Biochem. Physiol. 49: 509-518. -->

Vinogradov A.E. 2013. Density peaks of paralog pairs in human and mouse genomes. Gene 527: 55-61.

Vinogradov A.E. 2012. Minority of mammalian orthologs can be regarded as physiologically closest genes. Gene 509: 201-205.

Vinogradov A.E. 2012. Large scale of human duplicate genes divergence. J. Mol. Evol. 75: 25-33.

Vinogradov A.E. 2012. Human more complex than mouse at cellular level. PLoS One 7: e41753.

Anatskaya O.V., Sidorenko N.V., Beyer T.V. Vinogradov A.E. 2010. Neonatal gastroenteritis triggers long-term cardiomyocyte atrophy, remodeling and irreversible hyperpolyploidization. Kardiologiya 50(12): 35-44.

Anatskaya O.V., Vinogradov A.E. 2010. Somatic polyploidy promotes cell function under stress and energy depletion: evidence from tissue-specific mammal transcriptome. Funct. Integr. Genomics 10: 433-446.

Vinogradov A.E. 2010. Human transcriptome nexuses: basic-eukaryotic and metazoan. Genomics 95: 345-354.

Anatskaya O.V., Sidorenko N.V., Beyer T.V., Vinogradov A.E. 2010. Neonatal cardiomyocyte ploidy reveals critical windows of heart development. Int. J. Cardiol. 141: 81-91.

Vinogradov A.E. 2010. Systemic factors dominate mammal protein evolution. Proc. Roy. Soc. B 277: 1403-1408.

Anatskaya O.V., Vinogradov A.E. 2010. Somatic polyploidy-associated metabolic changes revealed by modular biology. Tsitologiya 52: 52-62 [in Russian].

Vinogradov A.E., Anatskaya O.V. 2009. Loss of protein interactions and regulatory divergence in yeast whole-genome duplicates. Genomics 93: 534-542.

Vinogradov A.E. 2009. Global versus local centrality in evolution of yeast protein network. J. Mol. Evol. 68: 192–196.

Vinogradov A.E. 2008. Modularity of cellular networks shows general center-periphery polarization. Bioinformatics 24: 2814-2817.

Анацкая О.В., Виноградов А.Е. 2008. Полиплоидия в сердце: защита и слабость. Химия и жизнь 9: 34-37.

Vinogradov A.E., Anatskaya O.V. 2007. Organismal complexity, cell differentiation and gene expression: human over mouse. Nucleic Acids Res. 35: 6350-6356.

Anatskaya O.V., Vinogradov A.E. 2007. Genome multiplication as adaptation to tissue survival: Evidence from gene expression in mammalian heart and liver. Genomics 89: 70-80.

Anatskaya O.V., Sidorenko N.V., Vinogradov A.E., Beyer T.V. 2007. Impact of neonatal cryptosporidial gastroenteritis on epigenetic programming of rat hepatocytes. Cell Biol. Int. 31: 420-427.

Vinogradov A.E. 2006. 'Genome design' model and multicellular complexity: golden middle. Nucleic Acids Res. 34: 5906–5914.

Vinogradov A.E., Anatskaya O.V. 2006. Genome size and metabolic intensity in tetrapods: a tale of two lines. Proc. Roy. Soc. Lond. B 273: 27-32.

Vinogradov A.E. 2006. "Genome design" model: evidence from conserved intronic sequence in human-mouse comparison. Genome Res. 16: 347-354.

Анацкая О.В., Виноградов А.Е. 2005. Зачем клеткам сердца "лишние" геномы? Наука в России 5: 46-51.

Vinogradov A.E. 2005. Dualism of gene GC content and CpG pattern in regard to expression in the human genome: magnitude versus breadth. Trends Genet. 21: 639-643.

Vinogradov A.E. 2005. Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic Acids Res. 33: 559-563.

Vinogradov A.E. 2005. Genome size and chromatin condensation in vertebrates. Chromosoma 113: 362-369.

Анацкая О.В., Виноградов А.Е. 2004. Полиплоидия: значение для функции кардиомиоцитов и потенциала работы сердца. Цитология 46: 105-113.

Anatskaya O.V., Vinogradov A.E. 2004. Paradoxical relationship between protein content and nucleolar activity in mammalian cardiomyocytes. Genome 47: 565-578.

Anatskaya O.V., Vinogradov A.E. 2004. Heart and liver as developmental bottlenecks of mammal design: evidence from cell polyploidization. Biol. J. Linn. Soc. 83: 175-186.

Vinogradov A.E. 2004. Testing genome complexity. Science 304: 389-390 [letter].

Vinogradov A.E. 2004. Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet. 20: 248-253.

Vinogradov A.E. 2004. Evolution of genome size: multi-level selection, mutation bias or dynamical chaos? Curr. Opin. Genet. Devel. 14: 620-626.

Vinogradov A.E. 2004. Genome size and extinction risk in vertebrates. Proc. Roy. Soc. Lond. B 271: 1701-1705.

Vinogradov A.E., Anatskaya O.V. 2004. Phenological resonance and quantum life-history. J. Theor. Biol. 228: 417-420.

Vinogradov A.E. 2003. Selfish DNA is maladaptive: evidence from the plant Red List. Trends Genet. 19: 609-614.

Vinogradov A.E. 2003. DNA helix: the importance of being GC-rich. Nucleic Acids Res. 31: 1838-1844.

Vinogradov A.E. 2003. Isochores and tissue-specificity. Nucleic Acids Res. 31: 5212-5220.

Vinogradov A.E. 2003. Silent DNA: speaking RNA language? Bioinformatics 9: 2167-2170.

Anatskaya O.V., Vinogradov A.E. 2002. Myocyte ploidy in heart chambers of birds with different locomotor activity. J. Exp. Zool. 293: 427-441.

Vinogradov A.E. 2002. Growth and decline of introns. Trends Genet. 18: 232-236.

Anatskaya O.V., Vinogradov A.E., Kudryavtsev B.N. 2001. Cardiomyocyte ploidy levels in birds with different growth rates. J. Exp. Zool. 289: 48-58.

Vinogradov A.E. 2002. Growth and decline of introns. Trends Genet. 18: 232-236.

Vinogradov A.E. 2001. Bendable genes of warm-blooded vertebrates. Mol. Biol. Evol. 18: 2195-2200.

Vinogradov A.E. 2001. Intron length and codon usage. J. Mol. Evol. 52: 2-5.

Vinogradov A.E. 2001. Within-intron correlation with base composition of adjacent exons in different genomes. Gene 276: 143-151.

Vinogradov A.E. 2001. Mirrored genome size distributions in monocot and dicot plants. Acta Biotheoretica 49: 43-51.

Vinogradov A.E., Anatskaya O.V., Kudryavtsev B.N. 2001. Relationship of hepatocyte ploidy levels with body size and growth rate in mammals. Genome 44: 350-360.

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Updated: January 2019