Bioinformatics Skills:

• NGS data analysis, metagenomics, transcriptomics, phylogenetics, regulation of mRNA translation initiation analysis
• programs and databases for nucleotides, proteins and NGS data analysis
• R, Python, Linux, GitHub
• Statistics, machine learning

Wet laboratory Skills:

• DNA cloning, primer design, PCR, DNA and proteins isolation, purification,
• agrobacterial transformation, plant transformation, transgenic plant cultivation,
• biochemistry analysis, ELISA

English knowledge: upper intermediate level.

Other skills: ability to make profound analysis of the literature, write articles, grants

Personal qualities: Learn fast, commitment, open to new information and methods.

Participation in grants 

2014-2016      RFBR grant “Model and prediction of mammalian RNA translation efficiency from its nucleotide sequence using data of ribosome profiling”, project leader

2009 -2010     RFBR grant “Research of mRNA eukaryotic features that enhances translation initiation from non- AUG start codon, and AUG codon, located in an unfavorable nucleotide context”, executor

2005 -2007     RFBR grant “Study of translation initiation signal and coding potential of eukaryotic mRNAs”, executor

2004 – 2006    RFBR grant “Study and formalized description of the processes taking place under the influence of excess of heavy metals exposure, conceptual models of the pathogenesis of lungs chronic non-infectious diseases and the optimization of their treatment”, executor

1996    ISSEP Student Soros grant.

Publications  

1. Bryanskaya A.V., Shipova A.A., Rozanov A.S., Kolpakova O.A., Lazareva E.V., Uvarova Yu.E., Efimov V.M., Zhmodik S.M., Taran O.P., Goryachkovskaya T.N., Peltek S.E. Metagenomic Insights into the Uncultured Diversity and Metabolism of the Microbial Communities in Hypersaline Lake (under review)
2. Kolpakova A.F., Sharipov R.N., Volkova O.A., Kolpakov F.A. The role of particulate matter air pollution in cancer pathogenesis. Siberian journal of oncology. 2021;20(2):102-109. (In Russ.) https://doi.org/10.21294/1814-4861-2021-20-2-102-109
3. Bryanskaya A.V., Shipova A.A., Rozanov A.S., Volkova O.A., Lazareva E.V., Uvarova Yu.E., Goryachkovskaya T.N., Peltek S.E. Metagenomics dataset used to characterize microbiome changes in water and sediments of the lake Solenoe (Novosibirsk region, Russia). Data Brief. 2021 Feb; 34: 106709. doi: 10.1016/j.dib.2020.106709
4. Kolpakova A.F., Sharipov R.N., Volkova O.A., Kolpakov F.A. Role of air pollution by particulate matter in the pathogenesis of cardiovascular diseases. Prevention measures. Cardiovascular Therapy and Prevention. 2020;19(3):2421. (In Russ.) https://doi.org/10.15829/1728-8800-2020-2421
5. Kolpakova A.F., Sharipov R.N., Volkova O.A., Kolpakov F.A. Particle pollution as a risk factor for lung carcinoma. Pulmonologiya. 2019;29(4):477-485. (In Russ.) https://doi.org/10.18093/0869-0189-2019-29-4-477-485
6. Trifonova, E.A., Ibragimova, S.M., Volkova, O.A., Shumny, V.K., & Kochetov A.V. A Ribonuclease activity as a new prospective disease resistance marker in potato. Vavilov Journal of Genetics and Breeding, 2018; 22(8), 987-991. DOI:18699/VJ18.441
7. Kolpakova A.F., Sharipov R.N., Volkova O.A. Correlation between type 2 diabetes mellitus and air pollution with suspended particles. Problems of Endocrinology. 2018;64(5):329-335. (In Russ.) https://doi.org/10.14341/probl9626
8. Volkova O.A., Kondrakhin Yu.V., Kashapov T.A., Sharipov R.N. Comparative analysis of protein-coding and long non-coding transcripts based on RNA sequence features. JBCB.2018. 16:02, DOI:1142/S0219720018400139
9. Kondrakhin Yu.V., Sharipov R.N., Volkova O.A. Start codons and mRNA translation efficiency prediction using Ribo-Seq-based weight matrices. Acta Natutae. 2017. 1:9, 25.
10. Yevshin I.S., Sharipov, R.N., Volkova O.A. Assessment of translation efficency from Ribo-Seq and mRNA-Seq data. Acta Natutae. 2017. 1:9, 28
11. Sharipov R.N., Yevshin I.S., Kondrakhin Yu.V., Volkova O.A. Ribo-Seq DB – a repository of selected human and mouse Ribo-Seq and RNA-Seq data. Acta Natutae. 2017. 1:9, 27.
12. Volkova O.A., Kondrakhin Yu.V., Yevshin IS, Valeev T.F., Sharipov R.N. Assessment of translational importance of mammalian mRNA sequence features based on Ribo-seq and mRNA-seq data Journal of Bioinformatics and Computational Biology. 2016, Vol. 14, No. 02, DOI: 10.1142/S0219720016410067
13. Volkova O.A., Kondrakhin Yu.V., Sharipov R.N. Estimation of translational importance of mammalian mRNA nucleotide sequence characteristics based on ribosome profiling data. Vavilov Journal of Genetics and Breeding. 2016. 20(6):779-786. DOI 10.18699/VJ16.195
14. Kolpakova A.F., Sharipov R.N., Volkova O.A. The impact of air pollution on the cardiovascular system. The Siberian Journal of Clinical and Experimental Medicine. 2015;30(3):7-12. (In Russ.) https://doi.org/10.29001/2073-8552-2015-30-3-7-12
15. Sharipov R.N., Yevshin I.S., Kondrakhin Yu.V., Volkova O.A. RiboSeqDB – a repository of selected human and mouse ribosome footprint and RNA-seq data. Virtual Biology, 2014, Virtual Biology, 2, 37-46, ISSN: 2306-8140, http://virtual-biology.org/vb/article/view/18
16. Kochetov A.V., Prayaga P.D., Volkova O.A. and Sankararamakrishnan R. Hidden coding potential of eukaryotic genomes: nonAUG started ORFs. J Biomol Struct Dyn, 2013; 31(1):103-14.
17. Kochetov A.V., Volkova O.A., Poliakov A., Dubchak I., Rogozin I.B. Tandem termintion signal in plant mRNAs. Gene. 2011. 481. 1-6.
18. Volkova O.A., Kochetov A.V. Interrelations between the nucleotide context of human start AUG codon, N-end amino acids of the encoded protein and initiation of translation. J Biomol. Struct. Dyn. 2010. 27 (5) 611-618.
19. Kochetov A.V., Ahmad S., Ivanisenko V., Volkova O.A., Kolchanov N.A., Sarai A. uORFs, reinitiation and alternative translation start sites in human mRNAs. FEBS Lett. 2008. 582. 1293-1297.
20. Volkova O.A., Titov S.E., Kochetov A.V. Interrelations between the translation initiation signal contextual organization and the N-terminus amino acid sequence of eukaryotic protein. Biofizika,. 2006. 51 (7): 11-17.
21. Volkova O.A., Kochetov A.V., Titov S.E. Kolchanov N.A. Potential open reading frames within 5'-untranslated regions of eukaryotic mRNAs. Biofizika, 2006;51(4):615-21.
22. Kochetov A.V., SyrnikA., Rogozin I.B., Glazko G.V., Komarova M.L., Shumny V.K. 5'- Context organization of mRNA 5'-untranslated regions of higher plants Mol Biol (Mosk) 2002;36(4):649-56.