Prof. Dr. Alexey Kochetov

Institute of Cytology and Genetics SB RAS, Novosibirsk
Prof. Dr. Alexey Kochetov

 

CURRICULUM VITAE

Name:
Alex V. Kochetov

Address:
10, pr. Lavrentieva,
Institute of Cytology and Genetics,
Novosibirsk, 630090, Russia

Affiliation:
Head of the Plant Gene Engineering Laboratory,
Institute of Cytology and Genetics,
Russian Academy of Sciences (Siberian Branch),
Novosibirsk, Russia

Education:

1991
Novosibirsk State University, Department of Biology.

1998
Ph.D. thesis: “mRNA sequence characteristics and expression of foreign genes in plant cells: experimental and computer analysis”, Novosibirsk, supervisors Prof., Dr.Sci V.K.Shumny, Dr.Sci. M.I.Rivkin

2004
Associate Professor

Skills:
molecular cloning, RNA-, DNA- and protein analysis, plant transgenesis, computer analysis of nucleotide sequences, bioinformatics, gene and mRNA organization

Interests:
molecular genetics, gene engineering, biotechnology, bioinformatics

Awards:
Belyaev’s Prize Laureate in Genetics, 1999, Siberian Branch of Russian Academy of Science
Chairman of society of young scientists of the Institute of Cytology and genetics (elected for 1999-2001 period). Vice-president of Society of young scientists of Siberian Division of Russian Academy of Sciences (biological division. elected for 1999-2001 period).

Member of Organizing and Program Committees:
2001, 2002 Lavrentiev’s Conference of junior researchers, Novosibirsk, Russia
2006 Pattern Recognition in Bioinformatics, Hong Kong
2006 Bioinformatics in Genome Regulation and Structure, Novosibirsk, Russia

Member of Bioinformatics Council, Siberian Branch of Russian Academy of Sciences

Selected Publications and Manuscripts (total, 90):

  1. Kochetov A.V. Alternative translation initiation sites and their impact to eukaryotic proteome. Russ. J. Mol. Biol. 2006 (in press).
  2. Volkova O.A., Kochetov A.V., Titov S.E., Kolchanov N.A. Potential open reading frames within eukaryotic mRNA 5′-untranslated regions. // Russ. J. Biophysics. 2006 (in press)
  3. Kolodiazhnaia IaS, Titov SE, Kochetov AV, Komarova ML, Romanova AV, Koval’ VS, Shumnyi VK Evaluation of salt tolerance in Nicotiana tabacum plants bearing an antisense suppressor of the proline dehydrogenase gene. Russ. J. Genetics. 2006 Feb;42(2):278-81
  4. Kochetov A.V., Sarai A., Rogozin I.B., Shumny V.K., Kolchanov N.A. The role of alternative translation start sites in generation of human protein diversity // Mol. Genet. Genomics 2005. 273. 491-496.
  5. Kochetov A.V. AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon context. Bioinformatics. 2005. V.21. P.837-840.
  6. Kochetov A.V., Sarai A. Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana // Bioinformatics. 2004. V.20. P.445-447.
  7. Vishnevsky O.V., Avdeeva I.V., Kochetov A.V. Study of the specific contextual features of translation initiation and termination sites in Saccharomyces cerevisiae // In: Bioinformatics of genome regulation and structure. Ed. by N. Kolchanov and R. Hofestaedt, Kluwer AcademicPublishers, Boston/Dordrecht/London, 2004, pp. 213-222.
  8. Matushkin Yu.G., Likhoshvai V.A., Kochetov A.V. Local secondary structure may be a critical characteristic influencing translation of unicellular organisms mRNA. // In: Bioinformatics Of Genome Regulation And Structure. Ed. By N. Kolchanov and R. Hofestaedt, Kluwer Academic Publishers, Boston/Dordrecht/London, 2004, pp. 103-114.
  9. Pichueva A.G., Kochetov A.V., Milanesi L., Kondrakhin Yu.V., Kolchanov N.A. Correlations between sequence features of yeast genes functional regions and the level of expression // In: Bioinformatics Of Genome Regulation And Structure. Ed. By N. Kolchanov and R. Hofestaedt, Kluwer Academic Publishers, Boston/Dordrecht/London, 2004, pp. 125-132.
  10. Trifonova EA, Komarova ML, Leonova NS, Shcherban AB, Kochetov AV, Malinovskii VI, Shumnyi VK. Transgenic potato (Solanum tuberosum L.) plants expressing the gene of secretory nuclease from Serratia marcescens. Dokl. Biochem. Biophys. 2004. V.394. P.39-41.
  11. Kochetov A.V., Titov C.E., Kolodyazhnaya J.S., Komarova M.L., Koval V.S., Trifonova E.A., Shumny V.K. Increase in proline content and cytoplasmic osmotic pressure in transformed tobacco plants bearing antisense suppressor of proline dehydrogenase // Russ. J. Genetics. 2004. V.40. P. 282-285.
  12. Kochetov A.V., Kolchanov N.A., Sarai A. Interrelations between the “strength” of translation start site and the sequence features of yeast mRNAs // Molecular Genetics & Genomics // 2003. V. 270. P. 442-447.
  13. Kochetov A.V., Sarai A., Vorob’ev D.G., Kolchanov N.A. The context organization of functional regions in yeast genes with high-level expression // Russ. J. Mol. Biol. 2002. V. 36. P. 1026-1034.
  14. Kochetov A.V., Sirnik O.A., Rogozin I.B., Glazko G.V., Komarova M.L., Shumny V.K. Context organization of mRNA 5′-untranslated regions of higher plants // Russ. J. Mol. Biol. 2002. V.36. P. 649-656.
  15. Trifonova E.A., Komarova M.L., Sirnik O.A., Kochetov A.V., Shumny V.K. Transgenic tobacco (Nicotiana tabacum SR1) plants expressing the gene coding for Serratia marcescens nuclease // Russ. J. Genetics 2002. V.38. P.274-277.
  16. Kochetov AV, Grigorovich D, Kolchanov NA, Sarai A. Database on mRNA-located eukaryotic expression signals influencing translation efficiency and specificity // Genome Informatics. Ser. 12. Edt: Matsuda et al. Universal Academy Press. Tokyo. Japan. 2001. P.492-493.
  17. Titov I.I., Kochetov A.V., Kolchanov N.A., Sarai A. Revealing mRNA translational signals by primary and secondary structure analysis // Genome Informatics. Ser. 12. Edt: Matsuda et al. Universal Academy Press. Tokyo. Japan. 2001. P.447-448.
  18. Kochetov A.V., Grigorovich D.A., Titov I.I., Vorob’ev D.G., Sirnik O.A., Vishnevsky O.V., Sarai A., Kolchanov N.A. mRNA-FAST (mRNA-Function, Activity, STructure) computer system // Russ. J. Mol. Biol. 2001. V.35. P. 1039-1047.
  19. Rogozin I.B., Kochetov A.V., Kondrashov F.A., Koonin E.V., Milanezi L. Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a “weak” context of the start codon // Bioinformatics. 2001. V. 17. P. 890-900.
  20. Trifonova E.A., Kochetov A.V., Shumny V.K. Role of nucleases in plant physiology // Advances in Modern Biology (review). 2000. V.120. P.395-405.
  21. Kochetov A.V., Ponomarenko M.P., Frolov A.S., Kisselev L.L., Kolchanov N.A. Prediction of eukaryotic mRNA translational properties // Bioinformatics J. 1999. V.15. P.704-712
  22. Kolchanov N.A., Ponomarenko M.P., Kel A.E., Kondrakhin Ju.V., Frolov A.S., Kolpakov F.A., Goryachkovskaya T.N., Kel O.V., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Babenko V.V., Vorobiev D.V., Lavryushev S.V., Ponomarenko Yu.V., Kochetov A.V., Kolesov G.N., Podkolodny N.L., Milanesi L., Wingender E., Heinemeyer T., Solovyev V., Overton G.C Genexpress 1.0: an WWW-oriented intergartor for the databases and computer systems for studying the eukaryotic gene expression // Bioinformatics J. 1999. V.15. P.669-686.
  23. Kochetov A.V., Pilugin M.V., Kolpakov F.A., Babenko V.N., Kolchanov N.A., Shumny V.K. 5’UTR of plant mRNAs: context of start AUG codon // Cytol. Genet. (Kiev) 1999. V.33. P. 3-9.
  24. Kolchanov N.A., Ponomarenko M.P., Kel A.E., Kondrakhin Ju.V., Frolov A.S., Kolpakov F.A., Goryachkovskaya T.N., Kel O.V., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Babenko V.V., Vorobiev D.V., Lavryushev S.V., Ponomarenko Yu.V., Kochetov A.V., Kolesov G.N., Podkolodny N.L., Milanesi L., Wingender E., Heinemeyer T., Solovyev V., Overton G.C GeneExpress: integrator for the databases and computer systems for studying the eukaryotic gene expression // Biofizika (Moscow). 1999. V.44. P.837-841.
  25. Kochetov A.V., Ischenko I.V., Vorobiev D.G., Kel A.E., Babenko V.N., Kisselev L.L., Kolchanov N.A. Eukaryotic mRNAs encoding abundant and scarce proteins are statistically dissimilar in many structural features // FEBS Lett. 1998. V.440. P.351-355.
  26. Deineko E.V., Zagorskaya A.A., Filipenko E.A., Filipenko M.L., Komarova N.I., Kochetov A.V., Shumny V.K. instability of the gene NPTII expression in transgenic tobacco (Nicotiana tabacum L.) plants during inbreeding// Russ. J. Genetics. 1998. V.34. P.1212-1219. 27. Kolchanov N.A., Ponomarenko M.P., Kel A. E., Kondrakhin Yu. V., Frolov A. S., Kolpakov F. A., Kel O. V., Ananko E. A., Ignatieva E.V., Podkolodnaya O. A., Stepanenko I. L., Merkulova T. I., Babenko V. N., Vorobiev D.G, Lavryushev S.V., Ponomarenko Yu. V., Kochetov A. V., Kolesov G.B., Podkolodny N. L., Milanesi L., Wingender E., Heinemeyer T., Solovyev V.V. GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences of the eukaryotic genome. // Proc. ISMB. 1998. V.6. P.95-104.
  27. Kochetov A.V. , Shumny V.K. Influence of mRNA sequence characteristics on translation intiation in plant cells (review) // Advances in current biology (Moscow). 1998. V.118. P.756-773.
  28. Gruntenko N.E., Kochetov A.V., Makarova K.S., Mishin V.P., Lukasheva V.V., Ptitsyn A.A., Kokoza V.A. Gene Nс73EF of Drosophila melanogaster encodes a protein highly homologous to E1 subunit of human 2-oxoglutarate dehydrogenase // Russ. J. Genetics. 1997.V.33. P.32-37.
  29. Kochetov A.V., Lukasheva V.V., Pilugin M.P., Konarova M.L., Deineko E.V., Rivkin M.I., McClean Ph., Shumny V.K. Exression of operons in plant cells // Cytology and Genetics (Kiev).1997. V.6. P.17-28.
  30. Kel A.E., Kolchnov N.A., Romaschenko A.G., Ananko E.A., Ignatieva E.V., Merkulova T.I., Podkolodnaya O.A. Kochetov A.V., Stepanenko I.A., Kolpako F.A., Podkolodny N.L., Naumochkin A.A.. TRRD: database on transcriptional regulatory regions of eukaryotic genes // Russ. J. Mol. Biol. 1997. V.31. P.626-636.
  31. Deineko E.V., Zagorskaya A.A., Filipenko E.A., Filipenko M.L., Novoselya T.V., Komarova M.L., Kochetov A.V., Shumny V.K. Instability of NPTII gene expression in the progeny of transgenic tobacco plants (Nicotiana tabacum L. and N.plumbaginifolia L.) // Biotechnology & Biotech.Equip. 1996. N4. P.89-92.
  32. Kochetov A.V., Lukasheva V.V., Komarova M.L., Pilugin M.V., Deineko E.V., Rivkin M.I., Shumny V.K. Expression of model bicistrones in transgenic plants // Reports of Russian Academy of Sciences. 1996. V.349. P.549-552.
  33. Rivkin M., Deineko E., Komarova M., Kochetov A., Malyshenko S., Talianskii M., Shumny V. Analysis of virus resistance of tobacco and alfalfa transgenic plants bearing human beta-interferon gene // Biotechnology & Biotech.Equip. 1995. N.1. P.40-44.
  34. Deineko E.V., Zagorskaya A.A., Filipenko M.L., Kochetov A.V., Shumny V.K. Variability in expression of marker NPTII gene in generations of transgenic tobacco plants // Reports of Russian Academy of Sciences 1995. V.344. P.407-411.
  35. Kochetov A.V., Lukasheva V.V., Filipenko M.L., Mertvetzov N.P., Rivkin M.I. Primary structure of coding sequence of the human pancreatic ribonuclease gene and its localization on chromosomes // Russ. J. Bioorg. Chem. 1995. V.21. P.691-694.