• Date of Birth: April 23, 1963;
• Marital status: Married
• Home Address: Sirenevaia 33-37, Novosibirsk, 630058, Russia
• Work Address: Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
• Telephone: +7(3832) 333118
• FAX: +7(3832) 331278
• Emails: bob@bionet.nsc.ru

• Statistical inferences on the genetic text features. Analysis of DNA, RNA context features, including

1. cDNA library oligonucleotide hybridization analysis

2. transcription factor binding sites revealing

3. Finding the statistical regularities in the non-coding regions

Full secondary school, 1970 - 1980

Novosibirsk State University (Mathematics Faculty), 1980-1985.

PhD courses in biology at Institute of Cytology and Genetics, Novosibirsk, Department of Biology, 1989 - 1992.

Degree: Ph.D. in Biology, May 26, 1992 (KD #064969 issued at Moscow, July/17/1992)

Title: " Analysis of tests for Hardy - Weinberg distribution"

Thesis advisor: Emil K. Ginsburg, Dr.Sci.

Institution: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia

"GenExpress"(an intellectual system for analysis of genomic regulatory sequences of humans and higher eukaryotes) - the particular programs realization.

"RGSiteScan": a computer program predicting the potential binding sites of 37 transcription factors, in the target DNA sequence - co-designer

(URL: http://wwwmgs.bionet.nsc.ru/mgs/programs/yura/rgscan1.html)

"RecGroup": a program aimed on construction of Recognition groups which are used further by the RGSiteScan for final result - co-designer

(URL: http://wwwmgs.bionet.nsc.ru/mgs/programs/yura/recgroup.html)

• Co-Principal Investigator, The SB RAS Competitive Support for Young Scientists, grant: “Theoretical and experimental investigation of the basic genetic processes”, 1998-1999
• Individual Grant fellowship by Open Society Archives, Budapest, 1998.
• Member of Russian/Vavilov National Geneticists and Breeders Society, 1992-present.

• 1998 P.S. Kosarev, MS (Thesis: contextual computer analysis of eukaryotic promoter regions) Novosibirsk State University, Biology
• 1997 M.A.Pozdnyakov, MS (Thesis: Analysis of spontaneous mutations in eukaryotic pseudogenes), Novosibirsk State University, Biology

1. Babenko, V.N., Kosarev, P.S., Basin, V.G., Frolov, A.S. The repeated motifs in promoter regions of eukaryotic genes. Biophysics, accepted.
2. Babenko, V.N., Kosarev, P.S., Basin, V.G. Searching for the repeats in regulatory regions of eukaryotic genes. Proc. Of International school of theoretical biophysics, Moscow, 1998, Russia, p.28.
3. Kosarev, P.S., Babenko, V.N. Promoters: AT/GC content and properties of TATA - box. Proc. of I International Conference on Bioinformatics of Genome Regulation and Structure, 1998. Novosibirsk, Russia, pp.119-124.
4. Kondrakhin, Yu. V., Babenko, V.N., Milanesi, L., Lavryushev, S.V., Kolchanov, N.A. Recognition groups: a new method for description and prediction of transcription factor binding sites. Bioinformatics, 1998, accepted

 

Oligonucleotides:

5. Kel, A.E., Ptitsyn, A.A. Babenko, V.N., Meier - Ewert, S., Lehrach, H. A genetic algorithm for designing gene family specific oligonucleotide sets for hybridization: The G protein-coupled receptor protein superfamily. Bioinformatics, 1998, v. 14, N. 3, pp.259-270;also: Proceedings of the German Conference on Bioinformatics GCB -97 (Mewes H.W. eds), MIPS-GSF Am Max-Planck Institut f. Biochemie 82152 Martinsried, Germany. pp.53-55.
6. Vishnevsky, O.V., Podkolodnaya, O.A., Babenko, V.N. Search for degenerate oligonucleotide motifs in transcription factor binding sites and eukaryotic promoters (Computer system ARGO). Proc. of I International Conference on Bioinformatics of Genome Regulation and Structure, 1998, Novosibirsk, Russia, pp.144-146.
7. Kolchanov, N.A., Babenko, V.N.,Vishnevsky, O.V., Kel, A.E. Oligonucleotide vocabularies of isofunctional gene families coding for proteins. Proceedings of Academy of Science (DAN). 1996, v.348, n5, pp.636-639 (in Russian).
8. Kel., A.E., Philippenko, M.V., Babenko, V.N., Kolchanov, N.A. Genetic algorithm for selection of oligonucleotides for identification by hybridization of genomic DNA fragments possessing gene potential. Proceedings of German Conference on Bioinformatics. Lepzig, 1996. pp.238-240.
9. Kolchanov, N.A., Vishnevsky, O.V., Babenko, V.N., Kel, A.E., Shindyalov, I.N. Identification of cDNA sequences by specific oligonucleotide sets. Computer tool and application. Proc. of 3-rd international conference on intelligent systems for molecular biology, London, 1995,pp.206-214.
10. Michailova, S.V., Babenko, V.N., Romachenko, A.G., Beliaeva, T.A., Melidi, N.N., Lavrinenko, V.A., Guvakova, T.V., Ivanova, L.N., Distribution of the Bsp-repeats transcripts of Canidae in the mink; structural similarity of Bsp-repeats with SINEs. Docl. Acad. Nauk. RAS, 1995, v. 343, n.2, p.260-264. (in Russian).

 

Databases and systems:

11. 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, pp.351-355.
12. Kochetov, A.V., Pilugin, M.V., Kolpakov F.A., Babenko, V.N., Kvashnina, E.V., Shumny, V.K. Structural and compositional features of 5’ untranslated regions of higher plant mRNAs. Proc. of I International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, pp.210-213.
13. Kochetov, A.V., Vorobiev, D.G., Babenko, V.N., Kisselev, I.L., Kolchanov, N.A. Translation control of gene expression in eukaryotes: mRNA encoding abundant and scarce proteins are dissimilar in many structural features. Int. School of Theoretical Biophysics, 1998, Moscow, Russia), p. 56.
14. Kolpakov, F.A., Babenko, V.N. MGL: An object- oriented computer system for molecular genetic data management, analysis and visualization. Proc. of I International Conference on Bioinformatics of Genome Regulation and Structure, 1998, Novosibirsk, Russia, pp.434-437.
15. Kolpakov, F.A., Babenko, V.N. Computer system MGL – tool for sample generation, visualization and analysis of regulatory genomic sequences. Molekularnaya Biologia, 1997, Vol.31. pp. 647-655. (Russ.)
16. Pozdnyakov, M.A., Rogozin, I.B., Babenko, V.N., Kolchanov, N.A. Analysis of Neighbor Base Influences on Spontaneous Mutations in Human Pseudogenes. Proceedings of Academy of Sciences, 1997, v.45. N.1, pp. 34-43 (in Russian).

      Population studies:

17. Baranov P.O., Babenko, V.N., Ivanova, A.V., Kobsev, V.F., Romaschenko, A.G., Voevoda, M.I. Peculiarities of mitochondrial genofond of Germans in Russia. Genetika, 1998, v. 35, N. 2, pp.210-215 (in Russian).
18. Babenko, V.N., Voevoda M.I. Testing the hypothesis on the selection in a population with sexual dimorphism. Proc. Of the 3-rd Siberian Congress on Applicational and Industrial Mathematics, INPRIM-98, Novosibirsk, Russia, pp. 111-112 (in Russian).
19. Kazakovtseva, M.A., Voevoda, M.I., Babenko, V.N., Osipova, L.P. Restriction - Site polymorphism of the Mitochondrial DNA Control Region in Populations of Russian Natives and Migrant Slavic Populations of Northern Siberia. Genetika, 1998, v. 34, N. 4, pp. 544-550 (in Russian).
20. Voevoda, M.I., Avksentiuk, A.V., Ivanova, A.V., Astakhova, T.I., Babenko, V.N., Kurilovitch, S.A., Duffy, L.K., Segal, B., Shields, G. Molecular- genetic studies in native inhabitants of Chuckchee peninsula. Analysis of polymorphism of mtDNA and alcohol metabolizing enzymes. Siberian Journal of Ecology, 1994, v.1, n.2, pp. 139-151.

 

Analysis of statistical tests:

21. Babenko, V.N., Rogozin, I.B. Application of rank correlation coefficient to compare mutational spectra. Biophysics (in Russian, accepted).
22. Deineko, E.V., Ceveleva, O.N., Peltek, S.E., Babenko, V.N., Sidorchuk, Ju. V., Shumny, V.K. Somaclonal variability of morphological and biochemical traits in regenerate plants of Medicago varia. Physiologia rastenii. 1997. v. 44, N. 5, pp. 775-781 (in Russian).
23. Ginsburg, E. Kh., Axenovich, T.I., Babenko, V.N. 1991. Comparison of asymptotic tests of Hardy - Weinberg distribution. Ann. Hum. Genet., 55, v.4, pp.329-338.
24. Ginsburg E.Kh., Svischova G.R., Babenko, V.N. Numerical comparison of tests for 2x2 tables. Proc. SD. Rus.Acad.Sci. (biol.ser.). 1992. v1, pp.13-24 (in Russian).
25. Babenko, V.N. Analysis of tests for Hardy-Weinberg distribution. Ph.D. Thesis., Novosibirsk. 1992. ICG Press, 16p. (in Russian).
26. Ginsburg, E.Kh., Axenovich, T.I., Babenko, V.N. Verification of Hardy-Weinberg distribution (analysis of tests). Novosibirsk. 1991. ICG Press, 75p. (in Russian).
27. Babenko, V.N., Ginsburg, E.Kh., Axenovich, T.I. Analysis of tests for Hardy-Weinberg distribution. in: Proc. Conf. on Mathematical and Computer Methods in Plant Breeding. Tver. 1991. Infor. Comp. Center Press. p 4.(in Russian).
28. Axenovich, T.I., Babenko, V.N. Analysis of tests for verification of Hardy-Weinberg distribution. in: Proc. Conf. II All-Union congress of med. geneticists, Moskow. 1990. p.10 (in Russian).
29. Ginsburg, E.Kh., Axenovich, T.I., Babenko, V.N. On adequacy of Haldane test for Hardy-Weinberg distribution. Novosibirsk. 1990. ICG Press, 14p. (in Russian).

Other papers

30. Babenko, V.N., Titov, I.I., Plato on PCR Amplification. Genetika, 1994. v.30 (Supplement), pp.10-11 (in Russian).
31. Ginsburg, E.Kh., Axenovich, T.I., Persova, T.I., Babenko, V.N. Software for genetic analysis of pedigrees of arbitrary structure. in: Proc. of 1-st Meeting of Medical Geneticists of Russia. Moscow. 1994. pp. 151-152. (in Russian).
32. Rauschenbach, I.V., Serova, L.I., Timokhina, I.S., Shumnaja, L.V., Chentsova, N.A., Babenko, V.N. Genetic Analysis of Differences in Metabolism of Dopamine in 2 Drosophila-Virilis Lines in Norm and Heat Stress. Genetika, 1993, v.29, N.6 pp. 935-949 (in Russian).