Denis G. Vorobiev, M.Sc.

Denis G. Vorobiev, M.Sc.

            Curriculum Vitae and List of Publications

November  1999

            Work Experience and Current Position:

1997 - present Post graduate student, Laboratory of Theoretical Molecular Genetics, Institute of Cytology and Genetics, Novosibirsk, Russia; Supervisor prof. N.A. Kolchanov
1996 - 1997 Technician, Laboratory of Theoretical Molecular Genetics, Institute of Cytology and Genetics, Novosibirsk, Russia
1995 - 1996 Ingineer, Department of Molecular Biology of Gene, Institute of Bioorganic Chemistry, Novosibirsk, Russia

            Area of Expertise:

Molecular biology, molecular biological databases, genetic text analysis, C/C++ programming languages, HTML design.

            Education Background:

Full secondary school, 1981 – 1991
Novosibirsk State University (Faculty of Natural Sciences, Biology), 1991-1997.

            The main author of the WWW resources:

“Samples” - a database of transcription factor binding sites
(URL: http://wwwmgs.bionet.nsc.ru/mgs/dbases/nsamples/)
“GIBBS” - a program for multiple local alignment of nucleotide sequences
(URL: http://wwwmgs.bionet.nsc.ru/mgs/programs/gibbs_nuc/)

            The co-author of the WWW resources:

“GenExpress” - an intellectual system for analysis of genomic regulatory sequences of humans and higher eukaryotes
(URL: http://wwwmgs.bionet.nsc.ru/mgs/systems/geneexpress/)

            Awards and Grants:

            Conferences and Workshops:

1999 - Congress of Russian Biophysicists, Moscow, Russia, poster
1998 - World Multiconference on Systemics, Cybernetics and Informatics, SCI'98, Orlando, FL, USA co-author of report
1998 - The International Conference on Systems, Signals, Control and Computers (SSCC'98), Durban, South Africa co-author of report
1998 - VI Intern. Conference of Intelligent Systems for Molecular Biology, Montreal, Quebec, Canada., co-author of report
1998 - I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, posters, co-author of reports
1998 - Theoretical Biophysics International School, Moscow, co-author of report
1996 - Computer Science and Biology. German Conference on Bioinformatics, (GSB’96), Liebigstr, Germany; co-author of report
1996 - V annual conference of Russian National Program "Human Genome", Chernogolovka (Moscow region)., poster

            Publications:

  1. Ponomarenko M.P., Ponomarenko J.V., Podkolodnaya O.A., Frolov A.S., Vorobyev D.G., Kolchanov N.A., and Overton G.C. Averaging the results of site recognition can increase the accuracy of human genome annotation // Biophysics (Rus.) - 1999 V.44(4) - p.649-654

  2. Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobyev D.G., Kolchanov N.A., and Overton G.C. Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.// Bioinformatics, 1999, V. 15, N. 7/8, P. 631-643.

  3. Ponomarenko J.V., Ponomarenko M.P., Frolov A.S., Vorobyev D.G., Overton G.C., and Kolchanov N.A., Conformational and physicochemical DNA features specific for transcription factor binding sites.// Bioinformatics, 1999, V. 15, N. 7/8, P. 654-668.

  4. Kolchanov N.A., Ponomarenko M.P., Frolov A.S., Ananko E.A., Kolpakov F.A., Ignatieva E.V., Podkolodnaya O.A., Goryachkovskaya T.N., Stepanenko I.L., Merkulova T.I., Babenko V.N., Ponomarenko J.V., Kochetov A.V., Podkolodny N.L., Vorobyev D.G., Lavrushev S.V., Grigorovich D.A., Kondrakhin Yu.V., Milanesi L., Wingender E., Solovyev V.V., and Overton G.C. Integrated databases and computer systems for studying eukaryotic gene expression. // Bioinformatics, 1999, V. 15, N. 7/8, P. 669-686.

  5. Ponomarenko J.V., Ponomarenko M.P., Frolov A.S., Podkolodny N.L., Vorobiev, D.G., Kolchanov, N.A. Transcription factor binding sites: conformational and physico-chemical codes of functioning. Proc. Theoretical Biophysics Int. School, 1999, Moscow, Russia), V.3, p. 971.

  6. 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.

  7. Kolchanov N.A., Ponomarenko M.P., Kel A.E., Kondrakhin Yu.V., Frolov A.S., Kolpakov F.A., Goryachkovsky T.N., Kel O.V., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Babenko V.N., Stepanenko I.L., Romashchenko A.G., Merkulova T.I., Vorobiev D.G., Lavryushev S.V., Ponomarenko Yu.V., Kochetov A.V., Kolesov G.B., Solovyev V.V., Milanesi L., Podkolodny N.L., Wingender E., Heinemeyer T. GENEEXPRESS: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome. // Proc. VI Intern. Conference of Intelligent Systems for Molecular Biology, Montreal, Quebec, Canada, 1998, pp. 95-104.

  8. Ponomarenko M.P., Kolchanov N.A., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobyev D.V., Podkolodny N.L., Overton G.C. Revealign the conformational and physico-chemical features applicable for predicting the activity of the functional DNA sites In: “ Advances in Systems, Signals, Control and Computers”, (Ed. Bajic V.B.) Published by IAAMSAD & SA branch of ANS, Durban, South Africa,  1998, V. 2, P. 326-330.

  9. Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Podkolodnaya O.A., Vorobyev D.V., Kolchanov N.A., Overton G.C. Mean-recognition: a systematic approach increasing the accuracy of the functional site recognition for the genomic DNA annotation. In: “Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics, SCI'98 ”, July 12-16, 1998, Orlando, Florida, (Eds. N. Callaos, L. Holmes) V. 4, P. 224-230.

  10. Kolchanov N.A., Ponomarenko M.P., Kel A.E., Kondrakhin Yu.V., Frolov A.S., Kolpakov F.A.,Kel A.E., Kel-Margoulis 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., Grigorovich D.A.,  Ponomarenko J.V., Kochetov A.V., Kolesov G.B., Podkolodny N.L., Wingender E., Heinemeyer T., Milanesi L.,  Solovyev V.V., Overton G.C. GENEEXPRESS SYSTEM: description, analysis and recognition of regulatory sequences in eukaryotic genomes. // Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 1998, p. 71-75.

  11. Vorobiev D.G., Ponomarenko J.V., Podkolodnaya O.A  SAMPLES AND ALIGNED: DATABASES FOR FUNCTIONAL SITE SEQUENCES. // Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 1998, p. 58-61.

  12. Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Vorobiev D.G., Levitsky V.G., Podkolodnaya O.A., Overton G.C., Kolchanov N.A. B-DNA-VIDEO: AN ACTIVE DATABASE FOR THE SIGNIFICANT B-DNA FEATURES OF TRANSCRIPTION FACTOR BINDING SITES. // Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 1998, p. 66-70

  13. Frolov A.S., Lavryushev S.V., Vorobiev D.G., Grigorovich D.A., A SYSTEM FOR ACTIVATION OF THE TRRD DATABASE: FURTHER DEVELOPMENT OF GENEEXPRESS. // Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 1998, p. 136-138

  14. Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Podkolodnaya O.A.,Vorobiev D.G. , Kolchanov N.A, Overton G.C., RECOGNITION ACCURACY OF DNA FUNCTIONAL SITES CAN BE INCREASED BY AVERAGING PARTIAL RECOGNITIONS. // Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 1998, p. 158-162

  15. Ponomarenko M.P., Kolchanov N.A, Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobiev D.G., Podkolodny N.L., Overton G.C., REVEALING THE CONFORMATIONAL AND PHYSICO-CHEMICAL DNA PROPERTIES APPLICABLE FOR PREDICTING THE ACTIVITY OF DNA FUNCTIONAL SITES. // Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 1998, p. 186-190

  16. Kochetov A.V., Ponomarenko M.P., Vorobiev D.G., Frolov A.S., Kisselev L.L.,  Kolchanov N.A, EUKARYOTIC mRNA ENCODING ABUNDANT AND SCARCE PROTEINS ARE DISSIMILAR IN MANY STRUCTURAL FEATURES OF 5’-UNTRANSLATED LEADERS. // Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 1998, p. 214-217

  17. Likhachev A.E., Ponomarenko M.P., Bogachev S., Kokoza E., Fisher P., Ponomarenko J.V., Vorobiev D.G. , Kolesov G.B., Kolchanov N.A, THE STRUCTURAL ANALYSIS OF THE DNA FRAGMENTS ASSOCIATED WITH THE NUCLEAR LAMINS IN DROSOPHILA MELANOGASTER. // Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 1998, p. 247-248

  18. Ponomarenko M.P., Vorobiev D.G., Ponomarenko J.V., Kuzin F.E., Gruzdev A.D., Kolchanov N.A, SIGNIFICANT B-DNA CONFORMATIONAL AND PHYSICO-CHEMICAL PROPERTIES OF THE DNA TOPOISOMERASE I SITES. // Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 1998, p. 446-447

  19. Kolchanov N.A., Ponomarenko M.P., Kel A.E., Kondrakhin Yu.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.N., Vorobiev D.G., Lavryushev S.V., Ponomarenko J.V., Kochetov A.V., Kolesov G.B., Podkolodny N.L., Milanesi L., Wingender E., Heinemeyer T., Solovyev V.V. GeneExpress: a WWW-oriented integrator for the databases and computer systems for studying the eukaryotic gene expression // Abstracts of Theoretical Biophysics International School, Moscow, 1998, p. 57.

  20. 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. Proc. Theoretical Biophysics Int. School, 1998, Moscow, Russia), p. 56.