Date of Birth: February 13, 1973

Marital status: Married with Svetlana L. Kivileva

Work Address: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospect Lavrenyieva 10, Novosibirsk, 630090, Russia

Tel.: (3832) 35-12-63 (off)

Fax: (3832) 35-65-58

E-Mail: fedor@bionet.nsc.ru

Work Experience and Current Position:

1995 - 1998 - Post-graduate course in Laboratory of Theoretical Molecular Genetics, Institute of Cytology and Genetics, Russia. Supervisor prof. N.A. Kolchanov

1998 - Present - Research Scientist, Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, 630090.

Object oriented programming and design (C++, Java)

Databases on molecular biology

Gene networks

Gene expression regulation

Functional sites analysis

Nucleotide sequences alignment

1980 - 1988 - secondary school.

1988 - 1990 - special physical-mathematical school

1990 - 1995 - Novosibirsk State University, Faculty of Natural Sciences, specialty molecular biology.

1995 - 1998 - Post-graduate course in Laboratory of Theoretical Molecular Genetics, Institute of Cytology and Genetics, Russia. Supervisor prof. N.A. Kolchanov

GeneNet - Java system for automated gene network visualization (GeneNet Viewer)

TRRD Viewer - Java system for automated visualization regulatory maps of genes from TRRD database. (TRRD Viewer)

MGL - Molecular Genetics object-oriented Library & Language (MGL Language)

 

1998 - the 1^st International Conference on Bioinformatics of Genome Regulation and Structure, (BGRS'98), Novosibirsk, Russia; report, posters and demonstration.

1998 - Dagstuhl seminar “Bioinformatics” Modelling and simulation of gene regulation and metabolic pathways, Germany; report and demonstration.

1998 - the 6^th Intern. Conference of Intelligent Systems for Molecular Biology, (ISMB'98), Montreal, Quebec, Canada; co-author of report.

1998 - Theoretical Biophysics International School, Moscow; co-author of reports.

1998 - the 3^rd Siberian Congress on Applied and Industrial Mathemetics, (INPRIM-98),
Novosibirsk, Russia; co-author of reports.

1996 - Computer Science and Biology. German Conference on Bioinformatics, (GSB’96), Liebigstr, Germany; co-author of report.

1996 - the 2^nd Siberian Congress on Applied and Industrial Mathemetics, (INPRIM-96),
Novosibirsk, Russia, report.

1996 - the 4^th International Conference on Intelligent Systems for Molecular Biology,
(ISMB’96)”, Washington University, St. Louis, USA, co-author of report.

1995 - the 3^rd Intern. Conference of Intelligent Systems for Molecular Biology, (ISMB'95) California, US, 1995; co-author of report.

1. Kolpakov F.A., Ananko E.A., Kolesov G.B. and Kolchanov N.A. GeneNet: a database for gene networks and its automated visualization // Bioinformatics, 1998, Vol.14. No. 6, p.
2. Kolpakov F.A., Babenko V.N. MGL - object-oriented computer system for molecular genetics data management, analysis and visualization // Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 1998, p. 434-437.
3. Kolpakov F.A, Frolov A.S., Ponomarenko M.P., Podkolodny N.L. MGL-PROT: the onthology-based query language for the user search for the 3D structures and functions of proteins in the WWW-available databases. // Ibid, p. 269-271.
4. Ananko E.A., Kolpakov F.A., Kolesov G.B. and Kolchanov N.A. Gene networks: a database and its automated visualization through the internet in the GeneNet computing system // Ibid, p. 82-85.
5. Seledtsov I.A., Kolpakov F.A. Rapid estimates of statistical significance of the pairwise nucleotide sequence alignment. //  Ibid, 1998, p. 301-304.
6. Kolesov G.B., Kolpakov F.A., Kolchanov N.A. New method for the study of the modular structure of transcription regulatory regions. // Ibid, p. 430-433.
7. Kochetov A.V., Pilugin M.V., Kolpakov F.A., Babenko V.N., Kvasnina E.V., Shumny V.K. Structural and compositional features of 5’ untranslated regions of higher plant mRNAs // Ibid, p. 210-213.
8. Kolchanov N.A., Igntieva E.V., Kel-Margoulis O.V., Kel A.E., Ananko E.A., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Goryachkovskaya T.N., Kolpakov F.A., Podkolodny N.L., Lavryushev S.V., Grigorovich D.A., Frolov A.S., Romaschenko A.G. Transcription regulatory regions database (TRRD): new possibilities provided by release 4.0. // Ibid, p. 25-28.
9. 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. // Ibid, p. 71-75.
10. 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.
11. Kolpakov F.A., Ananko E.A., Kolesov G.B. and Kolchanov N.A. GeneNet: a database for gene networks and its automated visualization through the Internet. // Dagstuhl seminar “Bioinformatics” Modelling and simulation of gene regulation and metabolic pathways, 1998.
12. Ananko E.A., Kel A.E., Kel O.V., Ignatieva E.V., Podkolodnaya O.A., Merkulova T.I., Merkulova I.L., Stepanenko I.L., Busigina T.V., Kozlova O.N., Kochetov A.V., Kolpakov F.A., Kolesov G.B., Lavryushev S.V., Grigorovich D.A., Podkolodny N.L., Frolov A.S., Romashchenko A.G., Kolchanov N.A. Transcription regulatory regions database (TRRD) as a global information system on transcription regulation of eukaryotic genes// Abstracts of Theoretical Biophysics International School, Moscow, 1998, p. 25.
13. Ananko E.A., Kolpakov F.A., Kolesov G.B. and Kolchanov N.A. Automatic generation of gene networks schemes from formalized description in the GeneNet database// Ibid, p. 26.
14. Ignatieva E.V., Ananko E.A., Kel O.V., Podkolodnaya O.A., Merkulova T.I., Stepanenko I.L., Busigina T.V., Kozlova O.N., Kolpakov F.A., Lavryushev S.V., Grigorovich D.A., Podkolodny N.L., Frolov A.S., Kel A.E., Kolchanov N.A. LM-TRRD: the first step toward understanding complex genetic word of lipid metabolism // Ibid, p. 52.
15. 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 // Ibid, p. 57.
16. Kolpakov F.A. Computer system MGL: a tool for sample generation, visualization, and analysis of regulatory genomic sequences // Ibid, p. 58.
17. Kolpakov F.A. Convergence in the evolution of promoters in higher eukaryotic genes transcribed by RNA-polymerase II // Ibid, p. 59.
18. Kolpakov F.A., Kolchanov N.A. Study of peculiarities of vertebrate promoter region evolution // Ibid, p. 60.
19. Heinemeyer T., Wingender E., Reuter H., Herjacob H., Kel A.E., Kel O.V., Ignatieva E.V., Ananko E.A., Podcolodnaya O.A., Kolpakov F.A., Podcolodny N.L., Kolchanov N.A. Databases on transcription regulation: TRANSFAC, TRRD and COMPEL. // Nucl. Acids Res., 1998, Vol.26, No. 1, pp. 362-367.
20. Kolchanov N.A., Ponamorenko M.P., Kel A.E., Ponomarenko J.V., Kolpakov F. A., Frolov A.S., Soloviev V.V., Romashchenko A.G., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Kel O.V., Merkulova T.I., Goryachkovskaya T.N., Kochetov A.V., Podkolodny N.L., Kolesov G.B., Lavryushev S.V., Kisselev L.L., GeneExpress: an intellectual system for analysis of genomic regulatory sequences of humans and higher eukaryotes, Abstract for HUGO'98.
21. Kolpakov F.A., Babenko V.N. Computer system MGL – tool for sample generation, visualization and analysis of regulatory genomic sequences. // Mol. Biol., 1997, Vol.31. pp. 647-655. (Russ.)
22. Kolpakov F.A., Kel A.E., Ponomarenko M.P., Kolchanov N.A. High heterogeneity of the promoters in higher eukaryotic genes transcribed by RNA-polymerase II. // Proc. of. Academy of Sciences, 1997, Vol. 357, No. 5, pp. 693-695. (Russ.)
23. Kel' A.E., Kolchanov N.A., Kel' O.V., Romashchenko A.G., Anan'ko E.A., Ignat'eva E.V., Merkulova T.I., Podkolodnaia O.A., Stepanenko I.L., Kochetov A.V., Kolpakov F.A., Podkolodnyi N.L., Naumochkin A.A. TRRD: a database of transcription regulatory regions in eukaryotic genes. // Mol. Biol., 1997, Vol. 31, pp.626-636 (Russ.)
24. Kolpakov F., Kel A., Kolchanov N. Convergenece in the evolution of promoters in higher eukaryotic genes transcribed by RNA-polymerase II. // 9^th International Congress on Genes, Gene Families and Isozymes San Antonio, Texas April 14-19, 1997.
25. Kolpakov F., Kolchanov N. Study of peculiarities of vertebrate promoter region evolution. // 2^nd Siberian Congress on Applied and Industrial Mathemetics, Novosibirsk, Russia, 1996, p. 27.
26. Kel A.E., Kolchanov N.A., Kel O.V., Kondrakhin Y.V., Kolpakov F.A., Lavrushov S., Ponomarenko M.P., Wingender E. Regulatory genomic sequences, databases and tools for analysis and recognition. // Abstr. of Intern. Symposium on Theoretical and Computational Genome Research, Deutsches Krebsforschungszentrum, Heidelberg, Germany, 1996, pp. 69-70.
27. Ponomarenko M.P., Savinkova L.K., Kel A.E., Kel O.V., Kolchanova A.N., Kondrakhin Y.V., Kolpakov F.A., Romaschenko A.G., Kolchanov N.A. The structure of eukariotic promoters and computer methods of its recognition. // Proc. Of Inter. Conference "Modelling and simulation of gene and cell regulation", Dagstuhl, Germany, 1996, p.12.
28. Kondrakhin Yu.V., Kolpakov F.A., Kel A.E., Milanezi L., Kolchanov N.A. Computer analysis and recognition of the transcription regulatory elements in eukaryotic genomes // Computer Science and Biology. Proc. of German Conference on Bioinformatics, GSB’96 (Eds: Hofestadt et al), Liebigstr, Germany, 1996.
29. Kel A., Kondrakhin Y., Kolpakov F., Wingender E., Kolchanov N. Computer analysis of the structure of transcroption factor binding sites // SAMS, 1995, Vol. 18-19, pp. 819-822.
30. Kel A.E., Kondrakhin Y.V., Kolpakov Ph.A., Kel O.V., Romaschenko A.G., Wingender E., Kolchanov N.A. Computer toll FUNSITE for analysis of eukaryotic regulatory genomic sequences // Proc. III Intern. Conference of Intelligent Systems for Molecular Biology, California, US, 1995, pp. 197-205.

Last update: 9 September 1998.