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Julia V. Ponomarenko, Ms.D.

Curriculum Vitae and List of Publications

Work Experience and Current Position:

2001 Visiting Scientist, GlaxoSmithKline Pharmaceuticals, King of Prussia, Pennsylvania, USA

1997 - present Research Associate, Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, 630090 Russia

1991 - 1997 Program Analyst, Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, 630090 Russia

Area of Scientific interest:

Development and implementation of programs and databases in the field of analysis of the protein binding sites in DNA and RNA. Many-years experience in RSX11M, MS DOS, and Windows operational systems, Fortran and C programming languages.

Education Background:

Full secondary school, 1973 - 1983

Special Physico-Mathematical school, 1982 - 1983.

Novosibirsk State University (Physical Faculty), 1983-1991.

Special courses "Chemical physics", "Molecular and Theoretical biology", 1988-1991.

Post-graduate courses in the Novosibirsk Institute of Cytology and Genetics, Department of Biology, 1996 - 1998.

 

The co-author of the WWW-server resourses:

rSNP_Guide - a system of databases documenting the influence of mutations in regulatory gene regions onto DNA interaction with nuclear proteins (http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/)

ACTIVITY - Distributed and intelligent database on functional site activity in DNA and RNA (http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/)

SELEX_DB - The activated database on selected randomized DNA/RNA sequences (http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/).

B-DNA-VIDEO - The activated database on significant B-DNA features of transcription factor binding sites (http://wwwmgs.bionet.nsc.ru/mgs/systems/bdnavideo/)

MATRIX - The database for the frequency matrixes of the functional DNA sites represented with using the oligonucleotide alphabets (http://wwwmgs.bionet.nsc.ru/mgs/systems/consfreq/)

SAMPLES - Database on sequence sets of functional sites in DNA, RNA , and proteins (http://wwwmgs.bionet.nsc.ru/Dbases/NSamples/auto1.exe)

GeneExpress- The integrated Web-based Computer system for discripting, analyzing, recognizing the potantial regulatory regions and functional sites in corse of the genome annotation (http://wwwmgs.bionet.nsc.ru/systems/GeneExpress/)

 

Conferences and Workshops:

2001 - Pacific Symposium on Biocomputing (PSB’2001), Hawaii, USA, posters

2000- WSES/MIUE/HNA International Conference: Mathematics and Computers in Biology and Chemistry (MCBC'2000), December 20-22, 2000, Montego Bay, Jamaica, report

2000 - The Eleventh Workshop on Genome Informatics (GIW 2000), December 18-19, 2000, Tokyo, Japan, posters

2000 - The Second International Conference of Bioinformatics of Genome Regulation and Structure (BGRS’2000), Novosibirsk, Russia, August 7-11, report, posters

2000 - The Second Meeting of Vavilov Society of Geneticists and Selectionists (VOGIS), February 1-5, S.-Peterburg, Russia, report

1999 - The First Cold Spring Harbor Workshop on computational biology “ Bridging the Gap between Sequences and Functions”, September 7-9, Cold Spring Harbor, New York, USA, co-author of report

1999 - Theory and Mathematics in Biology and Medicine, TMBM'99, June 29 - July 3, Amsterdam, Netherlands, poster

1999 - The British-Russian Digital Libraries Workshop, RBDLW'99, June 16-17, Moscow, Russia, co-author of report

1999 - The Sixth International Conference "Mathematics. Computer. Education." Puschino, Russia, January 25-30, report

1999 - The Workshop on Computer Science and Information Technologies (CSIT), Moscow, Russia, January 18 - 22, report

1998 - The International Conference on Systems, Signals, Control and Computers (SSCC'98), Durban, South Africa, co-author of report

1998 - The First International Conference of Bioinformatics of Genome Regulation and Structure (BGRS’98), Novosibirsk – Altai Mountains, Russia, August 24-31, report, posters

1998 - The World Multiconference on Systemics, Cybernetics and Informatics (SCI’98), Orlando, USA, July 12-16, co-author of report

1998 - The Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montreal, Canada, June 28 - July 1, co-author of report

1998 - The International school “Theoretical biophysics”, Moskow, Russia, 15-20 June, co-author of report

1998 - Pacific Symposium on Biocomputing (PSB’98), Hawaii, USA, co-author of report

1997 - Pacific Symposium on Biocomputing (PSB’97), Hawaii, USA, co-author of report

1997 - The 2nd international conference “Modern conceptions in evolution genetics”, Novosibirsk, co-author of two posters

1997 - A Newton Institute Workshop "Statistical analysis of DNA and protein sequences", co-author of report

1997 - German Conference on Bioinformatics “Computer science and biology”, Munih, Germany; abstract

1996 - The Engineering Foundation Conference “Recombinant DNA biotechnology: focus on metabolic engineering”, Danvers, Massachusetts, USA, abstract

1996 - The 11th Rinshoken International Coonference “Frontiers of Structural Biology” Tokyo, Japan, abstract

 

List of Publications:

Papers:

 

  1. Julia V. Ponomarenko, Tatyana I. Merkulova, Gennady V. Vasiliev, Zoya B. Levashova, Galina V. Orlova, Sergey V. Lavryushev, Oleg N. Fokin, Mikhail P. Ponomarenko, Anatoly S. Frolov, and Akinori Sarai (2001) rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. Nucleic Acids Research, 29, 312-316.
  2. Julia V. Ponomarenko, Dagmara P. Furman, Anatoly S. Frolov, Nikolay L. Podkolodny, Galina V. Orlova, Mikhail P. Ponomarenko, Nikolay A. Kolchanov, and Akinori Sarai (2001) ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. Nucleic Acids Research, 29, 284-287.
  3. Julia V. Ponomarenko, Mikhail P. Ponomarenko, Anatoly S. Frolov, Ivan Zvolsky (2000) Diffusion additive to TATA-box recognition score detects the non-contextual TBP-binding site at -30 position of TATA-less promoters. Proceedings of WSES/MIUE/HNA International Conference: Mathematics and Computers in Biology and Chemistry (MCBC'2000), December 20-22, 2000, Montego Bay, Jamaica.
  4. Julia V. Ponomarenko, Galina V. Orlova, Mikhail P. Ponomarenko, Sergey V. Lavryushev, Anatoly S. Frolov, Svetlana V. Zybova, Nikolay A. Kolchanov (2000) SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. Nucleic Acids Research, 28, 205-208. "Full-text (in PDF-format)"
  5. Vasiliev G.V., Merkulov V.M., Kobzev V.F., Merkulova T.I., Ponomarenko M.P., Podkolodnaya O.A., Ponomarenko J.V., and Kolchanov N.A. (2000) Point mutations within 663-666 bp of intron 6 of the human tryptophan oxigenase gene, associated with a number of psychiatric disorders, damage the YY-1 transcription factor binding site. Mol.Biol.(Mosk), 34(2), P. 214-222. (Russ)
  6. Kolchanov N.A., Ponomarenko M.P., Kel A.E., Kondrakhin Yu.V., Frolov A.S., Kolpakov F.A., Goriachkovsky T.N., Kel-Margulis O.V., Ananko E.A., Ignatieva E.V., Podkolodnaia O.A., Stepanenko I.L., Merkulova T.I., Babenko V.N., Vorobiev D.G., Lavrushev S.V., Ponomarenko J.V., Kochetove A.V., Kolesov G.N., Podkolodny N.L., Milanesi L., Wingender E., Heinemeier T., Solovyev V.V., Overton G.C. (1999) GeneExpress: a WWW-oriented integrator for databases and computer systems for studying the eukaryotic gene expression. Biofizika, 44, N. 5, P. 837-841. (Russ)
  7. Ponomarenko M.P., Ponomarenko J.V., Podkolodnaia O.A., Frolov A.S., Vorobiev D.G., Kolchanov N.A., and Overton G.C. (1999) Averaging the results of site recognition can increase the accuracy of human genome annotation. Biophysics, 44, N. 4, P. 631-635.
  8. Ponomarenko M.P., Ponomarenko J.V., Podkolodnaia O.A., Frolov A.S., Vorobiev D.G., Kolchanov N.A., and Overton G.C. (1999) Averaging the results of site recognition can increase the accuracy of human genome annotation. Biofizika, 44, N. 4, P. 649-654. (Russ)
  9. Ponomarenko M.P., Ponomarenko J.V., Kolchanov N.A., (1999) Contribution of signals and antisignals to the mutation spectrum of the td-intron homing site. Biophysics, 44, N. 4, P. 636-643.
  10. Ponomarenko M.P., Ponomarenko J.V., Kolchanov N.A., (1999) Contribution of signals and antisignals to the mutation spectrum of the td-intron homing site. Biofizika, 44, N. 4, P. 655-663. (Russ)
  11. Kolchanov N.A., Ponomarenko M.P., Frolov A.S., Ananko E.A., Kolpakov F.A., E., Ignatieva E.V., Podkolodnaya O.A., Goryachkovskaya T.N., Stepanenko I.L., Merkulova T.I., Babenko V.V., Ponomarenko Yu.V., Kochetov A.V., Podkolodny N.L., Vorobiev D.V., Lavryushev S.V., Grigorovich D.A., Kondrakhin Yu.V., Milanesi L., Wingender E., Solovyev V. and Overton G.C. (1999) Integrated databases and computer systems for studying eukaryotic gene expression. Bioinformatics, 15, 7/8, 669-686.
  12. Ponomarenko J.V., Ponomarenko M.P., Frolov A.S., Vorobyev D.G., Overton G.C., Kolchanov N.A. (1999) Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinformatics, 15, 7/8, 654-668.
  13. Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodny N.L., Savinkova L.K., Kolchanov N.A., Overton G.C. (1999) Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins. Bioinformatics, 15, 7/8, 687-703.
  14. Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobyev D.G., Kolchanov N.A., Overton G.C. (1999) Oligonucleotide frequency matrices addressed to recognising functional DNA sites. Bioinformatics, 15, 7/8, 631-643.
  15. Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobyev D.G., Kolchanov N.A., Overton G.C. (1999) Oligonucleotide frequency matrices addressed to recognising functional DNA sites. Bioinformatics, 15, 7/8, 631-643.
  16. Kolchanov N.A., Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodny N.L. (1998) Functional sites in pro- and eukaryotic genomes: computer models for predicting activity. Mol. Biol. (Mosk), V. 32(2), P. 255-267. (Russ)
  17. Ponomarenko M.P., Ponomarenko J.V., Titov I.I., Kolchanov N.A, Mazin A.V., Kowalczykowski S.C. (1998) DNA sequence specificity of RecA-filament correlates with genetic code, Docl. Acad. Sci., 1998, 363, P. 122-125. (Russ).
  18. 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. (1998) GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences of the eukaryotic genome. Proceedings of The Sixth International Conference on Intelligent Systems for Molecular Biology, ISMB-98. Ed.: Glasgow J. et al. June 28 - July 1, 1998, Montreal, Canada, AAAI Press, P. 95-104.
  19. Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Podkolodnaya O.A., Vorobyev D.V., Kolchanov N.A., Overton G.C. (1998) Mean-recognition: a systematic approach increasing the accuracy of the functional site recognition for the genomic DNA annotation. Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics, SCI’98, July 12-16, 1998, Orlando, Florida, Ed. N. Callaos, L. Holmes, Volume 4, P. 224-230.
  20. Ponomarenko M.P., Kolchanov N.A., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobyev D.V., Podkolodny N. L., Overton G.C. (1998) Revealing the conformational and physico-chemical DNA features applicable for predicting the activity of the functional DNA sites. Advances in Systems, Signals, Control and Computers, Ed.: Bajic V.B., September 22-24, Durban, South Africa, Published by IAAMSAD & the South Africa branch of the Academy of Nonlinear Sciences, Volume II, P. 326-330.
  21. Ponomarenko M.P., Savnikova L.K., Ponomarenko J.V., Kel A.E., Titov I.I., Kolchanov N.A. (1997) Modeling TATA-box sequences in eukaryotic genes. Mol Biol (Mosk). V. 31(4), P. 726-732. (Russ)
  22. Ponomarenko M.P., Ponomarenko J.V., Kel A.E., Kolchanov N.A., Karas H., Wingender E., Sklenar H. (1997) Computer analysis of conformational features of the eukaryotic TATA-box DNA promotors. Mol Biol (Mosk). V. 31(4), P. 733-740. (Russ)
  23. Ponomarenko M.P., Ponomarenko J.V., Kel A.E., Kolchanov N.A. (1997) Search for DNA conformational features for functional sites. Investigation of the TATA box. In: “Biocomputing: proceedings of the 1997 Pacific Symposium” (Altman, R., et al., eds.), Word Sci. Publ., Singapore, 1997, P. 340-351.

 

Other publications:

  1. Julia V. Ponomarenko, Galina V. Orlova, Mikhail P. Ponomarenko, Sergey V. Lavryushev, Svetlana V. Zybova, Anatoly S. Frolov (2000) SELEX_DB: an activated database on DNA/RNA sequences obtained in SELEX-experiments. Proceedings of The Second International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’2000, Novosibirsk, Russia, August 7-11, 2000, Ed. N.Kolchanov et al., ICG, Novosibirsk, V. 1, P. 37-40.
  2. Julia V. Ponomarenko, Dagmara P. Furman, Mikhail P. Ponomarenko, Galina V. Orlova, Anatoly S. Frolov, Nikolay L. Podkolodny, and Akinori Sarai (2000) ACTIVITY: a database on DNA regulatory sites activity, adapted for analyses of DNA-protein interactions. Proceedings of The Second International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’2000, Novosibirsk, Russia, August 7-11, 2000, Ed. N.Kolchanov et al., ICG, Novosibirsk, V. 1, P. 58-61.
  3. Julia V. Ponomarenko, Mikhail P. Ponomarenko (2000) Common B-DNA features of a definite transcription factor binding sites superclass. Proceedings of The Second International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’2000, Novosibirsk, Russia, August 7-11, 2000, Ed. N.Kolchanov et al., ICG, Novosibirsk, V. 1, P. 98-101.
  4. Julia V. Ponomarenko, Mikhail P. Ponomarenko, Ivan L. Zvolsky (2000) Conformation of TATA-promoters B-helix may govern diffusion of TBP along DNA towards -30 position of these promoters. Proceedings of The Second International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’2000, Novosibirsk, Russia, August 7-11, 2000, Ed. N.Kolchanov et al., ICG, Novosibirsk, V. 1, P. 102-105.
  5. Mikhail P. Ponomarenko, Julia V. Ponomarenko, Tatyana N. Goryachkovskaya, Galina V.Orlova, Akinory Sarai (2000) B-DNA features correlating with point mutations that influence DNA-protein binding free energy. Proceedings of The Second International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’2000, Novosibirsk, Russia, August 7-11, 2000, Ed. N.Kolchanov et al., ICG, Novosibirsk, V. 1, P. 111-114.
  6. Merkulova T.I., Vasiliev G.V., Ponomarenko M.P., Kobzev V.F., Podkolodnaya O.A., Ponomarenko J.V., and Kolchanov N.A. (2000) Analyses of the region of intron 6 of the human TDO2 gene in that point mutations associated with psychiatric disorders are located with the aid of computer and experimental approaches. Proceedings of The Second International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’2000, Novosibirsk, Russia, August 7-11, 2000, Ed. N.Kolchanov et al., ICG, Novosibirsk, V. 1, P. 134-137.
  7. Ponomarenko M.P., Merkulova T.I., Ponomarenko J.V., Orlova G.V. (2000) Method for prediction of ranscription factor binding to regulatory region, based on caused by point mutation alterations in the pattern of this region interaction with nuclear protein. Proceedings of The Second International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’2000, Novosibirsk, Russia, August 7-11, 2000, Ed. N.Kolchanov et al., ICG, Novosibirsk, V. 3, P. 65-68.
  8. Ponomarenko J.V., Orlova G.V. Ponomarenko M.P., Lavryushev S.V., Merkulova T.I., (2000) rSNP_Guide: a database documenting influence of substitutions in regulatory gene regions onto their interaction with nuclear proteins and predicting protein binding sites, damaged or appeared de novo due to these substitutions. Proceedings of The Second International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’2000, Novosibirsk, Russia, August 7-11, 2000, Ed. N.Kolchanov et al., ICG, Novosibirsk, V. 3, P. 69-72.
  9. Ponomarenko M.P., Kolchanov N.A., Kondrakhin Y.V., Frolov A.S., Kolpakov F.A., Kel A.E., 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., Grigorovich D.A., Ponomarenko J.V., Kochetov A.V., Kolesov G.B., Podkolodny N.L., Wingender E., Hainemeier T., Milanesi L., Solovyev V.V. (1998) GeneExpress: a computer system for investigating molecular mechanisms of gene expression. Abstracts of XVIII-th International Congress of Genetics, August 10-15, 1998, Beijing, China, P. 62
  10. Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Kolchanov N.A., Podkolodny N.L. (1998) A distributed and intelligent database for the activities of the functional sites in DNA and RNA. Abstracts of the 1998 Pacific Symposium on Biocomputing. Ed.: Altman R.S., Dunker A.K., Hunter L. and Klein T.E., World Scientific, 1998, P. 103-104
  11. Vorobiev D.G., Ponomarenko J.V., Podkolodnaya O.A. (1998) SAMPLES and ALIGNED: databases for functional site sequences. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 58-61.
  12. Ponomarenko J.V., Furman D.P., Mishchenko T.M., Katokhina L.V., Valuev V.P., Peregoedova E.L., Frolov A.S., Podkolodny N.L., Ponomarenko M.P. (1998) ACTIVITY: a database for activities of functional DNA and RNA sites. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 62-65.
  13. Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Vorobiev D.G., Levitsky V.G., Podkolodnaya O.A., Overton G.C., Kolchanov N.A. (1998) B-DNA-VIDEO: an active database for the significant B-DNA features of transcription factor binding sites. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 66-70.
  14. Kolchanov N.A., Ponomarenko M.P., Kondrakhin Y.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., Hainemeier T., Milanesi L., Solovyev V.V., Overton G.C. (1998) GeneExpress system: description, analysis, and recognition of regulatory sequences in eukaryotic genomes. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 71-76.
  15. Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Podkolodnaya O.A., Vorobiev D.G., Kolchanov N.A., Overton G.C. (1998) Recognition accuracy of DNA functional sites can be increased by averaging partial recognitions. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 158-162.
  16. Savinkova L.K., Sokolenko A.A., Rau V.A., Kobzev V.F., Ponomarenko M.P., Ponomarenko J.V., Kolchanov N.A. (1998) Quantitative computer-assisted analysis of the TATA-binding protein affinity for complementary duplexes of synthetic oligodeoxyribonucleotides. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 165-169.
  17. Ponomarenko M.P., Kolchanov N.A., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobiev D.G., Podkolodny N.L., Overton G.C. (1998) Revealing the conformational and physico-chemical DNA properties applicable for predicting the activity of DNA functional sites. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 186-190.
  18. Ponomarenko J.V. (1998) Classification of eukaryotic transcription factors based on significant B-DNA conformational and physico-chemical properties of their binding sites. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 191-194.
  19. Likhacheva E., Ponomarenko M.P., Bogachev S., Kokoza E., Fisher P., Ponomarenko J.V., Vorobiev D.G., Kolesov G.B., Kolchanov N.A. (1998) The structural analysis of the DNA fragments associated with the nuclear lamins in Drosophila melanogaster. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 247-248.
  20. Ponomarenko M.P., Ishchenko I.V., Frolov A.S., Ponomarenko J.V., Kolchanov N.A., Mikhailov Yu.I., Minina A.V., Ivashin S.A. (1998) Bioinformatics for humanitarians. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 417-418.
  21. Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Minina A.V., Ivashin S.A., Mikhailov Yu.I. (1998) Business game “Human Genome” for education in business, law and commerce. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 422-426.
  22. Ponomarenko M.P., Vorobiev D.G., Ponomarenko J.V., Kuzin F.E., Gruzdev A.D., Kolchanov N.A. (1998) Significant B-DNA conformational and physico-chemical properties of the DNA topoisomerase I sites. Proceedings of The First International Conference of Bioinformatics of Genome Regulation and Structure, BGRS’98, Novosibirsk – Altai Mountains, Russia, August 24-31, 1998, Ed. N.Kolchanov et al., ICG, Novosibirsk, P. 446-447.
  23. 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 J. V., Kochetov A. V., Kolesov G.B., Podkolodny N. L., Milanesi L., Wingender E., Heinemeyer T., Solovyev V.V. (1998) GeneExpress: a WWW-oriented integrator for the databases and computer systems for studying the eukaryotic gene expression. Abstracts of the International school “Theoretical biophysics”, Moskow, 15-20 June, 1998, P. 57.
  24. J.V. Ponomarenko, D.P. Furman, T.M. Mischenko, L.V. Katokhina, V.V. Valuev, E.L. Peregoedova, A.S. Frolov, N.L. Podkolodny, M.P. Ponomarenko, N.A. Kolchanov (1998) A Knowledge base for the functional DNA/RNA site ACTIVITY. Abstracts of the International school “Theoretical biophysics”, Moskow, 15-20 June, 1998, P. 80.
  25. M.P. Ponomarenko, J.V. Ponomarenko, O.A. Podkolodnaya,A.S. Frolov, D.V. Vorobyev, N.A. Kolchanov, G.C. Overton (1998) Mean-recognition can increase the genome annotation accuracy. Abstracts of the International school “Theoretical biophysics”, Moskow, 15-20 June, 1998, P. 81.
  26. M.P. Ponomarenko, I.I. Titov, J.V. Ponomarenko, N.A. Kolchanov, A.V. Mazin, Steven C. Kowalczykowski (1998) The contextual specificity of the ssDNA/RecA filament affinitycorrelates with genetic code characteristics. Abstracts of the International school “Theoretical biophysics”, Moskow, 15-20 June, 1998, P. 82.
  27. Ponomarenko M.P., Ponomarenko J.V., Kel A.E., Kolchanov N.A., Karas H., Wingender E., Sklenar H. (1997) Identification of the significant conformational features of functional sites in B-DNA. In: “Proceedings of the 1997 German conference on Bioinformatics “Computer science and biology” (Frishman D., Mewes H.W., eds), Munich Infirmation Center for Protein Science, P. 171.
  28. Ponomarenko M.P., Ponomarenko J.V., Kel A.E., Kolchanov N.A. (1997) The significant conformational B-DNA features of pro- and eukaryotic promoters are evolutionary optimized. In “Abstracts of The 2nd international conference “Modern concepts in evolution genetics”, (Markel A.L, et al., eds), Novosibirsk, V.2, P. 260-262.
  29. Ponomarenko M.P., Ponomarenko J.V., Savinkova L.K., Kel A.E., Kolchanov N.A. (1997) TBP/promoter-affinity increase with increasing evolutional level of eukaryotic taxa. In “Abstracts of The 2nd international conference “Modern concepts in evolution genetics”, (Markel A.L, et al., eds), Novosibirsk, V.2, P. 263-266.
  30. Ponomarenko M.P., Ponomarenko J.V., Kel A.E., Kolchanov N.A. (1996) Signals and anti-signals of the td intron homing site. In: “Abctracts of the Engineering Foundation Conference “Recombinant DNA biotechnology: focus on metabolic engineering” (Stephanopoulos G., ed.), Danvers, Massachusetts, USA, Poster #22.
  31. Ponomarenko M.P., Ponomarenko J.V., Kel A.E., Kolchanov N.A. (1996) Conformational features significant for the pro- and eukaryotic TATA boxes have been optimized via evolution. In: “Abstracts of the 11th Rinshoken International Conference “Frontiers of Structural Biology” (Ui M., et al., eds), The Tokyo Metropolitan Institute of Medical Science (Rinshoken), Tokyo, Japan, P. 87-88.

  

My hobbies:

I take interest in the known and new systems of physical jerks for people's health. I am a teacher of the woman health group in aerobics, shaping, stretching, and yoga gymnastics. I have a sport rank of a candidate in master of sports in free calisthenics. I am interested in philosophy and psychology. I enjoy cooking, playing with my children, listening to classic music, dancing, communing with nice people, reading classic literature, history and literary memoirs, especially those of women.