• Date of Birth: October 14, 1962;
• Marital status: Married.
• Home Address: 30 Kirov Street, Apt. 152, Berdsk, Novosibirsk region, 630190 Russia.
• Work Address: Institute of Cytology and Genetics, Novosibirsk, 630090 Russia
• Telephone: +7(3832) 333119
• FAX: +7(3832) 331278
• Emails: pon@bionet.nsc.ru

1999 Visiting Scientist, The Institute of Physical and Chemical Research (RIKEN), Tsukuba Life Science Center, BioInfo Bank, Japan

1998 Visiting Scientist, Center for Bioinformatics, University of Pennsylvania, Philadelphia, USA

1997 Visiting Scientist, University of California at Davis, Davis, California, USA

1996 Visiting Scientist, University of California at San Diego, San Diego, California, USA

1996 Visiting Scientist, San Diego Supercomputer Center, San Diego, California, USA

1995 Visiting Scientist, Gesellschaft für Biotechnologische Forschung mbH (GBF), Braunschweig, Germany

1993 - - present Senior Staff Scientist, Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, 630090 Russia

1992 - 1993 Research Scientist, Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, 630090 Russia

1991 - 1992 Visiting Scientist, Institute of Biomedical Advanced Technology of C.N.R., Milan, Italy; two visits.

1989 - 1992 Postgraduate Student, Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, 630090 Russia

1987 - 1989 Research Associate, Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, 630090 Russia

1985 - 1987 Program Analyst, Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, 630090 Russia

Structural organization and evolution of genetic macromolecules (DNA, RNA, and proteins). Development of theoretical methods based on Decision Making Theory, Zadeh’s fuzzy sets, and Pattern Recognition; analysis of biopolymer sequences and conformations; prediction of the activity of functional sites from sequences, simulation of sequences of functional sites with maximized activity; computer program code generation to predict activity and/or recognize location of functional site, “real-time search” through the complete PDB to find and 3D-align protein fragments being similar in conformation. The main author of several database and program resources for analysis of   protein, DNA, and RNA sequences; many-year experience (since 1982) in RSX11M, MS DOS, and Windows operational systems, Fortran and C programming languages.

Full secondary school, 1970 - 1980

Special Physico-Mathematical school, 1979 - 1980.

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

Special courses "Molecular and Theoretical biology", 1983-1985.

Post-graduate course in the Novosibirsk Institute of Cytology and Genetics, Department of Biology, 1989 - 1992.

Degree: Ph.D. in Biology, May 18, 1994 (Kn #006834 issued at Moscow, July 1, 1994)

Title: “Genetic text analysis using the computer technology SITEVIDEO”

Thesis advisor: Nikolay A. Kolchaniv, Prof., Dr.Sci.

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

Advisory

1990 Dmitry N. Benjukh " Theoretical study of proteins interacting DNA (RNA) by using the expert system technology ". Thesis for Ms.D. in Biology, Natural Science Department, Novosibirsk State University. Novosibirsk. Russia

1991 Yury L. Orlov " Searching for informative statistics of large-dimention data-sets ". Thesis for Ms.D. in Mathemetics, Mechanical-Mathematical Department, Novosibirsk State University. Novosibirsk. Russia

1992 Anna N. Kolchanova (Kosykh) " Theoretical aspects of interactions between proteins and nucleic acids: structural and functional features of protein motifs ". Thesis for Ms.D. in Biology, Natural Science Department, Novosibirsk State University. Novosibirsk. Russia

1999 Vadim P. Valuev " Computer analysis of protein structure-functional determinants ". Thesis for Ms.D. in Physics, Physical Department, Novosibirsk State University. Novosibirsk. Russia

Institute of Cytology and Genetics, Novosibirsk, Russia:

Institute of Cytology and Genetics, Novosibirsk, Russia:

rSNP_Guide - a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations (http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/)

SELEX_DB - Activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation (http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/)

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/mgs/systems/geneexpress/)

ACTIVITY - Distributed and Intelligent Database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another (http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/)

B-DNA-Video - Knowledge Base for the sequence-dependent conformational and physicochemical B-DNA features specific for the transcription factor binding sites. (http://wwwmgs.bionet.nsc.ru/mgs/systems/bdnavideo/)

SAMPLES - Database on DNA and RNA sequence sets of the only experimentaly detected natural sites binding proteins (http://wwwmgs.bionet.nsc.ru/mgs/dbases/nsamples/)

MATRIX - Activated database on oligonucleotide frequency matrixes devoted to recognition of the protein-binding sites on DNA (RNA) (http://wwwmgs.bionet.nsc.ru/mgs/dbases/matrix/)

LEADER - Knowledge Base addressed to predicting the High/Low-level dichotomy of gene expression via 5'UTR mRNA sequence analysis for this gene (http://wwwmgs.bionet.nsc.ru/mgs/systems/leaderrna/)

PredPackage - Predicting functional site activities and gene expression levels from sequences (http://wwwmgs.bionet.nsc.ru/mgs/programs/acts2/)

San Diego Supercomputer Center, California, USA:

LIKENESS - WWW-based real-time protein search and 3D-alignment though the complete PDB (http://cl.sdsc.edu/)

• co-Principal Investigator, The STA Fellow ID #499042: “ Computer analysis and prediction for the relative free energy change, ddG, induced by single nucleotide substitutions within DNA/protein complexes”, The Institute of Physical and Chemical Research (RIKEN), Tsukuba Life Science Center, BioInfo Bank, Japan, 1999
• Principal Investigator, The British Council travel grant: “ The participation for the Russian-British Digital Libraries Workshop, RBDLW'99 (June 16-17, 1999, Moscow, Russia)”, 1999
• Project Ivestigator, The Russian Fund for Basic Research grant: “ Digital Library on DNA, RNA and protein special structures and functions (as a part of the Digital Library of the Siberian Branch of Russian Academy of Sciences)”, #98-07-91078, 1999-2001
• Project Ivestigator, The INTAS grant: “ Development of early markers for detection environmental stress in aquatic organisms”, #INTAS 96-1787, 1998
• Principal Investigator, The Russian Fund for Basic Research travel grant: “ The participation for the 2nd World Multiconference on Systemics, Cybernetics and Informatics and the 4th International Conference on Information Sysytem Analysis and Synthesis (July 12-16, 1998, Orlando, Florida, USA)”, #98-07-93015, 1998
• Principal Investigator, The Russian Fund for Basic Research grant: “ The CORBA server for the automated generating the Java-applets for the molecular genetic investigations”, #98-07-90126, 1998-2000
• Principal Investigator, The SB RAS Competitive Support for Young Scientists, grant: “Theoretical and experimental investigation of the basic genetic processes”, 1998-1999
• Co-Principal Investigator, The SB RAS Integrative grant: “Development of program and information resources for the supercomputer-depended multisubjective inversigations”, IGSBRAS-97#13, 1997-1999
• Co-Principal Investigator, U.S. Civilian R&D Foundation for the Independent States of the Former Soviet Union: Collaborations in Biomedical and Behavior Sciences Proposal Development Program Travel grant " The role of DNA sequence-specificity in homologous recombination promoted by the RecA protein”, CRDF PDP #24, 1996
• Belyaev’s Prize Laureate in Genetics, SB RAS, Novosibirsk, 1995
• Principal Investigator, The Russian Fund for Basic Research grant: “Theoretical and computer analysis of the contextual features responsible for the activity values of functional sites in DNA and RNA”, #95-04-12469, 1995-1997
• Project Investigator, The Russian National Project "Human Genome" grant: "Computer system for automated analysis of nucleotide sequences from human genome", #307, 1989-1994
• Principal Investigator, The Russian National Project "Human Genome" grant: "Integrated database of protein structural-functional determinants", #309, 1989-1992
• Project Investigator, The Russian National Project "Human Genome" grant: "Computer system for functional classification and analysis of putative proteins inferred from human genome nucleotide sequences", #308, 1989-1992
• Principal Investigator, The Russian National Project GeneInform grant: "Expert system predicting the structural and functional features in proteins from their sequences", 1987-1990
• Project Investigator, The Russian National Project GeneInform grant: "A databank for biopolymer 3D-structures on the IBM PC platform", 1986-1990.
• Member of Russian National Genetisists and Selectionists Society, 1986 - present.
• Laureate in Physics, Russian National Graduate Students Competition, 1985.

2000 - The 2^dn International Conference “ Bioinformatics for Genome Regulation and Structure (BGRS'98)”, Novosibirsk, Russia, report, Member of Local Organazing Committee

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, report

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

1998 - The RFBR Workshop “ Digital Libraries: advanced methods and technologies, digital collections”, Moscow, Russia, report

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

1998 - The 1^st International Conference “ Bioinformatics for Genome Regulation and Structure (BGRS'98)”, Novosibirsk, Russia, report, Vice-Head of Local Organazing Committee

1998 - The 6^th International Conference on Intelligent Systems for Molecular Biology (ISMB'98), Montreal, Canada, co-author of report

1998 - The 3^rd Siberian Congress on Applied and Industrial Mathemetics, INPRIM-98, report

1998 - The XVIII International Congress on Genetics, Beijing, Chine, report

1998 - The 2^nd World Multiconference on Systemics, Cybernetics and Informatics and 4^th International Conference on Information Systems Analysis ans Sinthesis (SCI'98), Orlando, USA, report

1998 - The Moscow International Workshop on Biophysics, Moscow, Russia, report, chairman of session

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

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

1997 - The 2^nd International Conference “Modern Concepts in Evolution Genetics”, Novosibirsk, Russia, 3 posters

1997 - A Newton Institute Workshop "Statistical analysis of DNA and Protein sequences; Cambridge, UK, co-author of report

1997 - the 10^th German Conference on Bioinformatics: Computer Science and Biology, Munich, Germany; abstract

1996 - the Engineering Foundation Conference “Recombinant DNA Biotechnology: Focus on Metabolic Engineering”, Danvers, Massachusetts, USA, 2 abstracts

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

1996 - the 9^th German Conference on Bioinformatics: Computer Science and Biology, Leipzig, Germany, co-author of report

1996 - the International Symposium on Theoretical and Computational Genome Research, Deutsches Krebsforschungszentrum, Heidelberg, Germany, co-author of report

1996 - the International Summer School on Crystallographic Computing, Western Washington University, USA, co-author of report

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

1996 - the International Workshop on Computational Analysis of Eukaryutic Transcriptional Regulatory Elements”, Deutsches Krebsforschungszentrum, Heidelberg, Germany, co-author of report

1996 - the 11^th Rinshoken International Conference “Frontiers of Structural Biology” Tokyo, Japan, abstract

1995 - Gene-Finding and Gene Structure Prediction, Workshop, Penn Tower Hotel, Philadelphia, USA, poster

1995 - The 3rd International Conference on Intelligent Systems for Molecular Biology, Robinson College, Cambridge, England, poster

1995 - the Internetional Dagstuhl Seminar “Modelling and simulation of gene and cell regulation, Schloss Dagctuhl, Saarbrucken, Germany, report

1995 - the French-Russian Symposium on Regulation of Gene Expression”, Russian Fund for Basic Research, Novosibirsk, Russia, co-author of report and 2 posters

1994 - the 6th European Congress on Biotechnology (ECB6), Florence, Italy, co-author of report

1993 - the International Congress on Computer Systems and Applied Mathematics (CSAM'93)", St.Petersburg, Russia, 2 abstracts

1992 - International conference "Bioinformatics, Supercomputing, and Complex Genome Analysis", St.Petersburg, Florida, USA, co-author of 3 reports.

1992 - The 2dn European HUGO Congress “Human Genome Diversity”, Porto Conte, Italy, co-author of poster

1991 -  International conference "The role of biocomputing in the characterization of human genome sequences", Bari, Italy, co-author of 2 posters

1991 - the All-Union Annual Conference “HUMAN GENOME’91”, Moscow, USSR, co-author of 2 posters

1991 - the Genome Informatics Workshop II, Tokyo, Japan, co-author of report

1990 - the International Symposium "Modelling and Computer Methods in Molecular Biology and Genetics", Novosibirsk, report.

1988 - the All-Union symposium “Problems of Macro- and Micro-Evolution”, Moscow, Russia, co-author of report

1988, 1986, 1984 - 3d, 2d, and 1st Symposiums on Theoretical Investigations and Data Banks on Molecular Biology and Genetics, Novosibirsk, Russia, reports.

1987 - the Conference of Russian National Genetisists and Selectionists Society, Moscow, Russia, co-author of report

1986, 1983 - 6th and 5th All-Union Symposia on Molecular Mechanisms of Genetic Processes, Moscow, Russia, report and poster.

Author of 150 scientific publications, including 1 monograph and the following main publications:

Monographs:

1. Ponomarenko M.P. and co-authors, (2000) Current Conceptions in Natural Sciences. Genetic Informations: Regulatory Signals. Siberian Trade University, Pub.Dep., Novosibirsk, Russia, 30 p.
2. Ponomarenko M.P. and co-authors, (1994) 9 paragraphs In Computer analysis of Genetic Macromolecules. Structure, Function and Evolution. (eds. Kolchanov N.A., Lim H.A.), World World Sci., Pub.Co., Singapore, Singapore, 556 p.

Articles:

1. Ponomarenko J.V., Furman D.P., Frolov A.S., Podkolodny N.L., Orlova G.V., Ponomarenko M.P., Kolchanov N.A., and Sarai A. (2001) ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another Nucleic Acids Res.,V.29. N.1. P. 284-287.
2. Ponomarenko J.V., Merkulova T.I., Vasiliev G.V., Levashova Z.B., Orlova G.V., Lavryushev S.V., Fokin O.N., Ponomarenko M.P., Frolov A.S., and Sarai A. (2001) rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations Nucleic Acids Res.,V.29. N.1. P. 312-316.
3. Kolpakov F.A., Podkolodny N.L., Lavryushev S.V., Grigorovich D.A., Ponomarenko M.P., and Kolchanov N.A. (2000) Methods for integrating the heterogeneous molecular genetics information resources used within the digital library GENEEXPRESS. Programming (Mosk), V.1. N.3. P. 72-80. (Russ)
4. 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), V.34. N.2. P. 1-9. (Russ)
5. Ponomarenko J.V., Orlova G.V., Ponomarenko M.P., Lavryushev S.V., Frolov A.S., Zybova S.V., and Kolchanov N.A. (2000) SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. Nucleic Acids Res., V. 28, N. 1, P. 205-208.
6. Vasiliev G.V., Merkulov V.M., Kobzev V.F., Merkulova T.I., Ponomarenko M.P., and Kolchanov N.A. (1999) Point mutations within 663-666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY-1 transcription factor binding site. FEBS Lett., V. 462, N. 1/2, P. 85-88.
7. 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, V. 44, N. 5, P. 837-841. (Russ)
8. Ponomarenko M.P., Shindyalov I.N., Bourne P.E., and Kolchanov N.A. (1999) LIKENESS: a real-time system for searching and alining protein spatial structures. Biofizika, V. 44, N. 5, P. 821-831. (Russ)
9. 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, V. 44, N. 4, P. 649-654. (Russ)
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, V. 44, N. 4, P. 655-663. (Russ)
11. Levitsky V.G., Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., and Kolchanov N.A., (1999) Nucleosomal DNA property database. Bioinformatics, V. 15, N. 7/8, P. 582-592.
12. Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobyev D.G., Kolchanov N.A., and Overton G.C. (1999) Oligonucleotide frequency matrices addressed to recognizing functional DNA sites. Bioinformatics, V. 15, N. 7/8, P. 631-643.
13. Ponomarenko J.V., Ponomarenko M.P., Frolov A.S., Vorobyev D.G., Overton G.C., and Kolchanov N.A., (1999) Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinformatics, V. 15, N. 7/8, P. 654-668.
14. 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. (1999) Integrated databases and computer systems for studying eukaryotic gene expression. Bioinformatics, V. 15, N. 7/8, P. 669-686.
15. Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodny N.L., Savinkova L.K., Kolchanov N.A., and Overton G.C. (1999) Identification of sequence-dependent features correlating to activity of DNA sites interacting with proteins. Bioinformatics, V. 15, N. 7/8, P. 687-703.
16. Kochetov A.V., Ponomarenko M.P., Frolov A.S., Kisselev L.L., and Kolchanov N.A. (1999) Prediction of eukaryotic mRNA traslational properties. Bioinformatics, V. 15, N. 7/8, P. 704-712.
17. Ponomarenko M.P., Ponomarenko J.V., Frolov A.S, Kochetov A.V., Kolpakov F.A., Kolchanov N.A., Podkolodny N.L. (1999) A Knowledge Library for Genome DNA Annotation. Digital Labrary (Mosk, ISSN 1234-5678), V.2. N.3 (Russ). (http://www.iis.ru/el-bib/1999/199903/ponom/ponom.ru.html)
18. Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodny N.L., Kolchanov N.A. (1998) Database on functional DNA and RNA site activity, ACTIVITY. Russiant Patent Agency (RossPatent) Certificate No. 980059, Sept. 2, 1998, Moscow. Russia (Russ)
19. Ponomarenko M.P., Ponomarenko J.V., Titov I.I., Kolchanov N.A., Mazin A.V., Kowalczykowski S.C. (1998) Preference of the RecA-filament to DNA sequences is correlating Genetic Code. Dokl Acad Nauk, V. 363, P. 122-125 (Russ)
20. Erokhin G.H., Zabadaev I.C., Kuznetsov V.L., Marchuk A.G., Ponomarenko M.P., (1998) Development of program and information resources for the supercomputer-depended multisubjective inversigations In: “ Integrating Programs in Basic Research ”, Published by SB RAS, Novosibirsk, Russia, P. 159-173. (Russ)
21. Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Lavryushev S.V., Kolchanov N.A. (1998) Computer presentation and authomated generation for the knowledge on the functional activity of the DNA and RNA molecules. In: “ Proceedings of the Institute of the Computational Mathematics and Mathematical Geophysics ”, V. 5, P. 181-198. (Russ)
22. 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) 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, V. 2, P. 326-330.
23. 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. 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.
24. 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. ISMB, V. 6, P. 95-104.
25. 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)
26. 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 P. 726-732. (Russ)
27. 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)
28. Kolpakov F.A., Kel A.E., Ponomarenko M.P., Kolchanov N.A. (1997) High heterogeneity of higher eukaryotic gene promoters, transcribed by RNA polymerase II. Dokl. Akad. Nauk, V. 357, P. 693-695 (Russ)
29. Ponomarenko M.P., Savnikova L.K., Kel A.E., Kolchanov N.A. (1997) Computer modeling of TATA-box sequences of eukaryotic promoters. Dokl. Akad. Nauk, V. 355, P. 557-561 (Russ)
30. Ponomarenko M.P., Kolchanova A.N., Kolchanov N.A. (1997) Generating programs for predicting the activity of functional sites. J. Comput. Biol., V. 4, P. 83-90.
31. Kel A.E., Kel O.V., Vishnevsky O.V., Ponomarenko M.P., Ischenko I.V., Karas H., Kolchanov N.A., Slkenar H., Wingender E. (1997) TRRD and COMPEL databases on transcription linked to TRANSFACAS as tools for analysis and recognition of regulatory sequences. In: “ Lecture Notes in Computer Science: Bioinformatics, the 1996 German conference on bioinformatics, selected papers” (Hofestadt R., Lengauer T., Loffler M., Schomburg D., eds), Springer-Verlag, Berlin, P. 99-105.
32. 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. Pacif Symp Biocomp, V.2, P. 340-351.
33. 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 11^th Rinshoken International Coonference “Frontiers of Structural Biology” (Ui M., et al., eds), The Tokyo Metropolitan Institute of Medical Science (Rinshoken), Tokyo, Japan, P. 87-88.
34. Bourne P.E., Shindyalov I.N., Ponomarenko M.P. (1996) Keeping track of protein similarity. Gather/Scatter, V. 12, P. 2-3.
35. Ponomarenko M.P., I.N.Shindyalov I.N., Bourne P.E. (1996) Fast Substructure Searching Using the Conformational Likeness Method. In: “ Proceedings of the International Summer School on Crystallographic Computing” (Bourne P.E., Watenpaugh K., eds), P. 41-46.
36. Ponomarenko M.P., Kel A.E., Kolchanova A.N., Kolchanov N.A. (1996) Contextual signals and antisignals of the td intron homing site. Dokl. Akad. Nauk, V. 348, P. 424-427. (Russ)
37. Ponomarenko M.P., Savinkova L.K., Kel A.E., Kel O.V., Kolchanova A.N., Kondrakhin Y,V., Kolpakov F., Romaschenko A.G., Kolchanov N.A. (1996) The structure of eukaryotic promoters and computer methods of its recognition. In: “ Modelling and simulation of gene and cell regulation.” (Collado-Vides J., Hofestadt R., Loffler M., Mavrovouniotis M., eds), IBFI GmbH, Schloss Dagctuhl, 1995, Dagstuhl Seminar Report, V. 130, P. 12.
38. Kel A.E., Kondrakhin Y., Kolpakov Ph., Ponomarenko M.P., Wingender E., Kolchanov N.A. (1995) Computer analysis of the structure of transcription factor binding sites. SAMS, V. 18/19, P. 819-822.
39. Ponomarenko M.P., Savinkova L.K., Kolchanova A.N., Kel A.E., Kolchanov N.A. (1995) Quantitative analysis of dissociation constatn of transcription factor TFIID complex with synthetic ssDNA 15-mers. In: “Proceedings of the Gene-Finding and Gene Structure Prediction Workshop”, Penn Tower Hotel, Philadelphia, USA, P. 133- 141.
40. Milanesi L., Ishenko I.V., Rogozin I.B., Kapitonov V., Kolchanov N.A., Kel A.E., Ponomarenko M.P. (1994) Computer system for genes structure prediciton. In: “Progress in Biotechnology: ECB6, Proceedings of the 6th European Congress on Biotechnology" (Alberghina L, Frontali L, Sensi P, eds), Elsevier Science Publishers, Amsterdam, P. 657-660
41. Ponomarenko M.P., Kel A.E., Benjukh D.N., Ischenko I.V., Bokhonov V.B., Likhachev E.A., Kolchanov N.A. (1993) System SiteVideo: Recognition of functional sites using recursive context systems. In: "Computer analysis of genetic macromolecules: Structure, Function and Evolution."; (Kolchanov N.A., Lim H., eds), World Sci.Pub.Co., Singapore, P. 35-65.
42. Kel A.E., Ponomarenko M.P., Kolchanov N.A., Milanesi L., Likhachev E.A. (1993) Investigation of human splice sites by the SiteVideo system. In: "Computer analysis of genetic macromolecules: Structure, Function and Evolution" (Kolchanov N.A., Lim H., eds), World Sci.Pub.Co., Singapore, P. 66-81.
43. Kel A.E., Kolchanov N.A., Ponomarenko M.P., Milanesi L., Lim H. (1993) Analysis of facultative contextual features of site function. In: "Computer analysis of genetic macromolecules: Structure, Function and Evolution." (Kolchanov N.A., Lim H., eds), World Sci.Pub.Co., Singapore, P. 82-94.
44. Rogozin I.B., Milanesi L., Ischenko I.V., Kel A.E., Kolchanov N.A., Ponomarenko M.P., Orlov Y.L. (1993) Computer system "GenView" for Reconition of exon-intron structure of genes in human genome. In: "Computer analysis of genetic macromolecules: Structure, Function and Evolution." (Kolchanov N.A., Lim H., eds), World Sci.Pub.Co., Singapore, P. 142-153.
45. Ponomarenko M.P., Shindyalov I.N., Kolchanov N.A. (1993) Analysis of proteins structure and evolution using the topological apporoach. In: "Computer analysis of genetic macromolecules: Structure, Function and Evolution." (Kolchanov N.A., Lim H., eds), World Sci.Pub.Co., Singapore, P. 384-417.
46. Ponomarenko M.P., Benjukh D.N., Orlov Y.L., Kolchanov N.A. (1993) Method for recognition of structural-functional determinants of protein molecules. In: "Computer analysis of genetic macromolecules: Structure, Function and Evolution." (Kolchanov N.A., Lim H., eds), World Sci.Pub.Co., Singapore, P. 439-450.
47. Benjukh D.N., Ponomarenko M.P., Kosykh A.N., Kolchanov N.A. (1993) Classification of protein interacting with DNA(RNA) based on structural-functional determinants. In: "Computer analysis of genetic macromolecules: Structure, Function and Evolution." (Kolchanov N.A., Lim H., eds), World Sci.Pub.Co., Singapore, P. 451-459.
48. Ponomarenko M.P., Benjukh D.N., Salamov A.A., Solovyev V.V., Gushchin D.N., Kolchanov N.A. (1993) Reconstruction of the structural-functional organization of the N-end domain of histone H4 according to its amino acid sequencies. In: "Computer analysis of genetic macromolecules: Structure, Function and Evolution." (Kolchanov N.A., Lim H., eds), World Sci.Pub.Co., Singapore, P. 460-468.
49. Benjukh D.N., Silbergleit A.S., Ponomarenko M.P., Chepurin I.V., Kolchanov N.A., Lanzov V.A. (1993) Stractural-functional relationship in bacterial RecA protein: computer analysis of the primary structure of RecA protein family. In: "Computer analysis of genetic macromolecules: Structure, Function and Evolution." (Kolchanov N.A., Lim H., eds), World Sci.Pub.Co., Singapore, P. 469-477.
50. Kel A.E., Ponomarenko M.P., Likhachev E.A., Orlov Y.L., Ischenko I.V., Milanesi L., Kolchanov N.A. (1993) SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. CABIOS, V. 9, P. 617-627.
51. Kel A.E., Kolchanov N.A., Romaschenko A.G., Ponomarenko M.P., Likhachev E.A., Milanesi L., Lim H.A. (1993) Patterns of oligonucleotides distribution within DNA and RNA functional sites. In: “ Proceedings of the II International Conference on Bioinformatic, Supercomputing and Complex Genome Analysis” (H.A.Lim, J.W.Fickett, C.R.Cantor and R.J.Robbins, eds), World Sci.Publ.Co Pte Ltd, Singapore, P. 445-464.
52. Kolchanov N.A., Kel A.E., Kapitonov V.V., Ponomarenko M.P., Likhachev E.A., Milanesi L., Lim H.A. (1993) Computer analysis and recognition of functional sites on the base of oligonucleotide patterns distributions. In: “Proceedings of the II International Conference on Bioinformatic, Supercomputing and Complex Genome Analysis” (H.A.Lim, J.W.Fickett, C.R.Cantor and R.J.Robbins, eds), World Sci.Publ.Co Pte Ltd, Singapore, P. 521-544
53. Milanesi L., Kolchanov N.A., Rogozin I.B., Ischenko I.V., Kel A.E., Orlov Yu.L., Ponomarenko M.P., Vezzoni P. (1993) GenViewer: a computing tool for protein-coding regions prediction in nucleotide sequences. In: "Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis" (H.A.Lim, J.W.Fickett, C.R.Cantor and R.J.Robbins, eds), World Sci.Publ.Co Pte Ltd, Singapore, P. 573-588.
54. Kel A.E., Kolchanov N.A., Solovyev V.V., Ponomarenko M.P., Ischenko I.V., Orlov Y.L., Kapitonov V.V. (1992) Computer investigation of structural organization and evolution of functional sites in polynucleotide sequencies. In: "Modeling and computer methods in molecular biology and genetics" (Ratner V.A., Kolchanov N.A., eds), Nova Sci.Publ., Inc., New York, P. 49-62.
55. Ponomarenko M.P., Benjukh D.N., Salamov A.A., Solovyev V.V., Shindyalov I.N., Streletz V.B., Orlov Y.L., Kolchanov N.A. (1992) Computer system of protein structure and function.predictions. In: "Modeling and computer methods in molecular biology and genetics" (Ratner V.A., Kolchanov N.A., eds), Nova Sci.Publ., Inc., New York, P. 251-264.
56. Kel A.E., Ponomarenko M.P., Likhachev E.A., Kolchanov N.A., Milanezi L. (1991) Investigation of the human splice sites by using the SITEVIDEO system. In: Proceedings of the “HUMAN GENOME’91” (Baev A.A, ed.), Moscow: IMB AS USSSR, P. 155-157. (Russ)
57. Ponomarenko M.P., Kel A.E., Benjukh D.N., Orlov Yu.L., Bokhonov V.B., Kolchanov N.A., Milanezi L. (1991) Computer system SITEVIDEO for investigation of functional sites in biopolimers. In: Proceedings of the “HUMAN GENOME’91” (Baev A.A, ed.), Moscow: IMB AS USSSR, P. 166-168. (Russ)
58. Kolchanov N.A., Rogozin I.B., Kel A.E., Ponomarenko M.P., Lihachov J.A., Milanesi L. (1991) Computer analysis and recognition of human splice sites. In: "Genome Informatics Workshop II" (ed. Kanehisa M.), Tokyo, Japan, P. 104-107.
59. Ponomarenko M.P., Shindyalov I.N., Kolchanov N.A. (1991) Relationships between primary and topological structures in proteins and their evolution conservatism. In Proceedings of the 7^th All-Union symposium “Molecular mechanisms of genetic pocesses” (ed., Tarasov V.A.), Moscow, Nauka, P. 96-101. (Russ)
60. Ponomarenko M.P., Shindyalov I.N., Salamov A.A., Kolchanov N.A. (1991) Database for 3D-structures of proteins on the IBM PC platform. Databases in USSR, V. 2, P. 180. (Russ)
61. Ponomarenko M.P., Beniukh D.N., Orlov Y.L., Kolchanov N.A. (1991) Precise recognition method of structure-function determinants of protein molecules. Biofizika, V. 36, P. 943-956. (Russ)
62. Beniukh D.N., Ponomarenko M.P., Kolchanov N.A. (1991) Classification of DNA- and (RNA)-interacting proteins based on recognition of structure- function determinants. Biofizika, V. 36, P. 957-967. (Russ)
63. Ponomarenko M.P., Shindyalov I.N. (1990) Databank of biopolimer 3D-structure for IBM PC platform. IC&G SB RAS, Novosibirsk, V. 1 (57 p) and V. 2 (57 p.), (Russ).
64. Ponomarenko M.P., Shindyalov I.N., Kolchanov N.A. (1989) Expert system for predicting of protein topologies on the base of their amino acids sequences. In: Computer analysis of structure, function and evolution of genetic macromolecule: artificial intelligence approaches. (ed., Kolchanov N.A.), IC&G SB RAS, Novosibirsk, P. 168-196, (Russ).
65. Ponomarenko M.P., Orlov Y.L. (1989) Expert system for fast estimation of characteristics utility and defining biopolimers classification. In: Computer analysis of structure, function and evolution of genetic macromolecule: artificial intelligence approaches. (ed., Kolchanov N.A.), IC&G SB RAS, Novosibirsk, P. 197-220, (Russ).
66. Kel A.E., Ponomarenko M.P., Ischenko I.V., Mischenko T.M. Orlov Y.L. Likhachev E.A., Kolchanov N.A. (1989) Computer system for investigating of functional sites in polynucleotide sequences. In: Computer analysis of structure, function and evolution of genetic macromolecule: artificial intelligence approaches. (ed., Kolchanov N.A.), IC&G SB RAS, Novosibirsk, P. 221-242, (Russ).
67. Beniukh D.N., Ponomarenko M.P., Orlov Y.L., Kolchanov N.A. (1989) Computer system for investigating of DNA(RNA)-binding proteins. In: Computer analysis of structure, function and evolution of genetic macromolecule: artificial intelligence approaches. (ed., Kolchanov N.A.), IC&G SB RAS, Novosibirsk, P. 243-263, (Russ).
68. Ponomarenko M.P., Shindyalov I.N., Kolchanov N.A. (1989) Expert system for predicting of protein topologies by their amino acid sequences. IC&G SB AS USSR, Novosibirsk, V. 1 (29 p.), V. 2 (68 p.) and V. 3 (58 p.), (Russ).
69. Ponomarenko M.P., Shindyalov I.N., Kolchanov N.A. (1987) Databank of biopolimer 3D-structure for IBM PC platform (advertisement). IC&G SB RAS, Novosibirsk, 4 p., (Russ).
70. Ponomarenko M.P., Shindyalov I.N., Kolchanov N.A. (1986) Predicting the interresidue distances by using topological approach. In: “ Mathematical models for data transforms and problems of data processing” (ed., Drobyshev Y.P.), Computational Center SB AS USSR, Novosibirsk, P. 34-47, (Russ).
71. Ponomarenko M.P., Shindyalov I.N., Kolchanov N.A. (1984) Automated identification of the secondary structures in globula proteins by using a quantitative quality estimates. In: "Systems and methods for data analysis " (ed., Drobyshev Y.P.), Computational Center SB AS USSR, Novosibirsk, P. 111-126, (Russ).