Nikolay A. Kolchanov, Dr.Sci., Prof.

Curriculum Vitae and List of Publications

Work Experience and Current Position:

1974-1983 Research associate scientist, Theoretical Department,Institute of Cytology and Genetics, Novosibirsk, Russia

1992 - Present Deputy Director, Institute of Cytology and Genetics,Novosibirsk, Russia

1983-1989. Senior research scientist, Theoretical Department, Institute of Cytology and Genetics, Novosibirsk, Russia

1989 - Present. Head of the Laboratory of Theoretical Molecular Genetics,  Institute of Cytology and Genetics,Novosibirsk, Russia

 

Area of expertise:

Education Background:

Full secondary school, 1955 - 1965.

Novosibirsk State University, Faculty of Natural Sciences 1965-1972.

Novosibirsk State University, Faculty of Natural Sciences, Post-graduate course in the 1972 - 1974.

Degrees

1971: B.S. Mathematical Biology, Novosibirsk State University, Novosibirsk, Russia

1974: B.S.(Honors) Mathematical Biology, Novosibirsk State University, Novosibirsk, Russia

1975: Ph. D., Institute of Cytology and Genetics, Novosibirsk, Russia

1989: Dr.Sci., Institute of Cytology and Genetics, Novosibirsk, Russia

1992: Professor, Institute of Cytology and Genetics, Novosibirsk, Russia

2003 Corresponding member, Russian Academy of Sciences

Thesis

Degree: PhD. Genetics, 1975

Title: “Investigation of renin-angeotensin system based on mathematical and experimental models”.

Institution: Novosibirsk Institute of Cytology and Genetics

Thesis advisor: Vadim A.Ratner, Prof., Dr.Sci.

Degree: Dr.Sci. in Genetics, 1988

Title: “Theoretical investigation of structural-functional organization and evolution of genetic macromolecules”.

Institution: Novosibirsk Institute of Cytology and Genetics.

Scientific supervisor of studies resulted in creating WWW resourses

GeneExpress 2.1 http://wwwmgs.bionet.nsc.ru/mgs/gnw/

TRRD - database of transcription regulatory regions on eukaryotic genomes (TRRD); http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/

The GeneNet system is designed for formalized description and automated visualization of gene networks http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/

EnPDB database is made by reformatting PDB in a way allowing for extended search possibilities on PDB. http://wwwmgs.bionet.nsc.ru/mgs/gnw/enpdb/

GeneExpressSystem

DNA level

http://wwwmgs.bionet.nsc.ru/mgs/gnw/dna.shtml

RNA level

http://wwwmgs.bionet.nsc.ru/mgs/gnw/rna.shtml

Protein level

http://wwwmgs.bionet.nsc.ru/mgs/gnw/protein.shtml

Genenet works level

http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenetworks.shtml

Awards and Grants:

International Collaboration

  1. National Institutes of Health Grant “High Throughput Annotation of Genomic DNA Sequence” No.2 R01-HG-01539-04A2 (2000-2004)
  2. The Department of Energy Subgrant “Information Management Infrastructure for Systemic Annotation of Vertebrate Genomes” No. 535228 CFDA 81.049 (1999-2002)
  3. INTAS Project No. 21-2382 “Involvement of Epstein-Barr virus encoded proteins in signal transduction in virally transformed and in EBV-carrying malignant B cells“ (2002-2004).

4.        INTAS Monitoring Conference Grant, Conference Reference No. INTAS 01-MO-210 The Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002, Akademgorodok, Novosibirsk, Russia, 14-20, 2002.

5.        CONTRACT GRANT AGREEMENT ICA2-CT-2000-6003. PROJECT TITLE: "TWO-PHASES CONFERENCE ON BIODIVERSITY AND DYNAMICS OF ECOSYSTEMS IN NORTH EURASIA" To be held in Akademgorodok, Novosibirsk; the preliminary phase on August 21-26, 2000 and the final phase on July 9-14, 2001.

  1. INTAS-International Association for the promotion of co-operation with scientists from the New Independent States of the former Soviet Union grant: Development of early markers for detection of environmental stress in aquatic organisms. INTAS-96-1787. 1997-2000
  2. North Atlantic Treaty Organization grant: The link between data bases on regulatory genomic regions, 1996-1997
  3. Winner of travel award of U.S. Civilian R&D Foundation for the Independent States of the Former Soviet Union; 'Rllaborations in Biomedical and Behavior Sciences. Proposal development Program grant: Data base on transcriptional regulation of protooncogenes and related genes (1996)
  4. Office of Health and Environmental Research of the Department of Energy, U.S.A., grants: #OR00033-93CIS002 "Human genome computing" 1993-1994, Development of a Database on Transcription Regulatory Regions (1995-1996)
  5. Computer and theoretical analysis of hybridization of antisense oligonucleitides with tRNA INTAS-95-IN-RU-653
  6. German Ministry of Education, Science, Research and Technology grant: Establishment of Databases as tools for the analysis of regulatory genomic regions (1994-1997)
  7. Supplementary International Science Foundation Grant “Human genome computing" SBN000 (1994-1995)
  8. U.S. Man and Biosphere Program, Bureau of Oceans and International and Scientific Affairs, Department of State, U.S.A., (gr. N 1753-300217) Mutational Variability in Human Populations as an Indicator of Global Change 1993
  9. Knowledge Based Biological Modeling Information System 5-R01-RR04026-09
  10. Information management infrastructure for the Systematic Annotation of Vertebrate Genomes. Department of Energy USA DE-FG02-00ER62893

16.     CRDF PROJECT NUMBER RB0-1276 Developing Cancer Immunome Database (2001-2002)

Ministry of  Industry,  Science and Technology of Russian Federation

1.        Development of software for analysis of the structure–function properties of human genome (2002-2004)

2.        Development of new computer technologies and data bases for theoretical investigation of human, plant and animal genomes,

3.        Computer analysis of structural and functional organization of human and other eukaryotic genomes (1996-1998)

4.        Theoretical investigation of genome nucleotide sequences based on new informational and computer technologies (1993-1995)

5.        Mutational variability in blood genes induced by environmental antropogenic pollution, O?-156-95, (1995-1997)

6.        Russian State Committee of Science and Technical Policy. Program “Russian Universities” grant: Development of computer methods of prediction of possible changes in gene expressions in response to actions of environmental factors, O?-374-93 (1993-1997)

Russian Human Genome Program:

1.        Development of data bases on transcription regulatory regions in human genome and computer analysis of structural-functional organization of sequences controlling transcription,106-13/96, (1996-1998)

2.        Computer system for automatic analysis polynucleotide sequences in human genome 12312--5 (1993-1995)

3.        Computer system for automatical analysis of nucleotide sequences in human genome, 307, (1992),

4.        Computer system for functional classification and analysis of aminoacid sequences (308), Integrated data base on structural-functional characteristics of proteins (309) (1992),

5.        Development of set of programs for investigation of structural-functional organization and evolution of mobile genetic elements and repeated sequences in human and animal genomes (91) (1991-1992).

6.        Expert system for structural-functional classification, alignment of aminoacid sequences and data base on protein primary structures (1989),

Russian Foundation for Basic Research and others:

1.        Integrated Digital Library for 3D structures and function of DNA, RNA, Proteins and Gene nets, 01-07-90376 (1999-2002).

2.        Computer analysis of regulatory sequences controlling expressions of eukaryotic genes, 00-04-49229 (1999-2002)

3.        Software-informational support of studying complicated molecular-genetical systems (GeneNet system), 02-07-90359 (2002-2004).

4.        Research of structural-functional organization and evolution of gene networks: computer analysis and modeling, 03-04-48506 (2003-2005).

5.        System of computer-assisted support of experimental and theoretical research of transcription regulation mechanisms  03-07-90181-â (2003-2005).

6.        Investigation of transcription factor binding sites by experimental and theoretical approaches, 03-04-48469-à (2003-2005).

7.        The integrated database of arrangement and characteristic of nucleosome formation sites of genome DNA sequences, 03-04-48555-à (2003-2005).

8.        Interdisciplinary Integration Project on basic research No. 65 SB RAS "The simulation of basic genetic processes and systems” (2000-2002)

9.        Interdisciplinary Integration Project on basic research No. 66 SB RAS “Basic Problem in Biodiversity and Dynamics of Ecosystem” (2000-2002).

10.     Interdisciplinary Integration Project on basic research No. 119 SB RAS “Gene networks: theoretical analysis, computer simulation, and experimental construction” (2003-2005)

11.     Interdisciplinary Integration Project on basic research No. 145 SB RAS “Biodiversity and ecosystem dynamics: informational technologies and simulation” (2003-2005)

12.     Computer analysis and identification transcription regulatory regions in eukaryotic genes, 97-04-49740 (1997-1999)

13.     Knowledge based information system of biological modelling (1997)

14.     Russian State Committee of High Schools Development of theory of structural-functional organization of biopolymers,O-57-96, (1996-2000)

15.     Computer basis for mapping of functionally important regions in eukaryotic genomes 94-04-13241 (1994-1996).

16.     Russian Program “Frontiers in Genetics” Computer and theoretical analysis of principles of structural-functional organization and evolution of E.coli genome, 3.092-95, (1993-1995),

17.     Computer analysis of molecular-genetical mechanisms of mutagenesis and recombinations, 5-642, (1993-1995)

18.     Siberian Department of Russian Academy of Sciences grant: Theoretical investigation of genome nucleotide sequences based on new informational and computer technologies (1993-1995),

Ph.D. supervised:

Supervised about 20 PhD since 1985, including:

  1. Kondrakhin Y.V. <Computer analyzing and recognizing the transcription regulatory regions in eukaryotic genomes>, Institute Cytology and Genetics, Novosibirsk,1996.
  2. Ponomarenko M.P. <Investigating the genetic texts by using the computer technology SITEVIDEO>, Institute Cytology and Genetics, Novosibirsk, 1994.
  3. Streletz V.V. <Databanks and algorithms for aligning and classifying the nucleotide and aminoacid sequences>, Institute Cytology and Genetics, Novosibirsk, 1992.
  4. Kel' A.E. <Theoretical analyses of the structure, function and evolution of the short genomic repeats>, Institute Cytology and Genetics, Novosibirsk, 1991.
  5. Salamov A.A. "Computer system for investigation of globular protein secondary structure", Institute Cytology and Genetics, Novosibirsk, 1991.
  6. Rogozin I.B. " Theoretical analysis of the mechanisms of spontaneous and induced mutations" Institute Cytology and Genetics, Novosibirsk, 1990.

 

Memberships

Bibliography:

Author of more than 290 scientific publications, including 4 monographs, 3 educational books for university students and the following main publications:

Monographs:

  1. Computer Analysis of Genetic Macromolecules: Structure, Function and Evolution, July 1994, (N.A. Kolchanov and H.A. Lim, eds.), Singapore, New Jersey, London, Hong Kong, World Scientific Pub. co., Author (co-editor: with H.A. Lim) 556 pages
  2. Ratner V.A., Zharkikh A.A., Kolchanov N.A., Rodin S.N., Solovyov V.V., Antonov A.S. Molecular Evolution (Biomathematics: v. 24), 1996, pp 433 Springer-Verlag, Berlin Heidelberg New York
  3. "Modelling and computer methods in molecular biology and genetics". (Novosibirsk, August 28- September,1990). (eds V.A. Ratner and N.A. Kolchanov) Nova science Publishers, Inc., 1992.
  4. Ratner V.A.,Zharkikh A.A,Kolchanov N.A.,Rodin S.N.,Solovyev V.V. Shamin V.V. Problems of the theory of molecular evolution. ( R.I. Salganik ed.) "Science",Siberian Branch of the USSR Academy of Science, Novosibirsk, (Russ) 259 p.(1985).

Educational books for university students:

  1. Solovyev V.V., Kell A.E., Rogozin I.B., Kolchanov N.A. The application of computers in Molecular Biology. The theory of genetic texts. Novosibirsk State University (Russ),90,(1987).
  2. Kolchanov N.A.,Solovyev V.V.,Shindyalov I.N.,Strelets V.B. The application of computers in Molecular Biology. The structural organization of globular proteins. Novosibirsk State University (Russ),(1986),90 p.

7.        Kell A.E., Kolchanov N.A.,Solovyev V.V.The mathematical modeling in the molecular biology and genetics. The theory of the mutational process: deletions and duplications. Novosibirsk State University (1989),90 p.

8.    Articles (1997-2002):

  1. N.A. Kolchanov, M.A. Pozdnyakov, Y.L. Orlov, O.V. Vishnevsky, N.L. Podkolodny, E.E. Vityaev and B. Kovalerchuk. Computer System “Gene Discovery” for Promoter Structure Analysis. In: Artificial Intelligence and Heuristic Methods in Bioinformatics. Eds.: P. Frasconi and R. Shamir, IOS Press, 2003, P.173.

10.     Ananko E.A., Podkolodny N.L., Stepanenko I.L., Ignatieva E.V., Podkolodnaya O.A., Kolchanov N.A. GeneNet: a database on structure and functional organization of gene networks // Nucleic. Acid Research, 2002, 30 (1), pp. 398-401.

11.     Kolchanov N.A., Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Pozdnyakov M.A., Podkolodny N.L., Naumochkin A.N., Romashchenko A.G.  Transcription Regulatory Regions Database (TRRD): its status in 2002 // Nucleic. Acid Research, 2002, 30 (1), pp. 312-317.

12.     Kolchanov N.A., Nedosekina E.A., Ananko E.A., Likhoshvai V.A., Podkolodny N.L., Ratushny A.V., Stepanenko I.L., Podkolodnaya O.A., Ignatieva E.V., Matushkin Yu.G. GeneNet Database: Description and Modeling of Gene Networks // In Silico Biology, 2002, v.2, pp. 97-110.

13.     Kutsenko A.S., Gizatullin R.Z., Al-Amin A.N., Wang F., Kvasha S.M., Podowski R.M., Matushkin Yu.G., Gyanchandani A., Muravenko O.V., Levitsky V.G., Kolchanov N.A., Protopopov A.I.,  Kashuba V.I., Kisselev L.L., Wasserman W., Wahlestedt C., Zabarovsky E.R. NotI flanking sequences: a tool for gene discovery and verification of the human genome // Nucleic. Acid Research, 2002, 30 (14), pp. 3163-3170.

14.     Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Pozdnyakov M.A., Podkolodny N.L., Naumochkin A.N., Romashchenko A.G., Kolchanov N.A. TRANSCRIPTION REGULATORY REGIONS DATABASE (TRRD): ITS STATUS IN 2002 // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v. 1, pp. 10-13.

15.     Brunk B., Crabtree J., Diskin S., Mazzarelli J., Zigouras N., Alkalaeva E., Bogdanova V., Trifonoff V., Vorobjeva N., Katokhin A., Kolchanov N., Stoeckert C.MANUAL ANNOTATION OF THE HUMAN AND MOUSE GENE INDEX: WWW.ALLGENES.ORG // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v. 1, pp.182-184.

16.     Ananko E.A., Podkolodny N.L., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Kolchanov N.A. GENENET SYSTEM: ITS STATUS IN 2002 // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v. 2, pp.70-73.

17.     Kolchanov N.A., Podkolodny N.L., Likhoshvai V.A., Loktev K.A., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Nedosekina E.A., Matushkin Yu.G., Ratushny A.V., Tkachev Yu.A., Borisova I.A., Zagoruiko N.G., Dobrynin A.A., Makarov L.I., Fadeev S.I., Gainova I.A., Latypov A.F., Nikulichev Yu.V. COMPUTER SYSTEMIC BIOLOGY: INFORMATIONAL AND SOFTWARE TOOLSFOR COMPLEX MOLECULAR BIOLOGICAL SYSTEMS // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v. 2, pp. 140-142.

18.     Ratushny A.V., Likhoshvai V.A., Kolchanov N.A. ANALYSIS OF MUTATIONAL PORTRAITS OF GENE NETWORKS // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v. 2, pp. 157-159.

19.     Ratushny A.V., Likhoshvai V.A., Matushkin Yu.G., Kolchanov N.A. EVOLUTION OF DIPLOID GENE NETWORK OF CHOLESTEROL BIOSYNTHESIS REGULATION IN A CELL // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v. 2, pp. 160-162.

20.     Borisova I.A., Zagoruiko N.G., Likhoshvai V.A., Ratushny A.V., Kolchanov N.A. DIAGNOSTICS OF MUTATIONS BASED ON ANALYSIS OF GENE NETWORKS // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.2, pp.163-165.

21.     Latypov A.F., Nikulichev Yu.V., Likhoshvai V.A., Ratushny A.V., Matushkin Yu.G., Kolchanov N.A. PROBLEMS OF CONTROL OF GENE NETWORKS IN A SPACE OF STABLE STATES // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.2, pp.195-198.

22.     Latypov A.F., Nikulichev Yu.V., Likhoshvai V.A., Ratushny A.V., Matushkin Yu.G., Kolchanov N.A. A METHOD OF SOLVING PROBLEMS OF OPTIMAL CONTROL IN DINAMICS OF GENE NETWORKS // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.2, pp. 199-202.

23.     Kochetov A.V., Sarai A., Grigorovich D.A., Kolchanov N.A. DATABASE ON mRNA-LOCATED EUCARIOTIC TRANSLATIONAL SIGNALS // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 40-42.

24.     Titov I.I., Kochetov A.V., Kolchanov N.A., Sarai A. COMPUTER ANALYSIS OF mRNA UNTRANSLATED REGIONS OF HYPOXIA-INDUCED CORN GENES // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 46-48.

25.     Kochetov A.V., Kolchanov N.A., Sarai A. UNOPTIMAL TRANSLATION START SITE CORRELATES WITH INCREASED CONTENT OF IN-FRAME DOWNSTREAM AUG CODONS AT THE BEGINNING OF CDS OF EUKARYOTIC mRNAS // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp.52-54.

26.     Nikolaev S.V., Afonnikov D.A., Ivanisenko V.A., Bazhan S.I., Kolchanov N.A. COMPARISON OF METHODS FOR PREDICTING PROTEASOME CLEAVAGE MOTIFS // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 108-111.

27.     Nikolaev S.V., Ivanisenko V.A., Afonnikov D.A., Bazhan S.I., Kolchanov N.A. AN INDEX FOR ESTIMATING THE EFFICIENCY OF ANTIGENIC EPITOPE GENERATION DURING PROTEASOMAL PROTEOLYSIS // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp.112-114.

28.     Afonnikov D.A., Ivanisenko V.A., Grigorovich D.A., Valuev V.P., Nikolaev S.V., Kolchanov N.A. RESOURCES FOR THE ANALYSIS OF PROTEIN SEQUENCES AND STRUCTURES IN THE GENEEXPRESS SYSTEM // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp.138-140.

29.     Ivanisenko V.A., Grigorovich D.A., Kolchanov N.A. PDBSITE: A DATABASE ON PROTEIN ACTIVE SITES AND THEIR ENVIRONMENT // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp.145-148.

30.     Ivanisenko V.A., Debelov V.A., Pintus S.S., Matsokin A.M., Nikolaev S.V., Grigorovich D.A., Kolchanov N.A. PDBSITESCAN: A TOOL FOR SEARCH FOR THE BEST-MATCHING SUPERPOSITION IN THE DATABASE PDBSITE // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp.149-152.

31.     Likhoshvai V.A., Kochetov A.V., Matushkin Yu.G., Kolchanov N.A. STRUCTURAL FEATURES OF mRNA REGION AT THE TRANSLATION START SITE // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 55-57.

32.     Zagoruiko N.G., Pichueva A.G., Kutnenko O.A., Borisova I.A., Kochetov A.V., Ivanisenko V.A., Nikolaev S.V., Likhochvai V.A., Ratushny A.V., Kolchanov N.A. APPLICATION OF THE METHOD OF INTELLECTUAL DATA ANALYSIS TO SOLVING THE PROBLEMS OF BIOINFORMATICS // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 204-207.

33.     Kolchanov N.A., Valishev A.I., Popova N.A. ON SPECIALIZATION “BIOINFORMATICS” IN THE NOVOSIBIRSK STATE UNIVERSITY AND HIGH COLLEGE OF INFORMATICS OF NOVOSIBIRSK STATE UNIVERSITY // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp.220-221.

34.     Kolchanov N.À., Podkolodny N.L., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Lavryushev S.V., Grigorovich D.A., Kochetov A.V., Orlova G.V., Titov I.I., Vishnevsky Î.V.,Orlov Yu.L, Ivanisenko V.A., Vorobiev D.G.,  Oschepkov D.Yu., Omel'yanchuk N.A., Pozdnyakov M.A., Afonnikov D.A.,  Matushkin Yu.G., Likhoshvai V.A., Ratushny A.V., Katokhin A.V., Turnaev I.I., Proskura A.L., Suslov V.V., Nedosekina E.A. GENEEXPRESS – 2002: AN INTEGRATED SYSTEM ON GENE EXPRESSION REGULATION // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 232-234.

35.     Matushkin Yu.G., Levitsky V.G. , Likhoshvai V.A., Vishnevsky O.V., Kutsenko A.S., Protopopov A.I. , Zabarovsky E.R. Kolchanov N.A. ANALYSIS OF THE SECONDARY STRUCTURE AND NUCLEOSOMAL POTENTIAL OF NOT I SITES OF THE HUMAN GENOME // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 235-239.

36.     Vityaev E.E., Pozdnyakov M.A.,Orlov Yu.L., Vishnevsky O.V., Podkolodny N.L., Kolchanov N.A. GENE DISCOVERY COMPUTER SYSTEM FOR ANALYSIS OF REGULATORY REGIONS // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 257-259.

37.     Pozdnyakov M.A., Vityaev E.E., Ananko E.A., Busygina T.V., Ignatieva E.V., Proskura A.L., Podkolodnaya O.A., Podkolodny N.L., Merkulova T.I., Kolchanov N.A. DETECTION OF THE CORE STRUCTURE OF TRANSCRIPTION FACTOR BINDING SITES // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 251-254.

38.     Vityaev Å.E., Kostin V.S., Podkolodny N.L., Kolchanov N.A. NATURAL CLASSIFICATION OF NUCLEOTIDE SEQUENCES // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 197-199.

39.     Vishnevsky O.V., Avdeeva I.V., Kolchanov N.A. STUDY OF THE SPECIFIC CONTEXTUAL FEATURES OF TRANSLATION INITIATION AND TERMINATION REGIONS IN EUCARIOTES // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v.3, pp. 72-76.

40.     Stepanenko I.L., Podkolodnaya O.A., Kolchanov N.A. GENE NETWORKS: PRINCIPLES OF ORGANIZATION AND MECHANISMS OF OPERATION AND INTEGRATION // PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'2002), v. 2, pp.109-113.

41.     Valuev V.P., Afonnikov D.A., Ponomarenko M.P., Milanesi L., Kolchanov N.A.. ASPD (Artificial Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. // Nucleic. Acid Research., 2002, 30 (1), 200-202

42.     Ponomarenko J., Furman D., Frolov A., Podkolodny N., Orlova G., Ponomarenko M., Kolchanov N., Sarai A.. ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. // Nucl. Acids Research., 2001, 29, 284-287

43.     Levitsky V.G., Podkolodnaya O.A., Kolchanov N.A., Podkolodny N.L.. Nucleosome formation potential of eukaryotic DNA: tools for calculation and promoters analysis. // Bioinformatics, 2001, 17 (11), 988-1010

44.     Levitsky V.G., Podkolodnaya O.A., Kolchanov N.A., Podkolodny N.L.. Nucleosome formation potential of exons, introns, and Alu repeats. // Bioinformatics, 2001, 17 (11), 1062-1064

45.     Afonnikov D.A., Oschepkov D.Yu., Kolchanov N.A.. Detection of conserved physico-chemical characteristics of proteins by analysing clusters of positions with co-ordinated substitutions. // Bioinformatics, 2001, 17 (11), 1035-1046

46.     Valuev V.P., Afonnikov D.A., Ponomarenko M.P., Kolchanov N.A.. ASPD (Artificial Selected Proteins/Peptides Database) - a tool for proteomic studies. // European Journal of Biochemistry, 2001, 268 (Suppl. 1), 44

47.     Vityaev E.E., Orlov Yu.L., Vishnevsky O.V., Kovalerchuk B.K., Belenok A.S., Podkolodnii N.L., Kolchanov N.A.. Computer system "Gene Discovery" for functional annotation of DNA sequences. // in: ECML'2001 Workshop Machine Learning as Philosophy of Science Ed. K.B. Korb, H. Bensusan, Freiburg, Sept., 2001. p.1-11.  http://www.informatik.uni-freiburg.de/~ml/ecmlpkdd/WS-Proceedings/w02/index.html

48.     Orlov Yu.L., Filippov V.P., Potapov V.N., Kolchanov N.A.. Construction of stochastic context trees for genetical texts. // In: Proceedings of GCB '01, German Conference on Bioinformatics, October 7 - 10, 2001, Braunschweig, Germany, (ISBN 3-00-008114-3) p.212-214 (http://www.bioinfo.de/isb/gcb01/poster/index.html )

49.     Orlov Yu.L., Vityaev E.E., Vishnevsky O.V., Belenok A.S., Kovalerchuk B.K., Pozdnyakov M.A., Kolchanov N.A.. Program "Gene Discovery" for Pattern Matching in Promoter Sequences // In: Proceedings of the German Conference on Bioinformatics, GCB '01, October 7 - 10, 2001, Braunschweig, Germany, (ISBN 3-00-008114-3) p.215-216 (http://www.bioinfo.de/isb/gcb01/poster/index.html )

50.     Vishnevsky O.V., Katokhin A.V., Babenko V.N., Overton G.C., Kolchanov N.A.. Open reading frame reconstruction by using EST multiple alignment and dynamic programming. // Computational Technologies, 2000, v.5, Special Issue, 16-25

51.     Kolchanov N.A., Podkolodny N.L., Ananko E.A., Podkolodnaia O.A., Ignatieva E.V., Merkulova T.I., Goryachkovsky T.N., Stepanenko I.L., Kel-Margoulis O.V., Kel A.E., Naumochkin, I.M., Grigorovich D.A., Lokhova I.V., Romashchenko A.G.. Transcription regulatory regions database (TRRD): new possibilities. // Computational Technologies, 2000, v.5, Special Issue, 32-40

52.     Levitsky V.G., Katokhin A.V., Kolchanov N.A.. Inherent modular promoter structure and its application for recognition tools development. // Computational Technologies, 2000, v.5, Special Issue, 41-47

53.     Afonnikov D.A., Oshchepkov D.Yu., Kolchanov N.A.. A method of estimation of variances and covariances of protein physico-chemical characteristics in families of homologous sequences. // Computational Technologies, 2000, v.5, Special Issue, 79-86

54.     I.I. Titov, V.A. Ivanisenko, N.A. Kolchanov.. Fitness - a WWW-resource for RNA folding simulation based on genetic algorithm with local minimization. // Computational Technologies, 2000, v.5, Special Issue, 48-56

55.     Vasil'ev G.V., Merkulov V.M., Kobzev V.F., Merkulova T.I., Ponomarenko M.P., Podkolodnaia O.A., Ponomarenko Iu.V., Kolchanov N.A.. Point mutations in region 663-666 of intron 6 or the tryptophan oxygenase gene, connected with a series of mental disorders, disrupts the transcription factor YY1 binding site. // Mol. Biol. (Mosk), 2000, 34 (2), 214-222 [Article in Russian]

56.     Kel-Margoulis O.V., Romashchenko A.G., Kolchanov N.A., Wingender E., Kel A.E..COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. // Nucleic Acids Research., 2000, 28 (1), 311-315

57.     N.A. Kolchanov, O.A. Podkolodnaya, E.A. Ananko, E.V. Ignatieva, I.L. Stepanenko, O.V. Kel-Margoulis, A.E. Kel, T.I. Merkulova, T.N. Goryachkovskaya, T.V. Busygina, F.A. Kolpakov, N.L. Podkolodny, A.N. Naumochkin, I.M., Korostishevskaya, A.G. Romashchenko, G.C. Overton.. Transcription regulatory regions database (TRRD): its status in 2000. // Nucleic Acids Research., 2000, 28 (1), 298-301

58.     Ponomarenko J.V., Orlova G.V., Ponomarenko M.P., Lavryushev S.V., Frolov A.S., Zybova S.V., Kolchanov N.A.. SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. // Nucleic Acids Research., 2000, 28 (1), 205-208

59.     Ananko E.A., Podkolodnaya O.A., Ignatieva E.V., Kel-Margoulis O.V., Kel A.E., Merkulova T.I., Stepanenko I.L., Goryachkovskaya T. N., Podkolodny N.L., Grigorovich D.A., Naumochkin A.N., Korostishevskaya I.M., Lokhova I.V., Romashchenko A.G., Kolchanov N.À.. Transcription regulatory regions database (TRRD) // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 18-25

60.     Kel-Margoulis O.V., Romashchenko A.G., Deineko I.V., Kolchanov N.À.,Wingender E. Kel A.E.. Database on composite regulatory elements in eukaryotic genes (COMPEL). // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 45-49

61.     Kondrakhin Y.V., Milanesi L., Lavryushev S.V., Schug J., Kolchanov N.À.. Recognition groups: a new method for description and prediction of transcription factor binding sites. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 62-65

62.     Kochetov A.V., Vorobiev D.G., Sirinko.A., Kisselev L.L., Kolchanov N.À.. Contextual features of yeast mRNA 5'UTRs potentially important for their translational activity. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 67-70

63.     Kochetov A.V., Sirnik O.A., Komarova M.L., Trifonova E.A., Kolchanov N.À., Shumny V.K.. Translational Features of 5'UTR-located miniORFs. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 74-77

64.     Levitsky V.G., Kolchanov N.À.. Nucleosome organization of chromatin in eukaryotic genes and structure-functional genome regions. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 90-93

65.     Merkulova T.I., Vasiliev G.V., Ponomarenko M.P., Kobzev V.F., Podkolodnaya O.A., Ponomarenko Yu.V., Kolchanov N.A.. Analysis 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 ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 134-137

66.     Vityaev E.E., Podkolodny N.L., Vishnevsky O.V., Kosarev P.S., Ananko E.A., Ignatieva E.V., Podkolodnaya O.A., Kolchanov N.A.. Detecting patterns of structure-function organization of regulatory genomic sequences in a first order logic. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 150-152

67.     Levashova Z.B., Kaledin V.I., Ponomarenko M.P., Kobzev V.F., Vasiliev G.V., Ponomarenko J.V., Podkolodnaya O.A., Merkulova T.I., Kolchanov N.A.. Single nucleotide polymorphism in the region of 288-296 bp of intron 2 of the k-ras gene, related to lung tumor susceptibility, causes alteration in the set of proteins binding to this region. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 164-167

68.     Kolchanov N.A.. Regulatory genomic sequences: coding, organization, and function. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 168-172

69.     Ananko E.A., Kolpakov F.A., Kolchanov N.A.. GeneNet database: a technology for a formalized description of gene networks. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, 174-177

70.     Grigorovich D.A., Ivanisenko V.A., Kolchanov N.A.. Structure and format of the EnPDB database accumulating spatial structures of DNA, RNA and proteins. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, 119-121

71.     Vorobiev D.G., Titov I.I., Kochetov A.V., Kolchanov N.A.. Structural features of mRNA 5'UTRs of eukaryotic genes expressed at high and low levels. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, 135-137

72.     Titov I.I., Vorobiev D.G., Kolchanov N.A.. Mass analysis of RNA secondary structures using a genetic algorithm. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, 138-142

73.     Ivanisenko V.A., Grigorovich D.A., Kolchanov N.A.. PDBSite: a database on biologically active sites and their spatial surroundings in proteins with known tertiary structure. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, 171-174

74.     Valishev A.I., Kolchanov N.A., Podkolodny N.L., Melnikov V.N., Alsynbayeva L.G., Yaroslavtseva R.G., Haans W.J.A.. Bioinformatics: novel profile of vocational education. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, 232-234

75.     Titov I.I., Kolchanov N.A., Schroder H.C.. Model of phosphate high-affinity transport in bacteria. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.3, p. 62-64

76.     Ignatieva E.V., Podkolodny N.L., Kolchanov N.A.. Informational support of ontology for transcription regulation (ISOTR). // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.3, 99-102

77.     Ivanisenko V.A., Grigorovich D.A., Afonnikov D.A., Kuropatov D.A., Valuev V.P., Kolchanov N.A.. An informational system FrameProt on three-dimensional structures of DNA, RNA and proteins integrated with GeneExpress. // First Russian National Conference on DIGITAL LIBRARIES: ADVANCED METHODS AND TECHNOLOGIES, DIGITAL COLLECTIONS. October 19-21, 1999, Saint-Petersburg, Russia, p. 175-186

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

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

80.     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., Overton G.C.. Integrated databases and computer systems for studying eukaryotic gene expression. // Bioinformatics, 1999, 15 (7-8), 669-686

81.     Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodny N.L., Savinkova L.K., Kolchanov N.A., Overton G.C.. Identification of sequence-dependent features correlating to activity of DNA sites interacting with proteins. // Bioinformatics, 1999 15 (7-8), 687-703

82.     Levitsky V.G., Ponomarenko M.P., Ponomarenko Ju.V., Frolov A.S., Kolchanov N.A.. Nucleosomal DNA property database. // Bioinformatics, 1999, 15 (7), 582-592

83.     Kochetov A.V., Ponomarenko M.P., Frolov A.S., Kisselev L.L., Kolchanov N.A. Prediction of eukaryotic mRNA translational properties // Bioinformatics, 1999, 15 (8), 704-712

84.     Frolov A.S., Lavriushev S.V., Grigorovich D.A., Kel A.E., Ptitsyn A.A., Kolchanov N.A., Podkolodnyi N.L., Solov'ev V.V., Milanesi L., Bourne P., et al.. WWWMGS: an integrated server for molecular-genetic studies. // Biofizika 1999, 44 (5), 832-836 [Article in Russian]

85.     Vasiliev G.V., Merkulov V.M., Kobzev V.F., Merkulova T.I., Ponomarenko M.P., Kolchanov N.A.. 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 .,1999, 462 (1-2), 85-88

86.     Kolchanov N.A., Ananko E.A., Podkolodnaya O.A., Ignatieva E.V., Stepanenko I.L., Kel-Margoulis O.V., Kel A.E., Merkulova T.I., Goryachkovskaya T.N., Busygina T.V., Kolpakov F.A., Podkolodny N.L., Naumochkin A.N., Romashchenko A.G.. Transcription Regulatory Regions Database (TRRD):its status in 1999. // Nucleic. Acid Research, 1999, 303-306

87.     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., Lavryushev 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.. GeneExpress: a WWW-oriented integrator for databases and computer systems for studying the eukaryotic gene expression. // Biofizika, 1999, 44 (5), 837-841

88.     Ponomarenko M.P., Ponomarenko Iu.V., Podkolodnaia O.A., Frolov A.S., Vorob'ev D.V., Kolchanov N.A., Overton G.C.. Averaging results of site recognition can increase the accuracy of annotating the human genome. // Biofizika, 1999, 44 (4), 649-654 [Article in Russian]

89.     Ponomarenko M.P., Ponomarenko Iu.V., Kolchanov N.A.. Contribution of signals and antisignals in the mutational spectrum of the td-intron insertion site. // Biofizika, 1999, 44 (4), 655-663 [Article in Russian]

90.     Ponomarenko M.P., Shindialov I., Bourne P., Kolchanov N.A.. Likeness: a system for rapid retrieval of similar conformation of proteins and their spatial structures. // Biofizika, 1999, 44 (5), 821-831 [Article in Russian]

91.     Ignatieva E.V., Busyigina T.V., Podkolodnaya O.A., Ananko E.A., Merkulova T.I., Stepanenko I.L., Merkulov V.M., Mitina R., Kel-Margoulis O.V., Kolchanov N.A. Endocrine system transcription regulatory regions database (ES-TRRD). Genetic and developmental psychoneuroendocrinology. // Abstracts of the International Symposium dedicated to Prof.Eugene V.Naumenko, Novosibirsk, 12-16 July 1999, Russia, p. 39

92.     Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Merkulova T.I., Podkolodny N.L., Frolov A.S., Kolchanov N.A. The genes regulated by PPARs: the presentation in the TRRD database. // E2: Keystone Symposia on Molecular and Cellular Biology. The PPARs: Transcriptional Links to Obesity, Diabetes and Cardiovascular Disease. Organizers: Bruce M. Spiegelman and Ronald M. Evans, Keystone, Colorado, April 28 May 2, 1999, Abstract #126, p.34

93.     Ivanisenko V.A., Grigorovich D.A., Afonnikov D.A., Kuropatov D.A., Valuev V.P., Kolchanov N.A. Information system FrameProt on spatial structures of DNA, RNA and proteins as a part of GeneExpress system. Proceedings of the First Russian Conference "Digital Libraries: Advanced methods and Technologies, Digital Collections" 1999, Saint-Petersburg, Russia, p. 175-186 (in Russian)

94.     Ananko E.A., Kolpakov F.A., Podkolodnaya O.A., Ignatieva E.V., Goryachkovsky T.N., Stepanenko I.L., Busygina T.V., Kolesov G.B., Grigorovich D.A., Kolchanov N.A. Gene networks: formalized description and visualization in the GeneNet database. // Proc. of the international conference on Theory and Mathematics in Biology and Medicine. 1999. Amsterdam. The Netherlands, June 29 - July 3, 1999, p. 58-59

95.     Kolpakov F.A., Ananko E.A The GeneNet database: formalized description and visualization of gene networks dynamics based on experimental data. // Proc. of the international conference on Theory and Mathematics in Biology and Medicine. 1999. Amsterdam. The Netherlands, June 29 - July 3, 1999, p. 286

96.     Heinmeyer T., Wingender E., Reuter I., Hermjakob H., Kel A.E., Kel O.V., Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Kolpakov F.A., Podkolodny N.L., Kolchanov N.A.. Databases on transcription regulation: TRANSFAC, TRRD and COMPEL. //  Nucl. Acids Research., 1998, 26 (1), 362-367

97.     Ponomarenko M.P., Ponomarenko J.V., Titov I.I., Kolchanov N.A., Mazin A.V., Kowalczykowski S.C.. Preference of the RecA-filament to DNA sequences is correlating Genetic Code. //  Proc. Russian Acad. Scien., 1998, v.363, 22-125 [Article in Russian] 

98.     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.. GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences of the eukaryotic genome. // ISMB, 1998, v.6, 95-104

99.     Kolchanov N.A., Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodny N.L.. Functional sites in pro- and eukaryotic genomes: computer models for predicting activity. //  Mol. Biol. (Moscow), 1998 32(2),  255-267

100.  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, 440(3), 351-355

101.  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.. GeneExpress: a WWW-oriented integrator for the databases and computer systems for studying the eukaryotic gene expression. // Abstracts of the International school "Theoretical biophysics", Moscow, 15-20 June, 1998, p. 57

102.  M. Ponomarenko, N. Kolchanov, A. Kel, Y. Kondrakhin, A. Frolov, F. Kolpakov, O. Kel, E. Ananko, E. Ignatieva, O. Podkolodnaya, I. Stepanenko, T. Merkulova, V. Babenko, D. Vorobiev, S. Lavryushev, J. Ponomarenko, A. Kochetov, G. Kolesov N. Podkolodny (Russia), L. Milanesi (Italy), E. Wingender (Germany), T. Heinemeyer (Germany), and V. Solovyev (United Kingdom).. GeneExpress: a computer system for investigating molecular mechanisms of gene expression. // Abstracts XVIIIth International Congress of Genetics, August 10-15, 1998, Beijing, China, p. 62, 4S24

103.  N.A. Kolchanov, M.P. Ponamorenko, A.E. Kel, J.V. Ponomarenko, F. A. Kolpakov, A.S. Frolov, V.V. Soloviev, A.G. Romashchenko, E.A. Ananko, E.V. Ignatieva, O.A. Podkolodnaya, I.L. Stepanenko, O.V. Kel, T.I. Merkulova, T.N. Goryachkovskaya, A.V. Kochetov, N.L. Podkolodny, G.B. Kolesov, S.V. Lavryushev, L.L. Kisselev.. "GenExpress: an intellectual system for analysis of genomic regulatory sequences of humans and higher eukaryotes" // Abstract for HUGO'98

104.  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. // Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics, SCI’98, July 12-16, 1998, Orlando, Florida, Ed. N. Callaos, L. Holmes, v.4, p. 224-230.

105.  Ponomarenko M.P., Kolchanov N.A., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobyev D.V., Podkolodny N. L., Overton G.C.. 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., 1998 September 22-24, Durban, South Africa, Published by IAAMSAD & the South Africa branch of the Academy of Nonlinear Sciences, V. II, p. 326-330.

106.  Stoeckert S., Podkolodnaya O.A., Kel A.E., Brunk B., Haas J., Salas F., Stepanenko I.L., Ignatieva E.V., Kel-Margoulis O.V., Ananko E.A., Podkolodny N.L., Overton G.C., Kolchanov N.A.. EpoGERD: a database on regulation of eukaryotic gene expression. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 20-24

107.  Kolchanov N.A., Ignatieva E.V., Kel-Margoulis O.V., Kel A.E., Ananko E.A., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Goryachkovsky T.N., Kolpakov F.A., Podkolodny N.L., Lavryushev S.V., Grigorovich D.A., Frolov A.S., Romashchenko A.G.. Transcription Regulatory Regions Database (TRRD): new possibilities provided by release 4.0. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 25-28

108.  Kel-Margoulis O.V., Kel A.E., Frisch M., Romashchenko A.G., Kolchanov N.A., Wingender E.. COMPEL: a database on composite regulatory elements. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 54-57

109.  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. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 66-70

110.  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.. GeneExpress system: description, analysis, and recognition of regulatory sequences in eukaryotic genomes. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 71-76

111.  Ananko E.A., Kolpakov F.A., Kolesov G.B., Kolchanov N.A.. Gene Networks: a database and its automated visualization through the internet in the genenet computing system. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 82-85

112.  Kolchanov N.A., Matushkin Yu.G., Frolov A.S.. Regulation mechanisms in biological systems. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 111-114

113.  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. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 158-162

114.  Savinkova L.K., Sokolenko A.A., Rau V.A., Kobzev V.F., Ponomarenko M.P., Ponomarenko J.V., Kolchanov N.A.. Quantitative computer-assisted analysis of the TATA-binding protein affinity for complementary duplexes of synthetic oligodeoxyribonucleotides.// PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 165-169

115.  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. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 186-190

116.  Kochetov A.V., Ponomarenko M.P., Vorobiev D.G., Frolov A.S., Kisselev L.L.1, Kolchanov N.A.. Eukaryotic mRNAs encoding abundant and scarce proteins are dissimilar in many structural features of 5'-untranslated leaders. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, 214-217

117.  Likhacheva 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. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, 247-248

118.  Titov I.I., Ivanisenko V.A., Kolchanov N.A.. Predicting RNA folding by genetic algorithm with local exhaustion. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, 296

119.  Ponomarenko M.P., Kolchanov N.A., Shindyalov I., Bourne P.. Likeness: a system searching for and aligning similar protein conformations. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, 370-374

120.  Ponomarenko M.P., Ishchenko I.V., Frolov A.S., Ponomarenko J.V., Kolchanov N.A., Mikhailov Yu.I., Minina A.V., Ivashin S.A.. Bioinformatics for humanitarians. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, 417-418

121.  Kolesov G.B., Kolpakov F.A., Kolchanov N.A.. New method for the study of the modular structure of transcription regulatory regions. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, 430-433

122.  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. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, 446-447

123.  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, 14(6) 529-537

124.  Pozdniakov M.A., Rogozin I.B., Babenko V.N., Kolchanov N.A.. Neighboring base effect on emergence of spontaneous mutations in human pseudogenes. // Dokl Akad Nauk, 1997, 356(4), 566-568 [Article in Russian]

125.  Kel A.E., Kolchanov N.A., Kel O.V., Romaschenko A.G., Ananko E.A., Ignatieva E.V., Merkulova T.I., Podkolodnaya O.A., Stepanenko I.L., Kochetov A.V., Kolpakov F.A., Podkolodnyi N.L., Naumochkin A.N.. TRRD: Database on Transcription Regulatory Regions of Eukaryotic Genes. // Mol. Biol. (Moscow), 1997, v.31, 626-636

126.  Ponomarenko M.P., Savinkova L.K., Ponomarenko J.V., Kel A.E., Titov I.I., Kolchanov N.A.. Modeling TATA-box sequences in eukaryotic genes. // Mol Biol (Moscow), 1997, 31(4), 726-732

127.  Ponomarenko M.P., Ponomarenko J.V., Kel A.E., Kolchanov N.A., Karas H., Wingender E., Sklenar H.. Computer analysis of conformational features of the eukaryotic TATA-box DNA promoters. // Mol Biol (Moscow), 1997, 31 (4), 733-740

128.  Kolpakov F.A., Kel A.E., Ponomarenko M.P., Kolchanov N.A.. High heterogeneity of higher eukaryotic gene promoters, transcribed by RNA polymerase II. // Proc. Russian. Akad. Scien., 1997, v.357, 693-695 [Article in Russian] 

129.  Ponomarenko M.P., Savinkova L.K., Kel A.E., Kolchanov N.A.. Computer modeling of TATA-box sequences of eukaryotic promoters. // Proc. Russian Acad. Scien., 1997, v.355, 557-561 [Article in Russian]

130.  Ponomarenko M.P., Kolchanova A.N., Kolchanov N.A.. Generating programs for predicting the activity of functional sites. // J. Comput. Biol., 1997, v.4, 83-90

131.  Ponomarenko M.P., Ponomarenko J.V., Kel A.E., Kolchanov N.A.. Search for DNA conformational features for functional sites. Investigation of the TATA box.  // Pacif. Symp Biocomp, 1997, v.2, 340-351

132.  Kolchanov N.A.. Transcriptional regulation of eukaryotic genes: data bases and computer analysis. // Mol Biol (Mosk), 1997, 31(4), 581-583 [Article in Russian]

133.  Kel' O.V., Kel' A.E., Romashchenko A.G., Wingender E., Kolchanov N.A.. Composite regulatory elements: classification and description in the COMPEL database. // Mol Biol (Mosk), 1997, 31(4), 601-615 [Article in Russian]

134.  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 on transcription regulatory regions in eukaryotic genes. // Mol Biol (Mosk), 1997, 31(4), 626-636

135.  Karas H., Kel' E., Kel' O.V., Kolchanov N.A., Wingender E.. Integrating knowledge on transcriptional regulation of eukaryotic genes based on information from TRANSFAC, TRRD, and COMPEL databases. // Mol Biol (Mosk), 1997, 31(4), 637-646 [Article in Russian]

136.  Ponomarenko M.P., Kolchanova A.N., Kolchanov N.A.. Generating programs for predicting the activity of functional sites. // J Comput. Biol. 1997, 4(1), 83-90

137.  Wingender E., Kel A.E., Kel O.V., Karas H., Heinemeyer T., Dietze P., Knuppel R., Romaschenko A.G., Kolchanov N.A.. TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. // Nucleic Acids Research, 1997, v.25, 265-268

138.  Vishnevsky O.V., Kolchanov N.A., Babenko V.N., Kel A.E.. In silico selection of oligonucleotides for identification by hybridization of genomic DNA gene-bearing fragments. // 9th International Congress on Genes, Gene Families and Isozymes, San Antonio, Texas April 14-19, 1997

139.  F. Kolpakov, A. Kel, N. Kolchanov. Convergence in the evolution of promoters in higher eukaryotic genes transcribed by RNA-polymerase II. // 9th International Congress on Genes, Gene Families and Isozymes San Antonio, Texas April 14-19, 1997.

140.  Afonnikov D.A., Kondrakhin Yu.V., Titov I.I., Kolchanov N.A.. Detecting direct correlations between positions in multiple aligment of amino acid sequences. // In Mewes H.W. and Frishman D. (eds) Computer science and biology. Genome informatics: Function,structure,phylogeny, // Proc. of the German Conference on Bioinformatics, 1997. p.87-98

141.  Kolchanov N.A., Matushkin Yu.G.. A Biological Self-reproducing Systems: Principles of Organization and Evolution .// Russian Journal of Genetics, 1997, 33(8), 889-897 [Article in Russian]