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Kochetov A.V., Sarai A., Vorob'ev D.G., Kolchanov N.A. The context organization of functional regions in yeast genes with high-level expression. Mol Biol (Mosk), 2002, 36(6):1026-34.

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), 2002, 2:70-73.

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), 2002, 1:10-13.

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), 2002, 2:163-165.

Ivanisenko V.A., Grigorovich D.A., Kolchanov N.A. PDBSITE: A database on protein active sites and their environmen. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:145-148.

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), 2002, 3:149-152.

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), 2002, 2:140-142.

Kolchanov N.A., 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 O.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), 2002, 3:232-234.

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), 2002, 2:195-198.

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), 2002, 2:199-202.

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), 2002, 3:55-57.

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), 2002, 2:160-162.

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), 2002, 2:157-159.

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), 2002, 2:109-113.

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), 2002, 3:235-239.

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), 2002, 3:52-54.

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), 2002, 3:46-48.

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), 2002, 3:40-42.

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), 2002, 3:251-254.

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), 2002, 3:138-140.

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), 2002, 3:108-111.

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), 2002, 3:112-114.

Vishnevsky O.V., Avdeeva I.V., Kolchanov N.A. Study of the specific contextual features of translation initiation and termination regions in eukaryotes. Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2002), 2002, 3:72-76.

Vityaev E.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), 2002, 3:197-199.

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), 2002, 3:257-259.

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), 2002, 3;204-207.

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), 2002, 3;220-221.

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), 2002, 1:182-184.

Vityaev E.E., Orlov Yu.L., Pozdnyakov M.A., Vishnevsky O.V., Kolchanov N.A., Kovalerchuk B.K. Knowledge discovery for promoter structure analysis. Proceedings of the International Conference on Imaging Science, Systems, and Technology, Eds.: Hamid R. Arabnia, Youngsong Mun, Las Vegas, Nevada, USA, June 24-27, 2002, CSREA Press, v.1:122-128.

Vityaev E.E., OrlovYu.L., Vishnevsky O.V., Kovalerchuk B.Ya., Belenok A.S., Podkolodnii N.L., Kolchanov N.A. Knowledge discovery for gene regulatory regions analysis. In: Knowledge-Based Intelligent Information Engineering Systems and Allied Technologies, KES, 2002. (Eds. E.Damiani, R. Howlett, L.Jain, N. Ichalkaranje) IOS Press, Amsterdam, 2002, part 1, 487-491.

Ratushny A.V., Likhoshvai V.A., Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Matushkin Y.G., Kolchanov N.A. Computer dynamic modeling of gene networks and the analysis of the action of mutations. 10th Intern. Conf. on Intelligent Systems for Molecular Biology, Conf. program, 2002, 107.

Kolchanov N.A Bioinformatics of genomic regulation and structure. Mol Biol (Mosk). 2001,35(6):931-3.

Kolchanov N.A., Podkolodnaia O.A., Anan'ko E.A., Ignat'eva E.V., Podkolodnyi N.L., Merkulov V.M., Stepanenko I.L., Pozdniakov M.A., Belova O.E., Grigorovich D.A., Naumochkin A.N. Regulation of eukaryotic gene transcription: description in the TRRD database. Mol Biol (Mosk), 2001, 35(6):934-42.

Kochetov A.V., Grigorovich D.A., Titov, II, Vorob'ev D.G., Syrnik O.A., Vishnevskii O.V., Sarai A., Kolchanov N.A. mRNA-FAST (mRNA-Function, Activity, STructure) computer system. Mol Biol (Mosk), 2001, 35(6):1039-47.

Pozdniakov M.A., Vitiaev E.E., Anan'ko E.A., Ignat'eva E.V., Podkolodnaia O.A., Podkolodnyi N.L., Lavriushev S.V., Kolchanov N.A. Comparative analysis of methods for recognizing potential transcription factor binding sites. Mol Biol (Mosk), 2001, 35(6):961-9.

Vitiaev E.E., Orlov Iu L., Vishnevskii O.V., Belenok A.S., Kolchanov N.A. Computer system "Gene Discovery" for searching for regularities in organization of eukaryotic regulatory sequences. Mol Biol (Mosk), 2001, 35(6):952-960.

Afonnikov D.A., Kolchanov N.A. The conserved characteristics of DNA-binding domains belonging to the homeodomain class that are associated with coadaptive substitutions of amino acid residues. Dokl Biochem Biophys, 2001, 380:352-355.

Kolchanov N.A., Hodgman C. The 2nd international conference on the Bioinformatics of Genome Regulation and Structure (BGRS-2000), Novosibirsk, August 2000. Bioinformatics, 2001, 17:997.

Levitsky V.G., Podkolodnaya O.A., Kolchanov N.A., Podkolodny N.L. Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis. Bioinformatics, 2001, 17(11):998-1010.

Afonnikov D.A., Oshchepkov D.Y., Kolchanov N.A. Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. Bioinformatics, 2001, 17(11):1035-46.

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):1062-4.

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.

Ponomarenko J.V., Furman D.P., Frolov A.S., Podkolodny N.L., Orlova G.V., Ponomarenko M.P., Kolchanov N.A., Sarai A. ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. Nucleic Acids Res, 2001, 29(1):284-7.

Ponomarenko J., Ponomarenko M., Orlova G., Kolchanov N., Sarai A. Conformational B-helix DNA properties specific to DNA free energy of protein binding to DNA with point mutation focused on SNP-analysis. Proceedings of the Pacific Symposium on Biocomputing (PSB '2001), January 3-7, 2001, Hawaii, USA, (Eds. Altman R.S., et al.), Singapore: World Scientific, p. 118.

Kochetov A., Grigorovich D., Sarai A., Kolchanov N. Database on mRNA-located eukaryotic expression signals influencing translation efficiency and specificity. Proc. Int. Conf. "RNA as therapeutic and genomics target'2001" Novosibirsk, Russia. 2001, 64.

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. (Eds. Korb K.B., Bensusan H.) Freiburg, Sept., 2001, 1-11.

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 Res, 2000, 28(1):311-5.

Kolchanov N.A., Podkolodnaya O.A., Ananko E.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., Korostishevskaya I.M., Romashchenko A.G., Overton G.C. Transcription regulatory regions database (TRRD): its status in 2000. Nucleic Acids Res, 2000, 28(1):298-301.

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 Res, 2000, 28(1):205-8.

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