Publications

[dna] [rna] [protein] [genenetworks]

DNA integration level

Orlov Yu.L., Potapov V.N.. Estimation of stochastic complexity of genetical texts. // Computational Technologies. 2000, Vol.5, Special Issue, pp. 5-15

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, Vol.5, Special Issue, pp. 16-25.

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, Vol.5, Special Issue, pp. 32-40

Levitsky V.G., Katokhin A.V., Kolchanov N.A. (2000) Inherent modular promoter structure and its application for recognition tools development. // Computational technologies (Novosibirsk), 5, spec.issue, 41-47.

Grigorovich D.A., Ivanisenko V.A.. The EnPDB database on DNA, RNA and protein 3-dimensional structures. // Computational Technologies. 2000, Vol.5, Special Issue, pp. 64-66

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 Mar-Apr;34(2):214-22 [Article in Russian] ML: 20242219
[MEDLINE]

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 Jan 1;28(1):311-5 ML 20063292
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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 Res. 2000, V. 28, P. 298-301 ML 20063287
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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 Jan 1;28(1):205-8 ML 20063260
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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.

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 Jul-Aug;15(7-8):631-43 ML 99419254
[MEDLINE]

Babenko V.N., Kosarev P.S., Vishnevsky O.V., Levitsky V.G., Basin V.V., Frolov A.S. Investigating extended regulatory regions of genomic DNA sequences. Bioinformatics 1999 Jul-Aug;15(7-8):644-53 ML 99419255
[MEDLINE]

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 Jul-Aug;15(7-8):654-68 ML 99419256
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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, No. 7/8, P. 669-686. ML 99419257
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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. ML 99419258
[MEDLINE]

Levitsky V.G., Ponomarenko M.P., Ponomarenko Ju.V., Frolov A.S., Kolchanov N.A. Nucleosomal DNA property database // Bioinformatics. 1999. Vol. 15, No.7. p. 582-592 ML 99419249
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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 Sep-Oct;44(5):832-6 [Article in Russian] ML 20089648
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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 Nov 26;462(1-2):85-8 ML 20047832
[MEDLINE]

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. //NAR,1999, Jan 1;27(1), pp.303-306. ML 99063721
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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. (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. ML 20089649
[MEDLINE]

Levitsky V.G., Ponomarenko M.P., Ponomarenko J.P., Frolov A.S., Kolchanov N.A. (1999) Nucleosomal DNA property database. Bioinformatics, 15 (7/8), 582-592. ML 99419249
[MEDLINE]

Babenko V.N., Kosarev P.S., Vishnevsky O.V., Levitsky V.G., Basin V.V., Frolov A.S. Investigating extended regulatory regions of genomic DNA sequences. Bioinformatics, 1999, 15, 644-653. ML 99419255
[MEDLINE]

Levitsky V.G. (1999) The fine structure of the bending stiffness energy profile of nucleosomal DNA.Dokl Akad Nauk 364, 255-259.

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 Jul-Aug;44(4):649-54 [Article in Russian] ML 20012058
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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 Jul-Aug;44(4):655-63 [Article in Russian] ML 20012059
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Babenko V.N., Kosarev P.S., Bazin V.V., Frolov A.S.. [Repeating sequences in promoter regions of eukaryotic genes]. Biofizika 1999 Jul-Aug;44(4):664-7 [Article in Russian] ML 20012060
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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

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

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. pp.175-186 (in Russian)

Babenko V.N., Kosarev P.S., Levitsky V.G., Vishnevsky O.V., Basin V.V. and Frolov A.S. (1999) REGSCAN: Computer system for investigation extended regulatory regions of genomic DNA sequences. // Abstracts of II Congress of Russian Biophysicists, Moscow, Russia, V.3, P. 932.

Kosarev P.S., Babenko V.N. (1999) Complexity of nucleotide sequences of transcription factors binding sites. // Abstracts of II Congress of Russian Biophysicists, Moscow, Russia, V.3, P.957.

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., and Kolchanov N.A. (1998). Databases on transcription regulation: TRANSFAC, TRRD and COMPEL. Nucl. Acids Res. V. 26, No. 1, P. 362-367. ML 98062468
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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. Proc. Russian Acad. Scien. , V. 363, P. 122-125 (Russ) ML 99108349
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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. ML 98456543
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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. (Moscow), V. 32(2), P. 255-267. ML 98271915
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Kolchanov N. A., Ponomarenko M. P., Kel A. E., Kondrakhin Yu. V., Frolov A. S., Kolpakov F. A., Kel O. V., Ananko E. A., Ignatieva E.V., Podkolodnaya O. A., Stepanenko I. L., Merkulova T. I., Babenko V. N., Vorobiev D.G, Lavryushev S.V., Ponomarenko J. V., Kochetov A. V., Kolesov G.B., Podkolodny N. L., Milanesi L., Wingender E., Heinemeyer T., Solovyev V.V. (1998) GeneExpress: a WWW-oriented integrator for the databases and computer systems for studying the eukaryotic gene expression. Abstracts of the International school "Theoretical biophysics", Moscow, 15-20 June, 1998, P. 57.

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

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
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Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Podkolodnaya O.A., Vorobyev D.V., Kolchanov N.A., Overton G.C. (1998) Mean-recognition: a systematic approach increasing the accuracy of the functional site recognition for the genomic DNA annotation. Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics, SCI’98, July 12-16, 1998, Orlando, Florida, Ed. N. Callaos, L. Holmes, Volume 4, P. 224-230.
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Ponomarenko M.P., Kolchanov N.A., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobyev D.V., Podkolodny N. L., Overton G.C. (1998) Revealing the conformational and physico-chemical DNA features applicable for predicting the activity of the functional DNA sites. Advances in Systems, Signals, Control and Computers, Ed.: Bajic V.B., September 22-24, Durban, South Africa, Published by IAAMSAD & the South Africa branch of the Academy of Nonlinear Sciences, Volume II, P. 326-330.
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Babenko V.N., Kosarev P.S., Basin V.G. (1998) Searching for the repeats in regulatory regions of eukaryotic genes. // Abstracts of Theoretical Biophysics International School, Moscow, P.28.

Kosarev P.S. (1998) Analysis of eukaryotic promoters structure: distribution of nucleotides and repeats along the promoter sequences. // Abstracts of III Siberian Congress on Applied and Industrial Mathematics (INPRIM-98), Novosibirsk, Russia, V. 4, P.118-119.

Kosarev P.S. (1998) Analysis of vertebrate promoters structure: distribution of nucleotides and different types of repeats. // Abstracts of XXXVI International Scientific Students Conference, Novosibirsk, Russia, P.12.

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 Oct;356(4):566-8 [Article in Russian] ML 98065351
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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, P. 626-636. ML 97453248
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Podkolodnaya O.A., Stepanenko I.L.. Mechanisms of transcription regulation of erythroid-specific genes. Mol. Biol. (Moscow), 1997, V. 31, P.671-683. ML 97453252
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Ponomarenko M.P., Savinkova L.K., Ponomarenko J.V., Kel A.E., Titov I.I., Kolchanov N.A. (1997) Modeling TATA-box sequences in eukaryotic genes. Mol Biol (Moscow). V. 31 P. 726-732. ML 97453256
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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 promoters. Mol Biol (Moscow). V. 31 (4), P. 733-740. ML 97453257
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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. Proc. Russian. Akad. Scien, V. 357, P. 693-695 (Russ) ML 98154024
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Ponomarenko M.P., Savinkova L.K., Kel A.E., Kolchanov N.A. (1997) Computer modeling of TATA-box sequences of eukaryotic promoters. Proc. Russian Acad. Scien., V. 355, P. 557-561 (Russ) ML 98010813
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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. ML 97262831
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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. ML 98051977
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Kolchanov N.A.. [Transcriptional regulation of eukaryotic genes: data bases and computer analysis]. Mol Biol (Mosk) 1997 Jul-Aug;31(4):581-3 [Article in Russian] ML 97453244
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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 Jul-Aug;31(4):601-15 [Article in Russian] ML 97453246
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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 Jul-Aug;31(4):626-36 ML 97453248
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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 Jul-Aug;31(4):637-46 [Article in Russian] ML 97453249
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Kolpakov F.A., Babenko V.N. [The MGL computer system - an instrument for generating, graphically representing, and analyzing regulatory genomic sequences]. Mol Biol (Mosk) 1997 Jul-Aug;31(4):647-55 [Article in Russian] ML 97453250
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Kel' O.V., Kel' A.E.. [Intergenic interrelations in regulating the cell cycle: key role of E2F family transcription factors]. Mol Biol (Mosk) 1997 Jul-Aug;31(4):656-70 [Article in Russian] ML 97453251
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Podkolodnaia O.A., Stepanenko I.L. [Mechanisms of transcriptional regulation of erythroid specific genes]. Mol Biol (Mosk) 1997 Jul-Aug;31(4):671-83 [Article in Russian] ML 97453252
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Ignat'eva E.V., Merkulova T.I., Vishnevskii O.V., Kel' A.E.. [Transcriptional regulation of lipid metabolism genes: description in the TRDD database]. Mol Biol (Mosk) 1997 Jul-Aug;31(4):684-700 [Article in Russian] ML 97453253
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Anan'ko E.A., Bazhan S.I., Belova O.E., Kel' A.E.. [Mechanisms of transcriptional regulation of interferon-induced genes: description in the IIG-TRRD information system]. Mol Biol (Mosk) 1997 Jul-Aug;31(4):701-13 [Article in Russian] ML 97453254
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Merkulova T.I., Merkulov V.M., Mitina R.L.. [Mechanisms of glucocorticoid regulation and regulatory regions of genes, controlled by glucocorticoids: description in the TRDD database]. Mol Biol (Mosk) 1997 Jul-Aug;31(4):714-25 [Article in Russian] ML 97453255
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Ponomarenko M.P., Kolchanova A.N., Kolchanov N.A.. Generating programs for predicting the activity of functional sites. J Comput Biol 1997 Spring;4(1):83-90 ML 97262831
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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 Res (1997) 25, 265-268 ML 97169407
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Ignatieva E.V., Vishnevsky O.V., Kel A.E. Oligonucleotide composition of promoters for the apolipoprotein multigene family. 9th International Congress on Genes, Gene Families and Isozymes San Antonio, Texas April 14-19, 1997.

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.

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.
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Ptitsyn A.A., Rogozin I.B., Grigorovich D.A., Strelets V.B., Kel' A.E., Milanezi L., Kolchanov N.A.. [Computer system "AutoGene" for automatic analysis of nucleotide sequences]. Mol Biol (Mosk) 1996 Mar-Apr;30(2):432-41 [Article in Russian] ML 96320008
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Ponomarenko M.P., Kel A.E., Kolchanova A.N., Kolchanov N.A. (1996) Contextual signals and antisignals of the td intron homing site. Proc. Russian. Acad. Sci., V. 348, P. 424-427. (Russ) ML 96437358
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Ratner V.A., Zharkikh A.A., Kolchanov N.A., Rodin S.N., Solovyov V.V., Antonov A.S. Molecular Evolution (Biomathematics: v. 24), 1996, Springer-Verlag, Berlin Heidelberg New York. 433 p. //monogr

Rogozin I.B., Milanesi L., Kolchanov N.A. Gene structure prediction using information on homologous protein sequence. Comput Appl Biosci (1996) 12, 161-170 ML 97026204
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Rogozin I.B., Sredneva N.E., Kolchanov N.A. Somatic hypermutagenesis in immunoglobulin genes. III. Somatic mutations in the chicken light chain locus. Biochim Biophys Acta (1996) 1306, 171-178 ML 96221288
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A.E.Kel, O.V.Kel, O.V.Vishnevsky, M.P.Ponomarenko I.V.Ischenko, H.Karas, N.A.Kolchanov, H. Sklenar, E.Wingender. TRRD and COMPEL databases on transcription linked to TRANSFAC as tools for analysis and recognition of regulatory sequences. Special issue for Lecture Notes of Computer Science, Leipzig, September/October 1996 Selected Papers (Ralf Hofestaedt, Thomas Lengauer, Markus Loeffler, Dietmar Schomburg eds.) Springer-Verlag Berlin Heidelberg New York. P..99-105.

Kolchanov N.A., Babenko V.N., Vishnevsky O.V., Kel A.E. Oligonucleotide vocabularies of isofunctional protein-encoding gene families. Proc. of. Russian Academy of Sciences. 1996, V.348, N5, P. 696-699.(Russ) ML 96437365
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Kondrakhin Yu.V., Kolpakov F.A., Kel A.E., Milanesi L., Kolchanov N.A. Computer analysis and recognition of the transcription regulatory elements in eukaryotic genomes. Published in: Computer Science and Biology. Proc. of German Conference on Bioinformatics, GSB'96 (Eds: Hofestadt et al), Liebigstr, Germany, 1996
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Rogozin I.B., Milanesi L., Kolchanov N.A.. Gene structure prediction using information on homologous protein sequence. Comput Appl Biosci 1996 Jun;12(3):161-70 ML 97026204
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Kel O.V., Romaschenko A.G., Kel A.E., Wingender E., Kolchanov N.A.. A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucleic Acids Res 1995 Oct 25;23(20):4097-103 ML 96071170
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Kondrakhin Y.V., Kel A.E., Kolchanov N.A., Romashchenko A.G., Milanesi L..Eukaryotic promoter recognition by binding sites for transcription factors. Comput Appl Biosci 1995 Oct;11(5):477-88 ML 96163627
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Alexander Kel, Yury Kondrakhin, Phyodor Kolpakov, Mikhail Ponomarenko, Edgar Wingender, Nikolay Kolchanov. Computer analysis of the structure of transcription factor binding sites. SAMS, 1995, v. 18-19, pp. 819-822
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Ptitsyn A.A., Grigorovich D.A.. Object-oriented data handler for sequence analysis software development. Comput Appl Biosci 1995 Dec;11(6):583-9 ML 96404295
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Kel A.E., Kondrakhin Y.V., Kolpakov F.A., Kel O.V., Romashenko A.G.,Wingender E, Milanesi L., Kolchanov N.A.. Computer tool FUNSITE for analysis of eukaryotic regulatory genomic sequences. // Proc. III Intern. Conference of intelligent systems for molecular biology, California, US, 1995, pp. 197-205.
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Kolchanov N.A., Vishnevsky O.V., Babenko V.N., Kel A.E., Shyndyalov I.N.. Identification of cDNA sequences by specific oligonucleotide sets. Computer tool and application, In: procceedings of the Third International Conference on Intellegent Systems for Molecular Biology, AAAI Press, Menlo Park, Kalifornia, 1995. 206-214. ML 96038921
[MEDLINE]

Kel O.V., Romashchenko A.G., Kel A.E., Naumochkin A.N., Kolchanov N.A.. Data representation in the TRRD - a database of transcription regulatory regions of the eukaryotic genomes. Proceedings of the 28th Annual Hawaii International Conference on System Sciences [HICSS]. 1995. V. 5. Biotechnology Computing, IEE Computer Society Press: Los Alamos, California. P. 42 -51.

Kapitonov V.V., Titov I.I.. [Order of intron positioning and distant correlations in nucleotide sequences]. Dokl Akad Nauk 1994 Aug;337(6):810-2 [Article in Russian] ML 95072525
[MEDLINE]

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., 556 p. //monogr

Kel A.E., Ponomarenko M.P., Likhachev E.A., Orlov Yu.L., Ischenko I.V., Milanesi L., Kolchanov N.A.. SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. Comput Appl Biosci 1993 Dec;9(6):617-27 ML 94191996
[MEDLINE]

Likhoshvai V.A. Rare codons : fortunity or regularity?// in "Modeling and computer methods in molecular biology and genetics" (ed. by V.A.Ratner and N.A.Kolchanov, Nova Science Publishers, Inc., USA), 1992.,P. 463-469.

Rogozin I.B., Kolchanov N.A.. Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis. Biochim Biophys Acta 1992 Nov 15;1171(1):11-8 ML 93041998
[MEDLINE]

Beniukh D.N., Ponomarenko M.P., Kolchanov N.A.. [Classification of DNA- (RNA)-interacting proteins based on recognition of structure-function determinants]. Biofizika 1991 Nov-Dec;36(6):957-67 [Article in Russian] ML 92232819
[MEDLINE]

Rogozin I.B., Solovyov V.V., Kolchanov N.A.. Somatic hypermutagenesis in immunoglobulin genes. I. Correlation between somatic mutations and repeats. Somatic mutation properties and clonal selection. Biochim Biophys Acta 1991 Jun 13;1089(2):175-82 ML 91274346
[MEDLINE]

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, p.18-25

Ignatieva E.V., Busygina T.V., Ananko E.A., Podkolodnaya O.A., Merkulova T.I., Suslov V.V., Pozdnyakov M.A. Databases on endocrine system gene expression regulation: informational content and computer analysis. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 22-23
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Podkolodnaya O.A., Levitsky V.G. Locus control regions: description in a database. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 31-33

Podkolodnaya O.A., Stepanenko I.L., Ananko E.A., Vorobiev D.G., Representation of information on erythroid gene expression regulation in the GENEEXPRESS system. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 34-36
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Ponomarenko J.V., Orlova G.V., Ponomarenko M.P., Lavryushev S.V., Zybova S.V., Frolov A.S. SELEX_DB: an activated database on DNA/RNA sequences obtained in SELEX-experiments. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 37-40

Busygina T.V., Ignatieva E.V., Osadchuk A.V. Steroidogenesis-controlling gene transcription regulation: representation in TRRD database. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 41-44

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, p. 45-49

Ignatieva E.V., Likhoshvai V.A., Ratushny A.V., Kosarev P.S.. Knowledge base on molecular-genetical foundations of lipid metabolism regulation: current state and perspective. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 54-57
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Ponomarenko J.V., Furman D.P., Ponomarenko M.P., Orlova G.V., Frolov À.S., Podkolodny N.L., Sarai A.. ACTIVITY: a database on DNA regulatory sites activity, adapted for analysis of DNA-protein interactions. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 58-61

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, p. 62-65

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, p. 74-77

Kosarev P.S.. TRRDEXTR: computer program for extraction of regulatory sequences described in TRRD. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 84-85

Levitsky V.G., Katokhin A.V. Characteristic modular promoter structure and its application to development of recognition program software. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 90-93

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, p. 90-93

Levitsky V.G., Podkolodnaya O.A.. Analysis of relationships between nucleosome positioning in promoter regions and gene expression pattern. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 94-97

Ponomarenko J.V., Ponomarenko M.P. Common b-DNA features of a definite transcription factor binding sites superclass. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 98-101

Ponomarenko J.V., Pomonarenko M.P., Zvolsky I.L.. Conformation of TATA-promoters Â-helix may govern diffusion of tbp along DNA towards -30 position of these promoters. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 102-105

Rogozin I.B., Kondrakhin Yu.V., Naykova T.M., Yudin N.S., Voevoda M.I., Romaschenko A.G.. The module organization of the A and B boxes in the tRNA intragenic promoter. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 106-110

Ponomarenko M.P., Ponomarenko J.V., Goryachkovskaya T.N., Orlova G.V., Sarai A.. B-DNA features correlating with point mutations that influence DNA/protein-binding free energy. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 111-114

Orlov Yu.L., Kosarev P.S., Orlova N.G., Potapov V.N.. Analysis of context dependencies within regulatory gene regions in eukaryotes. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 115-117

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, p. 134-137

Kondrakhin Yu.V., Rogozin I.B., Romaschenko A.G.. Construction of the module structure model of the regulatory site on the base of the multiple relationships between site positions. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 147-149

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, p. 150-152

Orlov Yu.L., Levitsky V.G.. Nucleosome code analysis by estimating Markov dependencies. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 153-156

Oshchepkov D.Yu., Kuzin F.E., Afonnikov D.A.. Correlation analysis of DNa conformational characteristics of human topoisomerase I cleavage sites. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 157-160

Oshchepkov D.Yu., Stepanenko I.L., Afonnikov D.A., Schroeder H.C.. Correlation analysis of HSF binding sites conformational properties. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 161-163

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, p. 164-167

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, p. 168-172

Stepanenko I.L., Goryachkovsky T.N., Ibragimova S.S., Axenovich A.V., Omelyanchuk N.A., Lavryushev S.V., Podkolodny N.L.. Development of knowledge base on plant gene expression regulation. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 185-186
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Vishnevsky O.V., Katokhin A.V. Babenko V.N.. Reconstruction of the open reading frames by using est multiple alignment and dynamic programming. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 62-64

Likhoshvai V.A., Matushkin Yu.G.. On relationships between gene expression efficiency and nucleotide content of the protein-coding sequences. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 65-66

Orlov Yu.L., Potapov V.N.. Determining Markov model of genetical texts by stochastic complexity estimation. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 69-71

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, p. 119-121

Titov I.I.. Model of PCR kinetics. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 122-124

Afonnikov D.A.. Novel functional features of DNA-binding domain of the "homeodomain" class revealed by analysis of correlations of amino acid substitutions in its positions. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 149-151

Kolesnikov N.N., Nesterova T.B., Slobodyanyuk S.Y., Shevchenko A.V., Pavlova M.V., Rogozin I.B., Elisaphenko E.A., Kel A.E., Levitsky V.G., Brockdorff N., Zakian S.M.. Comparative characterization of the 5'-regions of the vole, human and mouse xist gene: conserved and repetitive sequences. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.3, p. 58

Stepanenko I.L., Levitsky V.G., Schroeder H.C.. Heat shock knowledge base. PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.3, p. 59-61
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Ponomarenko M.P., Merkulova T.I., Pomonarenko Yu.V., Orlova G.V.. Method for prediction of transcription factor binding to regulatory region, based on caused by point mutation alterations in the pattern of this region interaction with nuclear proteins. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.3, p. 65-68

Ponomarenko J.V., Orlova G.V., Ponomarenko M.P., Lavryushev S.V., Merkulova T.I.. rSNP_GUIDE: a database documenting influence of substitutions in regulatory gene regions onto their interaction with nuclear proteins and predicting protein binding sites, damaged or appeared de novo due to these substitutions. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.3, p. 69-72

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, p. 99-102

Nedosekina E.A., Pozdnyakov M.A.. Method of functional sites classification based on oligonucleotide frequencies. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.3, p. 103-104

Katokhin A.V., Levitsky V.G.. Drosophila promoter database EnDPD: project and the first steps of its realization. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.3, p. 105-108

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, p.25-28
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Ananko E.A., Naumochkin A.N., Fokin O.N., Frolov A.S.. Programs for data input to the Transcription Regulatory Regions Database. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.29-32
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Merkulova T.I., Merklov V.M., Kropatchev K.Y., Kaledin V.I.. The Glucocorticoid-Controlled Gene Regulatory Regions Database (GR-TRRD): the using for the elucidation of the mechanisms of chemical hepatocarcinogens action. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.33-36
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Ananko E.A., Bazhan S.I., Belova O.E.. Interferon-inducible genes - transcription regulatory regions database (IIG-TRRD). // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.37-40
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Podkolodnaya O.A., Stepanenko I.L.. The ESRG-TRRD: database of genes with specific transcription regulation in erythroid cells. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.41-44
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Ignatieva E.V. The Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD): transcription regulation of lipid metabolism genes. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.45-49
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Goryachkovsky T.N., Ananko E.A., Peltek S.E.. PLANT-TRRD database. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.50-53
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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, p.54-57
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Vorobiev D.G., Ponomarenko J.V., Podkolodnaya O.A.. SAMPLES and ALIGNED: databases for functional site sequences. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.58-61
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Ponomarenko J.V., Furman D.P., Mishchenko T.M., Katokhina L.V., Valuev V.P., Peregoedova E.L., Frolov A.S., Podkolodny N.L.1, Ponomarenko M.P.. ACTIVITY: a database for activities of functional DNA/RNA sites. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.62-65
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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, p.66-70
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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, p.71-76
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Kondrakhin Y.V., Overton G.C.. Recognition of the subset of eukaryotic promoters. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.124
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Kosarev P., Babenko V.N., Ponomarenko M.P.. Promoters: AT/GC content and properties of TATA box. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.125-129
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Frolov A.S., Lavryushev S.V., Vorobiev D.G., Grigorovich D.A.. A system for activation of the TRRD database: further development of geneexpress. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.136-138
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Vishnevsky O.V., Podkolodnaya O.A., Babenko V.N.. Search for degenerate oligonucleotide motifs in transcription factor binding sites and eukaryotic promoters (the system ARGO). // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.144-146
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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, p.158-162
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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, p.165-169
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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, p.186-190
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Ponomarenko J.V.. Classification of eukaryotic transcription factors based on significant B-DNA conformational and physico-chemical properties of their binding sites. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.191-194
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Levitsky V.G.. Fine structure of the profile of bending stiffness energy of nucleosomal DNA. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.195-198
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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, p.247-248
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Seledtsov I.A., Kolpakov F.A.. Rapid estimates of statistical significance of the pairwise nucleotide sequence alignment. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.301-304
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Matushkin Yu.G., Morozova I.N., Morozov P.S.. Theoretical analysis of mutation pattern of the cytochrome p450 superfamily. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.345-348
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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, p.430-433
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Kolpakov F.A., Babenko V.N.. MGL: an object-oriented computer system for molecular genetic data management, analysis, and visualization. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.434-437
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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, p.446-447
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A. E. Kel, N. A. Kolchanov, O. V. Kel, Yu. Kondrakhin, F. A. Kolpakov, S. V. Lavryushov, M. P. Ponomarcnko, E. Wingender. Regulatory genomic sequences, databases and tools for analysis and recognition.
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N.A. Kolchanov, M.P. Ponomarenko, J.V. Ponomarenko, A.S. Frolov, N.L. Podkolodny. Linear-additive approximation for predicting activity of the functional DNA and RNA sites.
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RNA integration level

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, Vol.5, Special Issue, pp. 48-56
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Likhoshvai V.A., Matushkin Yu.G.. Computer model for analysis of evolutionary drift of synonymous codons along mRNA. // Computational Technologies. 2000, Vol.5, Special Issue, pp. 57-63

Grigorovich D.A., Ivanisenko V.A.. The EnPDB database on DNA, RNA and protein 3-dimensional structures. // Computational Technologies. 2000, Vol.5, Special Issue, pp. 64-66

Kochetov A.V., Ponomarenko M.P., Frolov A.S., Kisselev L.L., Kolchanov N.A. Prediction of eukaryotic mRNA translational properties // Bioinformatics. 1999. Vol. 15, No.8., p704-712 ML 99419259
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Vitreshchak A., Bansal A.K., Titov I.I., Gel'fand M.S.. [Computer analysis of regulatory signals in complete bacterial genomes. Translation initiation of ribosomal protein operons]. Biofizika 1999 Jul-Aug;44(4):601-10 [Article in Russian] ML 20012051
[MEDLINE]

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 Dec 4;440(3):351-5 ML 99087406
[HTML] [MEDLINE]

Kolchanov N.A., Titov I.I., Vlassova I.E., Vlassov V.V.. Chemical and computer probing of RNA structure. Prog Nucleic Acid Res Mol Biol 1996;53:131-96 ML 96221752
[MEDLINE]

Kondrakhin Yu.V., Shamin V.V., Kolchanov N.A.. Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3'-terminal processing sites. Comput Appl Biosci 1994 Dec;10(6):597-603 ML 95219567
[MEDLINE]

Kondrakhin Iu.V., Shamin V.V.. [Design of the generalized consensus matrix for recognizing sites of 3'-terminal processing of vertebrate pre-mRNA]. Mol Biol (Mosk) 1994 May-Jun;28(3):511-20 [Article in Russian] ML 94329079
[MEDLINE]

Kravtchenko V.V., Shamin V.V, Gileva I.P., Likhoshvai V.A., Dobrinin V.N., Filipov S.A., Korobko V.G. Effectiveness of distal gene translation in polycistrons depends on mutual disposition of regulatory signals on the matrix. Bioorganicheskaya Khimiya., 1988, 14, P. 1372-1386.(In Russian). ML 96221752
[MEDLINE]

Kravtchenko V.V., Shamin V.V, Gileva I.P., Likhoshvai V.A., Dobrinin V.N., Filipov S.A., Korobko V.G. Influence of alternative secondary structure on effectiveness of polycistron mRNA translation. Izvestiya Akademii nauk SSSR, seriya biologicheskaya, 1988, 301, P. 480-484. (In Russian).

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, p. 67-70

Yudin N.S., Naykova T.M., Kondrakhin Yu.V., Kobzev V.F., Romaschenko A.G.. THE BSP-repeats from canidae contain a bidirectional promoter for the RNA polymerase III potentially capable of encoding double-stranded RNA. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 222-225

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, p. 135-137
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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, p. 138-142
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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, p.20-24
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Ponomarenko J.V., Furman D.P., Mishchenko T.M., Katokhina L.V., Valuev V.P., Peregoedova E.L., Frolov A.S., Podkolodny N.L., Ponomarenko M.P.. ACTIVITY: a database for activities of functional DNA/RNA sites. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.62-65
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Kochetov A.V., Pilugin M.V., Kolpakov F.A., Babenko V.N., Kvashnina E.V., Shumny V.K.. Structural and compositional features of 5' untranslated regions of higher plant mRNAs. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.1, p.210-213
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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, p.214-217
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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, p.296
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Titov I.I.. Statistical model of double helix growth. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.297-300
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Likhoshvai V.A., Matushkin Yu.G.. Theoretical analysis of possible evolutionary trends in codon distribution along the mRNA. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.341-344
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Alexey V. Kochetov*, Max V. Pilugin, Fedor V. Kolpakov, Vladimir N. Babenko, Nikolay A. Kolchanov, Vladimir K. Shumny. Sequence analysis of 5'-untranslated regions of plant mRNAs.
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N.A. Kolchanov, M.P. Ponomarenko, J.V. Ponomarenko, A.S. Frolov, N.L. Podkolodny. Linear-additive approximation for predicting activity of the functional DNA and RNA sites.
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Protein integration level

Grigorovich D.A., Ivanisenko V.A.. The EnPDB database on DNA, RNA and protein 3-dimensional structures. // Computational Technologies. 2000, Vol.5, Special Issue, pp. 64-66

Valuev V.P., Kuropatov D.A.. Automatic generation of recognition programs for amino acid sequences. // Computational Technologies. 2000, Vol.5, Special Issue, pp. 67-74

Afonnikov D.A., Valuev V.P., Kashinskaya Ju.O., Orlov Yu.L.. The ASPD database on synthetic peptides. // Computational Technologies. 2000, Vol.5, Special Issue, pp. 75-78

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, Vol.5, Special Issue, pp. 79-86

Karpenko L.I., Ivanisenko V.A., Pika I.A., Chikaev N.A., Eroshkin A.M., Veremeiko T.A., Ilyichev A.A.. Insertion of foreign epitopes in HBcAg: how to make the chimeric particle assemble. Amino Acids 2000;18(4):329-37 ML 20404849
[MEDLINE]

Karpenko L.I., Ivanisenko V.A., Pika I.S., Chikaev N.A., Eroshkin A.M., Melamed N.V., Veremeiko T.A., Il'ichev A.A.. [Analysis of foreign epitopes inserted in HBcAG. Possible routes for solving the problem of chimeric core particle self assembly]. Mol Biol (Mosk) 2000 Mar-Apr;34(2):223-9 [Article in Russian] ML 20242220
[MEDLINE]

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 Sep-Oct;44(5):821-31 [Article in Russian] ML 20089647
[MEDLINE]

Kuz'micheva G.A., Kuvshinov V.N., Razumov I.A., Ivanisenko V.A., Eroshkin A.M., Mishin V.P., Ushakova T.A., Loktev V.B., Il'ichev A.A.. [Use of a phage peptide library in mapping the group-specific hemagglutinating domain of alpha-virus glycoprotein E2]. Mol Gen Mikrobiol Virusol 1997;(4):25-9 [Article in Russian] ML 98031029
[MEDLINE]

Ivanisenko V.A., Eroshkin A.M.. [Search for sites containing functionally important substitutions in series of related or mutant proteins]. Mol Biol (Mosk) 1997 Sep-Oct;31(5):880-7 [Article in Russian] ML 98012324
[MEDLINE]

Afonnikov D.A., Kondrakhin Yu.V., Titov I.I. "Revealing of Correlated Positions of the DNA-binding region of the CREB and Ap-1 transcription factor families". Mol. Biol. (Moscow), 1997, 31 (4), 741-748. ML 97453258
[MEDLINE]

Kuz'micheva G.A., Kuvshinov V.N., Razumov I.A., Ivanisenko V.A., Eroshkin A.M., Mishin V.P., Oreshkova S.F., Loktev V.B., Il'ichev A.A., Sandakhchiev L.S.. [Localization of a group-specific, hemagglutinating epitope of alphavirus glycoprotein E2 using a phage peptide library]. Dokl Akad Nauk 1997 Jan;352(1):113-6 [Article in Russian] ML 97234934
[MEDLINE]

A.S. Frolov, I.S. Pika, A.M.Eroshkin. ProMSED: protein multiple sequence editor for Windows 3.11/95 CABIOS vol. 13 no. 3 1997 pp. 243-248. ML 97326707
[MEDLINE]

Kuznetsov I., Morozov P.S., Matushkin Yu.G. Prion proteins: evolution and preservation of secondary structure. FEBS Letters, 1997, 412, P. 429-432.

Afonnikov D.A., Kondrakhin Yu.V., Titov I.I. and Kolchanov N.A. (1997) 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. pp. 87-98.
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Rogozin I.B., Milanesi L., Kolchanov N.A.. Gene structure prediction using information on homologous protein sequence. Comput Appl Biosci 1996 Jun;12(3):161-70 ML 97026204
[MEDLINE]

Bourne P.E., Shindyalov I.N., Ponomarenko M.P. (1996) Keeping track of protein similarity. Gather/Scatter, V. 12, P. 2-3.

A. Frolov, A.Eroshkin. Interactive Multiple Protein Sequences Alignment with ProMSED, an application for Windows 3.11/95. BIOINFORMATICS<-->STRUCTURE. Jerusalem, Israel, November 17-21, 1996.

Eroshkin A.M., Fomin V.I., Zhilkin P.A., Ivanisenko V.V., Kondrakhin Y.V.. PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and for studying the structure--activity relationships in protein families. Comput Appl Biosci 1995 Feb;11(1):39-44 ML 95316690
[MEDLINE]

Shindyalov I.N., Kolchanov N.A., Sander C.. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng 1994 Mar;7(3):349-58 ML 94233038
[MEDLINE]

Korepanova A.V., Eroshkin A.M., Ivanisenko V.A., Lebedev L.R., Mikriukov N.N., Pustoshilova N.M., Petrenko V.A., Il'ichev A.A.. [Preparation of a mutant human tumor necrosis factor with increased resistance to proteases]. Mol Biol (Mosk) 1994 Jan-Feb;28(1):143-9 [Article in Russian] ML 94195289
[MEDLINE]

Eroshkina A.M., Minenkova O.O., Fomin V.I., Ivanisenko V.A., Il'ichev A.A.. [Analysis of peptide fragment insertions in the basic proteins of the bacteriophage M13, f1, and fd envelopes. Interconnection of structural characteristics of the envelope protein and viability of mutant phages]. Mol Biol (Mosk) 1993 Nov-Dec;27(6):1345-55 [Article in Russian] ML 94111721
[MEDLINE]

Streletc V.B., Shindyalov I.N., Kolchanov N.A., Milanesi L.. Fast, statistically based alignment of amino acid sequences on the base of diagonal fragments of DOT-matrices. Comput Appl Biosci 1992 Dec;8(6):529-34 ML 93105257
[MEDLINE]

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)

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) ML 92232818
[MEDLINE]

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)

Afonnikov D.A.. CRASP: software package for analysis of physicochemical parameters of aligned sequences of protein families. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 145-148

Valuev V. P., Afonnikov D.A., Petrenko O., Beylina A.G., Lokhova I.V., Grigorovich D.A., Fokin O.N., Ivanisenko V.A.. The database ASPD on experiments with application of phage display technique. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 160-163

Valuev V.P.. 3-dimensional protein structural class recognition. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 164-166

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, p. 171-174

Afonnikov D.A. Stability of partial correlation coefficient estimates for residue characteristics at different positions of amino acid sequences. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 207-210

Orlov Yu. L., Ivanisenko V.A., 1potapov V.N.. Context dependencies in amino acid sequencies of protein domains. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 211-216

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, p.20-24
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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, p.165-169
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Kolpakov F.A., Frolov A.S., Ponomarenko M.P., Podkolodny N.L.. MGL-PROT: the anthology-based query language for the user search for the 3d structures and functions of proteins in the WWW-available databases. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.269-271
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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, p.370-374
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Afonnikov D., Titov I.I.. Functional relationship between amino acid residues at N- and C-termini of DNA-binding regions of transcription factors CREB and AP-1 revealed by analyzing the pair correlations of amino acid substitutions. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.377-379
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Afonnikov D., Wingender E.. Statistical relation between the positions of the alpha-helix in the zinc-finger DNA-binding domain: results from the phage display data analysis. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.380-383
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Valuev V.P., Kuropatov D.A., Ponomarenko M.P.. Automatic generation of recognition programs for amino acid sequences. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.396-400
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Gene Networks integration level

Likhoshvay V.A., Matushkin Yu.G., Vatolin Yu.N., Bazhan S.I.. A generalized chemical-kinetic method for simulating complex biological systems. A computer model of l phage ontogenesis. // Computational Technologies. 2000, Vol.5, Special Issue, pp. 87-99

Kolpakov F.A., Ananko E.A. (1999) Interactive data input into the GeneNet database. Bioinformatics, V. 15 No. 7/8. P. 713-714 ML 99419260
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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.

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.

Kolpakov F.A., Ananko E.A., Kolesov G.B., and Kolchanov N.A. (1998) GeneNet: a database for gene networks and its automated visualization. // Bioinformatics, 1998, V. 14. N. 6. P. 529-537. ML 98362206
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Kolchanov N.A., Matushkin Yu.G. A Biological Self-reproducing Systems: Principles of Organization and Evolution. Russian Journal of Genetics, 1997, Vol.33, No.8, P.889-897

Bazhan S.I., Likhoshvay V.A., Belova,O.E. Theoretical analysis of the regulation of interferon expression during priming and blocking //Journal of Theoretical Biology, 1995, V.175, P.149-160.

Belova O.E., Likhoshvai V.A., Bazhan S.I., Kulichkov V.A. Computer system for investigation and integrated description of molecular-genetic system regulation of interferon induction and action //CABIOS, 1995, V.11, No.2, P.213-218.

Likhoshvai V.A., Bazhan S.I., Belova O.E. Mathematical modeling of molecular genetic system regulation of interferon induction and antiviral action // in "Modeling and computer methods in molecular biology and genetics" (ed. by V.A.Ratner and N.A.Kolchanov, Nova Science Publishers, Inc., USA), 1992.,P.293-299.

Kolchanov N.A., Shindyalov I.N.. A theoretical investigation of evolutionary in regulatory contoures in different types of selection. // in "Problems of genetics and theory of evolution." (ed. by Shumny V.K. and Ruvinsky A.O. Novosibirsk, "Nauka" Siberian division) 1991., P. 268-280. (In Russian).

Kravtchenko V.V., Shamin V.V, Gileva I.P., Likhoshvai V.A., Dobrinin, V.N., Filipov S.A., Korobko V.G. Model operon for study on coupled translation in E. coli cells. The role of stream of ribosomes. Bioorganicheskaya Khimiya., 1990, 16, P. 1161-1169. (In Russian).

Ignatieva E.V., Busygina T.V., Ananko E.A., Podkolodnaya O.A., Merkulova T.I., Suslov V.V., Pozdnyakov M.A.. Databases on endocrine system gene expression regulation: informational content and computer analysis. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 22-23

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, p. 174-177
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Logvinenko N.S., Ignatieva E.V., Ivanova L.N.. GeneNet-based model of two-stage aldosterone effect on principal cells of cortical collecting ducts. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 181-184

Goryachkovsky T.N., Ananko E.A., Kolpakov F.A.. Gene network on plant interaction with pathogen organisms. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 188-191

Likhoshvai V.A., Matushkin Yu.G.. Latent phenotype as an adaptation reserve: a simplest model of cell evolution. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 195-198

Ratushny A.V., Ignatieva E.V., Matushkin Yu.G., Likhoshvai V.A.. Mathematical model of cholesterol biosynthesis regulation in the cell. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 199-202
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Ratushny A.V., Podkolodnaya O.A., Ananko E.A., Likhoshvai V.A.. Mathematical model of erythroid cell differentiation regulation. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 203-206
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Stepananko I.L., Smirnova O.G., Konstantinov Yu.M.. Gene network of redox regulation and the problem of integrating local gene networks. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 207-209

Axenovich A.V., Goryachkovsky T.N., Ananko E.A., Omelyanchuk N.A., Stepanenko I.L.. Gene network on storage mobilization in seed. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 235-237

Goryachkovsky T.N., Ananko E.A., Kolpakov F.A., Stepanenko I.L.. Seed maturation in higher plants: gene networks on ontogenesis in storage tissues. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 238-242

Berezin A.Yu., Gainovai.A., Matushkin Yu.G., Likhoshvai V.A., Fadeev S.I.. Numerical study of mathematical models described dynamics of gene nets functioning: software package step. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.1, p. 243-245

Ponomarenko M.P., Ponomarenko J.V., Lavryushev S.V., Vorobiev D.G., Minina A.V., Ivashin S.A., Mikhailov Yu.I.. Education on the basis of the GENEEXPRESS system: business game "Regulatory Signals". // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 224-228

Valuev V.P., Afonnikov D.A.. Course "Introduction To Bioinformatics". // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.2, p. 229-231

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, p. 232-234

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

Suslov V.V., Ignatieva E.V., Osadchuk À.. Molecular-genetical mechanisms of thyroid system regulation: description in TRRD and GeneNet databases. // PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS-2000), v.3, p. 80-84

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, p.82-85
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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, p.111-114
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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, p.417-418
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Ponomarenko M.P., Ishchenko I.V., Frolov A.S., Minina A.V., Koneva E.I., Mikhailov Yu.I., Ivashin S.A.. Business game "Equilibrium" for education in economics, commerce, and law. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.419-420
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Afonnikov D., Kolesov G.B., Minina A.V., Mikhailov Yu.I., Ivashin S.A.. The practical study of the behavior of the complex dynamic systems on the basis of the "Life" game for education in economics, commerce, and law. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.421
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Ponomarenko M.P., Frolov A.S., Ponomarenko J.V., Minina A.V., Ivashin S.A., Mikhailov Yu.I.. Business game "Human Genome" for education in business, law and commerce. // PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE (BGRS'98), v.2, p.422-426
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