TRRD publications

ARTICLES

2002

N.A. Kolchanov, E.V. Ignatieva, E.A. Ananko, O.A. Podkolodnaya, I.L. Stepanenko, T.I. Merkulova, M.A. Pozdnyakov, N.L. Podkolodny, A.N. Naumochkin, and A.G. Romashchenko. (2002) Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic Acids Res., 30, 1, 312-317
[PDF]

2000

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 and G. C. Overton (2000) Transcription Regulatory Regions Database (TRRD): its status in 2000 Nucleic Acids Res., 28, 1, 298-301
[PMID: 10592253 ] [PDF]

1999

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. (1999) Transcription Regulatory Regions Database (TRRD):its status in 1999. Nucleic Acids Res.,  27, 1 :303-306.
[PMID: 9847210] [PDF]

Kolchanov N. A., M. P. Ponomarenko, A. S. Frolov, E. A. Ananko, F. A. Kolpakov, E. V. Ignatieva, O. A. Podkolodnaya, T. N. Goryachkovskaya, I. L. Stepanenko, T. I. Merkulova, V. V. Babenko, Yu. V. Ponomarenko, A. V. Kochetov, N. L. Podkolodny, D. V. Vorobiev, S. V. Lavryushev, D. A. Grigorovich, Yu. V. Kondrakhin, L. Milanesi, E. Wingender, V. Solovyev and G. C. Overton. (1999) Integrated databases and computer systems for studying eukaryotic gene expression. Bioinformatics.  V.15, Is. 7/8, P. 669-686
[PMID: 10487874]

1998

Kolchanov N.A., Ponomarenko M.P., Kel A. E., Kondrakhin Yu. V., Frolov A. S., Kolpakov F. A., Goryachkovsky T.N., 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

Heinemeyer 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. (1998) Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res. 26, 1, 362-367
[PMID: 9399875]

1997

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. (1997)  TRRD: a database of transcription regulatory regions in eukaryotic genes. Mol Biol (Mosk), 31, 4, 626-636
[PMID: 9340490]

Wingender E., Kel A.E., Kel O.V., Karas H., Heinemeyer T., Dietze P., Knuppel R., Romaschenko A.G., Kolchanov N.A. (1997) TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Res. 25, 1, 265-268
[PMID: 9016550]

Anan'ko E.A., Bazhan S.I., Belova O.E., Kel' A.E. (1997) Mechanisms of transcriptional regulation of interferon-induced genes: description in the IIG-TRRD information system Mol Biol (Mosk), 31, 4, 592-604
[PMID: 9340496]

Ignat'eva E.V., Merkulova T.I., Vishnevskii O.V., Kel' A.E. (1997) Transcriptional regulation of lipid metabolism genes: description in the TRDD database. Mol Biol (Mosk), 31, 4, 575-591
[PMID: 9340495]

Kel' O.V., Kel' A.E. (1997) Intergenic interrelations in regulating the cell cycle: key role of E2F family transcription factors Mol Biol (Mosk), 31, 4, 548-561
[PMID: 9340493]

Merkulova T.I., Merkulov V.M., Mitina R.L. (1997) Mechanisms of glucocorticoid regulation and regulatory regions of genes, controlled by glucocorticoids: description in the TRDD database. Mol Biol (Mosk),  31, 4, 605-615
[PMID: 9340497]

Podkolodnaia O.A., Stepanenko I.L. (1997) Mechanisms of transcriptional regulation of erythroid specific genes. Mol Biol (Mosk), 31, 4, 562-574
[PMID: 9340494]

1995

Kel O.V., Romashchenko A.G., Kel A.E., Naumochkin A.N., Kolchanov N.A. (1995) 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]. V. 5. Biotechnology Computing, IEE Computer Society Press: Los Alamos, California. P. 42 -51

PEPORTS

2000

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.A. (2000) Transcription Regulatory Regions Database (TRRD) Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure. (BGRS'2000), ICG, Novosibirsk, Russia, August 7-11, 1, 18-22

Ignatieva, E.V., Busygina, T.V., Ananko, Å.À. , Podkolodnaya, Î.À., Merkulova, T.I., Suslov,V.V., Pozdnyakov, Ì. (2000) 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), ICG, Novosibirsk, Russia, August 7-11, 1, 22-25.

Ignatieva, E.V., Likhoshvai, V.A., Ratushny, A.V., Kosarev,P.S. (2000) 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), ICG, Novosibirsk, Russia, August 7-11, 3, 54-57.

Kel-Margoulis,O.V. and Kel A.E. (2000) CYCLE-TRRD: a database on transcription regulation of cell cycle-dependent genes. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure. (BGRS'2000), ICG, Novosibirsk, Russia, August 7-11, 1, 28-30.

Podkolodnaya O.A., Stepanenko I.L., Ananko E.A., Vorobiev D.G. (2000) 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), ICG, Novosibirsk, Russia, August 7-11, 1, 34-36.

Stepanenko,I.L., Goryachkovsky,T.N., Ibragimova,S.S., Axenovich,A.V., Omelyanchuk,N.A., lavryushev,S.V., Podkolodny,N.L. (2000) Development of knowledge base on plant gene expression regulation. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure. (BGRS'2000), ICG, Novosibirsk, Russia, August 7-11, 1, 185-187.

Stepanenko,I.L., Levitsky,V.G., Schoeder,H.C. (2000) Heat Shock Knowledge Base. Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure. (BGRS'2000), ICG, Novosibirsk, Russia, August 7-11, 3, 59-61.

1999

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

Busyigina T.V, Ignatieva E.V., Kolchanov N.A., Osadchuk A.V. The transcription regulation of genes controlling steroidogenes: the description in the TRRD database. Genetic and developmental psychoneuroendocrinology. Abstracts of the International Symposium dedicated to Prof.Eugene V.Naumenko, Novosibirsk, 12-16 July 1999, Russia, p. 22

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.V., Ponomarenko Yu.V., Kochetov A.V., Podkolodny N.L., Vorobiev D.V., Lavryushev S.V., Grigorovich D.A., Kondrakhin Yu.V. The data base technology and the modern computer methods for studying the mechanisms of gene expression. Genetic and developmental psychoneuroendocrinology. Abstracts of the International Symposium dedicated to Prof.Eugene V.Naumenko, Novosibirsk, 12-16 July 1999, Russia, p. 46

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

1998

N.A. Kolchanov, E.V. Ignatieva, O.V. Kel-Margoulis, A.E. Kel, E.A. Ananko., O.A. Podkolodnaya, I.L. Stepanenko, T.I. Merkulova, T.N. Goryachkovskaya, F.A. Kolpakov, N.L. Podkolodny, S.V. Lavryushev, D.A. Grigorovich, A.S. Frolov, A.G. Romashchenko (1998) 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. Novosibirsk - Altai Mountains, Russia, August 24-31, 1998. P.25-28.
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T.I. Merkulova, V.M. Merkulov, K.Y. Kropatchev, V.I. Kaledin (1998) 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. Novosibirsk - Altai Mountains, Russia, August 24-31, 1998. P.33-36.
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E.A. Ananko, S.I. Bazhan, O.E. Belova (1998) Interferon-Inducible Genes - Transcription Regulatory Regions Database (IIG-TRRD). Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure. . BGRS’98. Novosibirsk - Altai Mountains, Russia, August 24-31, 1998. P.37-40.
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O.A. Podkolodnaya, I.L. Stepanenko (1998) 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. Novosibirsk - Altai Mountains, Russia, August 24-31, 1998. P.41-44.
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E.V. Ignatieva (1998) 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. 1998. BGRS’98. Novosibirsk - Altai Mountains, Russia, August 24-31, 1998. P.45-49.
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T.N. Goryachkovsky, E.A. Ananko, S.E. Peltek PLANT-TRRD Database. Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure. 1998. BGRS’98. Novosibirsk - Altai Mountains, Russia, August 24-31, 1998. P.50-53.
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