Publications 1988-1999

Chen, X., Dress, A., Karas, H., Reuter, I. and Wingender, E.:
A database framework for mapping expression patterns Computer Science and Biology.
Proceedings of the German Conference on Bioinformatics (GCB 1999). R. Giegerich, R. Hofestädt, T. Lengauer, W. Mewes, D. Schomburg, M. Vingron and E. Wingender GBF-Braunschweig and University of Bielefeld, pp. 174-178 (1999).

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, Y. V., Kochetov, A. V., Podkolodny, N. L., Vorobiev, D. V., Lavryushev, S. V., Grigorovich, D. A., Kondrakhin, Y. V., Milanesi, L., Wingender, E., Solovyev, V. and Overton, G. C.:
Integrated databases and computer systems for studying eukaryotic gene expression

Bioinformatics 15, 669-686 (1999). Medline

Kel, A., Kel-Margoulis, O., Babenko, V. and Wingender, E.:
Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells.
J. Mol. Biol. 288, 353-376 (1999). Medline

Heinemeyer, T., Chen, X., Karas, H., Kel, A. E., Kel, O. V., Liebich, I., Meinhardt, T., Reuter, I., Schacherer, F. and Wingender, E.:
Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms.

Nucleic Acids Res. 27, 318-322 (1999). Medline

Sacht, G., Marten, A., Deiters, U., Süssmuth, R., Jung, G., Wingender, E. and Mühlradt, P. F.:
Activation of nuclear factor-kappaB in macrophages by mycoplasmal lipopeptides.

Eur. J. Immunol. 28, 4207-4212 (1998). Medline

Reuter, I., Werner, T. and Wingender, E.:
Computer-assisted methods for the identification and characterization of polymerase II promoters.

Genetic Engineering: principles and methods, Vol. 20; J. K. Setlow (ed.), Plenum Press, New York and London, 25-40 (1998). Medline

Pickert, L., Reuter, I., Klawonn, F. and Wingender, E.:
Transcription regulatory region analysis using signal detection and fuzzy clustering.

Bioinformatics 14, 244-251 (1998). Medline

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. and Kolchanov, N. A.:
Databases on Transcriptional Regulation: TRANSFAC, TRRD, and COMPEL.

Nucleic Acids Res. 26, 362-367 (1998). Medline

Kel, O. V., Kel, A. E., Romashchenko, A. G., Wingender, E. and Kolchanov, N. A.:
Composite regulatory elements: classification and description in the COMPEL database.

Mol. Biol. (Mosk.) 31, 601-615 (1997). Mol. Biol. Engl. Tr. 31, 498-512 (1997). Medline

Flohé, L., Wingender, E. and Brigelius-Flohé, R.:
Regulation of glutathione peroxidases.
Oxidative stress and signal transduction; H. J. Forman, H. Cadenas (eds.), Chapman and Hall, New York, 415-440 (1997).

Kuhlenbäumer, G., Rothenburg, S., Matthes, M., Hollmann, C., Wingender, E., Thiele, H.-G., Koch-Nolte, F. and Haag, F.:
Expression of the RT6 mono(ADP-ribosyl)transferases is regulated by two promoter regions.
Adv. Exp. Med. Biol. 419, 265-270 (1997). Medline

Pickert, L., Klawonn, F. and Wingender, E.:
Fuzzy Cluster Analysis For Identification Of Gene Regulating Regions.
Proc. 7th International Fuzzy Systems Association World Congress (IFSA'97) Vol. IV, Academia, Prague, 56-61 (1997).

Pickert, L., Reuter, I., Klawonn, F. and Wingender, E.:
Transcription regulatory regions revealed by signal detection and fuzzy clustering.
Proceedings of the German Conference on Bioinformatics GCB '97, Kloster Irsee, Bavaria; H. W. Mewes, D. Frishman (eds.), 99-101 (1997).

Wingender, E.:
Classification scheme of eukaryotic transcription factors.
Molekularnaya Biologiya 31, 584-600 (1997). Mol. Biol. Engl. Tr. 31, 483-497 (1997). pdf

Kel, O. V., Kel, A. E., Romashchenko, A. G., Wingender, E. and Kolchanov, N. A.:
Composite regulatory elements: classification and description in the COMPEL database.
Mol. Biol. (Mosk.) 31, 601-615 (1997). Mol. Biol. Engl. Tr. 31, 498-512 (1997). Medline

Karas, H., Kel, A. E., Kel, O. V., Kolchanov, N. A. and Wingender, E.:
Integrating knowledge on transcriptional regulation of eukaryotic genes based on information from TRANSFAC, TRRD, and COMPEL databases.
Mol. Biol. (Mosk.) 31, 637-646 (1997). Mol. Biol. Engl. Tr. 31, 531-539 (1997). Medline

Ponomarkeno, M. P., Ponomarenko, I. V., Kel, A. E., Kolchanov, N. A., Karas, H., Wingender, E. and Sklenar, H.:
Computer analysis of conformational features of the eukaryotic TATA-box DNA promotors.
Mol. Biol. (Mosk.) 31, 733-740 (1997). Mol. Biol. Engl. Tr. 31, 623-630 (1997). Medline

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

Frech, K., Dietze, P., Werner, T.:
ConsInspector 3.0: new library and enhanced functionality.
Comp. Appl. Biosci. 13, 109-110 (1997). Medline

Wingender, E., Karas, H., Knüppel, R.:
TRANSFAC Database as a Bridge between Sequence Data Libraries and Biological Function.
Pacific Symposium on Biocomputing '97 (PSB'97), R. B. Altman, A. K. Dunker, L. Hunter, T. E. Klein (eds.). World Scientific, Singapore - New Jersey - London - Hong Kong 1996, pp. 477-485. Medline

Haag, F. A., Kuhlenbaeumer, G., Koch-Nolte, F., Wingender, E.,Thiele, H.-G.:
Structure of the gene encoding the rat T cell ecto-ADP-ribosyltransferase RT6.
J. Immunol. 157, 2022-2030 (1996). Medline

Karas, H., Knüppel, R., Schulz, W., Sklenar, H., Wingender, E.:
Combining structural analysis of DNA with search routines for detection of transcription regulatory elements.
Comput. Appl. Biosci. 12, 441-446 (1996). Medline

Wingender, E., Karas, H., Dietze, P., Knüppel, R., Sklenar, H.:
Combined approaches for the detection of regulatory DNA-regions.
Computer Science and Biology. Proceedings of the German Conference on Bioinformatics (GCB'96), R. Hofestaedt, T. Lengauer, M. Loeffler, D. Schomburg (eds.). University of Leipzig, Leipzig 1996, pp. 58-63.

Kel, A., Kel, O., Ischenko, I., Kolchanov, N., Karas, H., Wingender, E., Sklenar, H.:
TRRD and COMPEL databases on transcription linked to TRANSFAC as tools for analysis and recognition of regulatory sequences.
Computer Science and Biology. Proceedings of the German Conference on Bioinformatics (GCB'96), R. Hofestaedt, T. Lengauer, M. Loeffler, D. Schomburg (eds.). University of Leipzig, Leipzig 1996, pp. 113-117.

Wingender, E., Dietze, P., Karas, H., Knüppel, R.:
TRANSFAC: A database on transcription factors and their DNA binding sites.
Nucleic Acids Res., 24, 238-241 (1996). Medline

Quandt, K., Frech, K., Karas, H., Wingender, E., and Werner, T.:
MatInd and MatInspector - New fast and sensitive tools for detection of consensus matches in nucleotide sequence data
Nucleic Acids Res., 23, 4878-4884 (1995) Medline

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., 23, 4097-4103 (1995). Medline

Wingender, E., Knüppel, R., Dietze, P., Karas, H., Frech, K., Quandt, K., Werner, T.:
The TRANSFAC database and ConsInd program as tools for describing and understanding regulatory functions of the genome.
SAMS 18-19 (1995) pp. 823-826; Overseas PublishersAssociation, Amsterdam

Wingender, E., Knüppel, R., Dietze, P., Karas, H.:
TRANSFAC database as tool for the recognition of regulatory genomic sequences.
In: Bioinformatics and Genome Research, H.A. Lim and C.R. Cantor (Eds.), (World Scientific Publishing Co., Inc., New Jersey, 1995), pp. 275-282.

Knüppel, R., Dietze, P., Lehnberg, W., Frech, K., Wingender, E.:
TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins.
J. Comput. Biol. 1 (1994) 191-198 Medline

Wingender, E.:
Recognition of regulatory regions in genomic sequences.
J. Biotechnol. 35 (1994) 273-280 Medline

Brigelius-Flohe, R., Aumann, K.-D., Bloecker, H., Gross, G., Kiess, M., Kloeppel, K.-D., Maiorino, M., Roveri, A., Schuckelt, R., Ursini, F., Wingender, E., Flohe, L.:
Phospholipid hydroperoxide glutathione peroxidase: genomic DNA, cDNA, and deduced amino acid sequence.
J. Biol. Chem. 269 (1994) 7342-7348 Medline

Moeritz, A., Grzeschik, K.-H., Wingender, E., Fink, E.:
Organization and sequence of the gene encoding the human acrosin-trypsin inhibitor (HUSI-II).
Gene 123 (1993) 277-281 Medline

Scutt, A., Mayer, H., Wingender, E.:
New perspectives in the differentiation of bone-forming cells.
Biofactors 4 (1992) 1-13 Medline

Wingender, E., Heinemeyer, T., Lincoln, D.:
Regulatory DNA sequences: predictability of their function. Genome Analysis - From Sequence to Function.
BioTechForum- Advances in Molecular Genetics (J. Collins, A.J. Driesel, eds.) 4 (1991) 95-108

Rupp, E., Mayer, H., Wingender, E.:
The promoter of the human parathyroid hormone gene contains a functional cyclic AMP-response element.
Nucleic Acids Res. 18 (1990) 5677-5683 Medline

Wingender, E.:
Transcription regulating proteins and their recognition sequences
CRC Crit. Rev. in Eukaryotic Gene Expression 1 (1990) 11-48 Medline

Wingender, E.:
Compilation of transcription regulating proteins.
Nucleic Acids Res. 16 (1988) 1879-1902 Medline