Publications 2004-2005

Potapov, A. P., Voss, N., Sasse, N. and Wingender, E.:
Topology of mammalian transcription networks
Genome Inf. Ser. 16, 270-278 (2005). pdf

Krull, M. and Wingender, E.:
Eukaryotic regulatory sequences.
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Dunn, M. J., Jorde, L. B., Little, P. F. and Subramaniam S. (eds.), John Wiley & Sons, Ltd., UK (2005). link

Kel-Margoulis, O., Matys, V., Choi, C., Reuter, I., Krull, M., Potapov, A.P., Voss, N., Liebich, I., Kel, A., Wingender, E.:
Databases on Gene Regulation
Information Processing and Living Systems, Bajic, V. B. and Wee, T. T. (eds.), Imperial College Press, London, 709-727 (2005).

Kel, A., Kel-Margoulis, O., Borlak J., Tchekmenev, D., Wingender, E.:
Databases and tools for in silico analysis of regulation of gene expression
Handbook of Toxicogenomics, Borlak, J. (ed.), Wiley-VCH, Weinheim, 253-290 (2005). pdf

Guldener, U., Munsterkotter, M., Kastenmuller, G., Strack, N., van Helden, J., Lemer, C., Richelles, J., Wodak, S. J., Garcia-Martinez, J., Perez-Ortin, J. E., Michael, H., Kaps, A., Talla, E., Dujon, B., Andre, B., Souciet, J. L., De Montigny, J., Bon, E., Gaillardin, C. and Mewes, H. W.:
CYGD: the Comprehensive Yeast Genome Database.
Nucleic Acids Res. 33, D364-368 (2005). Medline

Kel, A., Tikunov, Y., Voss, N., Borlak, J. and Wingender, E.:
Application of kernel method to reveal subtypes of TF binding motifs. Causal analysis of gene expression data
Regulatory Genomics: RECOMB 2004 International Workshop, RRG 2004, San Diego, Ca, USA, March 26-27, 2004, Revised Selected Papers. Eleazar Eskin, Chris Workman (eds.), Lecture Notes in Computer Science 3318, 42-51 (2005). pdf

Shelest, E. and Wingender, E.:
Construction of predictive promoter models on the example of antibacterial response of human epithelial cells
Theor. Biol. Med. Model. 2, 2 (2005).link

Michael, H., Chen, X., Fricke, E., Haubrock, M., Ricanek, R. and Wingender, E.:
Deriving an ontology for human gene expression sources from the CYTOMER® database on human organs and cell types.
In Silico Biol. 5, 0007 (2004). link

Choi, C., Crass, T., Kel, A., Kel-Margoulis, O., Krull, M., Pistor, S., Potapov, A., Voss, N. and Wingender, E.:
Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database
Genome Inf. Ser. 15, 244-254 (2004). pdf

Stegmaier, P., Kel, A. E. and Wingender, E.:
Systematic DNA-binding domain classification of transcription factors
Genome Inf. Ser. 15, 276-286 (2004). pdf

Kel, A., Tikunov, Y., Voss, N. and Wingender, E.:
Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods
Bioinformatics 20, 1512-1516 (2004). Medline

Choi, C., Krull, M., Kel-Margoulis, O., Pistor, S., Potapov, A., Voss, N. and Wingender, E.:
TRANSPATH® - a high quality database focused on signal transduction
Comparative Functional Genomics 5, 163-168 (2004). link

Hehl, R., Steffens, N. O. and Wingender, E.:
Isolation and analysis of gene regulatory sequences
Handbook of Plant Biotechnology, Christou, P. and Klee, H. (eds.), Wiley and Sons Ltd., 81-102 (2004).

Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., Claussen, H., Ebeling, C., Ernst, P., Gailus-Durner, V., Glatting, K.H., Gohla, R., Gossling, F., Grote, K., Heidtke, K., Herrmann, A., O'Keeffe, S., Kiesslich, O., Kolibal, S., Korbel, J.O., Lengauer, T., Liebich, I., Van Der Linden, M., Luz, H., Meissner, K., Von Mering, C., Mevissen, H.T., Mewes, H.W., Michael, H., Mokrejs, M., Muller, T., Pospisil, H., Rarey, M., Reich, J.G., Schneider, R., Schomburg, D., Schulze-Kremer, S., Schwarzer, K.,Sommer, I., Springstubbe, S., Suhai, S., Thoppae, G., Vingron, M., Warfsmann, J., Werner, T., Wetzler, D., Wingender, E. and Zimmer, R.:
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
Bioinformatics 20, 268-270 (2004). Medline