Key publications for promoter analysis

Deyneko, I. V., Kel, A. E., Kel-Margoulis, O. V., Deineko, E. V., Wingender, E. and Weiss, S. (2013) MatrixCatch – a novel tool for the recognition of composite regulatory elements in promoters. BMC Bioinformatics 14, 241. Link

Stegmaier, P., Kel, A., Wingender, E., Borlak, J. (2013) A discriminative approach for unsupervised clustering of DNA sequence motifs. PLoS Comput. Biol. 9, e1002958. Link

Stegmaier P., Voss N., Meier T., Kel A., Wingender E., Borlak J. (2011) Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer. PLoS ONE 6, e17738. PubMed.

Wingender E. (2008) The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform. 9:326-332. PubMed.

Kel A., Konovalova T., Waleev T., Cheremushkin E., Kel-Margoulis O., Wingender, E. (2006) Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations. Bioinformatics 22:1190-1197. PubMed.

Waleev T. Shtokalo D., Konovalova T., Voss N., Cheremushkin E., Stegmaier P., Kel-Margoulis O., Wingender E., Kel A. (2006) Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm. Nucleic Acids Res. 34, W541-W545. PubMed.

Kel A.E., Gössling E., Reuter I., Cheremushkin E., Kel-Margoulis O.V., Wingender E. (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 31:3576-3579. PubMed