Eukaryotic Gene Regulation

We develop methods to predict the regulation of genes through transcription factors (TF) from the euchromatic sequence of co-regulated genes in eukaryotes. We look for overrepresented, putative binding motifs of TFs, exploiting the facts that (i) many eukaryotic genes have a homolog in related species and binding motifs are thus conserved; (ii) many transcription factors exhibit a positional preference when binding in a regulatory region; and (iii) most genes are controlled by a combination of factors with their corresponding binding sites forming homotypic or heterotypic clusters known as cis-regulatory modules.

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Sebastian J. Schultheiss

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Publications

• Schultheiss, SJ, Busch, W, Lohmann, JU, Kohlbacher, O, and Rätsch, G (2009).
  KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences
  Bioinformatics, 25(16):2126-2133.
  Supplementary website http://bioinformatics.oxfordjournals.org/cgi/content/full/25/16/2126
  Printable file

• Schultheiss, SJ, Busch, W, Lohmann, JU, Kohlbacher, O, and Rätsch, G (2008).
  KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences
  In: German Conference on Bioinformatics, ed. by A. Beyer and M. Schroeder, pp. 158-167, GI, Heidelberg, Springer Verlag. Lecture notes in Informatics.
  Supplementary website https://fml.ratschlab.org/projects/kirmes
  Printable file