Abstract. Morphogenesis and the spatial structure of an organism have repercussions on gene expression. These effects can influence the results of regulatory network reconstruction. An integrated,...
Abstract. Microarray technology has resulted in large sets of gene expression data. Using these data to derive knowledge about the underlying mechanisms that control gene expression dynamics has...
A scoring matrix approach to detecting miRNA target sites (2008)
Moxon, Simon, Moulton, Vincent, Kim, Jan T
Abstract Background Experimental identification of microRNA (miRNA) targets is a difficult and time consuming process. As a consequence several computational prediction methods have been devised in...
On the Effects of Transcription Factor Properties on the Information Content of Binding Sites (2008)
Jan T. Kim, Thomas Martinetz, Daniel Polani
Networks of genes which encode transcription factors (regulatory networks) play a central role in the realization of phenotypic traits based on genetic information. Sequence-specific recognition of...
Relevant information in optimized persistence vs. progeny strategies (2006)
Daniel Polani, Chrystopher L. Nehaniv, Thomas Martinetz, Jan T. Kim
Identifying and utilizing information is central to reproductive success. We study a scenario where a multicellular colony has to trade-off between utility of strategies for investment in persistence...
On the Stability and Robustness of Biological Systems (2005)
Biological systems are often remarkably robust to changing environmental conditions. This property can, however, not be generalised simplistically. In fact, in all biological systems, certain...
Jan T. Kim, Thomas Martinetz, Daniel Polani
Empirically, it has been observed in several cases that the information content of transcription factor binding site sequences (465798-:79;<97 ) approximately equals the information content of...
Dirk Repsilber, Jan T. Kim, Hans Liljenström, Thomas Martinetz
This contribution gives an initial report of a new project exploring the perspectives and limits of reversely engineering regulatory gene networks from gene expression data. The availability of such...
transsys: A Generic Formalism for Modelling Regulatory Networks in Morphogenesis (2001)
Abstract The formal language transsys is introduced as a tool for comprehensively representing regulatory gene networks in a way that makes them accessible to ALife modelling. As a first application,...
Münster, Thomas, Pahnke, Jens, Di Rosa, Alexandra, Kim, Jan T., Martin, William, Saedler, Heinz, ...
Flowers sensu lato are short, specialized axes bearing closely aggregated sporophylls. They are typical for seed plants (spermatophytes) and are prominent in flowering plants sensu stricto...
MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants
Winter, Kai-Uwe, Becker, Annette, Münster, Thomas, Kim, Jan T., Saedler, Heinz, Theissen, Günter
The evolutionary origin of the angiosperms (flowering plants sensu stricto) is still enigmatic. Answers to the question of angiosperm origins are intimately connected to the identification of their...
Münster, Thomas, Pahnke, Jens, Di Rosa, Alexandra, Kim, Jan T., Martin, William, Saedler, Heinz, ...
Flowers sensu lato are short, specialized axes bearing closely aggregated sporophylls. They are typical for seed plants (spermatophytes) and are prominent in flowering plants sensu stricto...
MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants
Winter, Kai-Uwe, Becker, Annette, Münster, Thomas, Kim, Jan T., Saedler, Heinz, Theissen, Günter
The evolutionary origin of the angiosperms (flowering plants sensu stricto) is still enigmatic. Answers to the question of angiosperm origins are intimately connected to the identification of their...