Simon H. Rasmussen

I’m a bioinformatician with interests in regulatory motifs discovery and method development. My main interest is Post-Transcriptional regulation by miRNAs and how they interact with RNA binding proteins, development of scientific algorithms and application of statistical theory.

Currently I’m doing my PhD in Anders Krogh’s group. Before this I have been working as Research Assistant doing projects within COAT and other collaborations. In COAT, all my research is highly relevant, I collaborate with a several people in the Center and I have done bioinformatics analyses of high throughput data produced by COAT collaborator.

I have Master’s in Bioinformatics; I did my thesis on cWords, a method that can find regulatory signatures of miRNAs given differential expression data. In my thesis work the main objective was application of statistical theory and optimization of a complex scientific algorithm. Furthermore, I have a Bachelor’s degree in Computer Science, with at solid foundation in scientific programming and algorithmics.


  • cWords – Regulatory motif discovery in high throughput data. This method has been used miRNA, RNBP, gapmer and mixmer binding and has been developed in collaboration with Anders Jacobsen.
  • Characterization of binding specificity of gapmers – Gapmers target RNA sequences for cleavage by RNAse H, we set out to identify off-target effect similar to those of siRNAs of different gapmers designed by Santaris Pharma.
  • Efficacy of miRNA targeting could depend on protein interaction of RISC and other proteins or limited accessibility. We will correlation of miRNA target site efficacy with protein occupancy and structure data. In collaboration with Lykke Pedersen and Mireya Plass.
  • Transcriptome–wide characterization of RNA binding proteins. This project focuses of building processing infrastructure for automatic CLIP-Seq processing. The project has the aim of standardized and systematic motif discovery in PAR-CLIP data.

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