Modifying SNEEP to account for averaged differential TF Binding

Project Description

In our lab, we developed a statistical approach (SNEEP, see project site) that identifies regulatory single nucleotide variants (SNVs) affecting transcription factor (TF) binding. Currently, the approach uses a maximization to identify the position with the strongest differential TF binding score. However, recent studies show that TFs might also bind at sites where several medium-strength binding sites overlap.

This project focuses on improving and adapting our SNEEP approach by modifying the underlying statistical model such that the above-described binding behavior is taken into account.

Research Goals

• Modify the SNEEP statistic to use an average differential TF binding score instead of the maximum
• Adapt the SNEEP software accordingly
• Test the new implementation
• Evaluate and compare the results to the previous version of SNEEP

Prerequisites

• C++ programming or motivation to learn it
• Basic knowlegde of genomics is helpful, but not required

How to Apply

Send an Email with a short motivation to the corresponding supervisor n.baumgarten|em.uni-frankfurt.de.