Publications

[mbelmadani]

Here, we can list publications providing background or ideas we can explore in this project. A few examples:

I'll start listing some papers that might provide context for this project. I'm not expecting anyone to read all of this, but definitely some of the ideas introduced in these can be relevant. I'll also update/edit this post with more content as I go.

Background:

• JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
• Regulatory elements: Putting enhancers into context
• MOODS: fast search for position weight matrix matches in DNA sequences

Potentially useful ideas from the literature:

• Reliable scaling of position weight matrices for binding strength comparisons between transcription factors
• The orientation of transcription factor binding site motifs in gene promoter regions: does it matter?
• Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers
• Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
• Variation in transcription factor binding among humans
• A systematic, large-scale comparison of transcription factor binding site models