Analysis of computational footprinting methods for DNase sequencing experiments

By Eduardo G. Gusmão, Manuel Allhoff, Martin Zenke, I. Costa. 2016

141 citations recorded by the source corpus.

Subfields: Cancer Research, Molecular Biology

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1. Philipp Goymann
2. J. Preussner
3. Anastasiia Petrova
4. Kathrin Klee
5. Thomas Braun
6. M. Looso
7. Johnny Kim
8. A. Fust

Citations in the corpus

• ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation (2020, methodology): “Reads within open chromatin peaks are then corrected by estimating the expected number of cuts per base pair and subtracting this from the observed cut sites as follows (modified from (4)): = − (1) for = ∗ (2) , = ∑ (3) , = ∑ (4)”
• Identification of transcription factor binding sites using ATAC-seq (2018, unknown): “Computational footprinting methods are crucial in the analysis of DNase-seq (Vierstra and Stamatoyannopoulos 2016; Gusmao et al. 2016).”