The DOI matches its Crossref record; 65 of the 65 references it cites were found in a registry or an index.
Identification of transcription factor binding sites using ATAC-seq
Open accessAbstract
Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering ATAC-seq protocol artifacts. HINT-ATAC uses a position dependency model to learn the cleavage preferences of the transposase. We observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints.
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Chromatin accessibility profiling methods
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Metadata
- Authors
- Li, Z., Schulz, M. H., Look, T., Begemann, M., Zenke, M., & Costa, I. G.
- Venue
- Genome Biology
- Published
- 2019-02-26
- Volume
- 20
- Issue
- 1
- Pages
- 45-45
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2925775506
- Cited by
- 452
- References
- 65
- FWCI
- 16.18
- Type
- journal article
- Language
- en
- Open access
- gold
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- Li, Z., Schulz, M. H., Look, T., Begemann, M., Zenke, M., & Costa, I. G. (2019). Identification of transcription factor binding sites using ATAC-seq. Genome Biology. https://doi.org/10.1186/s13059-019-1642-2
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