Talk:Preprint/K-mer
K-mers have also been shown to have a role in Epigenomics. In particular, for nucleosome positioning:
- Peckham,H.E. et al. (2007) Nucleosome positioning signals in genomic DNA. Genome Res., 17, 1170-1177.
- R Giancarlo, SE Rombo, F Utro. Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning. Bioinformatics 31 (18), 2939-2946, 2015.
- Akinori Awazu. Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition. Bioinformatics, Volume 33, Issue 1, 1 January 2017, Pages 42-48.
- R Giancarlo, SE Rombo, F Utro. In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes. Bioinformatics 34 (20), 3454-3460, 2018.
and for studying the variation in chromatin accessibility across cells:
- Schep, A. N., Wu, B., Buenrostro, J. D., & Greenleaf, W. J. (2017). chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nature methods, 14(10), 975-978. doi:10.1038/nmeth.4401
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