DNAshapeR: An R/Bioconductor package for DNA shape prediction and feature encoding

Bioinformatics

Volumn 32, Issue 8, 2016, Pages 1211-1213

  Chiu, Tsu Pei ^a   Comoglio, Federico ^b,d   Zhou, Tianyin ^a,e   Yang, Lin ^a   Paro, Renato ^b,c   Rohs, Remo ^a  

^a University of Southern California ^*  (United States)

^b ETH ZURICH   (Switzerland)

^c UNIVERSITY OF BASEL   (Switzerland)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e GOOGLE INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

COMPUTER LANGUAGE; GENOME; GENOMICS; SOFTWARE;

DNA; GENOME; GENOMICS; PROGRAMMING LANGUAGES; SOFTWARE;

EID: 84966549188     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv735     Document Type: Article

References (8)

1. Abe, N. et al. (2015) Deconvolving the recognition of DNA shape from sequence. Cell, 161, 307-318.
2. Chiu, T.P. et al. (2015) GBshape: a genome browser database for DNA shape annotations. Nucleic Acids Res, 43, D103-D109.
3. Comoglio, F. et al. (2015) High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins. Cell Rep., 11, 821-834.
4. He, Q. et al. (2015) ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. Nat. Biotechnol., 33, 395-401.
5. Murphy, M.W. et al. (2015) An ancient protein-DNA interaction underlying metazoan sex determination. Nat. Struct. Mol. Biol., 22, 442-451.
6. Yang, L. et al. (2014) TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res., 42(Database issue), D148-D155.
7. Zhou, T. et al. (2013) DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. Nucleic Acids Res., 41 (Web Server issue), W56-W62.
8. Zhou, T. et al. (2015) Quantitative modeling of transcription factor binding specificities using DNA shape. Proc. Natl. Acad. Sci. USA, 112, 4654-4659.