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Items: 1 to 20 of 203

1.

High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.

Chumsakul O, Nakamura K, Kurata T, Sakamoto T, Hobman JL, Ogasawara N, Oshima T, Ishikawa S.

DNA Res. 2013 Aug;20(4):325-38. doi: 10.1093/dnares/dst013. Epub 2013 Apr 11.

3.

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.

Yardımcı GG, Frank CL, Crawford GE, Ohler U.

Nucleic Acids Res. 2014 Oct 29;42(19):11865-78. doi: 10.1093/nar/gku810. Epub 2014 Oct 7.

4.

BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data.

Kähärä J, Lähdesmäki H.

Bioinformatics. 2015 Sep 1;31(17):2852-9. doi: 10.1093/bioinformatics/btv294. Epub 2015 May 7.

PMID:
25957350
9.

Analysis of computational footprinting methods for DNase sequencing experiments.

Gusmao EG, Allhoff M, Zenke M, Costa IG.

Nat Methods. 2016 Apr;13(4):303-9. doi: 10.1038/nmeth.3772. Epub 2016 Feb 22.

PMID:
26901649
10.
11.

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data.

Piper J, Elze MC, Cauchy P, Cockerill PN, Bonifer C, Ott S.

Nucleic Acids Res. 2013 Nov;41(21):e201. doi: 10.1093/nar/gkt850. Epub 2013 Sep 25. Erratum in: Nucleic Acids Res. 2014;42(17):11272.

12.
13.

The transition state transcription regulator abrB of Bacillus subtilis is a DNA binding protein.

Strauch MA, Spiegelman GB, Perego M, Johnson WC, Burbulys D, Hoch JA.

EMBO J. 1989 May;8(5):1615-21.

14.

Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation.

Chumsakul O, Takahashi H, Oshima T, Hishimoto T, Kanaya S, Ogasawara N, Ishikawa S.

Nucleic Acids Res. 2011 Jan;39(2):414-28. doi: 10.1093/nar/gkq780. Epub 2010 Sep 3.

15.

The DNA-binding specificity of the Bacillus anthracis AbrB protein.

Strauch MA, Ballar P, Rowshan AJ, Zoller KL.

Microbiology. 2005 Jun;151(Pt 6):1751-9.

PMID:
15941984
16.

Accurate prediction of inducible transcription factor binding intensities in vivo.

Guertin MJ, Martins AL, Siepel A, Lis JT.

PLoS Genet. 2012;8(3):e1002610. doi: 10.1371/journal.pgen.1002610. Epub 2012 Mar 29.

17.

Insights into the nature of DNA binding of AbrB-like transcription factors.

Sullivan DM, Bobay BG, Kojetin DJ, Thompson RJ, Rance M, Strauch MA, Cavanagh J.

Structure. 2008 Nov 12;16(11):1702-13. doi: 10.1016/j.str.2008.08.014.

18.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.

19.

Substitutional analysis of the C-terminal domain of AbrB revealed its essential role in DNA-binding activity.

Neubauer S, Dolgova O, Präg G, Borriss R, Makarewicz O.

PLoS One. 2014 May 15;9(5):e97254. doi: 10.1371/journal.pone.0097254. eCollection 2014.

20.

Precise Identification of DNA-Binding Proteins Genomic Location by Exonuclease Coupled Chromatin Immunoprecipitation (ChIP-exo).

Matteau D, Rodrigue S.

Methods Mol Biol. 2015;1334:173-93. doi: 10.1007/978-1-4939-2877-4_11.

PMID:
26404150

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