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Items: 1 to 20 of 101

1.

A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

Feehery GR, Yigit E, Oyola SO, Langhorst BW, Schmidt VT, Stewart FJ, Dimalanta ET, Amaral-Zettler LA, Davis T, Quail MA, Pradhan S.

PLoS One. 2013 Oct 28;8(10):e76096. doi: 10.1371/journal.pone.0076096. eCollection 2013.

2.

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias.

Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, Robinson MD, Clark SJ.

Epigenetics. 2011 Jan;6(1):34-44. doi: 10.4161/epi.6.1.13313. Epub 2011 Jan 1.

PMID:
20818161
3.

The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties.

Fraga MF, Ballestar E, Montoya G, Taysavang P, Wade PA, Esteller M.

Nucleic Acids Res. 2003 Mar 15;31(6):1765-74.

4.

Transcriptional repression by Drosophila methyl-CpG-binding proteins.

Roder K, Hung MS, Lee TL, Lin TY, Xiao H, Isobe KI, Juang JL, Shen CJ.

Mol Cell Biol. 2000 Oct;20(19):7401-9.

5.

The solution structure of the domain from MeCP2 that binds to methylated DNA.

Wakefield RI, Smith BO, Nan X, Free A, Soteriou A, Uhrin D, Bird AP, Barlow PN.

J Mol Biol. 1999 Sep 3;291(5):1055-65.

PMID:
10518942
6.

[Development of a method for methylated DNA enrichment with functionalized mesocellular silica foams immobilized with methyl CpG binding domain].

Chen YT, Han L, Zhao DY, Tu B, Ma D.

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2012 Jun;29(3):284-8. doi: 10.3760/cma.j.issn.1003-9406.2012.03.008. Chinese.

PMID:
22678790
7.

A novel method to capture methylated human DNA from stool: implications for colorectal cancer screening.

Zou H, Harrington J, Rego RL, Ahlquist DA.

Clin Chem. 2007 Sep;53(9):1646-51.

8.

Methyl-CpG-binding proteins. Targeting specific gene repression.

Ballestar E, Wolffe AP.

Eur J Biochem. 2001 Jan;268(1):1-6. Review.

9.

Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB.

Liu G, Weston CQ, Pham LK, Waltz S, Barnes H, King P, Sphar D, Yamamoto RT, Forsyth RA.

PLoS One. 2016 Jan 4;11(1):e0146064. doi: 10.1371/journal.pone.0146064. eCollection 2016.

10.

Mechanism of transcriptional regulation by methyl-CpG binding protein MBD1.

Fujita N, Shimotake N, Ohki I, Chiba T, Saya H, Shirakawa M, Nakao M.

Mol Cell Biol. 2000 Jul;20(14):5107-18.

11.

Kinetic and thermodynamic evidence for flipping of a methyl-CpG binding domain on methylated DNA.

Inomata K, Ohki I, Tochio H, Fujiwara K, Hiroaki H, Shirakawa M.

Biochemistry. 2008 Mar 11;47(10):3266-71. doi: 10.1021/bi7019029. Epub 2008 Feb 12.

PMID:
18266325
12.

The methyl-CpG binding domain and the evolving role of DNA methylation in animals.

Hendrich B, Tweedie S.

Trends Genet. 2003 May;19(5):269-77. Review.

PMID:
12711219
13.

Efficient depletion of host DNA contamination in malaria clinical sequencing.

Oyola SO, Gu Y, Manske M, Otto TD, O'Brien J, Alcock D, Macinnis B, Berriman M, Newbold CI, Kwiatkowski DP, Swerdlow HP, Quail MA.

J Clin Microbiol. 2013 Mar;51(3):745-51. doi: 10.1128/JCM.02507-12. Epub 2012 Dec 5.

14.

Exome capture from saliva produces high quality genomic and metagenomic data.

Kidd JM, Sharpton TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A, Guadalupe M, Guo X, Feng Q, Li Y, Liu X, Parham P, Hoal EG, Feldman MW, Pollard KS, Wall JD, Bustamante CD, Henn BM.

BMC Genomics. 2014 Apr 4;15:262. doi: 10.1186/1471-2164-15-262.

15.

Engineering a high-affinity methyl-CpG-binding protein.

Jørgensen HF, Adie K, Chaubert P, Bird AP.

Nucleic Acids Res. 2006 Aug 7;34(13):e96.

16.

Methylation-mediated transcriptional silencing in euchromatin by methyl-CpG binding protein MBD1 isoforms.

Fujita N, Takebayashi S, Okumura K, Kudo S, Chiba T, Saya H, Nakao M.

Mol Cell Biol. 1999 Sep;19(9):6415-26.

17.

A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation.

Yigit E, Feehery GR, Langhorst BW, Stewart FJ, Dimalanta ET, Pradhan S, Slatko B, Gardner AF, McFarland J, Sumner C, Davis TB.

Curr Protoc Mol Biol. 2016 Jul 1;115:7.26.1-7.26.14. doi: 10.1002/cpmb.12.

PMID:
27366894
18.

Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites.

Hogart A, Lichtenberg J, Ajay SS, Anderson S; NIH Intramural Sequencing Center, Margulies EH, Bodine DM.

Genome Res. 2012 Aug;22(8):1407-18. doi: 10.1101/gr.132878.111. Epub 2012 Jun 8.

19.
20.

On how mammalian transcription factors recognize methylated DNA.

Buck-Koehntop BA, Defossez PA.

Epigenetics. 2013 Feb;8(2):131-7. doi: 10.4161/epi.23632. Epub 2013 Jan 16. Review.

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