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Items: 1 to 20 of 100

1.

Mapping genome-wide transcription factor binding sites in frozen tissues.

Savic D, Gertz J, Jain P, Cooper GM, Myers RM.

Epigenetics Chromatin. 2013 Sep 16;6(1):30. doi: 10.1186/1756-8935-6-30.

2.

Genome-wide profiling of transcription factor binding and epigenetic marks in adipocytes by ChIP-seq.

Nielsen R, Mandrup S.

Methods Enzymol. 2014;537:261-79. doi: 10.1016/B978-0-12-411619-1.00014-8.

PMID:
24480351
3.

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, Keleş S.

PLoS Comput Biol. 2011 Jul;7(7):e1002111. doi: 10.1371/journal.pcbi.1002111. Epub 2011 Jul 14.

5.

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.

Mundade R, Ozer HG, Wei H, Prabhu L, Lu T.

Cell Cycle. 2014;13(18):2847-52. doi: 10.4161/15384101.2014.949201. Review.

6.

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.

7.

An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.

Cheng CY, Chu CH, Hsu HW, Hsu FR, Tang CY, Wang WC, Kung HJ, Chang PC.

BMC Genomics. 2014;15 Suppl 1:S1. doi: 10.1186/1471-2164-15-S1-S1. Epub 2014 Jan 24.

8.

Optimizing detection of transcription factor-binding sites in ChIP-seq experiments.

Kallio A, Elo LL.

Methods Mol Biol. 2013;1038:181-91. doi: 10.1007/978-1-62703-514-9_11.

PMID:
23872976
9.

Genome-wide transcription factor binding: beyond direct target regulation.

MacQuarrie KL, Fong AP, Morse RH, Tapscott SJ.

Trends Genet. 2011 Apr;27(4):141-8. doi: 10.1016/j.tig.2011.01.001. Epub 2011 Feb 4. Review.

10.

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

Yang JH, Li JH, Jiang S, Zhou H, Qu LH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D177-87. doi: 10.1093/nar/gks1060. Epub 2012 Nov 17.

11.

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M.

BMC Genomics. 2009 Jan 21;10:37. doi: 10.1186/1471-2164-10-37.

12.

Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.

Kuznetsov VA, Singh O, Jenjaroenpun P.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S12. doi: 10.1186/1471-2164-11-S1-S12.

13.

Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing.

Cotney JL, Noonan JP.

Cold Spring Harb Protoc. 2015 Feb 2;2015(2):191-9. doi: 10.1101/pdb.prot084848. Erratum in: Cold Spring Harb Protoc. 2015 Apr;2015(4):419.

PMID:
25646502
14.

Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite.

Wang X, Zhang X.

BMC Syst Biol. 2011;5 Suppl 2:S3. doi: 10.1186/1752-0509-5-S2-S3. Epub 2011 Dec 14.

15.

Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites.

Wong KC, Peng C, Li Y.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Nov-Dec;12(6):1416-28. doi: 10.1109/TCBB.2015.2424421.

PMID:
26671811
16.

Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation.

Gilchrist DA, Fargo DC, Adelman K.

Methods. 2009 Aug;48(4):398-408. doi: 10.1016/j.ymeth.2009.02.024. Epub 2009 Mar 9. Review.

17.

Characterising ChIP-seq binding patterns by model-based peak shape deconvolution.

Mendoza-Parra MA, Nowicka M, Van Gool W, Gronemeyer H.

BMC Genomics. 2013 Nov 26;14:834. doi: 10.1186/1471-2164-14-834.

18.

Next-generation sequencing applied to flower development: ChIP-Seq.

Graciet E, O'Maoiléidigh DS, Wellmer F.

Methods Mol Biol. 2014;1110:413-29. doi: 10.1007/978-1-4614-9408-9_24.

PMID:
24395273
19.

Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses.

Sokol M, Jessen KM, Pedersen FS.

APMIS. 2016 Jan-Feb;124(1-2):127-39. doi: 10.1111/apm.12477. Review.

PMID:
26818267
20.

On the identification of potential regulatory variants within genome wide association candidate SNP sets.

Chen CY, Chang IS, Hsiung CA, Wasserman WW.

BMC Med Genomics. 2014 Jun 11;7:34. doi: 10.1186/1755-8794-7-34.

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