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Items: 1 to 20 of 257

1.

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S.

Nat Methods. 2007 Aug;4(8):651-7. Epub 2007 Jun 11.

PMID:
17558387
2.

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.

Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ.

Genome Res. 2008 Dec;18(12):1906-17. doi: 10.1101/gr.078519.108. Epub 2008 Sep 11.

3.

MER41 repeat sequences contain inducible STAT1 binding sites.

Schmid CD, Bucher P.

PLoS One. 2010 Jul 6;5(7):e11425. doi: 10.1371/journal.pone.0011425.

4.

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.

5.

PICS: probabilistic inference for ChIP-seq.

Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, Jones S, Gottardo R.

Biometrics. 2011 Mar;67(1):151-63. doi: 10.1111/j.1541-0420.2010.01441.x.

PMID:
20528864
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.

Computational analysis of ChIP-seq data.

Ji H.

Methods Mol Biol. 2010;674:143-59. doi: 10.1007/978-1-60761-854-6_9.

PMID:
20827590
8.

Native chromatin immunoprecipitation (N-ChIP) and ChIP-Seq of Schistosoma mansoni: Critical experimental parameters.

Cosseau C, Azzi A, Smith K, Freitag M, Mitta G, Grunau C.

Mol Biochem Parasitol. 2009 Jul;166(1):70-6. doi: 10.1016/j.molbiopara.2009.02.015. Epub 2009 Mar 9.

PMID:
19428675
9.

Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing.

Hoffman BG, Jones SJ.

J Endocrinol. 2009 Apr;201(1):1-13. doi: 10.1677/JOE-08-0526. Epub 2009 Jan 9. Review.

10.

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.

Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E.

Nucleic Acids Res. 2010 Jun;38(11):e126. doi: 10.1093/nar/gkq217. Epub 2010 Apr 7.

11.

ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites.

Lefrançois P, Zheng W, Snyder M.

Methods Enzymol. 2010;470:77-104. doi: 10.1016/S0076-6879(10)70004-5. Epub 2010 Mar 1.

PMID:
20946807
12.

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments.

Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL.

BMC Genomics. 2009 Dec 18;10:618. doi: 10.1186/1471-2164-10-618.

13.

Mapping protein-DNA interactions using ChIP-sequencing.

Massie CE, Mills IG.

Methods Mol Biol. 2012;809:157-73. doi: 10.1007/978-1-61779-376-9_11.

PMID:
22113275
14.

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.

15.

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data.

Alawi M, Kurtz S, Beckstette M.

J Integr Bioinform. 2011 Jun 21;8(2):155. doi: 10.2390/biecoll-jib-2011-155.

PMID:
21690655
16.

Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans.

Brdlik CM, Niu W, Snyder M.

Methods Enzymol. 2014;539:89-111. doi: 10.1016/B978-0-12-420120-0.00007-4.

PMID:
24581441
17.

Genome-wide in vivo cross-linking of sequence-specific transcription factors.

Li XY, Biggin MD.

Methods Mol Biol. 2012;809:3-26. doi: 10.1007/978-1-61779-376-9_1.

PMID:
22113265
18.

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.

19.

Modeling ChIP sequencing in silico with applications.

Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M.

PLoS Comput Biol. 2008 Aug 22;4(8):e1000158. doi: 10.1371/journal.pcbi.1000158.

20.

Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification.

van Bakel H, van Werven FJ, Radonjic M, Brok MO, van Leenen D, Holstege FC, Timmers HT.

Nucleic Acids Res. 2008 Mar;36(4):e21. doi: 10.1093/nar/gkm1144. Epub 2008 Jan 7.

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