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Items: 1 to 20 of 120

1.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS.

Genome Res. 2008 Mar;18(3):393-403. doi: 10.1101/gr.7080508. Epub 2008 Feb 7.

2.

Comparison of sample preparation methods for ChIP-chip assays.

O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ.

Biotechniques. 2006 Nov;41(5):577-80.

3.

Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments.

Ghosh S, Hirsch HA, Sekinger E, Struhl K, Gingeras TR.

BMC Bioinformatics. 2006 Oct 5;7:434.

4.

HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data.

Taskesen E, Beekman R, de Ridder J, Wouters BJ, Peeters JK, Touw IP, Reinders MJ, Delwel R.

BMC Bioinformatics. 2010 May 21;11:275. doi: 10.1186/1471-2105-11-275.

5.

Model-based deconvolution of genome-wide DNA binding.

Reiss DJ, Facciotti MT, Baliga NS.

Bioinformatics. 2008 Feb 1;24(3):396-403. Epub 2007 Dec 1.

PMID:
18056063
6.

Poisson approximation for significance in genome-wide ChIP-chip tiling arrays.

Zhang Y.

Bioinformatics. 2008 Dec 15;24(24):2825-31. doi: 10.1093/bioinformatics/btn549. Epub 2008 Oct 25.

PMID:
18953047
7.

ChIP-Chip: algorithms for calling binding sites.

Liu XS, Meyer CA.

Methods Mol Biol. 2009;556:165-75. doi: 10.1007/978-1-60327-192-9_12.

8.

ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.

Ho JW, Bishop E, Karchenko PV, Nègre N, White KP, Park PJ.

BMC Genomics. 2011 Feb 28;12:134. doi: 10.1186/1471-2164-12-134.

9.

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.

Zacher B, Kuan PF, Tresch A.

BMC Bioinformatics. 2010 Apr 17;11:194. doi: 10.1186/1471-2105-11-194.

10.

Modeling and analysis of ChIP-chip experiments.

Gottardo R.

Methods Mol Biol. 2009;567:133-43. doi: 10.1007/978-1-60327-414-2_9. Review.

PMID:
19588090
11.

Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies.

Eeckhoute J, Lupien M, Brown M.

Methods Mol Biol. 2009;556:155-64. doi: 10.1007/978-1-60327-192-9_11.

PMID:
19488877
12.

Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays.

Wang Y, Barbacioru C, Hyland F, Xiao W, Hunkapiller KL, Blake J, Chan F, Gonzalez C, Zhang L, Samaha RR.

BMC Genomics. 2006 Mar 21;7:59.

13.

Efficient oligonucleotide probe selection for pan-genomic tiling arrays.

Phillippy AM, Deng X, Zhang W, Salzberg SL.

BMC Bioinformatics. 2009 Sep 16;10:293. doi: 10.1186/1471-2105-10-293.

14.

Normalization and experimental design for ChIP-chip data.

Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ.

BMC Bioinformatics. 2007 Jun 25;8:219.

15.

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.

16.

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.

Borneman AR, Zhang ZD, Rozowsky J, Seringhaus MR, Gerstein M, Snyder M.

Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19.

PMID:
17638031
17.

Chromatin immunoprecipitation using microarrays.

Durand-Dubief M, Ekwall K.

Methods Mol Biol. 2009;529:279-95. doi: 10.1007/978-1-59745-538-1_18.

PMID:
19381973
18.

rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments.

Droit A, Cheung C, Gottardo R.

Bioinformatics. 2010 Mar 1;26(5):678-9. doi: 10.1093/bioinformatics/btq023. Epub 2010 Jan 19.

PMID:
20089513
19.
20.

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data.

Chen Y, Meyer CA, Liu T, Li W, Liu JS, Liu XS.

Genome Biol. 2011;12(2):R11. doi: 10.1186/gb-2011-12-2-r11. Epub 2011 Feb 1.

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