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Items: 1 to 20 of 115


Multiple testing methods for ChIP-Chip high density oligonucleotide array data.

Keleş S, van der Laan MJ, Dudoit S, Cawley SE.

J Comput Biol. 2006 Apr;13(3):579-613.


A global map of p53 transcription-factor binding sites in the human genome.

Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y.

Cell. 2006 Jan 13;124(1):207-19.


ChIP-on-chip analysis of in vivo mutant p53 binding to selected gene promoters.

Dell'Orso S, Fontemaggi G, Stambolsky P, Goeman F, Voellenkle C, Levrero M, Strano S, Rotter V, Oren M, Blandino G.

OMICS. 2011 May;15(5):305-12. doi: 10.1089/omi.2010.0084. Epub 2011 Feb 19.


Distinct p53 genomic binding patterns in normal and cancer-derived human cells.

Botcheva K, McCorkle SR, McCombie WR, Dunn JJ, Anderson CW.

Cell Cycle. 2011 Dec 15;10(24):4237-49. doi: 10.4161/cc.10.24.18383. Epub 2011 Dec 15.


Integration of cap analysis of gene expression and chromatin immunoprecipitation analysis on array reveals genome-wide androgen receptor signaling in prostate cancer cells.

Takayama K, Tsutsumi S, Katayama S, Okayama T, Horie-Inoue K, Ikeda K, Urano T, Kawazu C, Hasegawa A, Ikeo K, Gojyobori T, Ouchi Y, Hayashizaki Y, Aburatani H, Inoue S.

Oncogene. 2011 Feb 3;30(5):619-30. doi: 10.1038/onc.2010.436. Epub 2010 Oct 4.


Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation.

Kubosaki A, Tomaru Y, Tagami M, Arner E, Miura H, Suzuki T, Suzuki M, Suzuki H, Hayashizaki Y.

Genome Biol. 2009;10(4):R41. doi: 10.1186/gb-2009-10-4-r41. Epub 2009 Apr 19.


Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR.

Cell. 2004 Feb 20;116(4):499-509.


Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome.

Bieda M, Xu X, Singer MA, Green R, Farnham PJ.

Genome Res. 2006 May;16(5):595-605. Epub 2006 Apr 10.


Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.

Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M.

Cell. 2005 Jul 15;122(1):33-43.


Distribution of NF-kappaB-binding sites across human chromosome 22.

Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M.

Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52. Epub 2003 Oct 3.


Chromatin immunoprecipitation (ChIP) on chip experiments uncover a widespread distribution of NF-Y binding CCAAT sites outside of core promoters.

Testa A, Donati G, Yan P, Romani F, Huang TH, Viganò MA, Mantovani R.

J Biol Chem. 2005 Apr 8;280(14):13606-15. Epub 2005 Jan 11.


p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy.

Lidor Nili E, Field Y, Lubling Y, Widom J, Oren M, Segal E.

Genome Res. 2010 Oct;20(10):1361-8. doi: 10.1101/gr.103945.109. Epub 2010 Aug 17.


Characterization of genome-wide p53-binding sites upon stress response.

Smeenk L, van Heeringen SJ, Koeppel M, van Driel MA, Bartels SJ, Akkers RC, Denissov S, Stunnenberg HG, Lohrum M.

Nucleic Acids Res. 2008 Jun;36(11):3639-54. doi: 10.1093/nar/gkn232. Epub 2008 May 12.


A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.


Nanobody(R)-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites.

Nguyen-Duc T, Peeters E, Muyldermans S, Charlier D, Hassanzadeh-Ghassabeh G.

Nucleic Acids Res. 2013 Mar 1;41(5):e59. doi: 10.1093/nar/gks1342. Epub 2012 Dec 28.


Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.

Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M.

Genome Res. 2007 Jun;17(6):898-909.


Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.


Myc-binding-site recognition in the human genome is determined by chromatin context.

Guccione E, Martinato F, Finocchiaro G, Luzi L, Tizzoni L, Dall' Olio V, Zardo G, Nervi C, Bernard L, Amati B.

Nat Cell Biol. 2006 Jul;8(7):764-70. Epub 2006 Jun 11.


TileMap: create chromosomal map of tiling array hybridizations.

Ji H, Wong WH.

Bioinformatics. 2005 Sep 15;21(18):3629-36. Epub 2005 Jul 26.


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