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PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.

Nat Biotechnol. 2009 Jan;27(1):66-75. doi: 10.1038/nbt.1518. Epub 2009 Jan 4.


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.


A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome.

Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ, Kuroda MI.

Cell. 2008 Aug 22;134(4):599-609. doi: 10.1016/j.cell.2008.06.033.


Fus3-triggered Tec1 degradation modulates mating transcriptional output during the pheromone response.

Chou S, Zhao S, Song Y, Liu H, Nie Q.

Mol Syst Biol. 2008;4:212. doi: 10.1038/msb.2008.47. Epub 2008 Aug 5.


High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies.

Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, Wang JD, Chen R.

PLoS Genet. 2008 Aug 1;4(8):e1000139. doi: 10.1371/journal.pgen.1000139.


High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G.

Nat Genet. 2008 Aug;40(8):987-93. doi: 10.1038/ng.195. Epub 2008 Jul 27.


Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing.

Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao Y, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones S, Hoodless PA.

Nucleic Acids Res. 2008 Aug;36(14):4549-64. doi: 10.1093/nar/gkn382. Epub 2008 Jul 8.


Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.

Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH.

Cell. 2008 Jun 13;133(6):1106-17. doi: 10.1016/j.cell.2008.04.043.


Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.

Nat Methods. 2008 Jul;5(7):621-8. doi: 10.1038/nmeth.1226. Epub 2008 May 30.


Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.

Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J.

Nature. 2008 Jun 26;453(7199):1239-43. doi: 10.1038/nature07002. Epub 2008 May 18.


Altered dosage and mislocalization of histone H3 and Cse4p lead to chromosome loss in Saccharomyces cerevisiae.

Au WC, Crisp MJ, DeLuca SZ, Rando OJ, Basrai MA.

Genetics. 2008 May;179(1):263-75. doi: 10.1534/genetics.108.088518. Epub 2008 May 5.


The transcriptional landscape of the yeast genome defined by RNA sequencing.

Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M.

Science. 2008 Jun 6;320(5881):1344-9. doi: 10.1126/science.1158441. Epub 2008 May 1.


Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR.

Cell. 2008 May 2;133(3):523-36. doi: 10.1016/j.cell.2008.03.029.


Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo.

Aparicio O, Geisberg JV, Struhl K.

Curr Protoc Cell Biol. 2004 Sep;Chapter 17:Unit 17.7. doi: 10.1002/0471143030.cb1707s23. Review.


Protein characterization of Saccharomyces cerevisiae RNA polymerase II after in vivo cross-linking.

Tardiff DF, Abruzzi KC, Rosbash M.

Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19948-53. Epub 2007 Dec 5.


Divergence of transcription factor binding sites across related yeast species.

Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M.

Science. 2007 Aug 10;317(5839):815-9.


Targeted high-throughput sequencing of tagged nucleic acid samples.

Meyer M, Stenzel U, Myles S, Prüfer K, Hofreiter M.

Nucleic Acids Res. 2007;35(15):e97. Epub 2007 Aug 1.


Nonhistone Scm3 and histones CenH3-H4 assemble the core of centromere-specific nucleosomes.

Mizuguchi G, Xiao H, Wisniewski J, Smith MM, Wu C.

Cell. 2007 Jun 15;129(6):1153-64.


A specialized nucleosome has a "point" to make.

Zhang W, Mellone BG, Karpen GH.

Cell. 2007 Jun 15;129(6):1047-9.


Scm3 is essential to recruit the histone h3 variant cse4 to centromeres and to maintain a functional kinetochore.

Camahort R, Li B, Florens L, Swanson SK, Washburn MP, Gerton JL.

Mol Cell. 2007 Jun 22;26(6):853-65. Epub 2007 Jun 14.

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