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A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome.

Jiang C, Pugh BF.

Genome Biol. 2009;10(10):R109. doi: 10.1186/gb-2009-10-10-r109. Epub 2009 Oct 8.


The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE.

Bioinformatics. 2009 Oct 15;25(20):2730-1. doi: 10.1093/bioinformatics/btp472. Epub 2009 Aug 4.


Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K.

Nat Struct Mol Biol. 2009 Aug;16(8):847-52. doi: 10.1038/nsmb.1636. Epub 2009 Jul 20.


Mechanisms that specify promoter nucleosome location and identity.

Hartley PD, Madhani HD.

Cell. 2009 May 1;137(3):445-58. doi: 10.1016/j.cell.2009.02.043.


Dissecting nucleosome free regions by a segmental semi-Markov model.

Sun W, Xie W, Xu F, Grunstein M, Li KC.

PLoS One. 2009;4(3):e4721. doi: 10.1371/journal.pone.0004721. Epub 2009 Mar 6.


Widespread bidirectional promoters are the major source of cryptic transcripts in yeast.

Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz LM, Jacquier A.

Nature. 2009 Feb 19;457(7232):1038-42. doi: 10.1038/nature07747. Epub 2009 Jan 25.


Bidirectional promoters generate pervasive transcription in yeast.

Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-M√ľnster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM.

Nature. 2009 Feb 19;457(7232):1033-7. doi: 10.1038/nature07728. Epub 2009 Jan 25.


A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome.

Venters BJ, Pugh BF.

Genome Res. 2009 Mar;19(3):360-71. doi: 10.1101/gr.084970.108. Epub 2009 Jan 5.


A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR.

Mol Cell. 2008 Dec 26;32(6):878-87. doi: 10.1016/j.molcel.2008.11.020.


The DNA-encoded nucleosome organization of a eukaryotic genome.

Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E.

Nature. 2009 Mar 19;458(7236):362-6. doi: 10.1038/nature07667. Epub 2008 Dec 17.


Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites.

Sasaki S, Mello CC, Shimada A, Nakatani Y, Hashimoto S, Ogawa M, Matsushima K, Gu SG, Kasahara M, Ahsan B, Sasaki A, Saito T, Suzuki Y, Sugano S, Kohara Y, Takeda H, Fire A, Morishita S.

Science. 2009 Jan 16;323(5912):401-4. doi: 10.1126/science.1163183. Epub 2008 Dec 11.


Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.

Core LJ, Waterfall JJ, Lis JT.

Science. 2008 Dec 19;322(5909):1845-8. doi: 10.1126/science.1162228. Epub 2008 Dec 4.


Divergent transcription from active promoters.

Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA.

Science. 2008 Dec 19;322(5909):1849-51. doi: 10.1126/science.1162253. Epub 2008 Dec 4.


The antisense transcriptomes of human cells.

He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW.

Science. 2008 Dec 19;322(5909):1855-7. doi: 10.1126/science.1163853. Epub 2008 Dec 4.


RNA exosome depletion reveals transcription upstream of active human promoters.

Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH.

Science. 2008 Dec 19;322(5909):1851-4. doi: 10.1126/science.1164096. Epub 2008 Dec 4.


Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome.

Cheung V, Chua G, Batada NN, Landry CR, Michnick SW, Hughes TR, Winston F.

PLoS Biol. 2008 Nov 11;6(11):e277. doi: 10.1371/journal.pbio.0060277.


Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.

Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E.

PLoS Comput Biol. 2008 Nov;4(11):e1000216. doi: 10.1371/journal.pcbi.1000216. Epub 2008 Nov 7.


The exosome: a multipurpose RNA-decay machine.

Schmid M, Jensen TH.

Trends Biochem Sci. 2008 Oct;33(10):501-10. doi: 10.1016/j.tibs.2008.07.003. Epub 2008 Sep 9. Review.


Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping.

Dutrow N, Nix DA, Holt D, Milash B, Dalley B, Westbroek E, Parnell TJ, Cairns BR.

Nat Genet. 2008 Aug;40(8):977-86. doi: 10.1038/ng.196. Epub 2008 Jul 20.


A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.

Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF.

Genome Res. 2008 Jul;18(7):1073-83. doi: 10.1101/gr.078261.108. Epub 2008 Jun 12.

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