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Items: 1 to 20 of 33

1.

Dynamic and complex transcription factor binding during an inducible response in yeast.

Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L, Gerstein MB, Snyder M.

Genes Dev. 2009 Jun 1;23(11):1351-63. doi: 10.1101/gad.1781909.

2.

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.

3.

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.

4.

FLO1 is a variable green beard gene that drives biofilm-like cooperation in budding yeast.

Smukalla S, Caldara M, Pochet N, Beauvais A, Guadagnini S, Yan C, Vinces MD, Jansen A, Prevost MC, Latgé JP, Fink GR, Foster KR, Verstrepen KJ.

Cell. 2008 Nov 14;135(4):726-37. doi: 10.1016/j.cell.2008.09.037.

5.

Model-based analysis of ChIP-Seq (MACS).

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS.

Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17.

6.

Species-specific transcription in mice carrying human chromosome 21.

Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VL, Fisher EM, Tavaré S, Odom DT.

Science. 2008 Oct 17;322(5900):434-8. doi: 10.1126/science.1160930. Epub 2008 Sep 11.

7.

High-resolution mapping of meiotic crossovers and non-crossovers in yeast.

Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM.

Nature. 2008 Jul 24;454(7203):479-85. doi: 10.1038/nature07135. Epub 2008 Jul 9.

8.

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.

PMID:
18228445
9.

Large-scale analysis of yeast filamentous growth by systematic gene disruption and overexpression.

Jin R, Dobry CJ, McCown PJ, Kumar A.

Mol Biol Cell. 2008 Jan;19(1):284-96. Epub 2007 Nov 7.

10.

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.

11.

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789.

Wei W, McCusker JH, Hyman RW, Jones T, Ning Y, Cao Z, Gu Z, Bruno D, Miranda M, Nguyen M, Wilhelmy J, Komp C, Tamse R, Wang X, Jia P, Luedi P, Oefner PJ, David L, Dietrich FS, Li Y, Davis RW, Steinmetz LM.

Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12825-30. Epub 2007 Jul 25.

12.

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
13.

Mapping determinants of gene expression plasticity by genetical genomics in C. elegans.

Li Y, Alvarez OA, Gutteling EW, Tijsterman M, Fu J, Riksen JA, Hazendonk E, Prins P, Plasterk RH, Jansen RC, Breitling R, Kammenga JE.

PLoS Genet. 2006 Dec 29;2(12):e222. Epub 2006 Nov 13.

14.

Genetics of global gene expression.

Rockman MV, Kruglyak L.

Nat Rev Genet. 2006 Nov;7(11):862-72. Review.

PMID:
17047685
15.

An improved map of conserved regulatory sites for Saccharomyces cerevisiae.

MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E.

BMC Bioinformatics. 2006 Mar 7;7:113.

16.

Target hub proteins serve as master regulators of development in yeast.

Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M.

Genes Dev. 2006 Feb 15;20(4):435-48. Epub 2006 Jan 31.

17.

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP.

Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. Epub 2005 Sep 30.

18.

Local regulatory variation in Saccharomyces cerevisiae.

Ronald J, Brem RB, Whittle J, Kruglyak L.

PLoS Genet. 2005 Aug;1(2):e25. Epub 2005 Aug 19.

19.

TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs.

Gordon DB, Nekludova L, McCallum S, Fraenkel E.

Bioinformatics. 2005 Jul 15;21(14):3164-5. Epub 2005 May 19.

PMID:
15905282
20.

Searching for the genome's second code.

Pennisi E.

Science. 2004 Oct 22;306(5696):632-5. No abstract available.

PMID:
15499005

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