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Items: 1 to 20 of 54

1.

Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae.

Kim Guisbert KS, Zhang Y, Flatow J, Hurtado S, Staley JP, Lin S, Sontheimer EJ.

RNA. 2012 Jun;18(6):1142-53. doi: 10.1261/rna.030510.111. Epub 2012 Apr 26.

2.

High-resolution view of the yeast meiotic program revealed by ribosome profiling.

Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS.

Science. 2012 Feb 3;335(6068):552-7. doi: 10.1126/science.1215110. Epub 2011 Dec 22.

3.

SignalP 4.0: discriminating signal peptides from transmembrane regions.

Petersen TN, Brunak S, von Heijne G, Nielsen H.

Nat Methods. 2011 Sep 29;8(10):785-6. doi: 10.1038/nmeth.1701. No abstract available.

PMID:
21959131
4.

RNA sequencing.

Waern K, Nagalakshmi U, Snyder M.

Methods Mol Biol. 2011;759:125-32. doi: 10.1007/978-1-61779-173-4_8.

PMID:
21863485
5.

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast.

Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP.

Mol Syst Biol. 2011 Jul 19;7:514. doi: 10.1038/msb.2011.48.

6.

The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae.

Chu D, Barnes DJ, von der Haar T.

Nucleic Acids Res. 2011 Aug;39(15):6705-14. doi: 10.1093/nar/gkr300. Epub 2011 May 9.

7.

Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation.

Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM.

Cell. 2010 Dec 10;143(6):1018-29. doi: 10.1016/j.cell.2010.11.020.

8.

Differential expression analysis for sequence count data.

Anders S, Huber W.

Genome Biol. 2010;11(10):R106. doi: 10.1186/gb-2010-11-10-r106. Epub 2010 Oct 27.

9.

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome.

Riordan DP, Herschlag D, Brown PO.

Nucleic Acids Res. 2011 Mar;39(4):1501-9. doi: 10.1093/nar/gkq920. Epub 2010 Oct 18.

10.

Comprehensive comparative analysis of strand-specific RNA sequencing methods.

Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A.

Nat Methods. 2010 Sep;7(9):709-15. doi: 10.1038/nmeth.1491. Epub 2010 Aug 15.

11.

The landscape of C. elegans 3'UTRs.

Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak SD, Mis E, Zegar C, Gutwein MR, Khivansara V, Attie O, Chen K, Salehi-Ashtiani K, Vidal M, Harkins TT, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F, Gunsalus KC, Kim JK.

Science. 2010 Jul 23;329(5990):432-5. doi: 10.1126/science.1191244. Epub 2010 Jun 3.

12.

Noncanonical transcript forms in yeast and their regulation during environmental stress.

Yoon OK, Brem RB.

RNA. 2010 Jun;16(6):1256-67. doi: 10.1261/rna.2038810. Epub 2010 Apr 26.

13.

RNA-Seq: a method for comprehensive transcriptome analysis.

Nagalakshmi U, Waern K, Snyder M.

Curr Protoc Mol Biol. 2010 Jan;Chapter 4:Unit 4.11.1-13. doi: 10.1002/0471142727.mb0411s89.

PMID:
20069539
14.

Predicting functional upstream open reading frames in Saccharomyces cerevisiae.

Selpi, Bryant CH, Kemp GJ, Sarv J, Kristiansson E, Sunnerhagen P.

BMC Bioinformatics. 2009;10:451. doi: 10.1186/1471-2105-10-451. Epub 2009 Dec 30.

15.

Transcriptome analysis by strand-specific sequencing of complementary DNA.

Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A.

Nucleic Acids Res. 2009 Oct;37(18):e123. doi: 10.1093/nar/gkp596. Epub 2009 Jul 20.

16.

Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi.

Hood HM, Neafsey DE, Galagan J, Sachs MS.

Annu Rev Microbiol. 2009;63:385-409. doi: 10.1146/annurev.micro.62.081307.162835. Review.

PMID:
19514854
17.

TopHat: discovering splice junctions with RNA-Seq.

Trapnell C, Pachter L, Salzberg SL.

Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16.

18.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

19.

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.

20.

Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast.

Lawless C, Pearson RD, Selley JN, Smirnova JB, Grant CM, Ashe MP, Pavitt GD, Hubbard SJ.

BMC Genomics. 2009 Jan 7;10:7. doi: 10.1186/1471-2164-10-7.

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