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Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae
Evan H Hurowitz, Patrick O Brown
Genome Biol. 2004; 5(1): R2. Published online 2003 December 22.
PMCID:
PMC395734
Abstract Full Text PDF–356K

Is Cited by the Following 34 Articles in this Archive:

Evolution of 5′ Untranslated Region Length and Gene Expression Reprogramming in Yeasts
Zhenguo Lin, Wen-Hsiung Li
Mol Biol Evol. 2012 January; 29(1): 81–89. Published online 2011 September 28. doi: 10.1093/molbev/msr143
PMCID:
PMC3245540
Free in PMC on 2013/01/01
Properties of untranslated regions of the S. cerevisiae genome
Tamir Tuller, Eytan Ruppin, Martin Kupiec
BMC Genomics. 2009; 10: 391. Published online 2009 August 22. doi: 10.1186/1471-2164-10-391
PMCID:
PMC2737003
Abstract Full Text PDF–757K Supplementary Material
Long 3′-UTRs target wild-type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae
Bessie W. Kebaara, Audrey L. Atkin
Nucleic Acids Res. 2009 May; 37(9): 2771–2778. Published online 2009 May. doi: 10.1093/nar/gkp146
PMCID:
PMC2685090
Abstract Full Text PDF–1.4M Supplementary Material
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast
Craig Lawless, Richard D Pearson, Julian N Selley, Julia B Smirnova, Christopher M Grant, Mark P Ashe, Graham D Pavitt, Simon J Hubbard
BMC Genomics. 2009; 10: 7. Published online 2009 January 7. doi: 10.1186/1471-2164-10-7
PMCID:
PMC2649001
Abstract Full Text PDF–1.4M Supplementary Material
Structural Characterization of the Rous Sarcoma Virus RNA Stability Element
Jason E. Weil, Michalis Hadjithomas, Karen L. Beemon
J Virol. 2009 March; 83(5): 2119–2129. Published online 2008 December 17. doi: 10.1128/JVI.02113-08
PMCID:
PMC2643715
Abstract Full Text PDF–958K Supplementary Material
Identification and characterization of extensive intra-molecular associations between 3′-UTRs and their ORFs
Naama Eldad, Yahav Yosefzon, Yoav Arava
Nucleic Acids Res. 2008 December; 36(21): 6728–6738. Published online 2008 December. doi: 10.1093/nar/gkn754
PMCID:
PMC2588509
Abstract Full Text PDF–4.9M
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne, Jan Komorowski
BMC Bioinformatics. 2008; 9: 484. Published online 2008 November 17. doi: 10.1186/1471-2105-9-484
PMCID:
PMC2629780
Abstract Full Text PDF–375K Supplementary Material
Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System
Daniel J Hogan, Daniel P Riordan, André P Gerber, Daniel Herschlag, Patrick O Brown
PLoS Biol. 2008 October; 6(10): e255. Published online 2008 October 28. doi: 10.1371/journal.pbio.0060255
PMCID:
PMC2573929
Abstract Full Text PDF–925K Supplementary Material
The 3′-UTR mediates the cellular localization of an mRNA encoding a short plasma membrane protein
Adi Loya, Lilach Pnueli, Yahav Yosefzon, Ydo Wexler, Michal Ziv-Ukelson, Yoav Arava
RNA. 2008 July; 14(7): 1352–1365. doi: 10.1261/rna.867208
PMCID:
PMC2441994
Abstract Full Text PDF–891K
Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae
Steve G. Hershman, Qijun Chen, Julia Y. Lee, Marina L. Kozak, Peng Yue, Li-San Wang, F. Brad Johnson
Nucleic Acids Res. 2008 January; 36(1): 144–156. Published online 2008 January. doi: 10.1093/nar/gkm986
PMCID:
PMC2248735
Abstract Full Text PDF–2.6M
Post-transcriptional gene regulation: From genome-wide studies to principles
R. E. Halbeisen, A. Galgano, T. Scherrer, A. P. Gerber
Cell Mol Life Sci. 2008 March; 65(5): 798–813. Published online 2007 November 26. doi: 10.1007/s00018-007-7447-6
PMCID:
PMC2771128
Abstract Full Text PDF–636K
Modeling SAGE tag formation and its effects on data interpretation within a Bayesian framework
Michael A Gilchrist, Hong Qin, Russell Zaretzki
BMC Bioinformatics. 2007; 8: 403. Published online 2007 October 18. doi: 10.1186/1471-2105-8-403
PMCID:
PMC2217564
Abstract Full Text PDF–408K Supplementary Material
Genome-wide polysomal analysis of a yeast strain with mutated ribosomal protein S9
Lilach Pnueli, Yoav Arava
BMC Genomics. 2007; 8: 285. Published online 2007 August 21. doi: 10.1186/1471-2164-8-285
PMCID:
PMC2020489
Abstract Full Text PDF–2.4M Supplementary Material
Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome
Traude H. Beilharz, Thomas Preiss
RNA. 2007 July; 13(7): 982–997. doi: 10.1261/rna.569407
PMCID:
PMC1894919
Abstract Full Text PDF–1.1M
Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions
Stephan Steigele, Wolfgang Huber, Claudia Stocsits, Peter F Stadler, Kay Nieselt
BMC Biol. 2007; 5: 25. Published online 2007 June 18. doi: 10.1186/1741-7007-5-25
PMCID:
PMC1914338
Abstract Full Text PDF–1.0M Supplementary Material
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
Paul G. Giresi, Jonghwan Kim, Ryan M. McDaniell, Vishwanath R. Iyer, Jason D. Lieb
Genome Res. 2007 June; 17(6): 877–885. doi: 10.1101/gr.5533506
PMCID:
PMC1891346
Abstract Full Text PDF–691K
Virtual Northern Analysis of the Human Genome
Evan H. Hurowitz, Iddo Drori, Victoria C. Stodden, David L. Donoho, Patrick O. Brown
PLoS ONE. 2007; 2(5): e460. Published online 2007 May 23. doi: 10.1371/journal.pone.0000460
PMCID:
PMC1866243
Abstract Full Text PDF–1.3M
Control of Signaling in a MAP-kinase Pathway by an RNA-Binding Protein
Susanne Prinz, Christine Aldridge, Stephen A. Ramsey, R. James Taylor, Timothy Galitski
PLoS ONE. 2007; 2(2): e249. Published online 2007 February 28. doi: 10.1371/journal.pone.0000249
PMCID:
PMC1803019
Abstract Full Text PDF–255K Supplementary Material
Evolutionary constraints on yeast protein size
Jonas Warringer, Anders Blomberg
BMC Evol Biol. 2006; 6: 61. Published online 2006 August 15. doi: 10.1186/1471-2148-6-61
PMCID:
PMC1560397
Abstract Full Text PDF–1.4M
Singular value decomposition of genome-scale mRNA lengths distribution reveals asymmetry in RNA gel electrophoresis band broadening
Orly Alter, Gene H. Golub
Proc Natl Acad Sci U S A. 2006 August 8; 103(32): 11828–11833. Published online 2006 July 28. doi: 10.1073/pnas.0604756103
PMCID:
PMC1524674
Abstract Full Text PDF–3.8M Supplementary Material
Deciphering principles of transcription regulation in eukaryotic genomes
Dat H Nguyen, Patrik D'haeseleer
Mol Syst Biol. 2006; 2: 2006.0012. Published online 2006 April 18. doi: 10.1038/msb4100054
PMCID:
PMC1681486
Abstract Full Text PDF–418K Supplementary Material
A high-resolution map of transcription in the yeast genome
Lior David, Wolfgang Huber, Marina Granovskaia, Joern Toedling, Curtis J. Palm, Lee Bofkin, Ted Jones, Ronald W. Davis, Lars M. Steinmetz
Proc Natl Acad Sci U S A. 2006 April 4; 103(14): 5320–5325. Published online 2006 March 28. doi: 10.1073/pnas.0601091103
PMCID:
PMC1414796
Abstract Full Text PDF–3.3M Supplementary Material
Evidence that Spt2/Sin1, an HMG-Like Factor, Plays Roles in Transcription Elongation, Chromatin Structure, and Genome Stability in Saccharomyces cerevisiae
Amine Nourani, Francois Robert, Fred Winston
Mol Cell Biol. 2006 February; 26(4): 1496–1509. doi: 10.1128/MCB.26.4.1496-1509.2006
PMCID:
PMC1367203
Abstract Full Text PDF–690K
Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast
Markus Ringnér, Morten Krogh
PLoS Comput Biol. 2005 December; 1(7): e72. Prepublished online 2005 November 9. Published online 2005 December 9. doi: 10.1371/journal.pcbi.0010072
PMCID:
PMC1309706
Abstract Full Text PDF–192K Supplementary Material
Gene Set Coregulated by the Saccharomyces cerevisiae Nonsense-Mediated mRNA Decay Pathway
Rachel Taylor, Bessie Wanja Kebaara, Tara Nazarenus, Ashley Jones, Rena Yamanaka, Rachel Uhrenholdt, Jason P. Wendler, Audrey L. Atkin
Eukaryot Cell. 2005 December; 4(12): 2066–2077. doi: 10.1128/EC.4.12.2066-2077.2005
PMCID:
PMC1317485
Abstract Full Text PDF–548K
Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae
Joseph A. Martens, Pei-Yun Jenny Wu, Fred Winston
Genes Dev. 2005 November 15; 19(22): 2695–2704. doi: 10.1101/gad.1367605
PMCID:
PMC1283962
Abstract Full Text PDF–434K
Dimethylation of Histone H3 at Lysine 36 Demarcates Regulatory and Nonregulatory Chromatin Genome-Wide
Bhargavi Rao, Yoichiro Shibata, Brian D. Strahl, Jason D. Lieb
Mol Cell Biol. 2005 November; 25(21): 9447–9459. doi: 10.1128/MCB.25.21.9447-9459.2005
PMCID:
PMC1265832
Abstract Full Text PDF–1.1M Supplementary Material
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs
Reut Shalgi, Michal Lapidot, Ron Shamir, Yitzhak Pilpel
Genome Biol. 2005; 6(10): R86. Published online 2005 September 30. doi: 10.1186/gb-2005-6-10-r86
PMCID:
PMC1257469
Abstract Full Text PDF–567K
Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes
Stephan Steigele, Kay Nieselt
Nucleic Acids Res. 2005; 33(16): 5034–5044. Published online 2005 September 7. doi: 10.1093/nar/gki804
PMCID:
PMC1201330
Abstract Full Text PDF–420K Supplementary Material
Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae
Chih Long Liu, Tommy Kaplan, Minkyu Kim, Stephen Buratowski, Stuart L Schreiber, Nir Friedman, Oliver J Rando
PLoS Biol. 2005 October; 3(10): e328. Published online 2005 August 30. doi: 10.1371/journal.pbio.0030328
PMCID:
PMC1195719
Abstract Full Text PDF–1.5M Supplementary Material
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