-
2
-
-
1442329652
-
Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae
-
Hurowitz EH, Brown PO (2003) Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol 5: R2.
-
(2003)
Genome Biol
, vol.5
-
-
Hurowitz, E.H.1
Brown, P.O.2
-
3
-
-
0035320036
-
MRNA localization: Message on the move
-
Jansen RP (2001) mRNA localization: Message on the move. Nat Rev Mol Cell Biol 2: 247-256.
-
(2001)
Nat Rev Mol Cell Biol
, vol.2
, pp. 247-256
-
-
Jansen, R.P.1
-
5
-
-
0036289532
-
Eukaryotic mRNPs may represent posttranscriptional operons
-
Keene JD, Tenenbaum SA (2002) Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell 9: 1161-1167.
-
(2002)
Mol Cell
, vol.9
, pp. 1161-1167
-
-
Keene, J.D.1
Tenenbaum, S.A.2
-
6
-
-
0037313537
-
Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery
-
Hieronymus H, Silver PA (2003) Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat Genet 33: 155-161.
-
(2003)
Nat Genet
, vol.33
, pp. 155-161
-
-
Hieronymus, H.1
Silver, P.A.2
-
7
-
-
19344365947
-
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
-
DOI: 10.1371/journal.pbio.0020079
-
Gerber AP, Herschlag D, Brown PO (2004) Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol 2: e79. DOI: 10.1371/journal.pbio.0020079
-
(2004)
PLoS Biol
, vol.2
, pp. 79
-
-
Gerber, A.P.1
Herschlag, D.2
Brown, P.O.3
-
8
-
-
0024546509
-
The scanning model for translation: An update
-
Kozak M (1989) The scanning model for translation: An update. J Cell Biol 108: 229-241.
-
(1989)
J Cell Biol
, vol.108
, pp. 229-241
-
-
Kozak, M.1
-
9
-
-
0021799353
-
Insertion mutagenesis to increase secondary structure within the 59 noncoding region of a eukaryotic mRNA reduces translational efficiency
-
Pelletier J, Sonenberg N (1985) Insertion mutagenesis to increase secondary structure within the 59 noncoding region of a eukaryotic mRNA reduces translational efficiency. Cell 40: 515-526.
-
(1985)
Cell
, vol.40
, pp. 515-526
-
-
Pelletier, J.1
Sonenberg, N.2
-
10
-
-
0023988840
-
MRNA structures influencing translation in the yeast Saccharomyces cerevisiae
-
Baim SB, Sherman F (1988) mRNA structures influencing translation in the yeast Saccharomyces cerevisiae. Mol Cell Biol 8: 1591-1601.
-
(1988)
Mol Cell Biol
, vol.8
, pp. 1591-1601
-
-
Baim, S.B.1
Sherman, F.2
-
11
-
-
0023665902
-
An analysis of 59-noncoding sequences from 699 vertebrate messenger RNAs
-
Kozak M (1987) An analysis of 59-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res 15: 8125-8148.
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 8125-8148
-
-
Kozak, M.1
-
12
-
-
0024414469
-
Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs
-
Kozak M (1989) Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs. Mol Cell Biol 9: 5134-5142.
-
(1989)
Mol Cell Biol
, vol.9
, pp. 5134-5142
-
-
Kozak, M.1
-
13
-
-
0028961870
-
Turnover mechanisms of the stable yeast PGK1 mRNA
-
Muhlrad D, Decker CJ, Parker R (1995) Turnover mechanisms of the stable yeast PGK1 mRNA. Mol Cell Biol 15: 2145-2156.
-
(1995)
Mol Cell Biol
, vol.15
, pp. 2145-2156
-
-
Muhlrad, D.1
Decker, C.J.2
Parker, R.3
-
14
-
-
0033005239
-
The role of the 59 untranslated region of an mRNA in translation regulation during development
-
van der Velden AW, Thomas AAM (1999) The role of the 59 untranslated region of an mRNA in translation regulation during development. Int J Biochem Cell Biol 31: 87-106.
-
(1999)
Int J Biochem Cell Biol
, vol.31
, pp. 87-106
-
-
Van Der Velden, A.W.1
Thomas, A.A.M.2
-
15
-
-
0035032444
-
The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 59 secondary structure
-
Svitkin YV, Pause A, Haghighat A, Pyronnet S, Witherell G, et al. (2001) The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 59 secondary structure. RNA 7: 382-394.
-
(2001)
RNA
, vol.7
, pp. 382-394
-
-
Svitkin, Y.V.1
Pause, A.2
Haghighat, A.3
Pyronnet, S.4
Witherell, G.5
-
16
-
-
0028202495
-
Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 59 to 39 digestion of the transcript
-
Muhlrad D, Decker CJ, Parker R (1994) Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 59 to 39 digestion of the transcript. Genes Dev 8: 855-866.
-
(1994)
Genes Dev
, vol.8
, pp. 855-866
-
-
Muhlrad, D.1
Decker, C.J.2
Parker, R.3
-
18
-
-
23944483135
-
Post-transcriptional control of gene expression: A genome-wide perspective
-
Mata J, Marguerat S, Bahler J (2005) Post-transcriptional control of gene expression: A genome-wide perspective. Trends Biochem Sci 30: 506-514.
-
(2005)
Trends Biochem Sci
, vol.30
, pp. 506-514
-
-
Mata, J.1
Marguerat, S.2
Bahler, J.3
-
19
-
-
0742288008
-
The enzymes and control of eukaryotic mRNA turnover
-
Parker R, Song H (2004) The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 11: 121-127.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 121-127
-
-
Parker, R.1
Song, H.2
-
20
-
-
0033790503
-
Mechanisms and control of mRNA decapping in Saccharomyces cerevisiae
-
Tucker M, Parker R (2000) Mechanisms and control of mRNA decapping in Saccharomyces cerevisiae. Annu Rev Biochem 69: 571-595.
-
(2000)
Annu Rev Biochem
, vol.69
, pp. 571-595
-
-
Tucker, M.1
Parker, R.2
-
21
-
-
0035983107
-
The role of the 59 untranslated region (UTR) in glucose-dependent mRNA decay
-
de la Cruz BJ, Prieto S, Scheffler IE (2002) The role of the 59 untranslated region (UTR) in glucose-dependent mRNA decay. Yeast 19: 887-902.
-
(2002)
Yeast
, vol.19
, pp. 887-902
-
-
Cruz, B.J.1
Prieto, S.2
Scheffler, I.E.3
-
22
-
-
0036021444
-
Emerging links between initiation of translation and human diseases
-
Kozak M (2002) Emerging links between initiation of translation and human diseases. Mamm Genome 13: 401-410.
-
(2002)
Mamm Genome
, vol.13
, pp. 401-410
-
-
Kozak, M.1
-
23
-
-
12344281782
-
The implications of structured 59 untranslated regions on translation and disease
-
Pickering BM, Willis AE (2005) The implications of structured 59 untranslated regions on translation and disease. Semin Cell Dev Biol 16: 39-47.
-
(2005)
Semin Cell Dev Biol
, vol.16
, pp. 39-47
-
-
Pickering, B.M.1
Willis, A.E.2
-
24
-
-
0037162469
-
Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
-
Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99: 9697-9702.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 9697-9702
-
-
Bernstein, J.A.1
Khodursky, A.B.2
Lin, P.H.3
Lin-Chao, S.4
Cohen, S.N.5
-
25
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, et al. (1994) Fast folding and comparison of RNA secondary structures. Monatsh Chem 125: 167-188.
-
(1994)
Monatsh Chem
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, S.4
Tacker, M.5
-
26
-
-
0032552882
-
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
-
Xia T, SantaLucia JJ, Burkard ME, Kierzek R, Schroeder SJ, et al. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37: 14719-14735.
-
(1998)
Biochemistry
, vol.37
, pp. 14719-14735
-
-
Xia, T.1
Santalucia, J.J.2
Burkard, M.E.3
Kierzek, R.4
Schroeder, S.J.5
-
27
-
-
0033572893
-
No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
-
Workman C, Krogh A (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res 27: 4816-4822.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 4816-4822
-
-
Workman, C.1
Krogh, A.2
-
28
-
-
17844391015
-
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency
-
Clote P, Ferre F, Kranakis E, Krizanc D (2005) Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA 11: 578-591.
-
(2005)
RNA
, vol.11
, pp. 578-591
-
-
Clote, P.1
Ferre, F.2
Kranakis, E.3
Krizanc, D.4
-
29
-
-
0022360113
-
Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage
-
Altschul SF, Erickson BW (1985) Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage. Mol Biol Evol 2: 526-538.
-
(1985)
Mol Biol e
, vol.2
, pp. 526-538
-
-
Altschul, S.F.1
Erickson, B.W.2
-
30
-
-
0037388094
-
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
-
Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, et al. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100: 3889-3894.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 3889-3894
-
-
Arava, Y.1
Wang, Y.2
Storey, J.D.3
Liu, C.L.4
Brown, P.O.5
-
31
-
-
10944232800
-
Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale
-
Beyer A, Hollunder J, Nasheuer HP, Wilhelm T (2004) Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics 3: 1083-1092.
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 1083-1092
-
-
Beyer, A.1
Hollunder, J.2
Nasheuer, H.P.3
Wilhelm, T.4
-
32
-
-
0037197892
-
Precision and functional specificity in mRNA decay
-
Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, et al. (2002)Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U SA 99: 5860-5865.
-
(2002)
Proc Natl Acad Sci U SA
, vol.99
, pp. 5860-5865
-
-
Wang, Y.1
Liu, C.L.2
Storey, J.D.3
Tibshirani, R.J.4
Herschlag, D.5
-
33
-
-
0032778953
-
Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae
-
Schwartz DC, Parker R (1999) Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae. Mol Cell Biol 19: 5247-5256.
-
(1999)
Mol Cell Biol
, vol.19
, pp. 5247-5256
-
-
Schwartz, D.C.1
Parker, R.2
-
34
-
-
0346801873
-
The Gene Ontology (GO) database and informatics resource
-
Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: 258-261.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 258-261
-
-
Harris, Ma.1
Clark, J.2
Ireland, A.3
Lomax, J.4
Ashburner, M.5
-
35
-
-
13244279520
-
Comparing functional annotation analyses with Catmap
-
Breslin T, Edén P, Krogh M (2004) Comparing functional annotation analyses with Catmap. BMC Bioinformatics 5: 193.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 193
-
-
Breslin, T.1
Edén, P.2
Krogh, M.3
-
36
-
-
0141519339
-
Widespread selection for local RNA secondary structure in coding regions of bacterial genes
-
Katz L, Burge CB (2003) Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res 13: 2042-2051.
-
(2003)
Genome Res
, vol.13
, pp. 2042-2051
-
-
Katz, L.1
Burge, C.B.2
-
37
-
-
0036137613
-
An integrated approach for finding overlooked genes in yeast
-
Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, et al. (2002) An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20: 58-63.
-
(2002)
Nat Biotechnol
, vol.20
, pp. 58-63
-
-
Kumar, A.1
Harrison, P.M.2
Cheung, K.H.3
Lan, N.4
Echols, N.5
-
38
-
-
0031832807
-
Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence
-
Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF (1998) Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8: 464-478.
-
(1998)
Genome Res
, vol.8
, pp. 464-478
-
-
Kim, J.M.1
Vanguri, S.2
Boeke, J.D.3
Gabriel, A.4
Voytas, D.F.5
-
39
-
-
2942561052
-
Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors
-
Grigull J, Mnaimneh S, Pootoolal J, Robinson MD, Hughes TR (2004) Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol 24: 5534-5547.
-
(2004)
Mol Cell Biol
, vol.24
, pp. 5534-5547
-
-
Grigull, J.1
Mnaimneh, S.2
Pootoolal, J.3
Robinson, M.D.4
Hughes, T.R.5
-
40
-
-
0019433557
-
Regulation of protein synthesis during heat shock
-
Lindquist S (1981) Regulation of protein synthesis during heat shock. Nature 293: 311-314.
-
(1981)
Nature
, vol.293
, pp. 311-314
-
-
Lindquist, S.1
-
41
-
-
9644275414
-
Translational regulation of Hsp90 mRNA. AUG-proximal 59-untranslated region elements essential for preferential heat shock translation
-
Ahmed R, Duncan RF (2004) Translational regulation of Hsp90 mRNA. AUG-proximal 59-untranslated region elements essential for preferential heat shock translation. J Biol Chem 279: 49919-49930.
-
(2004)
J Biol Chem
, vol.279
, pp. 49919-49930
-
-
Ahmed, R.1
Duncan, R.F.2
-
43
-
-
0041327747
-
Variations in yeast 39-processing cis-elements correlate with transcript stability
-
Graber JH (2003) Variations in yeast 39-processing cis-elements correlate with transcript stability. Trends Genet 19: 473-476.
-
(2003)
Trends Genet
, vol.19
, pp. 473-476
-
-
Graber, J.H.1
-
44
-
-
0347416978
-
Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 59 to 39 mRNA decay pathways in yeast
-
He F, Li X, Spatrick P, Casillo R, Dong S, et al. (2003) Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 59 to 39 mRNA decay pathways in yeast. Mol Cell 12: 1439-1452.
-
(2003)
Mol Cell
, vol.12
, pp. 1439-1452
-
-
He, F.1
Li, X.2
Spatrick, P.3
Casillo, R.4
Dong, S.5
-
45
-
-
0242384746
-
Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune sera
-
Tenenbaum SA, Carson CC, Atasoy U, Keene JD (2003) Genome-wide regulatory analysis using en masse nuclear run-ons and ribonomic profiling with autoimmune sera. Gene 317: 79-87.
-
(2003)
Gene
, vol.317
, pp. 79-87
-
-
Tenenbaum, S.A.1
Carson, C.C.2
Atasoy, U.3
Keene, J.D.4
-
46
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
-
(2000)
Mol Biol Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
-
47
-
-
0141920354
-
Comparing protein abundance and mRNA expression levels on a genomic scale
-
Greenbaum D, Colangelo C, Williams K, Gerstein M (2003) Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 4: 117.
-
(2003)
Genome Biol
, vol.4
, pp. 117
-
-
Greenbaum, D.1
Colangelo, C.2
Williams, K.3
Gerstein, M.4
-
48
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, et al. (2003) Global analysis of protein expression in yeast. Nature 425: 737-741.
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.K.2
Bower, K.3
Howson, R.W.4
Belle, A.5
-
49
-
-
0033119454
-
MRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences
-
Seffens W, Digby D (1999) mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res 27: 1578-1584.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 1578-1584
-
-
Seffens, W.1
Digby, D.2
-
50
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka R, Gentleman R (1996) R: A language for data analysis and graphics. J Comput Grap Stat 5: 299-314.
-
(1996)
J Comput Grap Stat
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
|