-
1
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M. and Snyder, M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349.
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
Gerstein, M.6
Snyder, M.7
-
2
-
-
0033016717
-
Correlation between protein and mRNA abundance in yeast
-
Gygi, S.P., Rochon, Y., Franza, B.R. and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol., 19, 1720-1730.
-
(1999)
Mol. Cell. Biol.
, vol.19
, pp. 1720-1730
-
-
Gygi, S.P.1
Rochon, Y.2
Franza, B.R.3
Aebersold, R.4
-
3
-
-
0023650543
-
The codon adaptation index a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp, P.M. and Li, W.H. (1987) The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res., 15, 1281-1295.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
4
-
-
34047223024
-
Posttranscriptional expression regulation: What determines translation rates
-
Brockmann, R., Beyer, A., Heinisch, J.J. and Wilhelm, T. (2007) Posttranscriptional expression regulation: what determines translation rates PLoS Comput. Biol., 3, e57.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Brockmann, R.1
Beyer, A.2
Heinisch, J.J.3
Wilhelm, T.4
-
5
-
-
4644280499
-
Solving the riddle of codon usage preferences: A test for translational selection
-
dos Reis, M., Savva, R. and Wernisch, L. (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res., 32, 5036-5044.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5036-5044
-
-
Dos Reis, M.1
Savva, R.2
Wernisch, L.3
-
6
-
-
84873570699
-
Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
-
Pechmann, S. and Frydman, J. (2013) Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nat. Struct. Mol. Biol., 20, 237-243.
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 237-243
-
-
Pechmann, S.1
Frydman, J.2
-
7
-
-
0035231288
-
Initiation factor eIF2 alpha phosphorylation in stress responses and apoptosis
-
Clemens, M.J. (2001) Initiation factor eIF2 alpha phosphorylation in stress responses and apoptosis. Prog. Mol. Subcell. Biol., 27, 57-89.
-
(2001)
Prog. Mol. Subcell. Biol.
, vol.27
, pp. 57-89
-
-
Clemens, M.J.1
-
8
-
-
12344305214
-
EIF2 and the control of cell physiology
-
Proud, C.G. (2005) eIF2 and the control of cell physiology. Semin. Cell Dev. Biol., 16, 3-12.
-
(2005)
Semin. Cell Dev. Biol.
, vol.16
, pp. 3-12
-
-
Proud, C.G.1
-
9
-
-
5044229348
-
Molecular mechanisms of translational control
-
Gebauer, F. and Hentze, M.W. (2004) Molecular mechanisms of translational control. Nat. Rev. Mol. Cell Biol., 5, 827-835.
-
(2004)
Nat. Rev. Mol. Cell Biol.
, vol.5
, pp. 827-835
-
-
Gebauer, F.1
Hentze, M.W.2
-
10
-
-
0031020341
-
Homologous segments in three subunits of the guanine nucleotide exchange factor eIF2B mediate translational regulation by phosphorylation of eIF2
-
Pavitt, G.D., Yang, W. and Hinnebusch, A.G. (1997) Homologous segments in three subunits of the guanine nucleotide exchange factor eIF2B mediate translational regulation by phosphorylation of eIF2. Mol. Cell. Biol., 17, 1298-1313.
-
(1997)
Mol. Cell. Biol.
, vol.17
, pp. 1298-1313
-
-
Pavitt, G.D.1
Yang, W.2
Hinnebusch, A.G.3
-
11
-
-
0030803256
-
Translational regulation of yeast GCN4. A window on factors that control initiator-trna binding to the ribosome
-
Hinnebusch, A.G. (1997) Translational regulation of yeast GCN4. A window on factors that control initiator-trna binding to the ribosome. J. Biol. Chem., 272, 21661-21664.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 21661-21664
-
-
Hinnebusch, A.G.1
-
12
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
Ingolia, N.T., Ghaemmaghami, S., Newman, J.R. and Weissman, J.S. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 218-223.
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.3
Weissman, J.S.4
-
13
-
-
27144465421
-
Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways
-
Smirnova, J.B., Selley, J.N., Sanchez-Cabo, F., Carroll, K., Eddy, A.A., McCarthy, J.E., Hubbard, S.J., Pavitt, G.D., Grant, C.M. and Ashe, M.P. (2005) Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways. Mol. Cell. Biol., 25, 9340-9349.
-
(2005)
Mol. Cell. Biol.
, vol.25
, pp. 9340-9349
-
-
Smirnova, J.B.1
Selley, J.N.2
Sanchez-Cabo, F.3
Carroll, K.4
Eddy, A.A.5
McCarthy, J.E.6
Hubbard, S.J.7
Pavitt, G.D.8
Grant, C.M.9
Ashe, M.P.10
-
14
-
-
0023720048
-
Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA
-
Pelletier, J. and Sonenberg, N. (1988) Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature, 334, 320-325.
-
(1988)
Nature
, vol.334
, pp. 320-325
-
-
Pelletier, J.1
Sonenberg, N.2
-
15
-
-
20444374113
-
Functional analysis of the pseudoknot structure in human telomerase RNA
-
discussion 8077-8089
-
Chen, J.L. and Greider, C.W. (2005) Functional analysis of the pseudoknot structure in human telomerase RNA. Proc. Natl Acad. Sci. USA, 102, 8080-8085; discussion 8077-8089.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 8080-8085
-
-
Chen, J.L.1
Greider, C.W.2
-
16
-
-
0038299558
-
Role of MicroRNAs in plant and animal development
-
Carrington, J.C. and Ambros, V. (2003) Role of MicroRNAs in plant and animal development. Science, 301, 336-338.
-
(2003)
Science
, vol.301
, pp. 336-338
-
-
Carrington, J.C.1
Ambros, V.2
-
17
-
-
54949148332
-
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
-
Hogan, D.J., Riordan, D.P., Gerber, A.P., Herschlag, D. and Brown, P.O. (2008) Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol., 6, e255.
-
(2008)
PLoS Biol.
, vol.6
-
-
Hogan, D.J.1
Riordan, D.P.2
Gerber, A.P.3
Herschlag, D.4
Brown, P.O.5
-
18
-
-
77954208849
-
Fusel alcohols regulate translation initiation by inhibiting eIF2B to reduce ternary complex in a mechanism that may involve altering the integrity and dynamics of the eIF2B body
-
Taylor, E.J., Campbell, S.G., Griffiths, C.D., Reid, P.J., Slaven, J.W., Harrison, R.J., Sims, P.F., Pavitt, G.D., Delneri, D. and Ashe, M.P. (2010) Fusel alcohols regulate translation initiation by inhibiting eIF2B to reduce ternary complex in a mechanism that may involve altering the integrity and dynamics of the eIF2B body. Mol. Biol. Cell, 21, 2202-2216.
-
(2010)
Mol. Biol. Cell
, vol.21
, pp. 2202-2216
-
-
Taylor, E.J.1
Campbell, S.G.2
Griffiths, C.D.3
Reid, P.J.4
Slaven, J.W.5
Harrison, R.J.6
Sims, P.F.7
Pavitt, G.D.8
Delneri, D.9
Ashe, M.P.10
-
19
-
-
33645217973
-
Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster
-
Gerber, A.P., Luschnig, S., Krasnow, M.A., Brown, P.O. and Herschlag, D. (2006) Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc. Natl Acad. Sci. USA, 103, 4487-4492.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 4487-4492
-
-
Gerber, A.P.1
Luschnig, S.2
Krasnow, M.A.3
Brown, P.O.4
Herschlag, D.5
-
20
-
-
84857401478
-
La-motif-dependent mRNA association with Slf1 promotes copper detoxification in yeast
-
Schenk, L., Meinel, D.M., Strasser, K. and Gerber, A.P. (2012) La-motif-dependent mRNA association with Slf1 promotes copper detoxification in yeast. RNA, 18, 449-461.
-
(2012)
RNA
, vol.18
, pp. 449-461
-
-
Schenk, L.1
Meinel, D.M.2
Strasser, K.3
Gerber, A.P.4
-
21
-
-
78649736872
-
A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes
-
Scherrer, T., Mittal, N., Janga, S.C. and Gerber, A.P. (2010) A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes. PLoS One, 5, e15499.
-
(2010)
PLoS One
, vol.5
-
-
Scherrer, T.1
Mittal, N.2
Janga, S.C.3
Gerber, A.P.4
-
22
-
-
77958594113
-
Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae
-
Tsvetanova, N.G., Klass, D.M., Salzman, J. and Brown, P.O. (2010) Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PLoS One, 5, e12671.
-
(2010)
PLoS One
, vol.5
-
-
Tsvetanova, N.G.1
Klass, D.M.2
Salzman, J.3
Brown, P.O.4
-
23
-
-
84878708955
-
Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNAbinding proteins in Saccharomyces cerevisiae
-
Klass, D.M., Scheibe, M., Butter, F., Hogan, G.J., Mann, M. and Brown, P.O. (2013) Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNAbinding proteins in Saccharomyces cerevisiae. Genome Res., 23, 1028-1038.
-
(2013)
Genome Res.
, vol.23
, pp. 1028-1038
-
-
Klass, D.M.1
Scheibe, M.2
Butter, F.3
Hogan, G.J.4
Mann, M.5
Brown, P.O.6
-
24
-
-
79952591194
-
Polysome analysis and RNA purification from sucrose gradients
-
Masek, T., Valasek, L. and Pospisek, M. (2011) Polysome analysis and RNA purification from sucrose gradients. Methods Mol. Biol., 703, 293-309.
-
(2011)
Methods Mol. Biol.
, vol.703
, pp. 293-309
-
-
Masek, T.1
Valasek, L.2
Pospisek, M.3
-
25
-
-
78650424915
-
Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins
-
Cridge, A.G., Castelli, L.M., Smirnova, J.B., Selley, J.N., Rowe, W., Hubbard, S.J., McCarthy, J.E., Ashe, M.P., Grant, C.M. and Pavitt, G.D. (2010) Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins. Nucleic Acids Res., 38, 8039-8050.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 8039-8050
-
-
Cridge, A.G.1
Castelli, L.M.2
Smirnova, J.B.3
Selley, J.N.4
Rowe, W.5
Hubbard, S.J.6
McCarthy, J.E.7
Ashe, M.P.8
Grant, C.M.9
Pavitt, G.D.10
-
26
-
-
65249176527
-
Stress-dependent coordination of transcriptome and translatome in yeast
-
Halbeisen, R.E. and Gerber, A.P. (2009) Stress-dependent coordination of transcriptome and translatome in yeast. PLoS Biol., 7, e105.
-
(2009)
PLoS Biol.
, vol.7
-
-
Halbeisen, R.E.1
Gerber, A.P.2
-
27
-
-
0035137667
-
Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source
-
Kuhn, K.M., DeRisi, J.L., Brown, P.O. and Sarnow, P. (2001) Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell. Biol., 21, 916-927.
-
(2001)
Mol. Cell. Biol.
, vol.21
, pp. 916-927
-
-
Kuhn, K.M.1
Derisi, J.L.2
Brown, P.O.3
Sarnow, P.4
-
28
-
-
29144508551
-
The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs
-
Lotan, R., Bar-On, V.G., Harel-Sharvit, L., Duek, L., Melamed, D. and Choder, M. (2005) The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Genes Dev., 19, 3004-3016.
-
(2005)
Genes Dev.
, vol.19
, pp. 3004-3016
-
-
Lotan, R.1
Bar-On, V.G.2
Harel-Sharvit, L.3
Duek, L.4
Melamed, D.5
Choder, M.6
-
29
-
-
45749090082
-
Yeast translational response to high salinity: Global analysis reveals regulation at multiple levels
-
Melamed, D., Pnueli, L. and Arava, Y. (2008) Yeast translational response to high salinity: global analysis reveals regulation at multiple levels. RNA, 14, 1337-1351.
-
(2008)
RNA
, vol.14
, pp. 1337-1351
-
-
Melamed, D.1
Pnueli, L.2
Arava, Y.3
-
30
-
-
33749379882
-
Global translational responses to oxidative stress impact upon multiple levels of protein synthesis
-
Shenton, D., Smirnova, J.B., Selley, J.N., Carroll, K., Hubbard, S.J., Pavitt, G.D., Ashe, M.P. and Grant, C.M. (2006) Global translational responses to oxidative stress impact upon multiple levels of protein synthesis. J. Biol. Chem., 281, 29011-29021.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 29011-29021
-
-
Shenton, D.1
Smirnova, J.B.2
Selley, J.N.3
Carroll, K.4
Hubbard, S.J.5
Pavitt, G.D.6
Ashe, M.P.7
Grant, C.M.8
-
31
-
-
80052865292
-
Glucose depletion inhibits translation initiation via eIF4A loss and subsequent 48S preinitiation complex accumulation, while the pentose phosphate pathway is coordinately up-regulated
-
Castelli, L.M., Lui, J., Campbell, S.G., Rowe, W., Zeef, L.A., Holmes, L.E., Hoyle, N.P., Bone, J., Selley, J.N., Sims, P.F. et al. (2011) Glucose depletion inhibits translation initiation via eIF4A loss and subsequent 48S preinitiation complex accumulation, while the pentose phosphate pathway is coordinately up-regulated. Mol. Biol. Cell, 22, 3379-3393.
-
(2011)
Mol. Biol. Cell
, vol.22
, pp. 3379-3393
-
-
Castelli, L.M.1
Lui, J.2
Campbell, S.G.3
Rowe, W.4
Zeef, L.A.5
Holmes, L.E.6
Hoyle, N.P.7
Bone, J.8
Selley, J.N.9
Sims, P.F.10
-
32
-
-
61649096857
-
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast
-
Lawless, C., Pearson, R.D., Selley, J.N., Smirnova, J.B., Grant, C.M., Ashe, M.P., Pavitt, G.D. and Hubbard, S.J. (2009) Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics, 10, 7.
-
(2009)
BMC Genomics
, vol.10
, pp. 7
-
-
Lawless, C.1
Pearson, R.D.2
Selley, J.N.3
Smirnova, J.B.4
Grant, C.M.5
Ashe, M.P.6
Pavitt, G.D.7
Hubbard, S.J.8
-
33
-
-
69849093394
-
Properties of untranslated regions of the S. Cerevisiae genome
-
Tuller, T., Ruppin, E. and Kupiec, M. (2009) Properties of untranslated regions of the S. cerevisiae genome. BMC Genomics, 10, 391.
-
(2009)
BMC Genomics
, vol.10
, pp. 391
-
-
Tuller, T.1
Ruppin, E.2
Kupiec, M.3
-
34
-
-
84877574893
-
Extensive transcriptional heterogeneity revealed by isoform profiling
-
Pelechano, V., Wei, W. and Steinmetz, L.M. (2013) Extensive transcriptional heterogeneity revealed by isoform profiling. Nature, 497, 127-131.
-
(2013)
Nature
, vol.497
, pp. 127-131
-
-
Pelechano, V.1
Wei, W.2
Steinmetz, L.M.3
-
35
-
-
33645785104
-
A high-resolution map of transcription in the yeast genome
-
David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C.J., Bofkin, L., Jones, T., Davis, R.W. and Steinmetz, L.M. (2006) A high-resolution map of transcription in the yeast genome. Proc. Natl Acad Sci. USA, 103, 5320-5325.
-
(2006)
Proc. Natl Acad Sci. USA
, vol.103
, pp. 5320-5325
-
-
David, L.1
Huber, W.2
Granovskaia, M.3
Toedling, J.4
Palm, C.J.5
Bofkin, L.6
Jones, T.7
Davis, R.W.8
Steinmetz, L.M.9
-
36
-
-
0035478854
-
Random forests
-
Breiman, L. (2001) Random forests. Mach. Learn., 45, 5-32.
-
(2001)
Mach. Learn.
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
37
-
-
33846446777
-
Puf3p, a Pumilio family RNA binding protein, localizes to mitochondria and regulates mitochondrial biogenesis and motility in budding yeast
-
Garcia-Rodriguez, L.J., Gay, A.C. and Pon, L.A. (2007) Puf3p, a Pumilio family RNA binding protein, localizes to mitochondria and regulates mitochondrial biogenesis and motility in budding yeast. J. Cell. Biol., 176, 197-207.
-
(2007)
J. Cell. Biol.
, vol.176
, pp. 197-207
-
-
Garcia-Rodriguez, L.J.1
Gay, A.C.2
Pon, L.A.3
-
38
-
-
0034388021
-
The Puf3 protein is a transcriptspecific regulator of mRNA degradation in yeast
-
Olivas, W. and Parker, R. (2000) The Puf3 protein is a transcriptspecific regulator of mRNA degradation in yeast. EMBO J., 19, 6602-6611.
-
(2000)
EMBO J.
, vol.19
, pp. 6602-6611
-
-
Olivas, W.1
Parker, R.2
-
39
-
-
84859586432
-
The response to heat shock and oxidative stress in Saccharomyces cerevisiae
-
Morano, K.A., Grant, C.M. and Moye-Rowley, W.S. (2012) The response to heat shock and oxidative stress in Saccharomyces cerevisiae. Genetics, 190, 1157-1195.
-
(2012)
Genetics
, vol.190
, pp. 1157-1195
-
-
Morano, K.A.1
Grant, C.M.2
Moye-Rowley, W.S.3
-
40
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Article3
-
Smyth, G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, Article3.
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
-
-
Smyth, G.K.1
-
41
-
-
58549109637
-
Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape
-
Knight, C.G., Platt, M., Rowe, W., Wedge, D.C., Khan, F., Day, P.J., McShea, A., Knowles, J. and Kell, D.B. (2009) Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape. Nucleic Acids Res., 37, e6.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Knight, C.G.1
Platt, M.2
Rowe, W.3
Wedge, D.C.4
Khan, F.5
Day, P.J.6
McShea, A.7
Knowles, J.8
Kell, D.B.9
-
42
-
-
77953351710
-
An application of Random Forests to a genome-wide association dataset: Methodological considerations & new findings
-
Goldstein, B.A., Hubbard, A.E., Cutler, A. and Barcellos, L.F. (2010) An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. BMC Genet., 11, 49.
-
(2010)
BMC Genet.
, vol.11
, pp. 49
-
-
Goldstein, B.A.1
Hubbard, A.E.2
Cutler, A.3
Barcellos, L.F.4
-
43
-
-
80053074684
-
CONSeQuence: Prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches
-
Eyers, C.E., Lawless, C., Wedge, D.C., Lau, K.W., Gaskell, S.J. and Hubbard, S.J. (2011) CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches. Mol. Cell. Proteom., 10, M110 003384.
-
(2011)
Mol. Cell. Proteom.
, vol.10
-
-
Eyers, C.E.1
Lawless, C.2
Wedge, D.C.3
Lau, K.W.4
Gaskell, S.J.5
Hubbard, S.J.6
-
44
-
-
77956167600
-
The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics
-
Ohta, S., Bukowski-Wills, J.C., Sanchez-Pulido, L., Alves Fde, L., Wood, L., Chen, Z.A., Platani, M., Fischer, L., Hudson, D.F., Ponting, C.P. et al. (2010) The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics. Cell, 142, 810-821.
-
(2010)
Cell
, vol.142
, pp. 810-821
-
-
Ohta, S.1
Bukowski-Wills, J.C.2
Sanchez-Pulido, L.3
Alves Fde, L.4
Wood, L.5
Chen, Z.A.6
Platani, M.7
Fischer, L.8
Hudson, D.F.9
Ponting, C.P.10
-
45
-
-
0030211964
-
Bagging predictors
-
Breiman, L. (1996) Bagging predictors. Mach. Learn., 24, 123-140.
-
(1996)
Mach. Learn.
, vol.24
, pp. 123-140
-
-
Breiman, L.1
-
46
-
-
27544491192
-
ROCR: Visualizing classifier performance in R
-
Sing, T., Sander, O., Beerenwinkel, N. and Lengauer, T. (2005) ROCR: visualizing classifier performance in R. Bioinformatics, 21, 3940-3941.
-
(2005)
Bioinformatics
, vol.21
, pp. 3940-3941
-
-
Sing, T.1
Sander, O.2
Beerenwinkel, N.3
Lengauer, T.4
-
47
-
-
77956340995
-
Comprehensive comparative analysis of strand-specific RNA sequencing methods
-
Levin, J.Z., Yassour, M., Adiconis, X., Nusbaum, C., Thompson, D.A., Friedman, N., Gnirke, A. and Regev, A. (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods, 7, 709-715.
-
(2010)
Nat. Methods
, vol.7
, pp. 709-715
-
-
Levin, J.Z.1
Yassour, M.2
Adiconis, X.3
Nusbaum, C.4
Thompson, D.A.5
Friedman, N.6
Gnirke, A.7
Regev, A.8
-
48
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M. and Schuster, P. (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, L.S.4
Tacker, M.5
Schuster, P.6
-
49
-
-
79952351662
-
Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome
-
Riordan, D.P., Herschlag, D. and Brown, P.O. (2011) Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome. Nucleic Acids Res., 39, 1501-1509.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 1501-1509
-
-
Riordan, D.P.1
Herschlag, D.2
Brown, P.O.3
-
50
-
-
0020363515
-
Preferential codon usage in prokaryotic genes: The optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes
-
Grosjean, H. and Fiers, W. (1982) Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene, 18, 199-209.
-
(1982)
Gene
, vol.18
, pp. 199-209
-
-
Grosjean, H.1
Fiers, W.2
-
51
-
-
33751375141
-
Impact of nonsensemediated mRNA decay on the global expression profile of budding yeast
-
Guan, Q., Zheng, W., Tang, S., Liu, X., Zinkel, R.A., Tsui, K.W., Yandell, B.S. and Culbertson, M.R. (2006) Impact of nonsensemediated mRNA decay on the global expression profile of budding yeast. PLoS Genet., 2, e203.
-
(2006)
PLoS Genet.
, vol.2
-
-
Guan, Q.1
Zheng, W.2
Tang, S.3
Liu, X.4
Zinkel, R.A.5
Tsui, K.W.6
Yandell, B.S.7
Culbertson, M.R.8
-
52
-
-
77958493102
-
The mRNA landscape at yeast translation initiation sites
-
Robbins-Pianka, A., Rice, M.D. and Weir, M.P. (2010) The mRNA landscape at yeast translation initiation sites. Bioinformatics, 26, 2651-2655.
-
(2010)
Bioinformatics
, vol.26
, pp. 2651-2655
-
-
Robbins-Pianka, A.1
Rice, M.D.2
Weir, M.P.3
-
53
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B, 57, 289-300.
-
(1995)
J. R. Stat. Soc. Series B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
54
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
55
-
-
0016155287
-
Mutants of yeast defective in iso 1 cytochrome c
-
Sherman, F., Stewart, J.W. and Jackson, M. (1974) Mutants of yeast defective in iso 1 cytochrome c. Genetics, 77, 255-284.
-
(1974)
Genetics
, vol.77
, pp. 255-284
-
-
Sherman, F.1
Stewart, J.W.2
Jackson, M.3
-
56
-
-
0032583570
-
Glutathione and catalase provide overlapping defenses for protection against hydrogen peroxide in the yeast Saccharomyces cerevisiae
-
Grant, C.M., Perrone, G. and Dawes, I.W. (1998) Glutathione and catalase provide overlapping defenses for protection against hydrogen peroxide in the yeast Saccharomyces cerevisiae. Biochem. Biophys. Res. Commun., 253, 893-898.
-
(1998)
Biochem. Biophys. Res. Commun.
, vol.253
, pp. 893-898
-
-
Grant, C.M.1
Perrone, G.2
Dawes, I.W.3
-
57
-
-
84873582146
-
Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae
-
Freeberg, M.A., Han, T., Moresco, J.J., Kong, A., Yang, Y.C., Lu, Z.J., Yates, J.R. and Kim, J.K. (2013) Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biol., 14, R13.
-
(2013)
Genome Biol.
, vol.14
-
-
Freeberg, M.A.1
Han, T.2
Moresco, J.J.3
Kong, A.4
Yang, Y.C.5
Lu, Z.J.6
Yates, J.R.7
Kim, J.K.8
-
58
-
-
84858588614
-
Saccharomyces genome database: The genomics resource of budding yeast
-
Cherry, J.M., Hong, E.L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E.T., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S.R. et al. (2012) Saccharomyces genome database: the genomics resource of budding yeast. Nucleic Acids Res., 40, D700-D705.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Cherry, J.M.1
Hong, E.L.2
Amundsen, C.3
Balakrishnan, R.4
Binkley, G.5
Chan, E.T.6
Christie, K.R.7
Costanzo, M.C.8
Dwight, S.S.9
Engel, S.R.10
-
59
-
-
0345602742
-
Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock
-
Preiss, T., Baron-Benhamou, J., Ansorge, W. and Hentze, M.W. (2003) Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nat. Struct. Biol., 10, 1039-1047.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 1039-1047
-
-
Preiss, T.1
Baron-Benhamou, J.2
Ansorge, W.3
Hentze, M.W.4
-
60
-
-
84859793036
-
Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast
-
Lackner, D.H., Schmidt, M.W., Wu, S., Wolf, D.A. and Bahler, J. (2012) Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast. Genome Biol., 13, R25.
-
(2012)
Genome Biol.
, vol.13
-
-
Lackner, D.H.1
Schmidt, M.W.2
Wu, S.3
Wolf, D.A.4
Bahler, J.5
-
61
-
-
19344365947
-
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
-
Gerber, A.P., Herschlag, D. and Brown, P.O. (2004) Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol., 2, E79.
-
(2004)
PLoS Biol
, vol.2
-
-
Gerber, A.P.1
Herschlag, D.2
Brown, P.O.3
-
62
-
-
77952703757
-
Translational repression by PUF proteins in vitro
-
Chritton, J.J. and Wickens, M. (2010) Translational repression by PUF proteins in vitro. RNA, 16, 1217-1225.
-
(2010)
RNA
, vol.16
, pp. 1217-1225
-
-
Chritton, J.J.1
Wickens, M.2
-
64
-
-
0037162703
-
Modular recognition of RNA by a human pumilio-homology domain
-
Wang, X., McLachlan, J., Zamore, P.D. and Hall, T.M.T. (2002) Modular recognition of RNA by a human pumilio-homology domain. Cell, 110, 501-512.
-
(2002)
Cell
, vol.110
, pp. 501-512
-
-
Wang, X.1
McLachlan, J.2
Zamore, P.D.3
Hall, T.M.T.4
-
65
-
-
0343750650
-
Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae
-
Jacobs Anderson, J.S. and Parker, R. (2000) Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae. Nucleic Acids Res., 28, 1604-1617.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1604-1617
-
-
Jacobs Anderson, J.S.1
Parker, R.2
-
66
-
-
52349122355
-
Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system
-
Galgano, A., Forrer, M., Jaskiewicz, L., Kanitz, A., Zavolan, M. and Gerber, A.P. (2008) Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS One, 3, e3164.
-
(2008)
PLoS One
, vol.3
-
-
Galgano, A.1
Forrer, M.2
Jaskiewicz, L.3
Kanitz, A.4
Zavolan, M.5
Gerber, A.P.6
-
67
-
-
79957869584
-
Repression of mitochondrial translation, respiration and a metabolic cycleregulated gene, SLF1, by the yeast Pumilio-family protein Puf3p
-
Chatenay-Lapointe, M. and Shadel, G.S. (2011) Repression of mitochondrial translation, respiration and a metabolic cycleregulated gene, SLF1, by the yeast Pumilio-family protein Puf3p. PLoS One, 6, e20441.
-
(2011)
PLoS One
, vol.6
-
-
Chatenay-Lapointe, M.1
Shadel, G.S.2
-
68
-
-
58249093939
-
How mitochondria produce reactive oxygen species
-
Murphy, M.P. (2009) How mitochondria produce reactive oxygen species. Biochem. J., 417, 1-13.
-
(2009)
Biochem. J.
, vol.417
, pp. 1-13
-
-
Murphy, M.P.1
-
69
-
-
79952351662
-
Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome
-
Riordan, D.P., Herschlag, D. and Brown, P.O. (2011) Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome. Nucleic Acids Res., 39, 1501-1509.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 1501-1509
-
-
Riordan, D.P.1
Herschlag, D.2
Brown, P.O.3
-
70
-
-
0032602952
-
Mitochondria oxidative stress, and antioxidant defences
-
Lenaz, G., Bovina, C., Formiggini, G. and Parenti Castelli, G. (1999) Mitochondria, oxidative stress, and antioxidant defences. Acta Biochim. Pol., 46, 1-21.
-
(1999)
Acta Biochim. Pol.
, vol.46
, pp. 1-21
-
-
Lenaz, G.1
Bovina, C.2
Formiggini, G.3
Parenti Castelli, G.4
-
71
-
-
48449096068
-
Yeast mitochondrial biogenesis: A role for the PUF RNA-binding protein Puf3p in mRNA localization
-
Saint-Georges, Y., Garcia, M., Delaveau, T., Jourdren, L., Le Crom, S., Lemoine, S., Tanty, V., Devaux, F. and Jacq, C. (2008) Yeast mitochondrial biogenesis: a role for the PUF RNA-binding protein Puf3p in mRNA localization. PLoS One, 3, e2293.
-
(2008)
PLoS One
, vol.3
-
-
Saint-Georges, Y.1
Garcia, M.2
Delaveau, T.3
Jourdren, L.4
Le Crom, S.5
Lemoine, S.6
Tanty, V.7
Devaux, F.8
Jacq, C.9
-
72
-
-
4644284749
-
Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast
-
Jackson, J.S. Jr, Houshmandi, S.S., Lopez Leban, F. and Olivas, W.M. (2004) Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast. RNA, 10, 1625-1636.
-
(2004)
RNA
, vol.10
, pp. 1625-1636
-
-
Jackson Jr., J.S.1
Houshmandi, S.S.2
Lopez Leban, F.3
Olivas, W.M.4
-
73
-
-
33749989519
-
Cap-dependent translational inhibition establishes two opposing morphogen gradients in Drosophila embryos
-
Cho, P.F., Gamberi, C., Cho-Park., Yoon, A., Cho-Park, I.B., Lasko, P. and Sonenberg, N. (2006) Cap-dependent translational inhibition establishes two opposing morphogen gradients in Drosophila embryos. Curr. Biol., 16, 2035-2041.
-
(2006)
Curr. Biol.
, vol.16
, pp. 2035-2041
-
-
Cho, P.F.1
Cho-Park, G.C.2
Yoon, A.3
Cho-Park, I.B.4
Lasko, P.5
Sonenberg, N.6
-
74
-
-
67649639495
-
The SESA network links duplication of the yeast centrosome with the protein translation machinery
-
Sezen, B., Seedorf, M. and Schiebel, E. (2009) The SESA network links duplication of the yeast centrosome with the protein translation machinery. Genes Dev., 23, 1559-1570.
-
(2009)
Genes Dev.
, vol.23
, pp. 1559-1570
-
-
Sezen, B.1
Seedorf, M.2
Schiebel, E.3
-
75
-
-
79960445493
-
Localization of mRNAs coding for mitochondrial proteins in the yeast Saccharomyces cerevisiae
-
Gadir, N., Haim-Vilmovsky, L., Kraut-Cohen, J. and Gerst, J.E. (2011) Localization of mRNAs coding for mitochondrial proteins in the yeast Saccharomyces cerevisiae. RNA, 17, 1551-1565.
-
(2011)
RNA
, vol.17
, pp. 1551-1565
-
-
Gadir, N.1
Haim-Vilmovsky, L.2
Kraut-Cohen, J.3
Gerst, J.E.4
-
76
-
-
0040932016
-
Grx5 glutaredoxin plays a central role in protection against protein oxidative damage in Saccharomyces cerevisiae
-
Rodriguez-Manzaneque, M.T., Ros, J., Cabiscol, E., Sorribas, A. and Herrero, E. (1999) Grx5 glutaredoxin plays a central role in protection against protein oxidative damage in Saccharomyces cerevisiae. Mol. Cell. Biol., 19, 8180-8190.
-
(1999)
Mol. Cell. Biol.
, vol.19
, pp. 8180-8190
-
-
Rodriguez-Manzaneque, M.T.1
Ros, J.2
Cabiscol, E.3
Sorribas, A.4
Herrero, E.5
-
77
-
-
83055163866
-
Protein expression regulation under oxidative stress
-
Vogel, C., Silva, G.M. and Marcotte, E.M. (2011) Protein expression regulation under oxidative stress. Mol. Cell. Proteom., 10, M111 009217.
-
(2011)
Mol. Cell. Proteom.
, vol.10
-
-
Vogel, C.1
Silva, G.M.2
Marcotte, E.M.3
-
78
-
-
33749986298
-
Free radicals and antioxidants in normal physiological functions and human disease
-
Valko, M., Leibfritz, D., Moncol, J., Cronin, M.T., Mazur, M. and Telser, J. (2007) Free radicals and antioxidants in normal physiological functions and human disease. Int. J. Biochem. Cell Biol., 39, 44-84.
-
(2007)
Int. J. Biochem. Cell Biol.
, vol.39
, pp. 44-84
-
-
Valko, M.1
Leibfritz, D.2
Moncol, J.3
Cronin, M.T.4
Mazur, M.5
Telser, J.6
-
79
-
-
79961042033
-
A yeast-based assay identifies drugs active against human mitochondrial disorders
-
Couplan, E., Aiyar, R.S., Kucharczyk, R., Kabala, A., Ezkurdia, N., Gagneur, J., St. Onge, R.P., Salin, B., Soubigou, F., Le Cann, M. et al. (2011) A yeast-based assay identifies drugs active against human mitochondrial disorders. Proc. Natl Acad. Sci. USA, 108, 11989-11994.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 11989-11994
-
-
Couplan, E.1
Aiyar, R.S.2
Kucharczyk, R.3
Kabala, A.4
Ezkurdia, N.5
Gagneur, J.6
St. Onge, R.P.7
Salin, B.8
Soubigou, F.9
Le Cann, M.10
|