-
1
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch, A. P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257 (2000).
-
(2000)
Mol. Biol. Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
-
3
-
-
0029361759
-
In vitro selection methodologies to probe RNA function and structure
-
Conrad, R. C., Baskerville, S. & Ellington, A. D. In vitro selection methodologies to probe RNA function and structure. Mol. Divers. 1, 69-78 (1995).
-
(1995)
Mol. Divers.
, vol.1
, pp. 69-78
-
-
Conrad, R.C.1
Baskerville, S.2
Ellington, A.D.3
-
4
-
-
46349083026
-
The distributions, mechanisms, and structures of metabolite-binding riboswitches
-
Barrick, J. E. & Breaker, R. R. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol. 8, R239 (2007).
-
(2007)
Genome Biol.
, vol.8
, pp. R239
-
-
Barrick, J.E.1
Breaker, R.R.2
-
5
-
-
80051989609
-
Understanding the transcriptome through RNA structure
-
Wan, Y., Kertesz, M., Spitale, R. C., Segal, E. & Chang, H. Y. Understanding the transcriptome through RNA structure. Nat. Rev. Genet. 12, 641-655 (2011).
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 641-655
-
-
Wan, Y.1
Kertesz, M.2
Spitale, R.C.3
Segal, E.4
Chang, H.Y.5
-
6
-
-
84963614962
-
Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria
-
Dar, D. et al. Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria. Science 352, aad9822 (2016).
-
(2016)
Science
, vol.352
, pp. aad9822
-
-
Dar, D.1
-
7
-
-
77956306662
-
Genome-wide measurement of RNA secondary structure in yeast
-
Kertesz, M. et al. Genome-wide measurement of RNA secondary structure in yeast. Nature 467, 103-107 (2010).
-
(2010)
Nature
, vol.467
, pp. 103-107
-
-
Kertesz, M.1
-
8
-
-
84897585709
-
In-line probing analysis of riboswitches
-
Regulski, E. E. & Breaker, R. R. In-line probing analysis of riboswitches. Methods Mol. Biol. 419, 53-67 (2008).
-
(2008)
Methods Mol. Biol.
, vol.419
, pp. 53-67
-
-
Regulski, E.E.1
Breaker, R.R.2
-
9
-
-
0037206833
-
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
-
Winkler, W., Nahvi, A. & Breaker, R. R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952-956 (2002).
-
(2002)
Nature
, vol.419
, pp. 952-956
-
-
Winkler, W.1
Nahvi, A.2
Breaker, R.R.3
-
10
-
-
0042320361
-
An mRNA structure that controls gene expression by binding S-adenosylmethionine
-
Winkler, W. C., Nahvi, A., Sudarsan, N., Barrick, J. E. & Breaker, R. R. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat. Struct. Biol. 10, 701-707 (2003).
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 701-707
-
-
Winkler, W.C.1
Nahvi, A.2
Sudarsan, N.3
Barrick, J.E.4
Breaker, R.R.5
-
11
-
-
84886739636
-
RegPrecise 3.0-a resource for genome-scale exploration of transcriptional regulation in bacteria
-
Novichkov, P. S. et al. RegPrecise 3.0-a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics 14, 745-2164-14-745 (2013).
-
(2013)
BMC Genomics
, vol.14
, pp. 45
-
-
Novichkov, P.S.1
-
12
-
-
4143149651
-
Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics
-
Washietl, S. & Hofacker, I. L. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J. Mol. Biol. 342, 19-30 (2004).
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 19-30
-
-
Washietl, S.1
Hofacker, I.L.2
-
13
-
-
84876034308
-
Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing
-
Li, S. & Breaker, R. R. Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing. Nucleic Acids Res. 41, 3022-3031 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 3022-3031
-
-
Li, S.1
Breaker, R.R.2
-
14
-
-
37849045636
-
Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs
-
Wachter, A. et al. Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 19, 3437-3450 (2007).
-
(2007)
Plant Cell
, vol.19
, pp. 3437-3450
-
-
Wachter, A.1
-
15
-
-
3843086171
-
Potential anti-infective targets in pathogenic yeasts: Structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans
-
Echt, S. et al. Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans. J. Mol. Biol. 341, 1085-1096 (2004).
-
(2004)
J. Mol. Biol.
, vol.341
, pp. 1085-1096
-
-
Echt, S.1
-
16
-
-
0037058920
-
An mRNA structure that controls gene expression by binding FMN
-
Winkler, W. C., Cohen-Chalamish, S. & Breaker, R. R. An mRNA structure that controls gene expression by binding FMN. Proc. Natl Acad. Sci. USA 99, 15908-15913 (2002).
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 15908-15913
-
-
Winkler, W.C.1
Cohen-Chalamish, S.2
Breaker, R.R.3
-
18
-
-
0029994841
-
A new efficient gene disruption cassette for repeated use in budding yeast
-
Guldener, U., Heck, S., Fielder, T., Beinhauer, J. & Hegemann, J. H. A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res. 24, 2519-2524 (1996).
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 2519-2524
-
-
Guldener, U.1
Heck, S.2
Fielder, T.3
Beinhauer, J.4
Hegemann, J.H.5
-
19
-
-
13944278373
-
SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
-
Das, R., Laederach, A., Pearlman, S. M., Herschlag, D. & Altman, R. B. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 11, 344-354 (2005).
-
(2005)
RNA
, vol.11
, pp. 344-354
-
-
Das, R.1
Laederach, A.2
Pearlman, S.M.3
Herschlag, D.4
Altman, R.B.5
-
20
-
-
82055164092
-
ViennaRNA Package 2.0
-
Lorenz, R. et al. ViennaRNA Package 2.0. Algorithms Mol. Biol. 6, 26-7188-6-26 (2011).
-
(2011)
Algorithms Mol. Biol.
, vol.6
, pp. 267188626
-
-
Lorenz, R.1
-
21
-
-
84891689485
-
V3 stain-free workflow for a practical, convenient, and reliable total protein loading control in western blotting
-
Posch, A., Kohn, J., Oh, K., Hammond, M. & Liu, N. V3 stain-free workflow for a practical, convenient, and reliable total protein loading control in western blotting. J. Vis. Exp. 82, 50948 (2013).
-
(2013)
J. Vis. Exp.
, vol.82
, pp. 50948
-
-
Posch, A.1
Kohn, J.2
Oh, K.3
Hammond, M.4
Liu, N.5
-
22
-
-
84862520770
-
Fiji: An open-source platform for biological-image analysis
-
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676-682 (2012).II
-
(2012)
Nat. Methods
, vol.9
, pp. 676-682
-
-
Schindelin, J.1
-
23
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
24
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344-1349 (2008).
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
-
25
-
-
78649240033
-
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq
-
Bruno, V. M. et al. Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Res. 20, 1451-1458 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1451-1458
-
-
Bruno, V.M.1
-
26
-
-
75249087100
-
K. EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.3
-
27
-
-
0025259313
-
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
-
Karlin, S. & Altschul, S. F. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA 87, 2264-2268 (1990).
-
(1990)
Proc. Natl Acad. Sci. USA
, vol.87
, pp. 2264-2268
-
-
Karlin, S.1
Altschul, S.F.2
-
28
-
-
8444247896
-
Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions
-
Tzeng, Y. H., Pan, R. & Li, W. H. Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 21, 2290-2298 (2004).
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 2290-2298
-
-
Tzeng, Y.H.1
Pan, R.2
Li, W.H.3
-
29
-
-
79960403324
-
GenBlastG: Using BLAST searches to build homologous gene models
-
She, R. et al. genBlastG: using BLAST searches to build homologous gene models. Bioinformatics 27, 2141-2143 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2141-2143
-
-
She, R.1
-
30
-
-
39749083331
-
The birth and death of microRNA genes in Drosophila
-
Lu, J. et al. The birth and death of microRNA genes in Drosophila. Nat. Genet. 40, 351-355 (2008).
-
(2008)
Nat. Genet.
, vol.40
, pp. 351-355
-
-
Lu, J.1
-
31
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
32
-
-
80052824121
-
MACSE: Multiple alignment of coding sequences accounting for frameshifts and stop codons
-
Ranwez, V., Harispe, S., Delsuc, F. & Douzery, E. J. MACSE: multiple alignment of coding sequences accounting for frameshifts and stop codons. PLoS One 6, e22594 (2011).
-
(2011)
PLoS One
, vol.6
, pp. e22594
-
-
Ranwez, V.1
Harispe, S.2
Delsuc, F.3
Douzery, E.J.4
-
33
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120 (1980).
-
(1980)
J. Mol. Evol.
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
34
-
-
34248669040
-
KaKs-Calculator: Calculating Ka and Ks through model selection and model averaging
-
Zhang, Z. et al. KaKs-Calculator: calculating Ka and Ks through model selection and model averaging. Genom. Proteom. Bioinform. 4, 259-263 (2006).
-
(2006)
Genom. Proteom. Bioinform.
, vol.4
, pp. 259-263
-
-
Zhang, Z.1
|