-
1
-
-
84872543206
-
A decade of riboswitches
-
Serganov A, Nudler E (2013) A decade of riboswitches. Cell 152(1-2):17-24.
-
(2013)
Cell
, vol.152
, Issue.1-2
, pp. 17-24
-
-
Serganov, A.1
Nudler, E.2
-
2
-
-
84858436083
-
Bacterial RNA thermometers: Molecular zippers and switches
-
Kortmann J, Narberhaus F (2012) Bacterial RNA thermometers: Molecular zippers and switches. Nat Rev Microbiol 10(4):255-265.
-
(2012)
Nat Rev Microbiol
, vol.10
, Issue.4
, pp. 255-265
-
-
Kortmann, J.1
Narberhaus, F.2
-
3
-
-
84908067413
-
Temperature-driven differential gene expression by RNA thermosensors
-
Krajewski SS, Narberhaus F (2014) Temperature-driven differential gene expression by RNA thermosensors. Biochim Biophys Acta 1839(10):978-988.
-
(2014)
Biochim Biophys Acta
, vol.1839
, Issue.10
, pp. 978-988
-
-
Krajewski, S.S.1
Narberhaus, F.2
-
4
-
-
0037031594
-
An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes
-
Johansson J, et al. (2002) An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 110(5):551-561.
-
(2002)
Cell
, vol.110
, Issue.5
, pp. 551-561
-
-
Johansson, J.1
-
5
-
-
0027141070
-
Temperature sensing in Yersinia pestis: Translation of the LcrF activator protein is thermally regulated
-
Hoe NP, Goguen JD (1993) Temperature sensing in Yersinia pestis: Translation of the LcrF activator protein is thermally regulated. J Bacteriol 175(24):7901-7909.
-
(1993)
J Bacteriol
, vol.175
, Issue.24
, pp. 7901-7909
-
-
Hoe, N.P.1
Goguen, J.D.2
-
6
-
-
84871714811
-
Concerted actions of a thermo-labile regulator and a unique intergenic RNA thermosensor control Yersinia virulence
-
Böhme K, et al. (2012) Concerted actions of a thermo-labile regulator and a unique intergenic RNA thermosensor control Yersinia virulence. PLoS Pathog 8(2):e1002518.
-
(2012)
PLoS Pathog
, vol.8
, Issue.2
, pp. e1002518
-
-
Böhme, K.1
-
7
-
-
84887247958
-
Role for cis-acting RNA sequences in the temperature-dependent expression of the multiadhesive lig proteins in Leptospira interrogans
-
Matsunaga J, Schlax PJ, Haake DA (2013) Role for cis-acting RNA sequences in the temperature-dependent expression of the multiadhesive lig proteins in Leptospira interrogans. J Bacteriol 195(22):5092-5101.
-
(2013)
J Bacteriol
, vol.195
, Issue.22
, pp. 5092-5101
-
-
Matsunaga, J.1
Schlax, P.J.2
Haake, D.A.3
-
8
-
-
84877989981
-
RNA-mediated thermoregulation of iron-acquisition genes in Shigella dysenteriae and pathogenic Escherichia coli
-
Kouse AB, Righetti F, Kortmann J, Narberhaus F, Murphy ER (2013) RNA-mediated thermoregulation of iron-acquisition genes in Shigella dysenteriae and pathogenic Escherichia coli. PLoS One 8(5):e63781.
-
(2013)
PLoS One
, vol.8
, Issue.5
, pp. e63781
-
-
Kouse, A.B.1
Righetti, F.2
Kortmann, J.3
Narberhaus, F.4
Murphy, E.R.5
-
9
-
-
84885611420
-
Temperature triggers immune evasion by Neisseria meningitidis
-
Loh E, et al. (2013) Temperature triggers immune evasion by Neisseria meningitidis. Nature 502(7470):237-240.
-
(2013)
Nature
, vol.502
, Issue.7470
, pp. 237-240
-
-
Loh, E.1
-
10
-
-
84908434445
-
Regulation of Pseudomonas aeruginosa virulence factors by two novel RNA thermometers
-
Grosso-Becerra MV, et al. (2014) Regulation of Pseudomonas aeruginosa virulence factors by two novel RNA thermometers. Proc Natl Acad Sci USA 111(43):15562-15567.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, Issue.43
, pp. 15562-15567
-
-
Grosso-Becerra, M.V.1
-
11
-
-
84907584473
-
RNA thermometer controls temperature-dependent virulence factor expression in Vibrio cholerae
-
Weber GG, Kortmann J, Narberhaus F, Klose KE (2014) RNA thermometer controls temperature-dependent virulence factor expression in Vibrio cholerae. Proc Natl Acad Sci USA 111(39):14241-14246.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, Issue.39
, pp. 14241-14246
-
-
Weber, G.G.1
Kortmann, J.2
Narberhaus, F.3
Klose, K.E.4
-
13
-
-
77956306662
-
Genome-wide measurement of RNA secondary structure in yeast
-
Kertesz M, et al. (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature 467(7311):103-107.
-
(2010)
Nature
, vol.467
, Issue.7311
, pp. 103-107
-
-
Kertesz, M.1
-
14
-
-
84868009378
-
Genome-wide measurement of RNA folding energies
-
Wan Y, et al. (2012) Genome-wide measurement of RNA folding energies. Mol Cell 48(2):169-181.
-
(2012)
Mol Cell
, vol.48
, Issue.2
, pp. 169-181
-
-
Wan, Y.1
-
15
-
-
84898949357
-
Mod-seq: Highthroughput sequencing for chemical probing of RNA structure
-
Talkish J, May G, Lin Y, Woolford JL, Jr, McManus CJ (2014) Mod-seq: Highthroughput sequencing for chemical probing of RNA structure. RNA 20(5):713-720.
-
(2014)
RNA
, vol.20
, Issue.5
, pp. 713-720
-
-
Talkish, J.1
May, G.2
Lin, Y.3
Woolford, J.L.4
McManus, C.J.5
-
16
-
-
84861121932
-
Global analysis of RNA secondary structure in two metazoans
-
Li F, et al. (2012) Global analysis of RNA secondary structure in two metazoans. Cell Reports 1(1):69-82.
-
(2012)
Cell Reports
, vol.1
, Issue.1
, pp. 69-82
-
-
Li, F.1
-
17
-
-
78049445573
-
Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis
-
Zheng Q, et al. (2010) Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet 6(9):e1001141.
-
(2010)
PLoS Genet
, vol.6
, Issue.9
, pp. e1001141
-
-
Zheng, Q.1
-
18
-
-
84871887837
-
Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome
-
Li F, et al. (2012) Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell 24(11):4346-4359.
-
(2012)
Plant Cell
, vol.24
, Issue.11
, pp. 4346-4359
-
-
Li, F.1
-
19
-
-
84893427735
-
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
-
Ding Y, et al. (2014) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505(7485):696-700.
-
(2014)
Nature
, vol.505
, Issue.7485
, pp. 696-700
-
-
Ding, Y.1
-
20
-
-
78649690492
-
FragSeq: Transcriptome-wide RNA structure probing using high-throughput sequencing
-
Underwood JG, et al. (2010) FragSeq: Transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods 7(12):995-1001.
-
(2010)
Nat Methods
, vol.7
, Issue.12
, pp. 995-1001
-
-
Underwood, J.G.1
-
21
-
-
84924584607
-
Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome
-
Incarnato D, Neri F, Anselmi F, Oliviero S (2014) Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome. Genome Biol 15(10):491.
-
(2014)
Genome Biol
, vol.15
, Issue.10
, pp. 491
-
-
Incarnato, D.1
Neri, F.2
Anselmi, F.3
Oliviero, S.4
-
22
-
-
84925777836
-
Structural imprints in vivo decode RNA regulatory mechanisms
-
Spitale RC, et al. (2015) Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519(7544):486-490.
-
(2015)
Nature
, vol.519
, Issue.7544
, pp. 486-490
-
-
Spitale, R.C.1
-
23
-
-
84893351549
-
Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
-
Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS (2014) Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505(7485): 701-705.
-
(2014)
Nature
, vol.505
, Issue.7485
, pp. 701-705
-
-
Rouskin, S.1
Zubradt, M.2
Washietl, S.3
Kellis, M.4
Weissman, J.S.5
-
24
-
-
84893358533
-
Landscape and variation of RNA secondary structure across the human transcriptome
-
Wan Y, et al. (2014) Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505(7485):706-709.
-
(2014)
Nature
, vol.505
, Issue.7485
, pp. 706-709
-
-
Wan, Y.1
-
25
-
-
84946606812
-
Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function
-
Del Campo C, Bartholomäus A, Fedyunin I, Ignatova Z (2015) Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function. PLoS Genet 11(10):e1005613.
-
(2015)
PLoS Genet
, vol.11
, Issue.10
, pp. e1005613
-
-
Del Campo, C.1
Bartholomäus, A.2
Fedyunin, I.3
Ignatova, Z.4
-
26
-
-
67249097456
-
Intrinsic thermal sensing controls proteolysis of Yersinia virulence regulator RovA
-
Herbst K, et al. (2009) Intrinsic thermal sensing controls proteolysis of Yersinia virulence regulator RovA. PLoS Pathog 5(5):e1000435.
-
(2009)
PLoS Pathog
, vol.5
, Issue.5
, pp. e1000435
-
-
Herbst, K.1
-
27
-
-
84987949523
-
Coregulation of host-adapted metabolism and virulence by pathogenic yersiniae
-
Heroven AK, Dersch P (2014) Coregulation of host-adapted metabolism and virulence by pathogenic yersiniae. Front Cell Infect Microbiol 4:146.
-
(2014)
Front Cell Infect Microbiol
, vol.4
, pp. 146
-
-
Heroven, A.K.1
Dersch, P.2
-
28
-
-
84926333299
-
Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs
-
Nuss AM, et al. (2015) Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs. PLoS Genet 11(3):e1005087.
-
(2015)
PLoS Genet
, vol.11
, Issue.3
, pp. e1005087
-
-
Nuss, A.M.1
-
29
-
-
13944268797
-
A novel method for accurate operon predictions in all sequenced prokaryotes
-
Price MN, Huang KH, Alm EJ, Arkin AP (2005) A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res 33(3):880-892.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.3
, pp. 880-892
-
-
Price, M.N.1
Huang, K.H.2
Alm, E.J.3
Arkin, A.P.4
-
30
-
-
80053019485
-
Regulation by small RNAs in bacteria: Expanding frontiers
-
Storz G, Vogel J, Wassarman KM (2011) Regulation by small RNAs in bacteria: Expanding frontiers. Mol Cell 43(6):880-891.
-
(2011)
Mol Cell
, vol.43
, Issue.6
, pp. 880-891
-
-
Storz, G.1
Vogel, J.2
Wassarman, K.M.3
-
31
-
-
84906346426
-
A direct link between the global regulator PhoP and the Csr regulon in Y. Pseudotuberculosis through the small regulatory RNA CsrC
-
Nuss AM, et al. (2014) A direct link between the global regulator PhoP and the Csr regulon in Y. pseudotuberculosis through the small regulatory RNA CsrC. RNA Biol 11(5):580-593.
-
(2014)
RNA Biol
, vol.11
, Issue.5
, pp. 580-593
-
-
Nuss, A.M.1
-
32
-
-
84933511144
-
Regulation of bacterial virulence by Csr (Rsm) systems
-
Vakulskas CA, Potts AH, Babitzke P, Ahmer BM, Romeo T (2015) Regulation of bacterial virulence by Csr (Rsm) systems. Microbiol Mol Biol Rev 79(2):193-224.
-
(2015)
Microbiol Mol Biol Rev
, vol.79
, Issue.2
, pp. 193-224
-
-
Vakulskas, C.A.1
Potts, A.H.2
Babitzke, P.3
Ahmer, B.M.4
Romeo, T.5
-
33
-
-
84862156384
-
Thermogenetic tools to monitor temperature-dependent gene expression in bacteria
-
Klinkert B, et al. (2012) Thermogenetic tools to monitor temperature-dependent gene expression in bacteria. J Biotechnol 160(1-2):55-63.
-
(2012)
J Biotechnol
, vol.160
, Issue.1-2
, pp. 55-63
-
-
Klinkert, B.1
-
34
-
-
0025166089
-
Secondary structure of the ribosome binding site determines translational efficiency: A quantitative analysis
-
de Smit MH, van Duin J (1990) Secondary structure of the ribosome binding site determines translational efficiency: A quantitative analysis. Proc Natl Acad Sci USA 87(19):7668-7672.
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, Issue.19
, pp. 7668-7672
-
-
De Smit, M.H.1
Van Duin, J.2
-
35
-
-
84909993101
-
The PqsR and RhlR transcriptional regulators determine the level of Pseudomonas quinolone signal synthesis in Pseudomonas aeruginosa by producing two different pqsABCDE mRNA isoforms
-
Brouwer S, et al. (2014) The PqsR and RhlR transcriptional regulators determine the level of Pseudomonas quinolone signal synthesis in Pseudomonas aeruginosa by producing two different pqsABCDE mRNA isoforms. J Bacteriol 196(23):4163-4171.
-
(2014)
J Bacteriol
, vol.196
, Issue.23
, pp. 4163-4171
-
-
Brouwer, S.1
-
36
-
-
84888227426
-
The cytotoxic necrotizing factor of Yersinia pseudotuberculosis (CNFY) enhances inflammation and Yop delivery during infection by activation of Rho GTPases
-
Schweer J, et al. (2013) The cytotoxic necrotizing factor of Yersinia pseudotuberculosis (CNFY) enhances inflammation and Yop delivery during infection by activation of Rho GTPases. PLoS Pathog 9(11):e1003746.
-
(2013)
PLoS Pathog
, vol.9
, Issue.11
, pp. e1003746
-
-
Schweer, J.1
-
37
-
-
84881469450
-
Cytotoxic necrotizing factor-Y boosts Yersinia effector translocation by activating Rac protein
-
Wolters M, et al. (2013) Cytotoxic necrotizing factor-Y boosts Yersinia effector translocation by activating Rac protein. J Biol Chem 288(32):23543-23553.
-
(2013)
J Biol Chem
, vol.288
, Issue.32
, pp. 23543-23553
-
-
Wolters, M.1
-
38
-
-
60549117099
-
The Yersinia pestis Ail protein mediates binding and Yop delivery to host cells required for plague virulence
-
Felek S, Krukonis ES (2009) The Yersinia pestis Ail protein mediates binding and Yop delivery to host cells required for plague virulence. Infect Immun 77(2):825-836.
-
(2009)
Infect Immun
, vol.77
, Issue.2
, pp. 825-836
-
-
Felek, S.1
Krukonis, E.S.2
-
39
-
-
77955292889
-
Ail binding to fibronectin facilitates Yersinia pestis binding to host cells and Yop delivery
-
Tsang TM, Felek S, Krukonis ES (2010) Ail binding to fibronectin facilitates Yersinia pestis binding to host cells and Yop delivery. Infect Immun 78(8):3358-3368.
-
(2010)
Infect Immun
, vol.78
, Issue.8
, pp. 3358-3368
-
-
Tsang, T.M.1
Felek, S.2
Krukonis, E.S.3
-
41
-
-
84892475803
-
Yersinia pseudotuberculosis uses Ail and YadA to circumvent neutrophils by directing Yop translocation during lung infection
-
Paczosa MK, Fisher ML, Maldonado-Arocho FJ, Mecsas J (2014) Yersinia pseudotuberculosis uses Ail and YadA to circumvent neutrophils by directing Yop translocation during lung infection. Cell Microbiol 16(2):247-268.
-
(2014)
Cell Microbiol
, vol.16
, Issue.2
, pp. 247-268
-
-
Paczosa, M.K.1
Fisher, M.L.2
Maldonado-Arocho, F.J.3
Mecsas, J.4
-
42
-
-
79960571755
-
Multiplexed RNA structure characterization with selective 2?-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
-
Lucks JB, et al. (2011) Multiplexed RNA structure characterization with selective 2?-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci USA 108(27):11063-11068.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.27
, pp. 11063-11068
-
-
Lucks, J.B.1
-
43
-
-
84928259454
-
Constitutive production of c-di-GMP is associated with mutations in a variant of Pseudomonas aeruginosa with altered membrane composition
-
Blanka A, et al. (2015) Constitutive production of c-di-GMP is associated with mutations in a variant of Pseudomonas aeruginosa with altered membrane composition. Sci Signal 8(372):ra36.
-
(2015)
Sci Signal
, vol.8
, Issue.372
, pp. ra36
-
-
Blanka, A.1
-
44
-
-
84877063192
-
Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing
-
Wan Y, Qu K, Ouyang Z, Chang HY (2013) Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nat Protoc 8(5):849-869.
-
(2013)
Nat Protoc
, vol.8
, Issue.5
, pp. 849-869
-
-
Wan, Y.1
Qu, K.2
Ouyang, Z.3
Chang, H.Y.4
-
45
-
-
70349667200
-
Fast mapping of short sequences with mismatches, insertions and deletions using index structures
-
Hoffmann S, et al. (2009) Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLOS Comput Biol 5(9):e1000502.
-
(2009)
PLOS Comput Biol
, vol.5
, Issue.9
, pp. e1000502
-
-
Hoffmann, S.1
-
46
-
-
82055164092
-
ViennaRNA Package 2.0
-
Lorenz R, et al. (2011) ViennaRNA Package 2.0. Algorithms Mol Biol 6:26.
-
(2011)
Algorithms Mol Biol
, vol.6
, pp. 26
-
-
Lorenz, R.1
-
47
-
-
67650727366
-
VARNA: Interactive drawing and editing of the RNA secondary structure
-
Darty K, Denise A, Ponty Y (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25(15):1974-1975.
-
(2009)
Bioinformatics
, vol.25
, Issue.15
, pp. 1974-1975
-
-
Darty, K.1
Denise, A.2
Ponty, Y.3
-
48
-
-
78650749888
-
Multiple layers of control govern expression of the Escherichia coli ibpAB heat-shock operon
-
Gaubig LC, Waldminghaus T, Narberhaus F (2011) Multiple layers of control govern expression of the Escherichia coli ibpAB heat-shock operon. Microbiology 157(Pt 1):66-76.
-
(2011)
Microbiology
, vol.157
, pp. 66-76
-
-
Gaubig, L.C.1
Waldminghaus, T.2
Narberhaus, F.3
-
49
-
-
0024252185
-
Extension inhibition analysis of translation initiation complexes
-
Hartz D, McPheeters DS, Traut R, Gold L (1988) Extension inhibition analysis of translation initiation complexes. Methods Enzymol 164:419-425.
-
(1988)
Methods Enzymol
, vol.164
, pp. 419-425
-
-
Hartz, D.1
McPheeters, D.S.2
Traut, R.3
Gold, L.4
|