-
1
-
-
58149177178
-
SRNAMap: Genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes
-
Huang, H. Y., Chang, H. Y., Chou, C. H., Tseng, C. P., Ho, S. Y., Yang, C. D., Ju, Y. W. and Huang, H. D. (2009) sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res., 37, D150-D154.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D150-D154
-
-
Huang, H.Y.1
Chang, H.Y.2
Chou, C.H.3
Tseng, C.P.4
Ho, S.Y.5
Yang, C.D.6
Ju, Y.W.7
Huang, H.D.8
-
2
-
-
78149343511
-
SRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments
-
Cao, Y., Wu, J., Liu, Q., Zhao, Y., Ying, X., Cha, L., Wang, L. and Li, W. (2010) sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments. RNA, 16, 2051-2057.
-
(2010)
RNA
, vol.16
, pp. 2051-2057
-
-
Cao, Y.1
Wu, J.2
Liu, Q.3
Zhao, Y.4
Ying, X.5
Cha, L.6
Wang, L.7
Li, W.8
-
3
-
-
84870324468
-
Predicting sRNAs and their targets in bacteria
-
Li, W., Ying, X., Lu, Q. and Chen, L. (2012) Predicting sRNAs and their targets in bacteria. Genomics Proteomics Bioinformatics, 10, 276-284.
-
(2012)
Genomics Proteomics Bioinformatics
, vol.10
, pp. 276-284
-
-
Li, W.1
Ying, X.2
Lu, Q.3
Chen, L.4
-
4
-
-
84860774336
-
SRNAs and the virulence of Salmonella enterica serovar Typhimurium
-
Hébrard, M., Kröger, C., Srikumar, S., Colgan, A., Händler, K. and Hinton, J. C. D. (2012) sRNAs and the virulence of Salmonella enterica serovar Typhimurium. RNA Biol., 9, 437-445.
-
(2012)
RNA Biol.
, vol.9
, pp. 437-445
-
-
Hébrard, M.1
Kröger, C.2
Srikumar, S.3
Colgan, A.4
Händler, K.5
Hinton, J.C.D.6
-
5
-
-
0031697252
-
Global regulation by the small RNA-binding protein CsrA and the non-coding RNA molecule CsrB
-
Romeo, T. (1998) Global regulation by the small RNA-binding protein CsrA and the non-coding RNA molecule CsrB. Mol Microbiol., 29, 1321-1330.
-
(1998)
Mol Microbiol.
, vol.29
, pp. 1321-1330
-
-
Romeo, T.1
-
6
-
-
34247169597
-
CsrB sRNA family: Sequestration of RNA-binding regulatory proteins
-
Babitzke, P. and Romeo, T. (2007) CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr. Opin. Microbiol., 10, 156-163.
-
(2007)
Curr. Opin. Microbiol.
, vol.10
, pp. 156-163
-
-
Babitzke, P.1
Romeo, T.2
-
7
-
-
70349736084
-
Experimental approaches for the discovery and characterization of regulatory small RNA
-
Sharma, C. M. and Vogel, J. (2009) Experimental approaches for the discovery and characterization of regulatory small RNA. Curr. Opin. Microbiol., 12, 536-546.
-
(2009)
Curr. Opin. Microbiol.
, vol.12
, pp. 536-546
-
-
Sharma, C.M.1
Vogel, J.2
-
8
-
-
34250709662
-
Target identification of small noncoding RNAs in bacteria
-
Vogel, J. and Wagner, E. G. (2007) Target identification of small noncoding RNAs in bacteria. Curr. Opin. Microbiol., 10, 262-270.
-
(2007)
Curr. Opin. Microbiol.
, vol.10
, pp. 262-270
-
-
Vogel, J.1
Wagner, E.G.2
-
9
-
-
84876543942
-
RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
-
Salgado, H., Peralta-Gil, M., Gama-Castro, S., Santos-Zavaleta, A., Muñiz-Rascado, L., García-Sotelo, J. S., Weiss, V., Solano-Lira, H., Martínez-Flores, I., Medina-Rivera, A. et al. (2013) RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res., 41, D203-D213.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D203-D213
-
-
Salgado, H.1
Peralta-Gil, M.2
Gama-Castro, S.3
Santos-Zavaleta, A.4
Muñiz-Rascado, L.5
García-Sotelo, J.S.6
Weiss, V.7
Solano-Lira, H.8
Martínez-Flores, I.9
Medina-Rivera, A.10
-
10
-
-
84864823820
-
SRNAdb: A small non-coding RNA database for gram-positive bacteria
-
Pischimarov, J., Kuenne, C., Billion, A., Hemberger, J., Cemić, F., Chakraborty, T. and Hain, T. (2012) sRNAdb: a small non-coding RNA database for gram-positive bacteria. BMC Genomics, 13, 384.
-
(2012)
BMC Genomics
, vol.13
, pp. 384
-
-
Pischimarov, J.1
Kuenne, C.2
Billion, A.3
Hemberger, J.4
Cemić, F.5
Chakraborty, T.6
Hain, T.7
-
11
-
-
84946094179
-
Rfam 12.0: Updates to the RNA families database
-
Nawrocki, E. P., Burge, S. W., Bateman, A., Daub, J., Eberhardt, R. Y., Eddy, S. R., Floden, E. W., Gardner, P. P., Jones, T. A., Tate, J. et al. (2015) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res., 43, D130-D137.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D130-D137
-
-
Nawrocki, E.P.1
Burge, S.W.2
Bateman, A.3
Daub, J.4
Eberhardt, R.Y.5
Eddy, S.R.6
Floden, E.W.7
Gardner, P.P.8
Jones, T.A.9
Tate, J.10
-
12
-
-
84876577653
-
BSRD: A repository for bacterial small regulatory RNA
-
Li, L., Huang, D., Cheung, M. K., Nong, W., Huang, Q. and Kwan, H. S. (2013) BSRD: a repository for bacterial small regulatory RNA. Nucleic Acids Res., 41, D233-D238.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D233-D238
-
-
Li, L.1
Huang, D.2
Cheung, M.K.3
Nong, W.4
Huang, Q.5
Kwan, H.S.6
-
13
-
-
84891773261
-
NPInter v2.0: An updated database of ncRNA interactions
-
Yuan, J., Wu, W., Xie, C., Zhao, G., Zhao, Y. and Chen, R. (2014) NPInter v2.0: an updated database of ncRNA interactions. Nucleic Acids Res., 42, D104-D108.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D104-D108
-
-
Yuan, J.1
Wu, W.2
Xie, C.3
Zhao, G.4
Zhao, Y.5
Chen, R.6
-
14
-
-
75249107453
-
Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1
-
Richter, A. S., Schleberger, C., Backofen, R. and Steglich, C. (2010) Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. Bioinformatics, 26, 1-5.
-
(2010)
Bioinformatics
, vol.26
, pp. 1-5
-
-
Richter, A.S.1
Schleberger, C.2
Backofen, R.3
Steglich, C.4
-
15
-
-
57249083988
-
IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
-
Busch, A., Richter, A. S. and Backofen, R. (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics, 24, 2849-2856.
-
(2008)
Bioinformatics
, vol.24
, pp. 2849-2856
-
-
Busch, A.1
Richter, A.S.2
Backofen, R.3
-
16
-
-
33744800020
-
Target prediction for small, noncoding RNAs in bacteria
-
Tjaden, B., Goodwin, S. S., Opdyke, J. A., Guillier, M., Fu, D. X., Gottesman, S. and Storz, G. (2006) Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res., 34, 2791-2802.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 2791-2802
-
-
Tjaden, B.1
Goodwin, S.S.2
Opdyke, J.A.3
Guillier, M.4
Fu, D.X.5
Gottesman, S.6
Storz, G.7
-
17
-
-
84904813263
-
TargetRNA2: Identifying targets of small regulatory RNAs in bacteria
-
Kery, M. B., Feldman, M., Livny, J. and Tjaden, B. (2014) TargetRNA2: identifying targets of small regulatory RNAs in bacteria. Nucleic Acids Res., 42, W124-W129.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. W124-W129
-
-
Kery, M.B.1
Feldman, M.2
Livny, J.3
Tjaden, B.4
-
18
-
-
79959937873
-
RNApredator: Fast accessibility-based prediction of sRNA targets
-
Eggenhofer, F., Tafer, H., Stadler, P. F. and Hofacker, I. L. (2011) RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res., 39, W149-W154.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W149-W154
-
-
Eggenhofer, F.1
Tafer, H.2
Stadler, P.F.3
Hofacker, I.L.4
-
19
-
-
74549172000
-
SRNATarget: A web server for prediction of bacterial sRNA targets
-
Cao, Y., Zhao, Y., Cha, L., Ying, X., Wang, L., Shao, N. and Li, W. (2009) sRNATarget: a web server for prediction of bacterial sRNA targets. Bioinformation, 3, 364-366.
-
(2009)
Bioinformation
, vol.3
, pp. 364-366
-
-
Cao, Y.1
Zhao, Y.2
Cha, L.3
Ying, X.4
Wang, L.5
Shao, N.6
Li, W.7
-
20
-
-
79960694944
-
STarPicker: A method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization
-
Ying, X., Cao, Y., Wu, J., Liu, Q., Cha, L. and Li, W. (2011) sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization. PLoS One, 6, e22705.
-
(2011)
PLoS One
, vol.6
, pp. e22705
-
-
Ying, X.1
Cao, Y.2
Wu, J.3
Liu, Q.4
Cha, L.5
Li, W.6
-
21
-
-
84883772639
-
Comparative genomics boosts target prediction for bacterial small RNAs
-
Wright, P. R., Richter, A. S., Papenfort, K., Mann, M., Vogel, J., Hess, W. R., Backofen, R. and Georg, J. (2013) Comparative genomics boosts target prediction for bacterial small RNAs. Proc. Natl. Acad. Sci. U. S. A., 110, E3487-E3496.
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. E3487-E3496
-
-
Wright, P.R.1
Richter, A.S.2
Papenfort, K.3
Mann, M.4
Vogel, J.5
Hess, W.R.6
Backofen, R.7
Georg, J.8
-
22
-
-
80855153001
-
Using binding profiles to predict binding sites of target RNAs
-
Poolsap, U., Kato, Y., Sato, K. and Akutsu, T. (2011) Using binding profiles to predict binding sites of target RNAs. J. Bioinform. Comput. Biol., 9, 697-713.
-
(2011)
J. Bioinform. Comput. Biol.
, vol.9
, pp. 697-713
-
-
Poolsap, U.1
Kato, Y.2
Sato, K.3
Akutsu, T.4
-
23
-
-
84941773183
-
Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks
-
Thébault, P., Bourqui, R., Benchimol, W., Gaspin, C., Sirand-Pugnet, P., Uricaru, R. and Dutour, I. (2015) Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks. Brief Bioinform., 16, 795-805.
-
(2015)
Brief Bioinform.
, vol.16
, pp. 795-805
-
-
Thébault, P.1
Bourqui, R.2
Benchimol, W.3
Gaspin, C.4
Sirand-Pugnet, P.5
Uricaru, R.6
Dutour, I.7
-
24
-
-
79952786136
-
Accessibility and evolutionary conservation mark bacterial small-RNA target-binding regions
-
Peer, A. and Margalit, H. (2011) Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions. J. Bacteriol., 193, 1690-1701.
-
(2011)
J. Bacteriol.
, vol.193
, pp. 1690-1701
-
-
Peer, A.1
Margalit, H.2
-
25
-
-
84904467798
-
Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli
-
Jai, J., Tree, S. G., Sean, P. M., David, T. and David, L. G. (2014) Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli. Mol. Cell., 55, 199-213.
-
(2014)
Mol. Cell.
, vol.55
, pp. 199-213
-
-
Jai, J.1
Tree, S.G.2
Sean, P.M.3
David, T.4
David, L.G.5
-
26
-
-
84866949691
-
Hfq proximity and orientation controls RNA annealing
-
Panja, S. and Woodson, S. A. (2012) Hfq proximity and orientation controls RNA annealing. Nucleic Acids Res., 40, 8690-8697.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 8690-8697
-
-
Panja, S.1
Woodson, S.A.2
-
27
-
-
84899831264
-
A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus
-
Eyraud, A., Tattevin, P., Chabelskaya, S. and Felden, B. (2014) A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus. Nucleic Acids Res., 42, 4892-4905.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 4892-4905
-
-
Eyraud, A.1
Tattevin, P.2
Chabelskaya, S.3
Felden, B.4
-
28
-
-
84893679350
-
Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria
-
Pandey, S. P., Winkler, J. A., Li, H., Camacho, D. M., Collins, J. J. and Walker, G. C. (2014) Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics, 15, 121.
-
(2014)
BMC Genomics
, vol.15
, pp. 121
-
-
Pandey, S.P.1
Winkler, J.A.2
Li, H.3
Camacho, D.M.4
Collins, J.J.5
Walker, G.C.6
-
29
-
-
84931570743
-
Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA
-
Miyakoshi, M., Chao, Y. and Vogel, J. (2015) Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA. EMBO J., 34, 1478-1492.
-
(2015)
EMBO J.
, vol.34
, pp. 1478-1492
-
-
Miyakoshi, M.1
Chao, Y.2
Vogel, J.3
-
30
-
-
80053651587
-
GenBank
-
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. and Sayers, E. W. (2013) GenBank. Nucleic Acids Res., 41, D36-D42.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D36-D42
-
-
Benson, D.A.1
Cavanaugh, M.2
Clark, K.3
Karsch-Mizrachi, I.4
Lipman, D.J.5
Ostell, J.6
Sayers, E.W.7
-
31
-
-
77956548953
-
Cytoscape Web: An interactive web-based network browser
-
Lopes, C. T., Franz, M., Kazi, F., Donaldson, S. L., Morris, Q. and Bader, G. D. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics, 26, 2347-2348.
-
(2010)
Bioinformatics
, vol.26
, pp. 2347-2348
-
-
Lopes, C.T.1
Franz, M.2
Kazi, F.3
Donaldson, S.L.4
Morris, Q.5
Bader, G.D.6
-
32
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang, D. W., Sherman, B. T. and Lempicki, R. A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc., 4, 44-57.
-
(2009)
Nat Protoc.
, vol.4
, pp. 44-57
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
33
-
-
33750297745
-
Conserved small non-coding RNAs that belong to the sigmaE regulon: Role in down-regulation of outer membrane proteins
-
Johansen, J., Rasmussen, A. A., Overgaard, M. and Valentin-Hansen, P. (2006) Conserved small non-coding RNAs that belong to the sigmaE regulon: role in down-regulation of outer membrane proteins. J. Mol. Biol., 364, 1-8.
-
(2006)
J. Mol. Biol.
, vol.364
, pp. 1-8
-
-
Johansen, J.1
Rasmussen, A.A.2
Overgaard, M.3
Valentin-Hansen, P.4
-
34
-
-
42549165769
-
Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis
-
Papenfort, K., Pfeiffer, V., Lucchini, S., Sonawane, A., Hinton, J. C. D. and Vogel, J. (2008) Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis. Mol. Microbiol., 68, 890-906.
-
(2008)
Mol. Microbiol.
, vol.68
, pp. 890-906
-
-
Papenfort, K.1
Pfeiffer, V.2
Lucchini, S.3
Sonawane, A.4
Hinton, J.C.D.5
Vogel, J.6
|