-
1
-
-
84860392511
-
Assessing computational tools for the discovery of small RNA genes in bacteria
-
PMID: 21768221
-
Lu X, Goodrich-Blair H, Tjaden B. Assessing computational tools for the discovery of small RNA genes in bacteria. RNA 2011; 17: 1635-47; PMID: 21768221; http: //dx. doi. org/10. 1261/rna. 2689811
-
(2011)
RNA
, vol.17
, pp. 1635-1647
-
-
Lu, X.1
Goodrich-Blair, H.2
Tjaden, B.3
-
2
-
-
84863924309
-
Bacterial small RNA regulators: Versatile roles and rapidly evolving variations
-
pii: a003798; PMID: 20980440
-
Gottesman S, Storz G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2011; 3: pii: a003798; PMID: 20980440; http: //dx. doi. org/10. 1101/cshperspect. a003798
-
(2011)
Cold Spring Harb Perspect Biol
, vol.3
-
-
Gottesman, S.1
Storz, G.2
-
3
-
-
80053019485
-
Regulation by small RNAs in bacteria: Expanding frontiers
-
PMID: 21925377
-
Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011; 43: 880-91; PMID: 21925377; http: //dx. doi. org/ 10. 1016/j. molcel. 2011. 08. 022
-
(2011)
Mol Cell
, vol.43
, pp. 880-891
-
-
Storz, G.1
Vogel, J.2
Wassarman, K.M.3
-
4
-
-
0344237410
-
RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria
-
PMID: 14602901
-
Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A, Wagner EG. RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res 2003; 31: 6435-43; PMID: 14602901; http: // dx. doi. org/10. 1093/nar/gkg867
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 6435-6443
-
-
Vogel, J.1
Bartels, V.2
Tang, T.H.3
Churakov, G.4
Slagter-Jager, J.G.5
Huttenhofer, A.6
Wagner, E.G.7
-
5
-
-
50849105413
-
Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
-
PMID: 18725932
-
Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 2008; 4: e1000163; PMID: 18725932; http: //dx. doi. org/10. 1371/journal. pgen. 1000163
-
(2008)
PLoS Genet
, vol.4
-
-
Sittka, A.1
Lucchini, S.2
Papenfort, K.3
Sharma, C.M.4
Rolle, K.5
Binnewies, T.T.6
Hinton, J.C.7
Vogel, J.8
-
6
-
-
55749083578
-
RNAplex: A fast tool for RNARNA interaction search
-
PMID: 18434344
-
Tafer H, Hofacker IL. RNAplex: a fast tool for RNARNA interaction search. Bioinformatics 2008; 24: 2657-63; PMID: 18434344; http: //dx. doi. org/10. 1093/ bioinformatics/btn193
-
(2008)
Bioinformatics
, vol.24
, pp. 2657-2663
-
-
Tafer, H.1
Hofacker, I.L.2
-
7
-
-
57249083988
-
IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
-
PMID: 18940824
-
Busch A, Richter AS, Backofen R. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 2008; 24: 2849-56; PMID: 18940824; http: //dx. doi. org/10. 1093/bioinformatics/btn544
-
(2008)
Bioinformatics
, vol.24
, pp. 2849-2856
-
-
Busch, A.1
Richter, A.S.2
Backofen, R.3
-
8
-
-
84859947721
-
LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
-
PMID: 22450757
-
Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R. LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA 2012; 18: 900-14; PMID: 22450757; http: //dx. doi. org/ 10. 1261/rna. 029041. 111
-
(2012)
RNA
, vol.18
, pp. 900-914
-
-
Will, S.1
Joshi, T.2
Hofacker, I.L.3
Stadler, P.F.4
Backofen, R.5
-
9
-
-
33645103560
-
GUUGle: A utility for fast exact matching under RNA complementary rules including G-U base pairing
-
PMID: 16403789
-
Gerlach W, Giegerich R. GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics 2006; 22: 762-4; PMID: 16403789; http: //dx. doi. org/ 10. 1093/bioinformatics/btk041
-
(2006)
Bioinformatics
, vol.22
, pp. 762-764
-
-
Gerlach, W.1
Giegerich, R.2
-
10
-
-
84867300120
-
RIsearch: Fast RNARNA interaction search using a simplified nearestneighbor energy model
-
PMID: 22923300
-
Wenzel A, Akbasli E, Gorodkin J. RIsearch: fast RNARNA interaction search using a simplified nearestneighbor energy model. Bioinformatics 2012; 28: 2738-46; PMID: 22923300; http: //dx. doi. org/10. 1093/ bioinformatics/bts519
-
(2012)
Bioinformatics
, vol.28
, pp. 2738-2746
-
-
Wenzel, A.1
Akbasli, E.2
Gorodkin, J.3
-
11
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
PMID: 10329189
-
Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999; 288: 911-40; PMID: 10329189; http: //dx. doi. org/10. 1006/jmbi. 1999. 2700
-
(1999)
J Mol Biol
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
12
-
-
11844254846
-
Secondary structure prediction of interacting RNA molecules
-
PMID: 15644199
-
Andronescu M, Zhang ZC, Condon A. Secondary structure prediction of interacting RNA molecules. J Mol Biol 2005; 345: 987-1001; PMID: 15644199; http: //dx. doi. org/10. 1016/j. jmb. 2004. 10. 082
-
(2005)
J Mol Biol
, vol.345
, pp. 987-1001
-
-
Andronescu, M.1
Zhang, Z.C.2
Condon, A.3
-
13
-
-
24744461715
-
Thermodynamically based DNA strand design
-
PMID: 16145053
-
Tulpan D, Andronescu M, Chang SB, Shortreed MR, Condon A, Hoos HH, Smith LM. Thermodynamically based DNA strand design. Nucleic Acids Res 2005; 33: 4951-64; PMID: 16145053; http: //dx. doi. org/ 10. 1093/nar/gki773
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4951-4964
-
-
Tulpan, D.1
Andronescu, M.2
Chang, S.B.3
Shortreed, M.R.4
Condon, A.5
Hoos, H.H.6
Smith, L.M.7
-
14
-
-
33744979613
-
Partition function and base pairing probabilities of RNA heterodimers
-
PMID: 16722605
-
Bernhart SH, Tafer H, Muckstein U, Flamm C, Stadler PF, Hofacker IL. Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol 2006; 1: 3; PMID: 16722605; http: //dx. doi. org/ 10. 1186/1748-7188-1-3
-
(2006)
Algorithms Mol Biol
, vol.1
, pp. 3
-
-
Bernhart, S.H.1
Tafer, H.2
Muckstein, U.3
Flamm, C.4
Stadler, P.F.5
Hofacker, I.L.6
-
15
-
-
48449101958
-
TargetRNA: A tool for predicting targets of small RNA action in bacteria
-
PMID: 18477632
-
Tjaden B. TargetRNA: a tool for predicting targets of small RNA action in bacteria. Nucleic Acids Res 2008; 36: W109-13; PMID: 18477632; http: //dx. doi. org/ 10. 1093/nar/gkn264
-
(2008)
Nucleic Acids Res
, vol.36
, pp. W109-W113
-
-
Tjaden, B.1
-
16
-
-
4644237189
-
Fast and effective prediction of microRNA/target duplexes
-
PMID: 15383676
-
Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA 2004; 10: 1507-17; PMID: 15383676; http: //dx. doi. org/10. 1261/rna. 5248604
-
(2004)
RNA
, vol.10
, pp. 1507-1517
-
-
Rehmsmeier, M.1
Steffen, P.2
Hochsmann, M.3
Giegerich, R.4
-
17
-
-
33747849920
-
RNAhybrid: MicroRNA target prediction easy, fast and flexible
-
PMID: 16845047
-
Kruger J, Rehmsmeier M. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 2006; 34: W451-4; PMID: 16845047; http: //dx. doi. org/10. 1093/nar/gkl243
-
(2006)
Nucleic Acids Res
, vol.34
, pp. W451-W454
-
-
Kruger, J.1
Rehmsmeier, M.2
-
18
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. Fast folding and comparison of RNA secondary structures. Monatsh Chem 1994; 125: 167-88; http: //dx. doi. org/10. 1007/BF00818163
-
(1994)
Monatsh Chem
, vol.125
, pp. 167-88;
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, L.S.4
Tacker, M.5
Schuster, P.6
-
19
-
-
33646877072
-
Thermodynamics of RNARNA binding
-
PMID: 16446276
-
Muckstein U, Tafer H, Hackermuller J, Bernhart SH, Stadler PF, Hofacker IL. Thermodynamics of RNARNA binding. Bioinformatics 2006; 22: 1177-82; PMID: 16446276; http: //dx. doi. org/10. 1093/ bioinformatics/btl024
-
(2006)
Bioinformatics
, vol.22
, pp. 1177-1182
-
-
Muckstein, U.1
Tafer, H.2
Hackermuller, J.3
Bernhart, S.H.4
Stadler, P.F.5
Hofacker, I.L.6
-
20
-
-
84883772639
-
Comparative genomics boosts target prediction for bacterial small RNAs
-
PMID: 23980183
-
Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J. Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci U S A 2013; 110: E3487-96; PMID: 23980183; http: //dx. doi. org/10. 1073/pnas. 1303248110
-
(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
-
21
-
-
84904810632
-
CopraRNA and IntaRNA: Predicting small RNA targets, networks and interaction domains
-
PMID: 24838564 Web Server issue
-
Wright PR, Georg J, Mann M, Sorescu DA, Richter AS, Lott S, Kleinkauf R, Hess WR, Backofen R. CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. Nucleic Acids Res 2014; 42 (Web Server issue): W119-23; PMID: 24838564
-
(2014)
Nucleic Acids Res
, vol.42
, pp. W119-W123
-
-
Wright, P.R.1
Georg, J.2
Mann, M.3
Sorescu, D.A.4
Richter, A.S.5
Lott, S.6
Kleinkauf, R.7
Hess, W.R.8
Backofen, R.9
-
22
-
-
84904813263
-
TargetRNA2: Identifying targets of small regulatory RNAs in bacteria
-
PMID: 24753424. Web Server issue
-
Kery MB, Feldman M, Livny J, Tjaden B. TargetRNA2: identifying targets of small regulatory RNAs in bacteria. Nucleic Acids Res 2014; 42(Web Server issue): W124-9; PMID: 24753424
-
(2014)
Nucleic Acids Res
, vol.42
, pp. W124-W129
-
-
Kery, M.B.1
Feldman, M.2
Livny, J.3
Tjaden, B.4
-
23
-
-
79952786136
-
Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions
-
PMID: 21278294
-
Peer A, Margalit H. Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions. J Bacteriol 2011; 193: 1690-701; PMID: 21278294; http: // dx. doi. org/10. 1128/JB. 01419-10
-
(2011)
J Bacteriol
, vol.193
, pp. 1690-1701
-
-
Peer, A.1
Margalit, H.2
-
24
-
-
85011941303
-
Computational prediction of sRNAs and their targets in bacteria
-
PMID: 20061798
-
Backofen R, Hess WR. Computational prediction of sRNAs and their targets in bacteria. RNA Biol 2010; 7: 33-42; PMID: 20061798; http: //dx. doi. org/10. 4161/ rna. 7. 1. 10655
-
(2010)
RNA Biol
, vol.7
, pp. 33-42
-
-
Backofen, R.1
Hess, W.R.2
-
25
-
-
79959937873
-
RNApredator: Fast accessibility-based prediction of sRNA targets
-
PMID: 21672960
-
Eggenhofer F, Tafer H, Stadler PF, Hofacker IL. RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res 2011; 39: W149-54; PMID: 21672960; http: //dx. doi. org/10. 1093/nar/gkr467
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W149-W154
-
-
Eggenhofer, F.1
Tafer, H.2
Stadler, P.F.3
Hofacker, I.L.4
-
26
-
-
84858862917
-
Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli
-
PMID: 22250746
-
Jorgensen MG, Nielsen JS, Boysen A, Franch T, Moller-Jensen J, Valentin-Hansen P. Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli. Mol Microbiol 2012; 84: 36-50; PMID: 22250746; http: //dx. doi. org/10. 1111/j. 1365-2958. 2012. 07976. x
-
(2012)
Mol Microbiol
, vol.84
, pp. 36-50
-
-
Jorgensen, M.G.1
Nielsen, J.S.2
Boysen, A.3
Franch, T.4
Moller-Jensen, J.5
Valentin-Hansen, P.6
-
27
-
-
79251559383
-
The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli
-
PMID: 21292161
-
Beisel CL, Storz G. The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Mol Cell 2011; 41: 286-97; PMID: 21292161; http: //dx. doi. org/ 10. 1016/j. molcel. 2010. 12. 027
-
(2011)
Mol Cell
, vol.41
, pp. 286-297
-
-
Beisel, C.L.1
Storz, G.2
-
28
-
-
0034730125
-
A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures
-
PMID: 10954740
-
Lease RA, Belfort M. A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc Natl Acad Sci U S A 2000; 97: 9919-24; PMID: 10954740; http: //dx. doi. org/10. 1073/pnas. 170281497
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 9919-9924
-
-
Lease, R.A.1
Belfort, M.2
-
29
-
-
68249156618
-
Coding sequence targeting byMicCRNA reveals bacterial mRNA silencing downstream of translational initiation
-
PMID: 19620966
-
Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J. Coding sequence targeting byMicCRNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 2009; 16: 840-6; PMID: 19620966; http: //dx. doi. org/10. 1038/nsmb. 1631
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 840-846
-
-
Pfeiffer, V.1
Papenfort, K.2
Lucchini, S.3
Hinton, J.C.4
Vogel, J.5
-
30
-
-
84880888853
-
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling
-
PMID: 23899370
-
Li S, Dong X, Su Z. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics 2013; 14: 520; PMID: 23899370; http: // dx. doi. org/10. 1186/1471-2164-14-520
-
(2013)
BMC Genomics
, vol.14
, pp. 520
-
-
Li, S.1
Dong, X.2
Su, Z.3
-
31
-
-
84867056798
-
Small RNA binding-site multiplicity involved in translational regulation of a polycistronic mRNA
-
PMID: 22988087
-
Rice JB, Balasubramanian D, Vanderpool CK. Small RNA binding-site multiplicity involved in translational regulation of a polycistronic mRNA. Proc Natl Acad Sci U S A 2012; 109: E2691-8; PMID: 22988087; http: //dx. doi. org/10. 1073/pnas. 1207927109
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. E2691-E2698
-
-
Rice, J.B.1
Balasubramanian, D.2
Vanderpool, C.K.3
-
32
-
-
78049393967
-
Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism
-
PMID: 20511587
-
Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, Skorski P, Borezée-Durant E, Barbet R, Jacquet E, Jacq A, et al. Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res 2010; 38: 6620-36; PMID: 20511587; http: //dx. doi. org/ 10. 1093/nar/gkq462
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 6620-6636
-
-
Bohn, C.1
Rigoulay, C.2
Chabelskaya, S.3
Sharma, C.M.4
Marchais, A.5
Skorski, P.6
Borezée-Durant, E.7
Barbet, R.8
Jacquet, E.9
Jacq, A.10
-
33
-
-
84865302975
-
Accessibility and conservation: General features of bacterial small RNA-mRNA interactions?
-
PMID: 22767260
-
Richter AS, Backofen R. Accessibility and conservation: general features of bacterial small RNA-mRNA interactions? RNA Biol 2012; 9: 954-65; PMID: 22767260; http: //dx. doi. org/10. 4161/rna. 20294
-
(2012)
RNA Biol
, vol.9
, pp. 954-965
-
-
Richter, A.S.1
Backofen, R.2
-
34
-
-
33847206046
-
Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding
-
PMID: 17268550
-
Vecerek B, Moll I, Blasi U. Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding. EMBO J 2007; 26: 965-75; PMID: 17268550; http: //dx. doi. org/10. 1038/sj. emboj. 7601553
-
(2007)
EMBO J
, vol.26
, pp. 965-975
-
-
Vecerek, B.1
Moll, I.2
Blasi, U.3
-
35
-
-
0034725539
-
fhlA repression by OxyS RNA: Kissing complex formation at two sites results in a stable antisense-target RNA complex
-
PMID: 10903857
-
Argaman L, Altuvia S. fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex. J Mol Biol 2000; 300: 1101-12; PMID: 10903857; http: //dx. doi. org/ 10. 1006/jmbi. 2000. 3942
-
(2000)
J Mol Biol
, vol.300
, pp. 1101-1112
-
-
Argaman, L.1
Altuvia, S.2
-
36
-
-
0037144546
-
A microRNA in a multipleturnover RNAi enzyme complex
-
PMID: 12154197
-
Hutvagner G, Zamore PD. A microRNA in a multipleturnover RNAi enzyme complex. Science 2002; 297: 2056-60; PMID: 12154197; http: //dx. doi. org/ 10. 1126/science. 1073827
-
(2002)
Science
, vol.297
, pp. 2056-2060
-
-
Hutvagner, G.1
Zamore, P.D.2
-
37
-
-
84928258164
-
Target repression induced by endogenous microRNAs: Large differences, small effects
-
PMID: 25141277
-
Kozomara A, Hunt S, Ninova M, Griffiths-Jones S, Ronshaugen M. Target repression induced by endogenous microRNAs: large differences, small effects. PloS One 2014; 9: e104286; PMID: 25141277; http: //dx. doi. org/10. 1371/journal. pone. 0104286
-
(2014)
PloS One
, vol.9
-
-
Kozomara, A.1
Hunt, S.2
Ninova, M.3
Griffiths-Jones, S.4
Ronshaugen, M.5
|