-
2
-
-
34247099372
-
Regulatory mechanisms employed by cis-encoded antisense RNAs
-
Brantl S (2007) Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 10:102-109.
-
(2007)
Curr Opin Microbiol
, vol.10
, pp. 102-109
-
-
Brantl, S.1
-
3
-
-
39049131090
-
RNA chaperones, RNA annealers and RNA helicases
-
Rajkowitsch L, et al. (2007) RNA chaperones, RNA annealers and RNA helicases. RNA Biol 4:118-130. (Pubitemid 351237913)
-
(2007)
RNA Biology
, vol.4
, Issue.3
, pp. 118-130
-
-
Rajkowitsch, L.1
Chen, D.2
Stampfl, S.3
Semrad, K.4
Waldsich, C.5
Mayer, O.6
Jantsch, M.F.7
Konrat, R.8
Blasi, U.9
Schroeder, R.10
-
4
-
-
36549086771
-
Toward reprogramming bacteria with small molecules and RNA
-
Gallivan JP (2007) Toward reprogramming bacteria with small molecules and RNA. Curr Opin Chem Biol 11:612-619.
-
(2007)
Curr Opin Chem Biol
, vol.11
, pp. 612-619
-
-
Gallivan, J.P.1
-
5
-
-
33747078696
-
Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes
-
DOI 10.1038/nbt1226, PII NBT1226
-
Pfleger BF, et al. (2006) Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 24:1027-1032. (Pubitemid 44215398)
-
(2006)
Nature Biotechnology
, vol.24
, Issue.8
, pp. 1027-1032
-
-
Pfleger, B.F.1
Pitera, D.J.2
Smolke, C.D.3
Keasling, J.D.4
-
6
-
-
3042741121
-
Engineered riboregulators enable post-transcriptional control of gene expression
-
DOI 10.1038/nbt986
-
Isaacs FJ, et al. (2004) Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol 22:841-847. (Pubitemid 38886602)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.7
, pp. 841-847
-
-
Isaacs, F.J.1
Dwyer, D.J.2
Ding, C.3
Pervouchine, D.D.4
Cantor, C.R.5
Collins, J.J.6
-
7
-
-
77957679279
-
Tracking, tuning, and terminating microbial physiology using synthetic riboregulators
-
Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR, Collins JJ (2010) Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc Natl Acad Sci USA 107:15898-15903.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 15898-15903
-
-
Callura, J.M.1
Dwyer, D.J.2
Isaacs, F.J.3
Cantor, C.R.4
Collins, J.J.5
-
8
-
-
69849092387
-
Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli
-
Nakashima N, Tamura T (2009) Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli. Nucleic Acids Res 37:e103.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Nakashima, N.1
Tamura, T.2
-
11
-
-
34447310821
-
A universal RNAi-based logic evaluator that operates in mammalian cells
-
DOI 10.1038/nbt1307, PII NBT1307
-
Rinaudo K, et al. (2007) A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 25:795-801. (Pubitemid 47052185)
-
(2007)
Nature Biotechnology
, vol.25
, Issue.7
, pp. 795-801
-
-
Rinaudo, K.1
Bleris, L.2
Maddamsetti, R.3
Subramanian, S.4
Weiss, R.5
Benenson, Y.6
-
12
-
-
54949106632
-
Model-guided design of ligand-regulated RNAi for programmable control of gene expression
-
Beisel CL, Bayer TS, Hoff KG, Smolke CD (2008) Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol Syst Biol 4:224.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 224
-
-
Beisel, C.L.1
Bayer, T.S.2
Hoff, K.G.3
Smolke, C.D.4
-
13
-
-
78649429678
-
Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins
-
Culler SJ, Hoff KG, Smolke CD (2010) Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330:1251-1255.
-
(2010)
Science
, vol.330
, pp. 1251-1255
-
-
Culler, S.J.1
Hoff, K.G.2
Smolke, C.D.3
-
14
-
-
84455174703
-
Model-driven engineering of RNA devices to quantitatively program gene expression
-
Carothers JM, Goler JA, Juminaga D, Keasling JD (2011) Model-driven engineering of RNA devices to quantitatively program gene expression. Science 334:1716-1719.
-
(2011)
Science
, vol.334
, pp. 1716-1719
-
-
Carothers, J.M.1
Goler, J.A.2
Juminaga, D.3
Keasling, J.D.4
-
15
-
-
68349141373
-
RNA synthetic biology inspired from bacteria: Construction of transcription attenuators under antisense regulation
-
Dawid A, Cayrol B, Isambert H (2009) RNA synthetic biology inspired from bacteria: Construction of transcription attenuators under antisense regulation. Phys Biol 6:025007.
-
(2009)
Phys Biol
, vol.6
, pp. 025007
-
-
Dawid, A.1
Cayrol, B.2
Isambert, H.3
-
16
-
-
79957700542
-
Versatile RNA-sensing transcriptional regulators for engineering genetic networks
-
Lucks JB, Qi L, Mutalik VK, Wang D, Arkin AP (2011) Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc Natl Acad Sci USA 108:8617-8622.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 8617-8622
-
-
Lucks, J.B.1
Qi, L.2
Mutalik, V.K.3
Wang, D.4
Arkin, A.P.5
-
17
-
-
84863226500
-
Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals
-
Qi L, Lucks JB, Liu CC, Mutalik VK, Arkin AP (2012) Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res 40:5775-5786.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 5775-5786
-
-
Qi, L.1
Lucks, J.B.2
Liu, C.C.3
Mutalik, V.K.4
Arkin, A.P.5
-
18
-
-
84859842558
-
Rationally designed families of orthogonal RNA regulators of translation
-
Mutalik VK, Qi L, Guimaraes JC, Lucks JB, Arkin AP (2012) Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol 8:447-454.
-
(2012)
Nat Chem Biol
, vol.8
, pp. 447-454
-
-
Mutalik, V.K.1
Qi, L.2
Guimaraes, J.C.3
Lucks, J.B.4
Arkin, A.P.5
-
19
-
-
79960697001
-
Organization of intracellular reactions with rationally designed RNA assemblies
-
Delebecque CJ, Lindner AB, Silver PA, Aldaye FA (2011) Organization of intracellular reactions with rationally designed RNA assemblies. Science 333:470-474.
-
(2011)
Science
, vol.333
, pp. 470-474
-
-
Delebecque, C.J.1
Lindner, A.B.2
Silver, P.A.3
Aldaye, F.A.4
-
20
-
-
33845411737
-
Enzyme-free nucleic acid logic circuits
-
DOI 10.1126/science.1132493
-
Seelig G, Soloveichik D, Zhang DY, Winfree E (2006) Enzyme-free nucleic acid logic circuits. Science 314:1585-1588. (Pubitemid 44907149)
-
(2006)
Science
, vol.314
, Issue.5805
, pp. 1585-1588
-
-
Seelig, G.1
Soloveichik, D.2
Zhang, D.Y.3
Winfree, E.4
-
21
-
-
38349121586
-
Programming biomolecular self-assembly pathways
-
Yin P, Choi HM, Calvert CR, Pierce NA (2008) Programming biomolecular self-assembly pathways. Nature 451:318-322.
-
(2008)
Nature
, vol.451
, pp. 318-322
-
-
Yin, P.1
Choi, H.M.2
Calvert, C.R.3
Pierce, N.A.4
-
22
-
-
70350683746
-
Molecular implementation of simple logic programs
-
Ran T, Kaplan S, Shapiro E (2009) Molecular implementation of simple logic programs. Nat Nanotechnol 4:642-648.
-
(2009)
Nat Nanotechnol
, vol.4
, pp. 642-648
-
-
Ran, T.1
Kaplan, S.2
Shapiro, E.3
-
23
-
-
27944493648
-
Computational design and experimental validation of oligonucleotide- sensing allosteric ribozymes
-
DOI 10.1038/nbt1155, PII N1155
-
Penchovsky R, Breaker RR (2005) Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat Biotechnol 23:1424-1433. (Pubitemid 41679396)
-
(2005)
Nature Biotechnology
, vol.23
, Issue.11
, pp. 1424-1433
-
-
Penchovsky, R.1
Breaker, R.R.2
-
24
-
-
34548606194
-
What's so great about RNA?
-
Ellington AD (2007) What's so great about RNA? ACS Chem Biol 2:445-448.
-
(2007)
ACS Chem Biol
, vol.2
, pp. 445-448
-
-
Ellington, A.D.1
-
25
-
-
0030793767
-
De novo protein design: Fully automated sequence selection
-
DOI 10.1126/science.278.5335.82
-
Dahiyat BI, Mayo SL (1997) De novo protein design: Fully automated sequence selection. Science 278:82-87. (Pubitemid 27446279)
-
(1997)
Science
, vol.278
, Issue.5335
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
26
-
-
0037108748
-
Folding free energy function selects native-like protein sequences in the core but not on the surface
-
DOI 10.1073/pnas.212068599
-
Jaramillo A, Wernisch L, Héry S, Wodak SJ (2002) Folding free energy function selects native-like protein sequences in the core but not on the surface. Proc Natl Acad Sci USA 99:13554-13559. (Pubitemid 35215420)
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.21
, pp. 13554-13559
-
-
Jaramillo, A.1
Wernisch, L.2
Hery, S.3
Wodak, S.J.4
-
27
-
-
0037022286
-
Protein topology and stability define the space of allowed sequences
-
Koehl P, Levitt M (2002) Protein topology and stability define the space of allowed sequences. Proc Natl Acad Sci USA 99:1280 -1285.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 1280-1285
-
-
Koehl, P.1
Levitt, M.2
-
28
-
-
0037102491
-
The non-Watson-Crick base pairs and their associated isostericity matrices
-
Leontis NB, Stombaugh J, Westhof E (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30:3497-3531. (Pubitemid 34919207)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.16
, pp. 3497-3531
-
-
Leontis, N.B.1
Stombaugh, J.2
Westhof, E.3
-
29
-
-
0034021259
-
RNA folding at elementary step resolution
-
DOI 10.1017/S1355838200992161
-
Flamm C, Fontana W, Hofacker IL, Schuster P (2000) RNA folding at elementary step resolution. RNA 6:325-338. (Pubitemid 30161278)
-
(2000)
RNA
, vol.6
, Issue.3
, pp. 325-338
-
-
Flamm, C.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
31
-
-
0029160643
-
How to search for RNA structures. Theoretical concepts in evolutionary biotechnology
-
Schuster P (1995) How to search for RNA structures. Theoretical concepts in evolutionary biotechnology. J Biotechnol 41:239-257.
-
(1995)
J Biotechnol
, vol.41
, pp. 239-257
-
-
Schuster, P.1
-
32
-
-
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 467:103-107.
-
(2010)
Nature
, vol.467
, pp. 103-107
-
-
Kertesz, M.1
-
33
-
-
84861541877
-
RNA folding with soft constraints: Reconciliation of probing data and thermodynamic secondary structure prediction
-
Washietl S, Hofacker IL, Stadler PF, Kellis M (2012) RNA folding with soft constraints: Reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Res 40:4261-4272.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 4261-4272
-
-
Washietl, S.1
Hofacker, I.L.2
Stadler, P.F.3
Kellis, M.4
-
34
-
-
80455124085
-
Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors
-
Rodrigo G, Carrera J, Jaramillo A (2011) Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors. Nucleic Acids Res 39:e138.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Rodrigo, G.1
Carrera, J.2
Jaramillo, A.3
-
35
-
-
0034730125
-
A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures
-
Lease RA, Belfort M (2000) A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc Natl Acad Sci USA 97:9919-9924.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 9919-9924
-
-
Lease, R.A.1
Belfort, M.2
-
36
-
-
77953090678
-
Positive regulation by small RNAs and the role of Hfq
-
Soper T, Mandin P, Majdalani N, Gottesman S, Woodson SA (2010) Positive regulation by small RNAs and the role of Hfq. Proc Natl Acad Sci USA 107:9602-9607.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 9602-9607
-
-
Soper, T.1
Mandin, P.2
Majdalani, N.3
Gottesman, S.4
Woodson, S.A.5
-
37
-
-
79952747147
-
Clustering to identify RNA conformations constrained by secondary structure
-
Sim AYL, Levitt M (2011) Clustering to identify RNA conformations constrained by secondary structure. Proc Natl Acad Sci USA 108:3590-3595.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 3590-3595
-
-
Sim, A.Y.L.1
Levitt, M.2
-
38
-
-
78650532236
-
Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA
-
Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J (2010) Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA. Proc Natl Acad Sci USA 107:20435-20440.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 20435-20440
-
-
Papenfort, K.1
Bouvier, M.2
Mika, F.3
Sharma, C.M.4
Vogel, J.5
-
39
-
-
79960433506
-
Hfq and its constellation of RNA
-
Vogel J, Luisi BF (2011) Hfq and its constellation of RNA. Nat Rev Microbiol 9:578-589.
-
(2011)
Nat Rev Microbiol
, vol.9
, pp. 578-589
-
-
Vogel, J.1
Luisi, B.F.2
-
40
-
-
0030861452
-
2 regulatory elements
-
DOI 10.1093/nar/25.6.1203
-
Lutz R, Bujard H (1997) Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res 25:1203-1210. (Pubitemid 27303212)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.6
, pp. 1203-1210
-
-
Lutz, R.1
Bujard, H.2
-
41
-
-
67650713931
-
The structural and functional diversity of metabolite-binding riboswitches
-
Roth A, Breaker RR (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 78:305-334.
-
(2009)
Annu Rev Biochem
, vol.78
, pp. 305-334
-
-
Roth, A.1
Breaker, R.R.2
-
42
-
-
79960959180
-
RNA mimics of green fluorescent protein
-
Paige JS, Wu KY, Jaffrey SR (2011) RNA mimics of green fluorescent protein. Science 333:642-646.
-
(2011)
Science
, vol.333
, pp. 642-646
-
-
Paige, J.S.1
Wu, K.Y.2
Jaffrey, S.R.3
-
43
-
-
70349964350
-
Automated design of synthetic ribosome binding sites to control protein expression
-
Salis HM, Mirsky EA, Voigt CA (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27:946-950.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 946-950
-
-
Salis, H.M.1
Mirsky, E.A.2
Voigt, C.A.3
-
44
-
-
0035396727
-
Internal ribosome entry sites in eukaryotic mRNA molecules
-
DOI 10.1101/gad.891101
-
Hellen CU, Sarnow P (2001) Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev 15:1593-1612. (Pubitemid 32702581)
-
(2001)
Genes and Development
, vol.15
, Issue.13
, pp. 1593-1612
-
-
Hellen, C.U.T.1
Sarnow, P.2
-
47
-
-
57049159362
-
A fast, robust and tunable synthetic gene oscillator
-
DOI 10.1038/nature07389, PII NATURE07389
-
Stricker J, et al. (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456:516-519. (Pubitemid 352759003)
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 516-519
-
-
Stricker, J.1
Cookson, S.2
Bennett, M.R.3
Mather, W.H.4
Tsimring, L.S.5
Hasty, J.6
-
48
-
-
0024672741
-
Genetic analysis of the rnc operon of Escherichia coli
-
Takiff HE, Chen SM, Court DL (1989) Genetic analysis of the rnc operon of Escherichia coli. J Bacteriol 171:2581-2590.
-
(1989)
J Bacteriol
, vol.171
, pp. 2581-2590
-
-
Takiff, H.E.1
Chen, S.M.2
Court, D.L.3
-
49
-
-
56749102636
-
Regulatory activity revealed by dynamic correlations in gene expression noise
-
Dunlop MJ, Cox RS, 3rd, Levine JH, Murray RM, Elowitz MB (2008) Regulatory activity revealed by dynamic correlations in gene expression noise. Nat Genet 40:1493-1498.
-
(2008)
Nat Genet
, vol.40
, pp. 1493-1498
-
-
Dunlop, M.J.1
Cox III, R.S.2
Levine, J.H.3
Murray, R.M.4
Elowitz, M.B.5
-
50
-
-
33845779493
-
Growth of E. coli BL21 in minimal media with different gluconeogenic carbon sources and salt contents
-
DOI 10.1007/s00253-006-0554-8
-
Paliy O, Gunasekera TS (2007) Growth of E. coli BL21 in minimal media with different gluconeogenic carbon sources and salt contents. Appl Microbiol Biotechnol 73:1169-1172. (Pubitemid 44974327)
-
(2007)
Applied Microbiology and Biotechnology
, vol.73
, Issue.5
, pp. 1169-1172
-
-
Paliy, O.1
Gunasekera, T.S.2
|