-
1
-
-
34247117654
-
Fast detection of common sequence structure patterns in RNAs
-
Backofen, R. and Siebert, S. (2007) Fast detection of common sequence structure patterns in RNAs. J. Discrete Algorithms, 5, 212-228.
-
(2007)
J. Discrete Algorithms
, vol.5
, pp. 212-228
-
-
Backofen, R.1
Siebert, S.2
-
4
-
-
46349083026
-
The distributions, mechanisms, and structures of metabolite-binding riboswitches
-
Barrick, J.E. and Breaker, R.R. (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol., 8, R239.
-
(2007)
Genome Biol.
, vol.8
-
-
Barrick, J.E.1
Breaker, R.R.2
-
6
-
-
77956650825
-
Development of aptamer therapeutics
-
Bunka, D.H.J. et al. (2010) Development of aptamer therapeutics. Curr. Opin. Pharmacol., 10, 557-562.
-
(2010)
Curr. Opin. Pharmacol.
, vol.10
, pp. 557-562
-
-
Bunka, D.H.J.1
-
7
-
-
67650727366
-
VARNA: Interactive drawing and editing of the RNA secondary structure
-
Darty, K. et al. (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974-1975.
-
(2009)
Bioinformatics
, vol.25
, pp. 1974-1975
-
-
Darty, K.1
-
8
-
-
23644448438
-
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
-
Ding, Y. et al. (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA, 11, 1157-1166.
-
(2005)
RNA
, vol.11
, pp. 1157-1166
-
-
Ding, Y.1
-
9
-
-
0028801335
-
In vitro selection of RNA ligands for the ribosomal L22 protein associated with Epstein-Barr virus-expressed RNA by using randomized and cDNA-derived RNA libraries
-
Dobbelstein, M. and Shenk, T. (1995) In vitro selection of RNA ligands for the ribosomal L22 protein associated with Epstein-Barr virus-expressed RNA by using randomized and cDNA-derived RNA libraries. J. Virol., 69, 8027-8034.
-
(1995)
J. Virol.
, vol.69
, pp. 8027-8034
-
-
Dobbelstein, M.1
Shenk, T.2
-
10
-
-
25844493154
-
RNA sequence and secondary structure participate in highaffinity CsrA-RNA interaction
-
Dubey, A.K. et al. (2005) RNA sequence and secondary structure participate in highaffinity CsrA-RNA interaction. RNA, 11, 1579-1587.
-
(2005)
RNA
, vol.11
, pp. 1579-1587
-
-
Dubey, A.K.1
-
11
-
-
13244255415
-
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
-
Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
12
-
-
80052441290
-
A neutralizing RNA aptamer against EGFR causes selective apoptotic cell death
-
Esposito, C.L. et al. (2011) A neutralizing RNA aptamer against EGFR causes selective apoptotic cell death. PloS One, 6, e24071.
-
(2011)
PloS One
, vol.6
-
-
Esposito, C.L.1
-
13
-
-
44949239504
-
Discovering sequence motifs with arbitrary insertions and deletions
-
Frith, M.C. et al. (2008) Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput. Biol., 4, e1000071.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Frith, M.C.1
-
14
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
Hertz, G.Z. and Stormo, G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
15
-
-
68549122907
-
Lightweight comparison of RNAs based on exact sequence- structure matches
-
Heyne, S. et al. (2009) Lightweight comparison of RNAs based on exact sequence- structure matches. Bioinformatics, 25, 2095-2102.
-
(2009)
Bioinformatics
, vol.25
, pp. 2095-2102
-
-
Heyne, S.1
-
16
-
-
33750212480
-
Using RNAsecondary structures to guide sequence motif finding towards single-stranded regions
-
Hiller, M. et al. (2006) Using RNAsecondary structures to guide sequence motif finding towards single-stranded regions. Nucleic Acids Res., 34, e117.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Hiller, M.1
-
19
-
-
78049275913
-
RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins
-
Kazan, H. et al. (2010) RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput. Biol., 6, e1000832.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Kazan, H.1
-
20
-
-
80054097776
-
An RNA aptamer that specifically binds pancreatic adenocarcinoma up-regulated factor inhibits migration and growth of pancreatic cancer cells
-
Kim, Y.-H. et al. (2011) An RNA aptamer that specifically binds pancreatic adenocarcinoma up-regulated factor inhibits migration and growth of pancreatic cancer cells. Cancer Lett., 313, 76-83.
-
(2011)
Cancer Lett.
, vol.313
, pp. 76-83
-
-
Kim, Y.-H.1
-
21
-
-
79956290589
-
Acyclic identification of aptamers for human alphathrombin using over-represented libraries and deep sequencing
-
Kupakuwana, G.V. et al. (2011) Acyclic identification of aptamers for human alphathrombin using over-represented libraries and deep sequencing. PLoS ONE, 6.
-
(2011)
PLoS ONE
, pp. 6
-
-
Kupakuwana, G.V.1
-
22
-
-
0346495950
-
Aptamer Database
-
Lee, J.F. et al. (2004) Aptamer Database. Nucleic Acids Res., 32, D95-D100.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Lee, J.F.1
-
23
-
-
79959289324
-
Aptamer selection for the detection of Escherichia coli K88
-
Li, H. et al. (2011) Aptamer selection for the detection of Escherichia coli K88. Can. J. Microbiol., 57, 453-459.
-
(2011)
Can. J. Microbiol.
, vol.57
, pp. 453-459
-
-
Li, H.1
-
24
-
-
0142240407
-
Selection of the simplest RNA that binds isoleucine
-
Lozupone, C. et al. (2003) Selection of the simplest RNA that binds isoleucine. RNA, 9, 1315-1322.
-
(2003)
RNA
, vol.9
, pp. 1315-1322
-
-
Lozupone, C.1
-
25
-
-
34147108104
-
In vitro selection and characterization ofRNAaptamers binding thyroxine hormone
-
Lvesque, D. et al. (2007) In vitro selection and characterization ofRNAaptamers binding thyroxine hormone. Biochem. J., 403, 129-138.
-
(2007)
Biochem. J.
, vol.403
, pp. 129-138
-
-
Lvesque, D.1
-
26
-
-
39149112830
-
FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments
-
Nagarajan, N. and Keich, U. (2008) FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments. Bioinformatics, 24, 577-578.
-
(2008)
Bioinformatics
, vol.24
, pp. 577-578
-
-
Nagarajan, N.1
Keich, U.2
-
27
-
-
28444479592
-
Computing the P-value of the information content from an alignment of multiple sequences
-
Nagarajan, N. et al. (2005) Computing the P-value of the information content from an alignment of multiple sequences. Bioinformatics, 21 (Suppl 1), i311-i318.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Nagarajan, N.1
-
28
-
-
80052228547
-
Nucleic acid aptamers: clinical applications and promising new horizons
-
Ni, X. et al. (2011) Nucleic acid aptamers: clinical applications and promising new horizons. Curr. Med. Chem., 18, 4206-4214.
-
(2011)
Curr. Med. Chem.
, vol.18
, pp. 4206-4214
-
-
Ni, X.1
-
29
-
-
78549255358
-
Aptamers embedded in polyacrylamide nanoparticles: a tool for in vivo metabolite sensing
-
Nielsen, L.J. et al. (2010) Aptamers embedded in polyacrylamide nanoparticles: a tool for in vivo metabolite sensing. ACS Nano, 4, 4361-4370.
-
(2010)
ACS Nano
, vol.4
, pp. 4361-4370
-
-
Nielsen, L.J.1
-
30
-
-
84871219030
-
Structure local multiple alignment of RNA
-
Lecture Notes in Informatics (LNI). Gesellschaft für Informatik (GI)
-
Otto, W. et al. (2008) Structure local multiple alignment of RNA. In Proceedings of German Conference on Bioinformatics (GCB'2008), volume P-136 of Lecture Notes in Informatics (LNI), pp. 178-188. Gesellschaft für Informatik (GI).
-
(2008)
Proceedings of German Conference on Bioinformatics (GCB'2008)
, vol.P-136
, pp. 178-188
-
-
Otto, W.1
-
31
-
-
2942694026
-
RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
-
Pavesi, G. et al. (2004) RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. Nucleic Acids Res., 32, 3258-3269.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 3258-3269
-
-
Pavesi, G.1
-
32
-
-
0022146059
-
Simultaneous solution of the RNA folding, alignment and protosequence problems
-
Sankoff, D. (1985) Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Applied Math., 45, 810-825.
-
(1985)
SIAM J. Applied Math.
, vol.45
, pp. 810-825
-
-
Sankoff, D.1
-
33
-
-
77950366829
-
Sequence-structure relationships in RNAloops: establishing the basis for loop homology modeling
-
Schudoma, C. et al. (2010) Sequence-structure relationships in RNAloops: establishing the basis for loop homology modeling. Nucleic Acids Res., 38, 970-980.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 970-980
-
-
Schudoma, C.1
-
34
-
-
0025194307
-
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
-
Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
-
(1990)
Science
, vol.249
, pp. 505-510
-
-
Tuerk, C.1
Gold, L.2
-
35
-
-
79960065507
-
The dual use ofRNAaptamer sequences for affinity purification and localization studies of RNAs and RNA-protein complexes
-
Walker, S.C. et al. (2011) The dual use ofRNAaptamer sequences for affinity purification and localization studies of RNAs and RNA-protein complexes. Method Mol. Biol., 714, 423-444.
-
(2011)
Method Mol. Biol.
, vol.714
, pp. 423-444
-
-
Walker, S.C.1
-
36
-
-
80052244344
-
Aptamers as Therapeutics in Cardiovascular Diseases
-
Wang, P. et al. (2011) Aptamers as Therapeutics in Cardiovascular Diseases. Curr. Med. Chem., 18, 4169-4174.
-
(2011)
Curr. Med. Chem.
, vol.18
, pp. 4169-4174
-
-
Wang, P.1
-
37
-
-
34247598415
-
Inferring noncoding RNAfamilies and classes by means of genome-scale structure-based clustering
-
Will, S. (2007) Inferring noncoding RNAfamilies and classes by means of genome-scale structure-based clustering. PLoS Comput. Biol., 3.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Will, S.1
-
38
-
-
0033080745
-
Complete suboptimal folding of rna and the stability of secondary structures
-
Wuchty, S. et al. (1999) Complete suboptimal folding of rna and the stability of secondary structures. Biopolymers, 49, 145-165.
-
(1999)
Biopolymers
, vol.49
, pp. 145-165
-
-
Wuchty, S.1
-
39
-
-
0034051357
-
A novel RNA motif that binds efficiently and specifically to the Ttat protein of HIV and inhibits the trans-activation by Tat of transcription in vitro and in vivo
-
Yamamoto, R. et al. (2000) A novel RNA motif that binds efficiently and specifically to the Ttat protein of HIV and inhibits the trans-activation by Tat of transcription in vitro and in vivo. Genes Cells, 5, 371-388.
-
(2000)
Genes Cells
, vol.5
, pp. 371-388
-
-
Yamamoto, R.1
-
40
-
-
78449303831
-
Real-time potentiometric detection of bacteria in complex samples
-
Zelada-Guilln, G.A. et al. (2010) Real-time potentiometric detection of bacteria in complex samples. Anal. Chem., 82, 9254-9260.
-
(2010)
Anal. Chem.
, vol.82
, pp. 9254-9260
-
-
Zelada-Guilln, G.A.1
-
41
-
-
0024477261
-
On finding all suboptimal foldings of an RNAmolecule
-
Zuker, M. (1989) On finding all suboptimal foldings of an RNAmolecule. Science, 244, 48-52.
-
(1989)
Science
, vol.244
, pp. 48-52
-
-
Zuker, M.1
-
42
-
-
0000616205
-
RNA secondary structures and their prediction
-
Zuker, M. and Sankoff, D. (1984) RNA secondary structures and their prediction. Bull. Math. Biol., 46, 591-621.
-
(1984)
Bull. Math. Biol.
, vol.46
, pp. 591-621
-
-
Zuker, M.1
Sankoff, D.2
|