-
1
-
-
0000568977
-
Ribonucleic acids from yeast which contain a fifth nucleotide
-
Davis, F. F. & Allen, F. W. Ribonucleic acids from yeast which contain a fifth nucleotide. J. Biol. Chem. 227, 907-915 (1957).
-
(1957)
J. Biol. Chem.
, vol.227
, pp. 907-915
-
-
Davis, F.F.1
Allen, F.W.2
-
2
-
-
0028239805
-
Gln complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure
-
Gln complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure. Biochemistry 33, 7560-7567 (1994).
-
(1994)
Biochemistry
, vol.33
, pp. 7560-7567
-
-
Arnez, J.G.1
Steitz, T.A.2
-
3
-
-
0033935223
-
Pseudouridine in RNA: What, where, how, and why
-
Charette, M. & Gray, M. W. Pseudouridine in RNA: what, where, how, and why. IUBMB Life 49, 341-351 (2000).
-
(2000)
IUBMB Life
, vol.49
, pp. 341-351
-
-
Charette, M.1
Gray, M.W.2
-
4
-
-
0025922011
-
Phe from hisT mutants: A structural role for pseudouridine
-
Phe from hisT mutants: a structural role for pseudouridine. Biochemistry 30, 4223-4231 (1991).
-
(1991)
Biochemistry
, vol.30
, pp. 4223-4231
-
-
Davis, D.R.1
Poulter, C.D.2
-
6
-
-
0025805268
-
Properties of a U1/mRNA 5′ splice site duplex containing pseudouridine as measured by thermodynamic and NMR methods
-
Hall, K. B. & Mclaughlin, L. W. Properties of a U1/mRNA 5′ splice site duplex containing pseudouridine as measured by thermodynamic and NMR methods. Biochemistry 30, 1795-1801 (1991).
-
(1991)
Biochemistry
, vol.30
, pp. 1795-1801
-
-
Hall, K.B.1
Mclaughlin, L.W.2
-
7
-
-
84886027613
-
Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides
-
Hudson, G. A., Bloomingdale, R. & Znosko, B. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides. RNA 19, 1474-1482 (2013).
-
(2013)
RNA
, vol.19
, pp. 1474-1482
-
-
Hudson, G.A.1
Bloomingdale, R.2
Znosko, B.3
-
8
-
-
0033199501
-
Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39
-
Yarian, C. S. et al. Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39. Nucleic Acids Res. 27, 3543-3549 (1999).
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 3543-3549
-
-
Yarian, C.S.1
-
9
-
-
84881477474
-
Unusual base pairing during the decoding of a stop codon by the ribosome
-
Fernández, I. S. et al. Unusual base pairing during the decoding of a stop codon by the ribosome. Nature 500, 107-110 (2013).
-
(2013)
Nature
, vol.500
, pp. 107-110
-
-
Fernández, I.S.1
-
10
-
-
79959284255
-
Converting nonsense codons into sense codons by targeted pseudouridylation
-
Karijolich, J. & Yu, Y.-T. Converting nonsense codons into sense codons by targeted pseudouridylation. Nature 474, 395-398 (2011).
-
(2011)
Nature
, vol.474
, pp. 395-398
-
-
Karijolich, J.1
Yu, Y.-T.2
-
11
-
-
2442691791
-
Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA)
-
Bykhovskaya, Y., Casas, K., Mengesha, E., Inbal, A. & Fischel-Ghodsian, N. Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA). Am. J. Hum. Genet. 74, 1303-1308 (2004).
-
(2004)
Am. J. Hum. Genet.
, vol.74
, pp. 1303-1308
-
-
Bykhovskaya, Y.1
Casas, K.2
Mengesha, E.3
Inbal, A.4
Fischel-Ghodsian, N.5
-
12
-
-
0031799895
-
X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions
-
Heiss, N. S. et al. X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. Nature Genet. 19, 32-38 (1998).
-
(1998)
Nature Genet.
, vol.19
, pp. 32-38
-
-
Heiss, N.S.1
-
13
-
-
84861697187
-
Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis
-
Mei, Y.-P. et al. Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis. Oncogene 31, 2794-2804 (2012).
-
(2012)
Oncogene
, vol.31
, pp. 2794-2804
-
-
Mei, Y.-P.1
-
14
-
-
78651335915
-
The RNA Modification Database, RNAMDB: 2011 update
-
Cantara, W. A. et al. The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res. 39, D195-D201 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D195-D201
-
-
Cantara, W.A.1
-
15
-
-
84880360716
-
Characterization and comparison of human nuclear and cytosolic editomes
-
Chen, L. Characterization and comparison of human nuclear and cytosolic editomes. Proc. Natl Acad. Sci. USA 110, E2741-E2747 (2013).
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. E2741-E2747
-
-
Chen, L.1
-
17
-
-
66349122954
-
Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
-
Li, J. B. et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324, 1210-1213 (2009).
-
(2009)
Science
, vol.324
, pp. 1210-1213
-
-
Li, J.B.1
-
18
-
-
84862649489
-
Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons
-
Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635-1646 (2012).
-
(2012)
Cell
, vol.149
, pp. 1635-1646
-
-
Meyer, K.D.1
-
19
-
-
84860751168
-
Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA
-
Squires, J. E. et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 40, 5023-5033 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 5023-5033
-
-
Squires, J.E.1
-
20
-
-
0027438034
-
Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: Analysis by the application of a new sequencing technique
-
Bakin, A. & Ofengand, J. Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique. Biochemistry 32, 9754-9762 (1993).
-
(1993)
Biochemistry
, vol.32
, pp. 9754-9762
-
-
Bakin, A.1
Ofengand, J.2
-
21
-
-
78650905534
-
U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP
-
Wu, G., Xiao, M., Yang, C. & Yu, Y.-T. U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP. EMBO J. 30, 79-89 (2011).
-
(2011)
EMBO J.
, vol.30
, pp. 79-89
-
-
Wu, G.1
Xiao, M.2
Yang, C.3
Yu, Y.-T.4
-
23
-
-
0033546399
-
Pseudouridine synthetase Pus1 of Saccharomyces cerevisiae: Kinetic characterisation, tRNA structural requirement and real-time analysis of its complex with tRNA
-
Arluison, V., Buckle, M. & Grosjean, H. Pseudouridine synthetase Pus1 of Saccharomyces cerevisiae: kinetic characterisation, tRNA structural requirement and real-time analysis of its complex with tRNA. J. Mol. Biol. 289, 491-502 (1999).
-
(1999)
J. Mol. Biol.
, vol.289
, pp. 491-502
-
-
Arluison, V.1
Buckle, M.2
Grosjean, H.3
-
24
-
-
0031565927
-
Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the TΨ-loop of yeast tRNAs
-
Becker, H. F., Motorin, Y., Sissler, M., Florentz, C. & Grosjean, H. Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the TΨ-loop of yeast tRNAs. J. Mol. Biol. 274, 505-518 (1997).
-
(1997)
J. Mol. Biol.
, vol.274
, pp. 505-518
-
-
Becker, H.F.1
Motorin, Y.2
Sissler, M.3
Florentz, C.4
Grosjean, H.5
-
25
-
-
0142147324
-
The Saccharomyces cerevisiae U2 snRNA:Pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Ψ-synthase also acting on tRNAs
-
Behm-Ansmant, I. et al. The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Ψ-synthase also acting on tRNAs. RNA 9, 1371-1382 (2003).
-
(2003)
RNA
, vol.9
, pp. 1371-1382
-
-
Behm-Ansmant, I.1
-
26
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
Kudla, G., Murray, A. W., Tollervey, D. & Plotkin, J. B. Coding-sequence determinants of gene expression in Escherichia coli. Science 324, 255-258 (2009).
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
Murray, A.W.2
Tollervey, D.3
Plotkin, J.B.4
-
27
-
-
84879345901
-
Rate-limiting steps in yeast protein translation
-
Shah, P., Ding, Y., Niemczyk, M., Kudla, G. & Plotkin, J. B. Rate-limiting steps in yeast protein translation. Cell 153, 1589-1601 (2013).
-
(2013)
Cell
, vol.153
, pp. 1589-1601
-
-
Shah, P.1
Ding, Y.2
Niemczyk, M.3
Kudla, G.4
Plotkin, J.B.5
-
28
-
-
0027494569
-
Ribosomal pausing during translation of an RNA pseudoknot
-
Somogyi, P., Jenner, A. J., Brierley, I. & Inglis, S. C. Ribosomal pausing during translation of an RNA pseudoknot. Mol. Cell. Biol. 13, 6931-6940 (1993).
-
(1993)
Mol. Cell. Biol.
, vol.13
, pp. 6931-6940
-
-
Somogyi, P.1
Jenner, A.J.2
Brierley, I.3
Inglis, S.C.4
-
29
-
-
34247329067
-
Cis-acting determinants of asymmetric, cytoplasmic RNA transport
-
Jambhekar, A. & Derisi, J. L. Cis-acting determinants of asymmetric, cytoplasmic RNA transport. RNA 13, 625-642 (2007).
-
(2007)
RNA
, vol.13
, pp. 625-642
-
-
Jambhekar, A.1
Derisi, J.L.2
-
30
-
-
84863012654
-
Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy
-
Tan, X. et al. Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy. Proc. Natl Acad. Sci. USA 109, 869-874 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 869-874
-
-
Tan, X.1
-
31
-
-
0031820288
-
Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae
-
Longtine, M. S. et al. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14, 953-961 (1998).
-
(1998)
Yeast
, vol.14
, pp. 953-961
-
-
Longtine, M.S.1
-
32
-
-
0033529707
-
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis
-
Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
-
(1999)
Science
, vol.285
, pp. 901-906
-
-
Winzeler, E.A.1
-
35
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10-12 (2011).
-
(2011)
EMBnet.Journal
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
36
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R36
-
-
Kim, D.1
-
37
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
38
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
39
-
-
60549108380
-
Bidirectional promoters generate pervasive transcription in yeast
-
Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033-1037 (2009).
-
(2009)
Nature
, vol.457
, pp. 1033-1037
-
-
Xu, Z.1
-
40
-
-
33847270751
-
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA
-
Piekna-Przybylska, D., Decatur, W. A. & Fournier, M. J. New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 13, 305-312(2007).
-
(2007)
RNA
, vol.13
, pp. 305-312
-
-
Piekna-Przybylska, D.1
Decatur, W.A.2
Fournier, M.J.3
-
41
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks, G. E., Hon, G., Chandonia, J.-M. & Brenner, S. E. WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190 (2004).
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.-M.3
Brenner, S.E.4
-
42
-
-
67650727366
-
VARNA: Interactive drawing and editing of the RNA secondary structure
-
Darty, K., Denise, A. & Ponty, Y. VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics 25, 1974-1975 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1974-1975
-
-
Darty, K.1
Denise, A.2
Ponty, Y.3
-
43
-
-
58149191272
-
tRNAdb 2009: Compilation of tRNA sequences and tRNA genes
-
Jühling, F. et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 37, D159-D162 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D159-D162
-
-
Jühling, F.1
-
44
-
-
34247493236
-
Matplotlib: A 2D graphics environment
-
Hunter, J. D. Matplotlib: A 2D graphics environment. Comput. Sci. Eng. 9, 90-95 (2007).
-
(2007)
Comput. Sci. Eng.
, vol.9
, pp. 90-95
-
-
Hunter, J.D.1
|