-
1
-
-
84860779086
-
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
-
Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201-206 (2012).
-
(2012)
Nature
, vol.485
, pp. 201-206
-
-
Dominissini, D.1
-
2
-
-
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
-
3
-
-
84922180958
-
Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells
-
Carlile, T. M. et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515, 143-146 (2014).
-
(2014)
Nature
, vol.515
, pp. 143-146
-
-
Carlile, T.M.1
-
4
-
-
84907527348
-
Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA
-
Schwartz, S. et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159, 148-162 (2014).
-
(2014)
Cell
, vol.159
, pp. 148-162
-
-
Schwartz, S.1
-
5
-
-
84937514684
-
Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome
-
Li, X. et al. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nature Chem. Biol. 11, 592-597 (2015).
-
(2015)
Nature Chem. Biol
, vol.11
, pp. 592-597
-
-
Li, X.1
-
6
-
-
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
-
7
-
-
84877350071
-
Identification of direct targets and modified bases of RNA cytosine methyltransferases
-
Khoddami, V. & Cairns, B. R. Identification of direct targets and modified bases of RNA cytosine methyltransferases. Nature Biotechnol. 31, 458-464 (2013).
-
(2013)
Nature Biotechnol
, vol.31
, pp. 458-464
-
-
Khoddami, V.1
Cairns, B.R.2
-
8
-
-
84898814417
-
Gene expression regulation mediated through reversible m6A RNA methylation
-
Fu, Y., Dominissini, D., Rechavi, G. & He, C. Gene expression regulation mediated through reversible m6A RNA methylation. Nature Rev. Genet. 15, 293-306 (2014).
-
(2014)
Nature Rev. Genet
, vol.15
, pp. 293-306
-
-
Fu, Y.1
Dominissini, D.2
Rechavi, G.3
He, C.4
-
9
-
-
84906852434
-
The pivotal regulatory landscape of RNA modifications
-
Li, S. & Mason, C. E. The pivotal regulatory landscape of RNA modifications. Annu. Rev. Genomics Hum. Genet. 15, 127-150 (2014).
-
(2014)
Annu. Rev. Genomics Hum. Genet
, vol.15
, pp. 127-150
-
-
Li, S.1
Mason, C.E.2
-
10
-
-
84875692043
-
MODOMICS: A database of RNA modification pathways-2013 update
-
Machnicka, M. A. et al. MODOMICS: a database of RNA modification pathways-2013 update. Nucleic Acids Res. 41, D262-D267 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D262-D267
-
-
Machnicka, M.A.1
-
11
-
-
0000475679
-
The occurrence of 1-methyladenine in ribonucleic acid
-
Dunn, D. B. The occurrence of 1-methyladenine in ribonucleic acid. Biochim. Biophys. Acta 46, 198-200 (1961).
-
(1961)
Biochim. Biophys. Acta
, vol.46
, pp. 198-200
-
-
Dunn, D.B.1
-
12
-
-
50549156133
-
Method for isolation of 2'-O-methylribonucleotides and N1-methyladenosine from ribonucleic acid
-
Hall, R. H. Method for isolation of 2'-O-methylribonucleotides and N1-methyladenosine from ribonucleic acid. Biochim. Biophys. Acta 68, 278-283 (1963).
-
(1963)
Biochim. Biophys. Acta
, vol.68
, pp. 278-283
-
-
Hall, R.H.1
-
13
-
-
84870152928
-
Biosynthesis and function of posttranscriptional modifications of transfer RNAs
-
El Yacoubi, B., Bailly, M. & de Crécy-Lagard, V. Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Annu. Rev. Genet. 46, 69-95 (2012).
-
(2012)
Annu. Rev. Genet
, vol.46
, pp. 69-95
-
-
El Yacoubi, B.1
Bailly, M.2
De Crécy-Lagard, V.3
-
14
-
-
84878583858
-
Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae
-
Sharma, S., Watzinger, P., Kötter, P. & Entian, K. D. Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae. Nucleic Acids Res. 41, 5428-5443 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 5428-5443
-
-
Sharma, S.1
Watzinger, P.2
Kötter, P.3
Entian, K.D.4
-
16
-
-
0014340979
-
1-Methyladenosine. Dimroth rearrangement and reversible reduction
-
Macon, J. B. & Wolfenden, R. 1-Methyladenosine. Dimroth rearrangement and reversible reduction. Biochemistry 7, 3453-3458 (1968).
-
(1968)
Biochemistry
, vol.7
, pp. 3453-3458
-
-
Macon, J.B.1
Wolfenden, R.2
-
17
-
-
0016285746
-
Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells
-
Desrosiers, R., Friderici, K. & Rottman, F. Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells. Proc. Natl Acad. Sci. USA 71, 3971-3975 (1974).
-
(1974)
Proc. Natl Acad. Sci. USA
, vol.71
, pp. 3971-3975
-
-
Desrosiers, R.1
Friderici, K.2
Rottman, F.3
-
18
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
-
(2008)
Genome Biol
, vol.9
, pp. R137
-
-
Zhang, Y.1
-
19
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
-
Ingolia, N. T., Lareau, L. F. & Weissman, J. S. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789-802 (2011).
-
(2011)
Cell
, vol.147
, pp. 789-802
-
-
Ingolia, N.T.1
Lareau, L.F.2
Weissman, J.S.3
-
20
-
-
84866267681
-
Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution
-
Lee, S. et al. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc. Natl Acad. Sci. USA 109, E2424-E2432 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. E2424-E2432
-
-
Lee, S.1
-
21
-
-
84926190005
-
Quantitative profiling of initiating ribosomes in vivo
-
Gao, X. et al. Quantitative profiling of initiating ribosomes in vivo. Nature Methods 12, 147-153 (2015).
-
(2015)
Nature Methods
, vol.12
, pp. 147-153
-
-
Gao, X.1
-
22
-
-
84923878470
-
Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI)
-
Takuma, H. et al. Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI). J. Biol. Chem. 290, 5912-5925 (2015).
-
(2015)
J. Biol. Chem
, vol.290
, pp. 5912-5925
-
-
Takuma, H.1
-
23
-
-
23644456550
-
The bipartite structure of the tRNA m1A58 methyltransferase from S. Cerevisiae is conserved in humans
-
Ozanick, S., Krecic, A., Andersland, J. & Anderson, J. T. The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans. RNA 11, 1281-1290 (2005).
-
(2005)
RNA
, vol.11
, pp. 1281-1290
-
-
Ozanick, S.1
Krecic, A.2
Andersland, J.3
Anderson, J.T.4
-
24
-
-
27144555357
-
Regulation of translation via mRNA structure in prokaryotes and eukaryotes
-
Kozak, M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361, 13-37 (2005).
-
(2005)
Gene
, vol.361
, pp. 13-37
-
-
Kozak, M.1
-
25
-
-
0037109157
-
Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: A potential mechanism for the activity of the IME4 gene
-
Clancy, M. J., Shambaugh, M. E., Timpte, C. S. & Bokar, J. A. Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene. Nucleic Acids Res. 30, 4509-4518 (2002).
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4509-4518
-
-
Clancy, M.J.1
Shambaugh, M.E.2
Timpte, C.S.3
Bokar, J.A.4
-
26
-
-
84890107723
-
High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis
-
Schwartz, S. et al. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 155, 1409-1421 (2013).
-
(2013)
Cell
, vol.155
, pp. 1409-1421
-
-
Schwartz, S.1
-
27
-
-
84875410311
-
Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA
-
Peifer, C. et al. Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA. Nucleic Acids Res. 41, 1151-1163 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 1151-1163
-
-
Peifer, C.1
-
28
-
-
81355146483
-
N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO
-
Jia, G. et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nature Chem. Biol. 7, 885-887 (2011).
-
(2011)
Nature Chem. Biol
, vol.7
, pp. 885-887
-
-
Jia, G.1
-
29
-
-
0037456369
-
Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA
-
Aas, P. A. et al. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature 421, 859-863 (2003).
-
(2003)
Nature
, vol.421
, pp. 859-863
-
-
Aas, P.A.1
-
30
-
-
4944254870
-
AlkB restores the biological function of mRNA and tRNA inactivated by chemical methylation
-
Ougland, R. et al. AlkB restores the biological function of mRNA and tRNA inactivated by chemical methylation. Mol. Cell 16, 107-116 (2004).
-
(2004)
Mol. Cell
, vol.16
, pp. 107-116
-
-
Ougland, R.1
-
31
-
-
84880766519
-
New universal rules of eukaryotic translation initiation fidelity
-
Zur, H. & Tuller, T. New universal rules of eukaryotic translation initiation fidelity. PLOS Comput. Biol. 9, e1003136 (2013).
-
(2013)
PLOS Comput. Biol
, vol.9
-
-
Zur, H.1
Tuller, T.2
-
32
-
-
79953052296
-
mRNA helicases: The tacticians of translational control
-
Parsyan, A. et al. mRNA helicases: the tacticians of translational control. Nature Rev. Mol. Cell Biol. 12, 235-245 (2011).
-
(2011)
Nature Rev. Mol. Cell Biol
, vol.12
, pp. 235-245
-
-
Parsyan, A.1
-
33
-
-
0032867610
-
A Watson-Crick base-pair-disrupting methyl group (m1A9) is sufficient for cloverleaf folding of human mitochondrial tRNALys
-
Helm, M., Giegé, R. & Florentz, C. A Watson-Crick base-pair-disrupting methyl group (m1A9) is sufficient for cloverleaf folding of human mitochondrial tRNALys. Biochemistry 38, 13338-13346 (1999).
-
(1999)
Biochemistry
, vol.38
, pp. 13338-13346
-
-
Helm, M.1
Giegé, R.2
Florentz, C.3
-
34
-
-
84879969127
-
Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
-
Guttman, M., Russell, P., Ingolia, N. T., Weissman, J. S. & Lander, E. S. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154, 240-251 (2013).
-
(2013)
Cell
, vol.154
, pp. 240-251
-
-
Guttman, M.1
Russell, P.2
Ingolia, N.T.3
Weissman, J.S.4
Lander, E.S.5
-
35
-
-
77955235019
-
Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system
-
Lu, L., Yi, C., Jian, X., Zheng, G. & He, C. Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system. Nucleic Acids Res. 38, 4415-4425 (2010).
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 4415-4425
-
-
Lu, L.1
Yi, C.2
Jian, X.3
Zheng, G.4
He, C.5
-
36
-
-
25844499232
-
A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. Coli Ada
-
He, C. et al. A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli Ada. Mol. Cell 20, 117-129 (2005).
-
(2005)
Mol. Cell
, vol.20
, pp. 117-129
-
-
He, C.1
-
37
-
-
84891280075
-
Identification of a selective polymerase enables detection of N6- methyladenosine in RNA
-
Harcourt, E. M., Ehrenschwender, T., Batista, P. J., Chang, H. Y. & Kool, E. T. Identification of a selective polymerase enables detection of N6- methyladenosine in RNA. J. Am. Chem. Soc. 135, 19079-19082 (2013).
-
(2013)
J. Am. Chem. Soc
, vol.135
, pp. 19079-19082
-
-
Harcourt, E.M.1
Ehrenschwender, T.2
Batista, P.J.3
Chang, H.Y.4
Kool, E.T.5
-
38
-
-
60149091189
-
Regulation of translation initiation in eukaryotes: Mechanisms and biological targets
-
Sonenberg, N. & Hinnebusch, A. G. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136, 731-745 (2009).
-
(2009)
Cell
, vol.136
, pp. 731-745
-
-
Sonenberg, N.1
Hinnebusch, A.G.2
-
39
-
-
84930621650
-
N6-methyladenosine modulates messenger RNA translation efficiency
-
Wang, X. et al. N6-methyladenosine modulates messenger RNA translation efficiency. Cell 161, 1388-1399 (2015).
-
(2015)
Cell
, vol.161
, pp. 1388-1399
-
-
Wang, X.1
-
40
-
-
0042161864
-
The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines
-
Kierzek, E. & Kierzek, R. The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines. Nucleic Acids Res. 31, 4472-4480 (2003).
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 4472-4480
-
-
Kierzek, E.1
Kierzek, R.2
-
41
-
-
84922780316
-
Structure and thermodynamics of N6-methyladenosine in RNA: A spring-loaded base modification
-
Roost, C. et al. Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. J. Am. Chem. Soc. 137, 2107-2115 (2015).
-
(2015)
J. Am. Chem. Soc
, vol.137
, pp. 2107-2115
-
-
Roost, C.1
-
42
-
-
84957828213
-
Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome
-
Li, X. et al. Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome. Nat. Chem. Biol. http://dx.doi.org/10.1038/ nchembio.2040 (2016).
-
(2016)
Nat. Chem. Biol
-
-
Li, X.1
-
43
-
-
84922342926
-
M6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation
-
Geula, S. et al. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science 347, 1002-1006 (2015).
-
(2015)
Science
, vol.347
, pp. 1002-1006
-
-
Geula, S.1
-
44
-
-
84892372347
-
N6-methyladenosine-dependent regulation of messenger RNA stability
-
Wang, X. et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117-120 (2014).
-
(2014)
Nature
, vol.505
, pp. 117-120
-
-
Wang, X.1
-
45
-
-
84875160429
-
Total synthesis of the hypermodified RNA bases wybutosine and hydroxywybutosine and their quantification together with other modified RNA bases in plant materials
-
Hienzsch, A., Deiml, C., Reiter, V. & Carell, T. Total synthesis of the hypermodified RNA bases wybutosine and hydroxywybutosine and their quantification together with other modified RNA bases in plant materials. Chemistry 19, 4244-4248 (2013).
-
(2013)
Chemistry
, vol.19
, pp. 4244-4248
-
-
Hienzsch, A.1
Deiml, C.2
Reiter, V.3
Carell, T.4
-
46
-
-
79954592362
-
LC-MS based quantification of 2'-ribosylated nucleosides Ar(p) and Gr(p) in tRNA
-
Pearson, D. et al. LC-MS based quantification of 2'-ribosylated nucleosides Ar(p) and Gr(p) in tRNA. Chem. Commun. (Camb.) 47, 5196-5198 (2011).
-
(2011)
Chem. Commun. (Camb.)
, vol.47
, pp. 5196-5198
-
-
Pearson, D.1
-
47
-
-
84951734126
-
The reverse transcription signature of N-1- methyladenosine in RNA-Seq is sequence dependent
-
Hauenschild, R. et al. The reverse transcription signature of N-1- methyladenosine in RNA-Seq is sequence dependent. Nucleic Acids Res. 43, 9950-9964 10.1093/nar/gkv895 (2015).
-
(2015)
Nucleic Acids Res
, vol.43
, pp. 9950-9964
-
-
Hauenschild, R.1
-
48
-
-
33947490122
-
Purine Nucleosides. III. Methylation studies of certain naturally occurring purine nucleosides
-
Jones, J. W. & Robins, R. K. Purine Nucleosides. III. Methylation studies of certain naturally occurring purine nucleosides. J. Am. Chem. Soc. 85, 193-201 (1963).
-
(1963)
J. Am. Chem. Soc
, vol.85
, pp. 193-201
-
-
Jones, J.W.1
Robins, R.K.2
-
49
-
-
35549008047
-
Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine
-
Dai, Q. et al. Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Res. 35, 6322-6329 (2007).
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 6322-6329
-
-
Dai, Q.1
-
50
-
-
0142071287
-
The synthesis of 2'-O-[(triisopropylsilyl)oxy] methyl (TOM) phosphoramidites of methylated ribonucleosides (m1G, m2G, m2 2G, m1I, m3U, m4C, m6A, m2 6A) for use in automated RNA solid-phase synthesis
-
Hobartner, C. et al. The synthesis of 2'-O-[(triisopropylsilyl)oxy] methyl (TOM) phosphoramidites of methylated ribonucleosides (m1G, m2G, m2 2G, m1I, m3U, m4C, m6A, m2 6A) for use in automated RNA solid-phase synthesis. Monatsh. Chem. 134, 851-873 (2003).
-
(2003)
Monatsh. Chem
, vol.134
, pp. 851-873
-
-
Hobartner, C.1
-
51
-
-
84872032385
-
Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing
-
Dominissini, D., Moshitch-Moshkovitz, S., Salmon-Divon, M., Amariglio, N. & Rechavi, G. Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing. Nature Protocols 8, 176-189 (2013).
-
(2013)
Nature Protocols
, vol.8
, pp. 176-189
-
-
Dominissini, D.1
Moshitch-Moshkovitz, S.2
Salmon-Divon, M.3
Amariglio, N.4
Rechavi, G.5
-
52
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357-359 (2012).
-
(2012)
Nature Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
53
-
-
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
-
54
-
-
84928987900
-
HTSeq-a Python framework to work with high-throughput sequencing data
-
Anders, S., Pyl, P. T. & Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
55
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
56
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol. 28, 511-515 (2010).
-
(2010)
Nature Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
-
57
-
-
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
-
58
-
-
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
-
59
-
-
77955183656
-
PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci
-
Salmon-Divon, M., Dvinge, H., Tammoja, K. & Bertone, P. PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. BMC Bioinformatics 11, 415 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 415
-
-
Salmon-Divon, M.1
Dvinge, H.2
Tammoja, K.3
Bertone, P.4
-
60
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
61
-
-
82055164092
-
ViennaRNA Package 2.0
-
Lorenz, R. et al. ViennaRNA Package 2.0. Algorithms Mol. Biol. 6, 26 (2011).
-
(2011)
Algorithms Mol. Biol
, vol.6
, pp. 26
-
-
Lorenz, R.1
-
62
-
-
84914680429
-
On the normalization of the minimum free energy of RNAs by sequence length
-
Trotta, E. On the normalization of the minimum free energy of RNAs by sequence length. PLoS One 9, e113380 (2014).
-
(2014)
PLoS One
, vol.9
-
-
Trotta, E.1
-
63
-
-
84877063192
-
Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing
-
Wan, Y., Qu, K., Ouyang, Z. & Chang, H. Y. Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nature Protocols 8, 849-869 (2013).
-
(2013)
Nature Protocols
, vol.8
, pp. 849-869
-
-
Wan, Y.1
Qu, K.2
Ouyang, Z.3
Chang, H.Y.4
-
64
-
-
77956306662
-
Genome-wide measurement of RNA secondary structure in yeast
-
Kertesz, M. et al. Genome-wide measurement of RNA secondary structure in yeast. Nature 467, 103-107 (2010).
-
(2010)
Nature
, vol.467
, pp. 103-107
-
-
Kertesz, M.1
-
65
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
-
66
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey, T. L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36 (1994).
-
(1994)
Proc. Int. Conf. Intell. Syst. Mol. Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
67
-
-
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
-
68
-
-
84938417580
-
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome
-
Linder, B. et al. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nature Methods 12, 767-772 (2015).
-
(2015)
Nature Methods
, vol.12
, pp. 767-772
-
-
Linder, B.1
-
69
-
-
33644874573
-
The UCSC Genome Browser Database: Update 2006
-
Hinrichs, A. S. et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34, D590-D598 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D590-D598
-
-
Hinrichs, A.S.1
-
70
-
-
84857938446
-
Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins
-
Geiger, T., Wehner, A., Schaab, C., Cox, J. & Mann, M. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol. Cell Proteomics http://dx.doi.org/10.1074/mcp. M111.014050 (2012).
-
(2012)
Mol. Cell Proteomics
-
-
Geiger, T.1
Wehner, A.2
Schaab, C.3
Cox, J.4
Mann, M.5
-
71
-
-
42649132889
-
Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5, 111 proteins
-
Graumann, J. et al. Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5, 111 proteins. Mol. Cell. Proteomics 7, 672-683 (2008).
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 672-683
-
-
Graumann, J.1
-
72
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwanhäusser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337-342 (2011).
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwanhäusser, B.1
-
73
-
-
84895756743
-
System wide analyses have underestimated protein abundances and the importance of transcription in mammals
-
Li, J. J., Bickel, P. J. & Biggin, M. D. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ 2, e270 (2014).
-
(2014)
PeerJ
, vol.2
-
-
Li, J.J.1
Bickel, P.J.2
Biggin, M.D.3
-
74
-
-
84907338120
-
Quantitative analysis of mammalian translation initiation sites by FACS-seq
-
Noderer, W. L. et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol. Syst. Biol. 10, 748 (2014).
-
(2014)
Mol. Syst. Biol
, vol.10
, pp. 748
-
-
Noderer, W.L.1
-
75
-
-
56049121180
-
G-quadruplexes: The beginning and end of UTRs
-
Huppert, J. L., Bugaut, A., Kumari, S. & Balasubramanian, S. G-quadruplexes: the beginning and end of UTRs. Nucleic Acids Res. 36, 6260-6268 (2008).
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 6260-6268
-
-
Huppert, J.L.1
Bugaut, A.2
Kumari, S.3
Balasubramanian, S.4
-
76
-
-
77957058196
-
5'-UTR G-quadruplex structures acting as translational repressors
-
Beaudoin, J. D. & Perreault, J. P. 5'-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res. 38, 7022-7036 (2010).
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 7022-7036
-
-
Beaudoin, J.D.1
Perreault, J.P.2
-
77
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20 (2005).
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
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