-
1
-
-
84902830900
-
Insights into RNA structure and function from genome-wide studies
-
Mortimer S.A., Kidwell M.A., Doudna J.A. Insights into RNA structure and function from genome-wide studies. Nat Rev Genet 2014, 15:469-479.
-
(2014)
Nat Rev Genet
, vol.15
, pp. 469-479
-
-
Mortimer, S.A.1
Kidwell, M.A.2
Doudna, J.A.3
-
2
-
-
84877928424
-
Cytotopic localization by long noncoding RNAs
-
Batista P.J., Chang H.Y. Cytotopic localization by long noncoding RNAs. Curr Opin Cell Biol 2013, 25:195-199.
-
(2013)
Curr Opin Cell Biol
, vol.25
, pp. 195-199
-
-
Batista, P.J.1
Chang, H.Y.2
-
3
-
-
80051989609
-
Understanding the transcriptome through RNA structure
-
Wan Y., Kertesz M., Spitale R.C., Segal E., Chang H.Y. Understanding the transcriptome through RNA structure. Nat Rev Genet 2011, 12:641-655.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 641-655
-
-
Wan, Y.1
Kertesz, M.2
Spitale, R.C.3
Segal, E.4
Chang, H.Y.5
-
4
-
-
77955475692
-
TRANSAT - method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures
-
Wiebe N.J., Meyer I.M. TRANSAT - method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures. PLoS Comput Biol 2010, 6:e1000823.
-
(2010)
PLoS Comput Biol
, vol.6
, pp. e1000823
-
-
Wiebe, N.J.1
Meyer, I.M.2
-
6
-
-
0023665268
-
Probing the structure of RNAs in solution
-
Ehresmann C., Baudin F., Mougel M., Romby P., Ebel J.P., Ehresmann B. Probing the structure of RNAs in solution. Nucleic Acids Res 1987, 15:9109-9128.
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 9109-9128
-
-
Ehresmann, C.1
Baudin, F.2
Mougel, M.3
Romby, P.4
Ebel, J.P.5
Ehresmann, B.6
-
7
-
-
16244412610
-
RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)
-
Merino E.J., Wilkinson K.A., Coughlan J.L., Weeks K.M. RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc 2005, 127:4223-4231.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 4223-4231
-
-
Merino, E.J.1
Wilkinson, K.A.2
Coughlan, J.L.3
Weeks, K.M.4
-
8
-
-
77956306662
-
Genome-wide measurement of RNA secondary structure in yeast
-
Kertesz M., Wan Y., Mazor E., Rinn J.L., Nutter R.C., Chang H.Y., Segal E. Genome-wide measurement of RNA secondary structure in yeast. Nature 2010, 467:103-107.
-
(2010)
Nature
, vol.467
, pp. 103-107
-
-
Kertesz, M.1
Wan, Y.2
Mazor, E.3
Rinn, J.L.4
Nutter, R.C.5
Chang, H.Y.6
Segal, E.7
-
9
-
-
84893358533
-
Landscape and variation of RNA secondary structure across the human transcriptome
-
Wan Y., Qu K., Zhang Q.C., Flynn R.A., Manor O., Ouyang Z., Zhang J., Spitale R.C., Snyder M.P., Segal E., et al. Landscape and variation of RNA secondary structure across the human transcriptome. Nature 2014, 505:706-709.
-
(2014)
Nature
, vol.505
, pp. 706-709
-
-
Wan, Y.1
Qu, K.2
Zhang, Q.C.3
Flynn, R.A.4
Manor, O.5
Ouyang, Z.6
Zhang, J.7
Spitale, R.C.8
Snyder, M.P.9
Segal, E.10
-
10
-
-
78649690492
-
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing
-
Underwood J.G., Uzilov A.V., Katzman S., Onodera C.S., Mainzer J.E., Mathews D.H., Lowe T.M., Salama S.R., Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods 2010, 7:995-1001.
-
(2010)
Nat Methods
, vol.7
, pp. 995-1001
-
-
Underwood, J.G.1
Uzilov, A.V.2
Katzman, S.3
Onodera, C.S.4
Mainzer, J.E.5
Mathews, D.H.6
Lowe, T.M.7
Salama, S.R.8
Haussler, D.9
-
11
-
-
78049445573
-
Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis
-
Zheng Q., Ryvkin P., Li F., Dragomir I., Valladares O., Yang J., Cao K., Wang L.S., Gregory B.D. Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet 2010, 6:e1001141.
-
(2010)
PLoS Genet
, vol.6
, pp. e1001141
-
-
Zheng, Q.1
Ryvkin, P.2
Li, F.3
Dragomir, I.4
Valladares, O.5
Yang, J.6
Cao, K.7
Wang, L.S.8
Gregory, B.D.9
-
12
-
-
84864116955
-
RNA structure prediction: an overview of methods
-
Seetin M.G., Mathews D.H. RNA structure prediction: an overview of methods. Methods Mol Biol 2012, 905:99-122.
-
(2012)
Methods Mol Biol
, vol.905
, pp. 99-122
-
-
Seetin, M.G.1
Mathews, D.H.2
-
13
-
-
84925301356
-
The RNA structurome: transcriptome-wide structure probing with next-generation sequencing
-
Kwok C.K., Tang Y., Assmann S.M., Bevilacqua P.C. The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. Trends Biochem Sci 2015, 40:221-232.
-
(2015)
Trends Biochem Sci
, vol.40
, pp. 221-232
-
-
Kwok, C.K.1
Tang, Y.2
Assmann, S.M.3
Bevilacqua, P.C.4
-
14
-
-
85027948185
-
RNA structural analysis by evolving SHAPE chemistry
-
Spitale R.C., Flynn R.A., Torre E.A., Kool E.T., Chang H.Y. RNA structural analysis by evolving SHAPE chemistry. Wiley Interdiscip Rev RNA 2014, 5:867-881.
-
(2014)
Wiley Interdiscip Rev RNA
, vol.5
, pp. 867-881
-
-
Spitale, R.C.1
Flynn, R.A.2
Torre, E.A.3
Kool, E.T.4
Chang, H.Y.5
-
15
-
-
77955787630
-
Advances in RNA structure analysis by chemical probing
-
Weeks K.M. Advances in RNA structure analysis by chemical probing. Curr Opin Struct Biol 2010, 20:295-304.
-
(2010)
Curr Opin Struct Biol
, vol.20
, pp. 295-304
-
-
Weeks, K.M.1
-
16
-
-
84893427735
-
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
-
Ding Y., Tang Y., Kwok C.K., Zhang Y., Bevilacqua P.C., Assmann S.M. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 2014, 505:696-700.
-
(2014)
Nature
, vol.505
, pp. 696-700
-
-
Ding, Y.1
Tang, Y.2
Kwok, C.K.3
Zhang, Y.4
Bevilacqua, P.C.5
Assmann, S.M.6
-
17
-
-
84893351549
-
Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
-
Rouskin S., Zubradt M., Washietl S., Kellis M., Weissman J.S. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 2014, 505:701-705.
-
(2014)
Nature
, vol.505
, pp. 701-705
-
-
Rouskin, S.1
Zubradt, M.2
Washietl, S.3
Kellis, M.4
Weissman, J.S.5
-
18
-
-
84871298684
-
RNA SHAPE analysis in living cells
-
Spitale R.C., Crisalli P., Flynn R.A., Torre E.A., Kool E.T., Chang H.Y. RNA SHAPE analysis in living cells. Nat Chem Biol 2013, 9:18-20.
-
(2013)
Nat Chem Biol
, vol.9
, pp. 18-20
-
-
Spitale, R.C.1
Crisalli, P.2
Flynn, R.A.3
Torre, E.A.4
Kool, E.T.5
Chang, H.Y.6
-
19
-
-
84925777836
-
Structural imprints in vivo decode RNA regulatory mechanisms
-
Spitale R.C., Flynn R.A., Zhang Q.C., Crisalli P., Lee B., Jung J.W., Kuchelmeister H.Y., Batista P.J., Torre E.A., Kool E.T., et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 2015, 519:486-490.
-
(2015)
Nature
, vol.519
, pp. 486-490
-
-
Spitale, R.C.1
Flynn, R.A.2
Zhang, Q.C.3
Crisalli, P.4
Lee, B.5
Jung, J.W.6
Kuchelmeister, H.Y.7
Batista, P.J.8
Torre, E.A.9
Kool, E.T.10
-
20
-
-
84898949357
-
Mod-seq: high-throughput sequencing for chemical probing of RNA structure
-
Talkish J., May G., Lin Y., Woolford J.L., McManus C.J. Mod-seq: high-throughput sequencing for chemical probing of RNA structure. RNA 2014, 20:713-720.
-
(2014)
RNA
, vol.20
, pp. 713-720
-
-
Talkish, J.1
May, G.2
Lin, Y.3
Woolford, J.L.4
McManus, C.J.5
-
21
-
-
80052729501
-
Understanding the errors of SHAPE-directed RNA structure modeling
-
Kladwang W., VanLang C.C., Cordero P., Das R. Understanding the errors of SHAPE-directed RNA structure modeling. Biochemistry 2011, 50:8049-8056.
-
(2011)
Biochemistry
, vol.50
, pp. 8049-8056
-
-
Kladwang, W.1
VanLang, C.C.2
Cordero, P.3
Das, R.4
-
22
-
-
33646838978
-
A periodic pattern of mRNA secondary structure created by the genetic code
-
Shabalina S.A., Ogurtsov A.Y., Spiridonov N.A. A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res 2006, 34:2428-2437.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 2428-2437
-
-
Shabalina, S.A.1
Ogurtsov, A.Y.2
Spiridonov, N.A.3
-
23
-
-
84947936380
-
Detection of RNA-protein interactions in living cells with SHAPE
-
Smola M.J., Calabrese J.M., Weeks K.M. Detection of RNA-protein interactions in living cells with SHAPE. Biochemistry 2015, 54:6867-6875.
-
(2015)
Biochemistry
, vol.54
, pp. 6867-6875
-
-
Smola, M.J.1
Calabrese, J.M.2
Weeks, K.M.3
-
24
-
-
84924072927
-
N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions
-
Liu N., Dai Q., Zheng G., He C., Parisien M., Pan T. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 2015, 518:560-564.
-
(2015)
Nature
, vol.518
, pp. 560-564
-
-
Liu, N.1
Dai, Q.2
Zheng, G.3
He, C.4
Parisien, M.5
Pan, T.6
-
25
-
-
84922780316
-
Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification
-
Roost C., Lynch S.R., Batista P.J., Qu K., Chang H.Y., Kool E.T. Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. J Am Chem Soc 2015, 137:2107-2115.
-
(2015)
J Am Chem Soc
, vol.137
, pp. 2107-2115
-
-
Roost, C.1
Lynch, S.R.2
Batista, P.J.3
Qu, K.4
Chang, H.Y.5
Kool, E.T.6
-
26
-
-
84907190326
-
Single-molecule correlated chemical probing of RNA
-
Homan P.J., Favorov O.V., Lavender C.A., Kursun O., Ge X., Busan S., Dokholyan N.V., Weeks K.M. Single-molecule correlated chemical probing of RNA. Proc Natl Acad Sci U S A 2014, 111:13858-13863.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 13858-13863
-
-
Homan, P.J.1
Favorov, O.V.2
Lavender, C.A.3
Kursun, O.4
Ge, X.5
Busan, S.6
Dokholyan, N.V.7
Weeks, K.M.8
-
27
-
-
85027926010
-
RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)
-
Siegfried N.A., Busan S., Rice G.M., Nelson J.A., Weeks K.M. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat Methods 2014, 11:959-965.
-
(2014)
Nat Methods
, vol.11
, pp. 959-965
-
-
Siegfried, N.A.1
Busan, S.2
Rice, G.M.3
Nelson, J.A.4
Weeks, K.M.5
-
28
-
-
84876935138
-
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding
-
Helwak A., Kudla G., Dudnakova T., Tollervey D. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 2013, 153:654-665.
-
(2013)
Cell
, vol.153
, pp. 654-665
-
-
Helwak, A.1
Kudla, G.2
Dudnakova, T.3
Tollervey, D.4
-
29
-
-
79959946169
-
Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast
-
Kudla G., Granneman S., Hahn D., Beggs J.D., Tollervey D. Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast. Proc Natl Acad Sci U S A 2011, 108:10010-10015.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 10010-10015
-
-
Kudla, G.1
Granneman, S.2
Hahn, D.3
Beggs, J.D.4
Tollervey, D.5
-
30
-
-
84925799191
-
HiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1
-
Sugimoto Y., Vigilante A., Darbo E., Zirra A., Militti C., D'Ambrogio A., Luscombe N.M., Ule J. hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1. Nature 2015, 519:491-494.
-
(2015)
Nature
, vol.519
, pp. 491-494
-
-
Sugimoto, Y.1
Vigilante, A.2
Darbo, E.3
Zirra, A.4
Militti, C.5
D'Ambrogio, A.6
Luscombe, N.M.7
Ule, J.8
-
31
-
-
84941087441
-
High-throughput determination of RNA structure by proximity ligation
-
Ramani V., Qiu R., Shendure J. High-throughput determination of RNA structure by proximity ligation. Nat Biotechnol 2015, 33:980-984.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 980-984
-
-
Ramani, V.1
Qiu, R.2
Shendure, J.3
-
32
-
-
84937061323
-
Consistent global structures of complex RNA states through multidimensional chemical mapping
-
Cheng C.Y., Chou F.C., Kladwang W., Tian S., Cordero P., Das R. Consistent global structures of complex RNA states through multidimensional chemical mapping. Elife 2015, 4:e07600.
-
(2015)
Elife
, vol.4
, pp. e07600
-
-
Cheng, C.Y.1
Chou, F.C.2
Kladwang, W.3
Tian, S.4
Cordero, P.5
Das, R.6
-
33
-
-
84855863141
-
IRES-mediated translation of cellular messenger RNA operates in eIF2alpha- independent manner during stress
-
Thakor N., Holcik M. IRES-mediated translation of cellular messenger RNA operates in eIF2alpha- independent manner during stress. Nucleic Acids Res 2012, 40:541-552.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 541-552
-
-
Thakor, N.1
Holcik, M.2
-
34
-
-
84875173647
-
DEAD box RNA helicase functions in cancer
-
Fuller-Pace F.V. DEAD box RNA helicase functions in cancer. RNA Biol 2013, 10:121-132.
-
(2013)
RNA Biol
, vol.10
, pp. 121-132
-
-
Fuller-Pace, F.V.1
|