-
1
-
-
70350569286
-
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches
-
Chen M, Manley JL. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 2009, 10:741-754.
-
(2009)
Nat Rev Mol Cell Biol
, vol.10
, pp. 741-754
-
-
Chen, M.1
Manley, J.L.2
-
2
-
-
72849106592
-
RNA processing and its regulation: global insights into biological networks
-
Licatalosi DD, Darnell RB. RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 2010, 11:75-87.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 75-87
-
-
Licatalosi, D.D.1
Darnell, R.B.2
-
3
-
-
57749195712
-
RNA-Seq: a revolutionary tool for transcriptomics
-
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
4
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
Kingsmore, S.F.7
Schroth, G.P.8
Burge, C.B.9
-
5
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40:1413-1415.
-
(2008)
Nat Genet
, vol.40
, pp. 1413-1415
-
-
Pan, Q.1
Shai, O.2
Lee, L.J.3
Frey, B.J.4
Blencowe, B.J.5
-
6
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628.
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
7
-
-
47649124124
-
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
-
Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008, 321:956-960.
-
(2008)
Science
, vol.321
, pp. 956-960
-
-
Sultan, M.1
Schulz, M.H.2
Richard, H.3
Magen, A.4
Klingenhoff, A.5
Scherf, M.6
Seifert, M.7
Borodina, T.8
Soldatov, A.9
Parkhomchuk, D.10
Schmidt, D.11
O'Keeffe, S.12
Haas, S.13
Vingron, M.14
Lehrach, H.15
Yaspo, M.L.16
-
8
-
-
84867163995
-
Extensive alternative polyadenylation during zebrafish development
-
Ulitsky I, Shkumatava A, Jan CH, Subtelny AO, Koppstein D, Bell GW, Sive H, Bartel DP. Extensive alternative polyadenylation during zebrafish development. Genome Res 2012, 22:2054-2066.
-
(2012)
Genome Res
, vol.22
, pp. 2054-2066
-
-
Ulitsky, I.1
Shkumatava, A.2
Jan, C.H.3
Subtelny, A.O.4
Koppstein, D.5
Bell, G.W.6
Sive, H.7
Bartel, D.P.8
-
9
-
-
84855320189
-
Accurate identification of A-to-I RNA editing in human by transcriptome sequencing
-
Bahn JH, Lee JH, Li G, Greer C, Peng G, Xiao X. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res 2012, 22:142-150.
-
(2012)
Genome Res
, vol.22
, pp. 142-150
-
-
Bahn, J.H.1
Lee, J.H.2
Li, G.3
Greer, C.4
Peng, G.5
Xiao, X.6
-
10
-
-
84863229628
-
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
-
Peng Z, Cheng Y, Tan BC, Kang L, Tian Z, Zhu Y, Zhang W, Liang Y, Hu X, Tan X, Guo J, Dong Z, Liang Y, Bao L, Wang J. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 2012, 30:253-260.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 253-260
-
-
Peng, Z.1
Cheng, Y.2
Tan, B.C.3
Kang, L.4
Tian, Z.5
Zhu, Y.6
Zhang, W.7
Liang, Y.8
Hu, X.9
Tan, X.10
Guo, J.11
Dong, Z.12
Liang, Y.13
Bao, L.14
Wang, J.15
-
11
-
-
84859935298
-
High levels of RNA-editing site conservation amongst 15 laboratory mouse strains
-
Danecek P, Nellåker C, McIntyre RE, Buendia-Buendia JE, Bumpstead S, Ponting CP, Flint J, Durbin R, Keane TM, Adams DJ. High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. Genome Biol 2012, 13:26.
-
(2012)
Genome Biol
, vol.13
, pp. 26
-
-
Danecek, P.1
Nellåker, C.2
McIntyre, R.E.3
Buendia-Buendia, J.E.4
Bumpstead, S.5
Ponting, C.P.6
Flint, J.7
Durbin, R.8
Keane, T.M.9
Adams, D.J.10
-
12
-
-
84860779086
-
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
-
Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, Cesarkas K, Jacob-Hirsch J, Amariglio N, Kupiec M, Sorek R, Rechavi G. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 2012, 485:201-206.
-
(2012)
Nature
, vol.485
, pp. 201-206
-
-
Dominissini, D.1
Moshitch-Moshkovitz, S.2
Schwartz, S.3
Salmon-Divon, M.4
Ungar, L.5
Osenberg, S.6
Cesarkas, K.7
Jacob-Hirsch, J.8
Amariglio, N.9
Kupiec, M.10
Sorek, R.11
Rechavi, G.12
-
13
-
-
84862649489
-
Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons
-
Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell 2012, 149:1635-1646.
-
(2012)
Cell
, vol.149
, pp. 1635-1646
-
-
Meyer, K.D.1
Saletore, Y.2
Zumbo, P.3
Elemento, O.4
Mason, C.E.5
Jaffrey, S.R.6
-
14
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458:223-227.
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
Amit, I.2
Garber, M.3
French, C.4
Lin, M.F.5
Feldser, D.6
Huarte, M.7
Zuk, O.8
Carey, B.W.9
Cassady, J.P.10
Cabili, M.N.11
Jaenisch, R.12
Mikkelsen, T.S.13
Jacks, T.14
Hacohen, N.15
Bernstein, B.E.16
Kellis, M.17
Regev, A.18
Rinn, J.L.19
Lander, E.S.20
more..
-
15
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011, 25:1915-1927.
-
(2011)
Genes Dev
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
Trapnell, C.2
Goff, L.3
Koziol, M.4
Tazon-Vega, B.5
Regev, A.6
Rinn, J.L.7
-
16
-
-
84865839598
-
Long noncoding RNAs are rarely translated in two human cell lines
-
Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, Brown JB, Lipovich L. Long noncoding RNAs are rarely translated in two human cell lines. Genome Res 2012, 22:1646-1657.
-
(2012)
Genome Res
, vol.22
, pp. 1646-1657
-
-
Bánfai, B.1
Jia, H.2
Khatun, J.3
Wood, E.4
Risk, B.5
Gundling, W.E.6
Kundaje, A.7
Gunawardena, H.P.8
Yu, Y.9
Xie, L.10
Krajewski, K.11
Strahl, B.D.12
Chen, X.13
Bickel, P.14
Giddings, M.C.15
Brown, J.B.16
Lipovich, L.17
-
17
-
-
84879969127
-
Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
-
Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 2013, 154:240-251.
-
(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
-
18
-
-
84857066786
-
Modular regulatory principles of large non-coding RNAs
-
Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature 2012, 482:339-346.
-
(2012)
Nature
, vol.482
, pp. 339-346
-
-
Guttman, M.1
Rinn, J.L.2
-
19
-
-
84861904178
-
Genome regulation by long noncoding RNAs
-
Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem 2012, 81:145-166.
-
(2012)
Annu Rev Biochem
, vol.81
, pp. 145-166
-
-
Rinn, J.L.1
Chang, H.Y.2
-
20
-
-
84876839218
-
Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing
-
Pandit S, Zhou Y, Shiue L, Coutinho-Mansfield G, Li H, Qiu J, Huang J, Yeo GW, Ares M, Fu XD. Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell 2013, 50:223-235.
-
(2013)
Mol Cell
, vol.50
, pp. 223-235
-
-
Pandit, S.1
Zhou, Y.2
Shiue, L.3
Coutinho-Mansfield, G.4
Li, H.5
Qiu, J.6
Huang, J.7
Yeo, G.W.8
Ares, M.9
Fu, X.D.10
-
21
-
-
84861161751
-
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins
-
Huelga SC, Vu AQ, Arnold JD, Liang TY, Liu PP, Yan BY, Donohue JP, Shiue L, Hoon S, Brenner S, Ares M, Yeo GW. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep 2012, 1:167-178.
-
(2012)
Cell Rep
, vol.1
, pp. 167-178
-
-
Huelga, S.C.1
Vu, A.Q.2
Arnold, J.D.3
Liang, T.Y.4
Liu, P.P.5
Yan, B.Y.6
Donohue, J.P.7
Shiue, L.8
Hoon, S.9
Brenner, S.10
Ares, M.11
Yeo, G.W.12
-
22
-
-
0242497663
-
CLIP identifies Nova-regulated RNA networks in the brain
-
Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB. CLIP identifies Nova-regulated RNA networks in the brain. Science 2003, 302:1212-1215.
-
(2003)
Science
, vol.302
, pp. 1212-1215
-
-
Ule, J.1
Jensen, K.B.2
Ruggiu, M.3
Mele, A.4
Ule, A.5
Darnell, R.B.6
-
23
-
-
59649107040
-
An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells
-
Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol 2009, 16:130-137.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 130-137
-
-
Yeo, G.W.1
Coufal, N.G.2
Liang, T.Y.3
Peng, G.E.4
Fu, X.D.5
Gage, F.H.6
-
24
-
-
84865201988
-
Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins
-
Wang ET, Cody NA, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB. Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 2012, 150:710-724.
-
(2012)
Cell
, vol.150
, pp. 710-724
-
-
Wang, E.T.1
Cody, N.A.2
Jog, S.3
Biancolella, M.4
Wang, T.T.5
Treacy, D.J.6
Luo, S.7
Schroth, G.P.8
Housman, D.E.9
Reddy, S.10
Lécuyer, E.11
Burge, C.B.12
-
25
-
-
0025324948
-
A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro
-
Ge H, Manley JL. A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro. Cell 1990, 62:25-34.
-
(1990)
Cell
, vol.62
, pp. 25-34
-
-
Ge, H.1
Manley, J.L.2
-
26
-
-
0028077730
-
Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors
-
Caceres JF, Stamm S, Helfman DM, Krainer AR. Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors. Science 1994, 265:1706-1709.
-
(1994)
Science
, vol.265
, pp. 1706-1709
-
-
Caceres, J.F.1
Stamm, S.2
Helfman, D.M.3
Krainer, A.R.4
-
27
-
-
84875429298
-
Reflections on the history of pre-mRNA processing and highlights of current knowledge: a unified picture
-
Darnell JE. Reflections on the history of pre-mRNA processing and highlights of current knowledge: a unified picture. RNA 2013, 19:443-460.
-
(2013)
RNA
, vol.19
, pp. 443-460
-
-
Darnell, J.E.1
-
28
-
-
84887624226
-
RNA catalyses nuclear pre-mRNA splicing
-
Fica SM, Tuttle N, Novak T, Li NS, Lu J, Koodathingal P, Dai Q, Staley JP, Piccirilli JA. RNA catalyses nuclear pre-mRNA splicing. Nature 2013, 503:229-234.
-
(2013)
Nature
, vol.503
, pp. 229-234
-
-
Fica, S.M.1
Tuttle, N.2
Novak, T.3
Li, N.S.4
Lu, J.5
Koodathingal, P.6
Dai, Q.7
Staley, J.P.8
Piccirilli, J.A.9
-
29
-
-
79959411466
-
The mechanism of peptidyl transfer catalysis by the ribosome
-
Leung EK, Suslov N, Tuttle N, Sengupta R, Piccirilli JA. The mechanism of peptidyl transfer catalysis by the ribosome. Annu Rev Biochem 2011, 80:527-555.
-
(2011)
Annu Rev Biochem
, vol.80
, pp. 527-555
-
-
Leung, E.K.1
Suslov, N.2
Tuttle, N.3
Sengupta, R.4
Piccirilli, J.A.5
-
30
-
-
0035656688
-
Non-coding RNA genes and the modern RNA world
-
Eddy SR. Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2001, 2:919-929.
-
(2001)
Nat Rev Genet
, vol.2
, pp. 919-929
-
-
Eddy, S.R.1
-
31
-
-
0347444723
-
MicroRNAs: genomics, biogenesis, mechanism, and function
-
Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
32
-
-
79953089167
-
PIWI-interacting small RNAs: the vanguard of genome defence
-
Siomi MC, Sato K, Pezic D, Aravin AA. PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 2011, 12:246-258.
-
(2011)
Nat Rev Mol Cell Biol
, vol.12
, pp. 246-258
-
-
Siomi, M.C.1
Sato, K.2
Pezic, D.3
Aravin, A.A.4
-
33
-
-
80052869283
-
LincRNAs act in the circuitry controlling pluripotency and differentiation
-
Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011, 477:295-300.
-
(2011)
Nature
, vol.477
, pp. 295-300
-
-
Guttman, M.1
Donaghey, J.2
Carey, B.W.3
Garber, M.4
Grenier, J.K.5
Munson, G.6
Young, G.7
Lucas, A.B.8
Ach, R.9
Bruhn, L.10
Yang, X.11
Amit, I.12
Meissner, A.13
Regev, A.14
Rinn, J.L.15
Root, D.E.16
Lander, E.S.17
-
34
-
-
77957243921
-
Long noncoding RNAs with enhancer-like function in human cells
-
Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010, 143:46-58.
-
(2010)
Cell
, vol.143
, pp. 46-58
-
-
Ørom, U.A.1
Derrien, T.2
Beringer, M.3
Gumireddy, K.4
Gardini, A.5
Bussotti, G.6
Lai, F.7
Zytnicki, M.8
Notredame, C.9
Huang, Q.10
Guigo, R.11
Shiekhattar, R.12
-
35
-
-
79953748673
-
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
-
Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011, 472:120-124.
-
(2011)
Nature
, vol.472
, pp. 120-124
-
-
Wang, K.C.1
Yang, Y.W.2
Liu, B.3
Sanyal, A.4
Corces-Zimmerman, R.5
Chen, Y.6
Lajoie, B.R.7
Protacio, A.8
Flynn, R.A.9
Gupta, R.A.10
Wysocka, J.11
Lei, M.12
Dekker, J.13
Helms, J.A.14
Chang, H.Y.15
-
36
-
-
60149099385
-
Evolution and functions of long noncoding RNAs
-
Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009, 136:629-641.
-
(2009)
Cell
, vol.136
, pp. 629-641
-
-
Ponting, C.P.1
Oliver, P.L.2
Reik, W.3
-
37
-
-
84879987789
-
LincRNAs: genomics, evolution, and mechanisms
-
Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell 2013, 154:26-46.
-
(2013)
Cell
, vol.154
, pp. 26-46
-
-
Ulitsky, I.1
Bartel, D.P.2
-
38
-
-
77953928753
-
HITS-CLIP: panoramic views of protein-RNA regulation in living cells
-
Darnell RB. HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip Rev RNA 2010, 1:266-286.
-
(2010)
Wiley Interdiscip Rev RNA
, vol.1
, pp. 266-286
-
-
Darnell, R.B.1
-
39
-
-
54949148332
-
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
-
Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLOS Biol 2008, 6:e255.
-
(2008)
PLOS Biol
, vol.6
-
-
Hogan, D.J.1
Riordan, D.P.2
Gerber, A.P.3
Herschlag, D.4
Brown, P.O.5
-
40
-
-
19344365947
-
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
-
Gerber AP, Herschlag D, Brown PO. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLOS Biol 2004, 2:E79.
-
(2004)
PLOS Biol
, vol.2
-
-
Gerber, A.P.1
Herschlag, D.2
Brown, P.O.3
-
41
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 2009, 324:218-223.
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.3
Weissman, J.S.4
-
42
-
-
0029763191
-
Purification of telomerase from Euplotes aediculatus: requirement of a primer 3' overhang
-
Lingner J, Cech TR. Purification of telomerase from Euplotes aediculatus: requirement of a primer 3' overhang. Proc Natl Acad Sci U S A 1996, 93:10712-10717.
-
(1996)
Proc Natl Acad Sci U S A
, vol.93
, pp. 10712-10717
-
-
Lingner, J.1
Cech, T.R.2
-
43
-
-
0037168541
-
Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method
-
Hartmuth K, Urlaub H, Vornlocher HP, Will CL, Gentzel M, Wilm M, Lührmann R. Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method. Proc Natl Acad Sci U S A 2002, 99:16719-16724.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 16719-16724
-
-
Hartmuth, K.1
Urlaub, H.2
Vornlocher, H.P.3
Will, C.L.4
Gentzel, M.5
Wilm, M.6
Lührmann, R.7
-
44
-
-
34249053165
-
RNA-based affinity purification reveals 7SK RNPs with distinct composition and regulation
-
Hogg JR, Collins K. RNA-based affinity purification reveals 7SK RNPs with distinct composition and regulation. RNA 2007, 13:868-880.
-
(2007)
RNA
, vol.13
, pp. 868-880
-
-
Hogg, J.R.1
Collins, K.2
-
45
-
-
84861969926
-
Insights into RNA biology from an atlas of mammalian mRNA-binding proteins
-
Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, Krijgsveld J, Hentze MW. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 2012, 149:1393-1406.
-
(2012)
Cell
, vol.149
, pp. 1393-1406
-
-
Castello, A.1
Fischer, B.2
Eichelbaum, K.3
Horos, R.4
Beckmann, B.M.5
Strein, C.6
Davey, N.E.7
Humphreys, D.T.8
Preiss, T.9
Steinmetz, L.M.10
Krijgsveld, J.11
Hentze, M.W.12
-
46
-
-
84883741725
-
The RNA-binding protein repertoire of embryonic stem cells
-
Kwon SC, Yi H, Eichelbaum K, Föhr S, Fischer B, You KT, Castello A, Krijgsveld J, Hentze MW, Kim VN. The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol 2013, 20:1122-1130.
-
(2013)
Nat Struct Mol Biol
, vol.20
, pp. 1122-1130
-
-
Kwon, S.C.1
Yi, H.2
Eichelbaum, K.3
Föhr, S.4
Fischer, B.5
You, K.T.6
Castello, A.7
Krijgsveld, J.8
Hentze, M.W.9
Kim, V.N.10
-
47
-
-
72149117411
-
Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping
-
Xue Y, Zhou Y, Wu T, Zhu T, Ji X, Kwon YS, Zhang C, Yeo G, Black DL, Sun H, Fu XD, Zhang Y. Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol Cell 2009, 36:996-1006.
-
(2009)
Mol Cell
, vol.36
, pp. 996-1006
-
-
Xue, Y.1
Zhou, Y.2
Wu, T.3
Zhu, T.4
Ji, X.5
Kwon, Y.S.6
Zhang, C.7
Yeo, G.8
Black, D.L.9
Sun, H.10
Fu, X.D.11
Zhang, Y.12
-
48
-
-
77954838957
-
Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls
-
Zhang C, Frias MA, Mele A, Ruggiu M, Eom T, Marney CB, Wang H, Licatalosi DD, Fak JJ, Darnell RB. Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science 2010, 329:439-443.
-
(2010)
Science
, vol.329
, pp. 439-443
-
-
Zhang, C.1
Frias, M.A.2
Mele, A.3
Ruggiu, M.4
Eom, T.5
Marney, C.B.6
Wang, H.7
Licatalosi, D.D.8
Fak, J.J.9
Darnell, R.B.10
-
49
-
-
55349109963
-
Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome
-
Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008, 322:750-756.
-
(2008)
Science
, vol.322
, pp. 750-756
-
-
Zhao, J.1
Sun, B.K.2
Erwin, J.A.3
Song, J.J.4
Lee, J.T.5
-
50
-
-
34250729138
-
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
-
Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007, 129:1311-1323.
-
(2007)
Cell
, vol.129
, pp. 1311-1323
-
-
Rinn, J.L.1
Kertesz, M.2
Wang, J.K.3
Squazzo, S.L.4
Xu, X.5
Brugmann, S.A.6
Goodnough, L.H.7
Helms, J.A.8
Farnham, P.J.9
Segal, E.10
Chang, H.Y.11
-
51
-
-
67650921949
-
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
-
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 2009, 106:11667-11672.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
Guttman, M.2
Huarte, M.3
Garber, M.4
Raj, A.5
Rivea Morales, D.6
Thomas, K.7
Presser, A.8
Bernstein, B.E.9
van Oudenaarden, A.10
Regev, A.11
Lander, E.S.12
Rinn, J.L.13
-
52
-
-
0036713096
-
Partial reconstitution of human RNase P in HeLa cells between its RNA subunit with an affinity tag and the intact protein components
-
Li Y, Altman S. Partial reconstitution of human RNase P in HeLa cells between its RNA subunit with an affinity tag and the intact protein components. Nucleic Acids Res 2002, 30:3706-3711.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3706-3711
-
-
Li, Y.1
Altman, S.2
-
53
-
-
34748916981
-
Quantitative mass spectrometry in proteomics: a critical review
-
Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 2007, 389:1017-1031.
-
(2007)
Anal Bioanal Chem
, vol.389
, pp. 1017-1031
-
-
Bantscheff, M.1
Schirle, M.2
Sweetman, G.3
Rick, J.4
Kuster, B.5
-
54
-
-
56549105330
-
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
-
Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 2008, 456:464-469.
-
(2008)
Nature
, vol.456
, pp. 464-469
-
-
Licatalosi, D.D.1
Mele, A.2
Fak, J.J.3
Ule, J.4
Kayikci, M.5
Chi, S.W.6
Clark, T.A.7
Schweitzer, A.C.8
Blume, J.E.9
Wang, X.10
Darnell, J.C.11
Darnell, R.B.12
-
55
-
-
77954387023
-
ICLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
-
König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 2010, 17:909-915.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 909-915
-
-
König, J.1
Zarnack, K.2
Rot, G.3
Curk, T.4
Kayikci, M.5
Zupan, B.6
Turner, D.J.7
Luscombe, N.M.8
Ule, J.9
-
56
-
-
77950920903
-
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
-
Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141:129-141.
-
(2010)
Cell
, vol.141
, pp. 129-141
-
-
Hafner, M.1
Landthaler, M.2
Burger, L.3
Khorshid, M.4
Hausser, J.5
Berninger, P.6
Rothballer, A.7
Ascano, M.8
Jungkamp, A.C.9
Munschauer, M.10
Ulrich, A.11
Wardle, G.S.12
Dewell, S.13
Zavolan, M.14
Tuschl, T.15
-
57
-
-
67649854477
-
Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs
-
Granneman S, Kudla G, Petfalski E, Tollervey D. Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs. Proc Natl Acad Sci U S A 2009, 106:9613-9618.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 9613-9618
-
-
Granneman, S.1
Kudla, G.2
Petfalski, E.3
Tollervey, D.4
-
58
-
-
78650253763
-
Genome-wide identification of Polycomb-associated RNAs by RIP-seq
-
Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M, Lee JT. Genome-wide identification of Polycomb-associated RNAs by RIP-seq. Mol Cell 2010, 40:939-953.
-
(2010)
Mol Cell
, vol.40
, pp. 939-953
-
-
Zhao, J.1
Ohsumi, T.K.2
Kung, J.T.3
Ogawa, Y.4
Grau, D.J.5
Sarma, K.6
Song, J.J.7
Kingston, R.E.8
Borowsky, M.9
Lee, J.T.10
-
59
-
-
84894247159
-
RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes
-
doi:10.1016/j.ymeth.2013.09.013
-
Singh G, Ricci EP, Moore MJ. RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes. Methods 2013, doi:10.1016/j.ymeth.2013.09.013.
-
(2013)
Methods
-
-
Singh, G.1
Ricci, E.P.2
Moore, M.J.3
-
60
-
-
79959813870
-
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins
-
Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M. A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat Methods 2011, 8:559-564.
-
(2011)
Nat Methods
, vol.8
, pp. 559-564
-
-
Kishore, S.1
Jaskiewicz, L.2
Burger, L.3
Hausser, J.4
Khorshid, M.5
Zavolan, M.6
-
61
-
-
79960230895
-
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
-
Zhang C, Darnell RB. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 2011, 29:607-614.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 607-614
-
-
Zhang, C.1
Darnell, R.B.2
-
62
-
-
84887419464
-
Promiscuous RNA binding by Polycomb repressive complex 2
-
Davidovich C, Zheng L, Goodrich KJ, Cech TR. Promiscuous RNA binding by Polycomb repressive complex 2. Nat Struct Mol Biol 2013, 20:1250-1257.
-
(2013)
Nat Struct Mol Biol
, vol.20
, pp. 1250-1257
-
-
Davidovich, C.1
Zheng, L.2
Goodrich, K.J.3
Cech, T.R.4
-
63
-
-
33845275018
-
RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts
-
Keene JD, Komisarow JM, Friedersdorf MB. RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 2006, 1:302-307.
-
(2006)
Nat Protoc
, vol.1
, pp. 302-307
-
-
Keene, J.D.1
Komisarow, J.M.2
Friedersdorf, M.B.3
-
64
-
-
35348971338
-
Comprehensive analysis of diverse ribonucleoprotein complexes
-
Oeffinger M, Wei KE, Rogers R, DeGrasse JA, Chait BT, Aitchison JD, Rout MP. Comprehensive analysis of diverse ribonucleoprotein complexes. Nat Methods 2007, 4:951-956.
-
(2007)
Nat Methods
, vol.4
, pp. 951-956
-
-
Oeffinger, M.1
Wei, K.E.2
Rogers, R.3
DeGrasse, J.A.4
Chait, B.T.5
Aitchison, J.D.6
Rout, M.P.7
-
65
-
-
80054759888
-
Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1
-
Creamer TJ, Darby MM, Jamonnak N, Schaughency P, Hao H, Wheelan SJ, Corden JL. Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1. PLoS Genet 2001, 7:e1002329.
-
(2001)
PLoS Genet
, vol.7
-
-
Creamer, T.J.1
Darby, M.M.2
Jamonnak, N.3
Schaughency, P.4
Hao, H.5
Wheelan, S.J.6
Corden, J.L.7
-
66
-
-
7044272280
-
Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses
-
Mili S, Steitz JA. Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA 2004, 10:1692-1694.
-
(2004)
RNA
, vol.10
, pp. 1692-1694
-
-
Mili, S.1
Steitz, J.A.2
-
67
-
-
84875418596
-
Noncoding RNA and Polycomb recruitment
-
Brockdorff N. Noncoding RNA and Polycomb recruitment. RNA 2013, 19:429-442.
-
(2013)
RNA
, vol.19
, pp. 429-442
-
-
Brockdorff, N.1
-
68
-
-
77954572735
-
Long noncoding RNA as modular scaffold of histone modification complexes
-
Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010, 329:689-693.
-
(2010)
Science
, vol.329
, pp. 689-693
-
-
Tsai, M.C.1
Manor, O.2
Wan, Y.3
Mosammaparast, N.4
Wang, J.K.5
Lan, F.6
Shi, Y.7
Segal, E.8
Chang, H.Y.9
-
69
-
-
84879642373
-
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome
-
Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 2013, 341:1237973.
-
(2013)
Science
, vol.341
, pp. 1237973
-
-
Engreitz, J.M.1
Pandya-Jones, A.2
McDonel, P.3
Shishkin, A.4
Sirokman, K.5
Surka, C.6
Kadri, S.7
Xing, J.8
Goren, A.9
Lander, E.S.10
Plath, K.11
Guttman, M.12
-
70
-
-
0242668706
-
Role of histone H3 lysine 27 methylation in X inactivation
-
Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y. Role of histone H3 lysine 27 methylation in X inactivation. Science 2003, 300:131-135.
-
(2003)
Science
, vol.300
, pp. 131-135
-
-
Plath, K.1
Fang, J.2
Mlynarczyk-Evans, S.K.3
Cao, R.4
Worringer, K.A.5
Wang, H.6
de la Cruz, C.C.7
Otte, A.P.8
Panning, B.9
Zhang, Y.10
-
71
-
-
79960918737
-
Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability
-
Mukherjee N, Corcoran DL, Nusbaum JD, Reid DW, Georgiev S, Hafner M, Ascano M, Tuschl T, Ohler U, Keene JD. Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell 2011, 43:327-339.
-
(2011)
Mol Cell
, vol.43
, pp. 327-339
-
-
Mukherjee, N.1
Corcoran, D.L.2
Nusbaum, J.D.3
Reid, D.W.4
Georgiev, S.5
Hafner, M.6
Ascano, M.7
Tuschl, T.8
Ohler, U.9
Keene, J.D.10
-
72
-
-
77955323879
-
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response
-
Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks T, Rinn JL. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010, 142:409-419.
-
(2010)
Cell
, vol.142
, pp. 409-419
-
-
Huarte, M.1
Guttman, M.2
Feldser, D.3
Garber, M.4
Koziol, M.J.5
Kenzelmann-Broz, D.6
Khalil, A.M.7
Zuk, O.8
Amit, I.9
Rabani, M.10
Attardi, L.D.11
Regev, A.12
Lander, E.S.13
Jacks, T.14
Rinn, J.L.15
-
73
-
-
0024274359
-
Intra-RNA and RNA-protein cross-linking techniques in Escherichia coli ribosomes
-
Brimacombe R, Stiege W, Kyriatsoulis A, Maly P. Intra-RNA and RNA-protein cross-linking techniques in Escherichia coli ribosomes. Methods Enzymol 1988, 164:287-309.
-
(1988)
Methods Enzymol
, vol.164
, pp. 287-309
-
-
Brimacombe, R.1
Stiege, W.2
Kyriatsoulis, A.3
Maly, P.4
-
74
-
-
27944508215
-
CLIP: a method for identifying protein-RNA interaction sites in living cells
-
Ule J, Jensen K, Mele A, Darnell RB. CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 2005, 37:376-386.
-
(2005)
Methods
, vol.37
, pp. 376-386
-
-
Ule, J.1
Jensen, K.2
Mele, A.3
Darnell, R.B.4
-
75
-
-
67649840910
-
CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo
-
Wang Z, Tollervey J, Briese M, Turner D, Ule J. CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. Methods 2009, 48:287-293.
-
(2009)
Methods
, vol.48
, pp. 287-293
-
-
Wang, Z.1
Tollervey, J.2
Briese, M.3
Turner, D.4
Ule, J.5
-
76
-
-
84869090905
-
The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus
-
Singh G, Kucukural A, Cenik C, Leszyk JD, Shaffer SA, Weng Z, Moore MJ. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell 2012, 151:750-764.
-
(2012)
Cell
, vol.151
, pp. 750-764
-
-
Singh, G.1
Kucukural, A.2
Cenik, C.3
Leszyk, J.D.4
Shaffer, S.A.5
Weng, Z.6
Moore, M.J.7
-
77
-
-
78649807567
-
Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA
-
Kaneko S, Li G, Son J, Xu CF, Margueron R, Neubert TA, Reinberg D. Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev 2010, 24:2615-2620.
-
(2010)
Genes Dev
, vol.24
, pp. 2615-2620
-
-
Kaneko, S.1
Li, G.2
Son, J.3
Xu, C.F.4
Margueron, R.5
Neubert, T.A.6
Reinberg, D.7
-
78
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 2011, 8:469-477.
-
(2011)
Nat Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
79
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010, 11:R106.
-
(2010)
Genome Biol
, vol.11
-
-
Anders, S.1
Huber, W.2
-
80
-
-
84883644707
-
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
-
Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol 2013, 14:R95.
-
(2013)
Genome Biol
, vol.14
-
-
Rapaport, F.1
Khanin, R.2
Liang, Y.3
Pirun, M.4
Krek, A.5
Zumbo, P.6
Mason, C.E.7
Socci, N.D.8
Betel, D.9
-
81
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012, 7:562-578.
-
(2012)
Nat Protoc
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
Pimentel, H.7
Salzberg, S.L.8
Rinn, J.L.9
Pachter, L.10
-
82
-
-
84864269662
-
Ultraviolet shadowing of RNA can cause significant chemical damage in seconds
-
Kladwang W, Hum J, Das R. Ultraviolet shadowing of RNA can cause significant chemical damage in seconds. Sci Rep 2012, 2:517.
-
(2012)
Sci Rep
, vol.2
, pp. 517
-
-
Kladwang, W.1
Hum, J.2
Das, R.3
-
83
-
-
0021111044
-
Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site
-
Carey J, Cameron V, de Haseth PL, Uhlenbeck OC. Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site. Biochemistry 1983, 22:2601-2610.
-
(1983)
Biochemistry
, vol.22
, pp. 2601-2610
-
-
Carey, J.1
Cameron, V.2
de Haseth, P.L.3
Uhlenbeck, O.C.4
-
84
-
-
78149342808
-
A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes
-
Slobodin B, Gerst JE. A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes. RNA 2010, 16:2277-2290.
-
(2010)
RNA
, vol.16
, pp. 2277-2290
-
-
Slobodin, B.1
Gerst, J.E.2
-
85
-
-
79957986263
-
Quantitative profiling of in vivo-assembled RNA-protein complexes using a novel integrated proteomic approach
-
Tsai BP, Wang X, Huang L, Waterman ML. Quantitative profiling of in vivo-assembled RNA-protein complexes using a novel integrated proteomic approach. Mol Cell Proteomics 2011, 10:M110.007385.
-
(2011)
Mol Cell Proteomics
, vol.10
-
-
Tsai, B.P.1
Wang, X.2
Huang, L.3
Waterman, M.L.4
-
86
-
-
0025145063
-
Purification of RNA and RNA-protein complexes by an R17 coat protein affinity method
-
Bardwell VJ, Wickens M. Purification of RNA and RNA-protein complexes by an R17 coat protein affinity method. Nucleic Acids Res 1990, 18:6587-6594.
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 6587-6594
-
-
Bardwell, V.J.1
Wickens, M.2
-
87
-
-
84875832964
-
RNA-protein analysis using a conditional CRISPR nuclease
-
Lee HY, Haurwitz RE, Apffel A, Zhou K, Smart B, Wenger CD, Laderman S, Bruhn L, Doudna JA. RNA-protein analysis using a conditional CRISPR nuclease. Proc Natl Acad Sci U S A 2013, 110:5416-5421.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 5416-5421
-
-
Lee, H.Y.1
Haurwitz, R.E.2
Apffel, A.3
Zhou, K.4
Smart, B.5
Wenger, C.D.6
Laderman, S.7
Bruhn, L.8
Doudna, J.A.9
-
88
-
-
0032758073
-
StreptoTag: a novel method for the isolation of RNA-binding proteins
-
Bachler M, Schroeder R, von Ahsen U. StreptoTag: a novel method for the isolation of RNA-binding proteins. RNA 1999, 5:1509-1516.
-
(1999)
RNA
, vol.5
, pp. 1509-1516
-
-
Bachler, M.1
Schroeder, R.2
von Ahsen, U.3
-
89
-
-
84892981981
-
An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins
-
doi:10.1093/nar/gkt956
-
Leppek K, Stoecklin G. An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins. Nucleic Acids Res 2013, doi:10.1093/nar/gkt956.
-
(2013)
Nucleic Acids Res
-
-
Leppek, K.1
Stoecklin, G.2
-
90
-
-
0035001466
-
Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins
-
Srisawat C, Engelke DR. Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins. RNA 2001, 7:632-6341.
-
(2001)
RNA
, vol.7
, pp. 632-6341
-
-
Srisawat, C.1
Engelke, D.R.2
-
91
-
-
67649774581
-
Unbiased RNA-protein interaction screen by quantitative proteomics
-
Butter F, Scheibe M, Morl M, Mann M. Unbiased RNA-protein interaction screen by quantitative proteomics. Proc Natl Acad Sci U S A 2009, 106:10626-10631.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 10626-10631
-
-
Butter, F.1
Scheibe, M.2
Morl, M.3
Mann, M.4
-
92
-
-
31944452549
-
In vivo identification of ribonucleoprotein-RNA interactions
-
Zielinski J, Kilk K, Peritz T, Kannanayakal T, Miyashiro KY, Eiríksdóttir E, Jochems J, Langel U, Eberwine J. In vivo identification of ribonucleoprotein-RNA interactions. Proc Natl Acad Sci U S A 2006, 103:1557-1562.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 1557-1562
-
-
Zielinski, J.1
Kilk, K.2
Peritz, T.3
Kannanayakal, T.4
Miyashiro, K.Y.5
Eiríksdóttir, E.6
Jochems, J.7
Langel, U.8
Eberwine, J.9
-
93
-
-
34548736002
-
A protocol for PAIR: PNA-assisted identification of RNA binding proteins in living cells
-
Zeng F, Peritz T, Kannanayakal TJ, Kilk K, Eiríksdóttir E, Langel U, Eberwine J. A protocol for PAIR: PNA-assisted identification of RNA binding proteins in living cells. Nat Protoc 2006, 1:920-927.
-
(2006)
Nat Protoc
, vol.1
, pp. 920-927
-
-
Zeng, F.1
Peritz, T.2
Kannanayakal, T.J.3
Kilk, K.4
Eiríksdóttir, E.5
Langel, U.6
Eberwine, J.7
-
94
-
-
84861997955
-
The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts
-
Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, Wyler E, Bonneau R, Selbach M, Dieterich C, Landthaler M. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell 2012, 46:674-690.
-
(2012)
Mol Cell
, vol.46
, pp. 674-690
-
-
Baltz, A.G.1
Munschauer, M.2
Schwanhäusser, B.3
Vasile, A.4
Murakawa, Y.5
Schueler, M.6
Youngs, N.7
Penfold-Brown, D.8
Drew, K.9
Milek, M.10
Wyler, E.11
Bonneau, R.12
Selbach, M.13
Dieterich, C.14
Landthaler, M.15
-
95
-
-
46849099222
-
Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions
-
Sutherland BW, Toews J, Kast J. Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions. J Mass Spectrom 2008, 43:699-715.
-
(2008)
J Mass Spectrom
, vol.43
, pp. 699-715
-
-
Sutherland, B.W.1
Toews, J.2
Kast, J.3
-
96
-
-
84872051030
-
Global analysis of yeast mRNPs
-
Mitchell SF, Jain S, She M, Parker R. Global analysis of yeast mRNPs. Nat Struct Mol Biol 2013, 20:127-133.
-
(2013)
Nat Struct Mol Biol
, vol.20
, pp. 127-133
-
-
Mitchell, S.F.1
Jain, S.2
She, M.3
Parker, R.4
-
97
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376-386.
-
(2002)
Mol Cell Proteomics
, vol.1
, pp. 376-386
-
-
Ong, S.E.1
Blagoev, B.2
Kratchmarova, I.3
Kristensen, D.B.4
Steen, H.5
Pandey, A.6
Mann, M.7
-
98
-
-
84864607962
-
Mrhl RNA, a long noncoding RNA, negatively regulates Wnt signaling through its protein partner Ddx5/p68 in mouse spermatogonial cells
-
Arun G, Akhade VS, Donakonda S, Rao MR. mrhl RNA, a long noncoding RNA, negatively regulates Wnt signaling through its protein partner Ddx5/p68 in mouse spermatogonial cells. Mol Cell Biol 2012, 32:3140-3152.
-
(2012)
Mol Cell Biol
, vol.32
, pp. 3140-3152
-
-
Arun, G.1
Akhade, V.S.2
Donakonda, S.3
Rao, M.R.4
-
99
-
-
47949100595
-
Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing
-
Newman MA, Thomson JM, Hammond SM. Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing. RNA 2008, 14:1539-1549.
-
(2008)
RNA
, vol.14
, pp. 1539-1549
-
-
Newman, M.A.1
Thomson, J.M.2
Hammond, S.M.3
-
100
-
-
0037068447
-
Comprehensive proteomic analysis of the human spliceosome
-
Zhou Z, Licklider LJ, Gygi SP, Reed R. Comprehensive proteomic analysis of the human spliceosome. Nature 2002, 419:182-185.
-
(2002)
Nature
, vol.419
, pp. 182-185
-
-
Zhou, Z.1
Licklider, L.J.2
Gygi, S.P.3
Reed, R.4
-
101
-
-
84868100738
-
Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions
-
Scheibe M, Butter F, Hafner M, Tuschl T, Mann M. Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions. Nucleic Acids Res 2012, 40:9897-9902.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 9897-9902
-
-
Scheibe, M.1
Butter, F.2
Hafner, M.3
Tuschl, T.4
Mann, M.5
-
102
-
-
84875169786
-
System-wide identification of RNA-binding proteins by interactome capture
-
Castello A, Horos R, Strein C, Fischer B, Eichelbaum K, Steinmetz LM, Krijgsveld J, Hentze MW. System-wide identification of RNA-binding proteins by interactome capture. Nat Protoc 2013, 8:491-500.
-
(2013)
Nat Protoc
, vol.8
, pp. 491-500
-
-
Castello, A.1
Horos, R.2
Strein, C.3
Fischer, B.4
Eichelbaum, K.5
Steinmetz, L.M.6
Krijgsveld, J.7
Hentze, M.W.8
-
103
-
-
84873582146
-
Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae
-
Freeberg MA, Han T, Moresco JJ, Kong A, Yang YC, Lu ZJ, Yates JR, Kim JK. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biol 2013, 14:R13.
-
(2013)
Genome Biol
, vol.14
-
-
Freeberg, M.A.1
Han, T.2
Moresco, J.J.3
Kong, A.4
Yang, Y.C.5
Lu, Z.J.6
Yates, J.R.7
Kim, J.K.8
-
104
-
-
84883741725
-
The RNA-binding protein repertoire of embryonic stem cells
-
Kwon SC, Yi H, Eichelbaum K, Föhr S, Fischer B, You KT, Castello A, Krijgsveld J, Hentze MW, Kim VN. The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol 2013, 20:1122-1130.
-
(2013)
Nat Struct Mol Biol
, vol.20
, pp. 1122-1130
-
-
Kwon, S.C.1
Yi, H.2
Eichelbaum, K.3
Föhr, S.4
Fischer, B.5
You, K.T.6
Castello, A.7
Krijgsveld, J.8
Hentze, M.W.9
Kim, V.N.10
-
105
-
-
84891697468
-
RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
-
Silverman IM, Li F, Alexander A, Goff L, Trapnell C, Rinn JL, Gregory BD. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Genome Biol 2014, 15:R3.
-
(2014)
Genome Biol
, vol.15
-
-
Silverman, I.M.1
Li, F.2
Alexander, A.3
Goff, L.4
Trapnell, C.5
Rinn, J.L.6
Gregory, B.D.7
-
106
-
-
84892412330
-
Differential protein occupancy profiling of the mRNA transcriptome
-
Schueler M, Munschauer M, Gregersen LH, Finzel A, Loewer A, Chen W, Landthaler M, Dieterich C. Differential protein occupancy profiling of the mRNA transcriptome. Genome Biol 2014, 15:RX.
-
(2014)
Genome Biol
, vol.15
-
-
Schueler, M.1
Munschauer, M.2
Gregersen, L.H.3
Finzel, A.4
Loewer, A.5
Chen, W.6
Landthaler, M.7
Dieterich, C.8
-
107
-
-
84878708955
-
Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae
-
Klass DM, Scheibe M, Butter F, Hogan GJ, Mann M, Brown PO. Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae. Genome Res 2013, 23:1028-1038.
-
(2013)
Genome Res
, vol.23
, pp. 1028-1038
-
-
Klass, D.M.1
Scheibe, M.2
Butter, F.3
Hogan, G.J.4
Mann, M.5
Brown, P.O.6
|