-
1
-
-
84874086395
-
Beyond secondary structure: Primary-sequence determinants license pri-miRNA hairpins for processing
-
Auyeung VC, Ulitsky I, McGeary SE, Bartel DP. 2013. Beyond secondary structure: Primary-sequence determinants license pri-miRNA hairpins for processing. Cell 152: 844-858.
-
(2013)
Cell
, vol.152
, pp. 844-858
-
-
Auyeung, V.C.1
Ulitsky, I.2
McGeary, S.E.3
Bartel, D.P.4
-
2
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
3
-
-
22844440427
-
Identification of hundreds of conserved and nonconserved human microRNAs
-
Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, et al. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37: 766-770.
-
(2005)
Nat Genet
, vol.37
, pp. 766-770
-
-
Bentwich, I.1
Avniel, A.2
Karov, Y.3
Aharonov, R.4
Gilad, S.5
Barad, O.6
Barzilai, A.7
Einat, P.8
Einav, U.9
Meiri, E.10
-
4
-
-
79955369794
-
Insights into Polyomaviridae microRNA function derived from study of the bandicoot papillomatosis carcinomatosisviruses
-
Chen CJ, Kincaid RP, Seo GJ, Bennett MD, Sullivan CS. 2011. Insights into Polyomaviridae microRNA function derived from study of the bandicoot papillomatosis carcinomatosisviruses. J Virol 85: 4487-4500.
-
(2011)
J Virol
, vol.85
, pp. 4487-4500
-
-
Chen, C.J.1
Kincaid, R.P.2
Seo, G.J.3
Bennett, M.D.4
Sullivan, C.S.5
-
5
-
-
84884351427
-
Divergent microRNA targetomes of closely related circulating strains of a polyomavirus
-
Chen CJ, Cox JE, Kincaid RP, Martinez A, Sullivan CS. 2013. Divergent microRNA targetomes of closely related circulating strains of a polyomavirus. J Virol 87: 11135-11147.
-
(2013)
J Virol
, vol.87
, pp. 11135-11147
-
-
Chen, C.J.1
Cox, J.E.2
Kincaid, R.P.3
Martinez, A.4
Sullivan, C.S.5
-
6
-
-
77952368550
-
Mammalian microRNAs: Experimental evaluation of novel and previously annotated genes
-
Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, et al. 2010. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 24: 992-1009.
-
(2010)
Genes Dev
, vol.24
, pp. 992-1009
-
-
Chiang, H.R.1
Schoenfeld, L.W.2
Ruby, J.G.3
Auyeung, V.C.4
Spies, N.5
Baek, D.6
Johnston, W.K.7
Russ, C.8
Luo, S.9
Babiarz, J.E.10
-
7
-
-
9144224451
-
Processing of primary microRNAs by the Microprocessor complex
-
Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ. 2004. Processing of primary microRNAs by the Microprocessor complex. Nature 432: 231-235.
-
(2004)
Nature
, vol.432
, pp. 231-235
-
-
Denli, A.M.1
Tops, B.B.2
Plasterk, R.H.3
Ketting, R.F.4
Hannon, G.J.5
-
8
-
-
52649112259
-
The sequence selectivity of KSRP explains its flexibility in the recognition of the RNA targets
-
García-Mayoral MF, Díaz-Moreno I, Hollingworth D, Ramos A. 2008. The sequence selectivity of KSRP explains its flexibility in the recognition of the RNA targets. Nucleic Acids Res 36: 5290-5296.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 5290-5296
-
-
García-Mayoral, M.F.1
Díaz-Moreno, I.2
Hollingworth, D.3
Ramos, A.4
-
9
-
-
9144225636
-
The Microprocessor complex mediates the genesis of microRNAs
-
Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R. 2004. The Microprocessor complex mediates the genesis of microRNAs. Nature 432: 235 -240.
-
(2004)
Nature
, vol.432
, pp. 235-240
-
-
Gregory, R.I.1
Yan, K.P.2
Amuthan, G.3
Chendrimada, T.4
Doratotaj, B.5
Cooch, N.6
Shiekhattar, R.7
-
10
-
-
17844364875
-
Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. Elegans developmental timing
-
Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC. 2001. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106: 23-34.
-
(2001)
Cell
, vol.106
, pp. 23-34
-
-
Grishok, A.1
Pasquinelli, A.E.2
Conte, D.3
Li, N.4
Parrish, S.5
Ha, I.6
Baillie, D.L.7
Fire, A.8
Ruvkun, G.9
Mello, C.C.10
-
11
-
-
10644234841
-
The Drosha-DGCR8 complex in primary microRNA processing
-
Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN. 2004. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18: 3016-3027.
-
(2004)
Genes Dev
, vol.18
, pp. 3016-3027
-
-
Han, J.1
Lee, Y.2
Yeom, K.H.3
Kim, Y.K.4
Jin, H.5
Kim, V.N.6
-
12
-
-
33744520104
-
Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex
-
Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT, Kim VN. 2006. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125: 887-901.
-
(2006)
Cell
, vol.125
, pp. 887-901
-
-
Han, J.1
Lee, Y.2
Yeom, K.H.3
Nam, J.W.4
Heo, I.5
Rhee, J.K.6
Sohn, S.Y.7
Cho, Y.8
Zhang, B.T.9
Kim, V.N.10
-
13
-
-
0035800521
-
A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA
-
Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD. 2001. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293: 834-838.
-
(2001)
Science
, vol.293
, pp. 834-838
-
-
Hutvagner, G.1
McLachlan, J.2
Pasquinelli, A.E.3
Balint, E.4
Tuschl, T.5
Zamore, P.D.6
-
14
-
-
0035887005
-
Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. Elegans
-
Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ, Plasterk RH. 2001. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 15: 2654-2659.
-
(2001)
Genes Dev
, vol.15
, pp. 2654-2659
-
-
Ketting, R.F.1
Fischer, S.E.2
Bernstein, E.3
Sijen, T.4
Hannon, G.J.5
Plasterk, R.H.6
-
15
-
-
0142165224
-
Functional siRNAs and miRNAs exhibit strand bias
-
Khvorova A, Reynolds A, Jayasena SD. 2003. Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216.
-
(2003)
Cell
, vol.115
, pp. 209-216
-
-
Khvorova, A.1
Reynolds, A.2
Jayasena, S.D.3
-
16
-
-
18344369543
-
MicroRNA biogenesis: Coordinated cropping and dicing
-
Kim VN. 2005. MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6: 376-385.
-
(2005)
Nat Rev Mol Cell Biol
, vol.6
, pp. 376-385
-
-
Kim, V.N.1
-
18
-
-
10344248903
-
The human DiGeorge syndrome critical region gene 8 and its D. Melanogaster homolog are required for miRNA biogenesis
-
Landthaler M, Yalcin A, Tuschl T. 2004. The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 14: 2162-2167.
-
(2004)
Curr Biol
, vol.14
, pp. 2162-2167
-
-
Landthaler, M.1
Yalcin, A.2
Tuschl, T.3
-
19
-
-
0141843656
-
The nuclear RNase III Drosha initiates microRNA processing
-
Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Rådmark O, Kim S, et al. 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415-419.
-
(2003)
Nature
, vol.425
, pp. 415-419
-
-
Lee, Y.1
Ahn, C.2
Han, J.3
Choi, H.4
Kim, J.5
Yim, J.6
Lee, J.7
Provost, P.8
Rådmark, O.9
Kim, S.10
-
20
-
-
4444368187
-
Argonaute2 is the catalytic engine of mammalian RNAi
-
Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua-Tor L, Hannon GJ. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441.
-
(2004)
Science
, vol.305
, pp. 1437-1441
-
-
Liu, J.1
Carmell, M.A.2
Rivas, F.V.3
Marsden, C.G.4
Thomson, J.M.5
Song, J.J.6
Hammond, S.M.7
Joshua-Tor, L.8
Hannon, G.J.9
-
21
-
-
84890835664
-
Lower and upper stem-single-stranded RNA junctions together determine the Drosha cleavage site
-
Ma H, Wu Y, Jang-Gi C, Wu H. 2013. Lower and upper stem-single-stranded RNA junctions together determine the Drosha cleavage site. Proc Natl Acad Sci 110: 20687 -20692.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. 20687-20692
-
-
Ma, H.1
Wu, Y.2
Jang-Gi, C.3
Wu, H.4
-
22
-
-
30844438338
-
Structural basis for double-stranded RNA processing by Dicer
-
MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. 2006. Structural basis for double-stranded RNA processing by Dicer. Science 311: 195-198.
-
(2006)
Science
, vol.311
, pp. 195-198
-
-
MacRae, I.J.1
Zhou, K.2
Li, F.3
Repic, A.4
Brooks, A.N.5
Cande, W.Z.6
Adams, P.D.7
Doudna, J.A.8
-
23
-
-
34948901976
-
Structural determinants of RNA recognition and cleavage by Dicer
-
MacRae IJ, Zhou K, Doudna JA. 2007. Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol 14: 934-940.
-
(2007)
Nat Struct Mol Biol
, vol.14
, pp. 934-940
-
-
MacRae, I.J.1
Zhou, K.2
Doudna, J.A.3
-
24
-
-
79960049624
-
Detection of viral microRNAs by Northern blot analysis
-
McClure LV, Lin YT, Sullivan CS. 2011. Detection of viral microRNAs by Northern blot analysis. Methods Mol Biol 721: 153-171.
-
(2011)
Methods Mol Biol
, vol.721
, pp. 153-171
-
-
McClure, L.V.1
Lin, Y.T.2
Sullivan, C.S.3
-
25
-
-
21844477027
-
Human microRNA prediction through a probabilistic co-learning model of sequence and structure
-
Nam J, Shin K, Han J, Lee Y, Kim VN. 2005. Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res 33: 3570-3581.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 3570-3581
-
-
Nam, J.1
Shin, K.2
Han, J.3
Lee, Y.4
Kim, V.N.5
-
26
-
-
40449139010
-
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
-
Parisien M, Major F. 2008. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452: 51-55.
-
(2008)
Nature
, vol.452
, pp. 51-55
-
-
Parisien, M.1
Major, F.2
-
27
-
-
79960185923
-
Dicer recognizes the 5′ end of RNA for efficient and accurate processing
-
Park J, Heo I, Tian Y, Simanshu DK, Chang H, Jee D, Patel DJ, Kim VN. 2011. Dicer recognizes the 5′ end of RNA for efficient and accurate processing. Nature 475: 201-205.
-
(2011)
Nature
, vol.475
, pp. 201-205
-
-
Park, J.1
Heo, I.2
Tian, Y.3
Simanshu, D.K.4
Chang, H.5
Jee, D.6
Patel, D.J.7
Kim, V.N.8
-
28
-
-
4444221565
-
UCSF Chimera - A visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. 2004. UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 13: 1605-1612.
-
(2004)
J Comput Chem
, vol.13
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
29
-
-
84873365736
-
Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the Drosha cleavage site
-
Quarles KA, Sahu D, Havens MA, Forsyth ER, Wostenberg C, Hastings ML, Showalter SA. 2013. Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the Drosha cleavage site. Biochemistry 52: 795-807.
-
(2013)
Biochemistry
, vol.52
, pp. 795-807
-
-
Quarles, K.A.1
Sahu, D.2
Havens, M.A.3
Forsyth, E.R.4
Wostenberg, C.5
Hastings, M.L.6
Showalter, S.A.7
-
30
-
-
67049159825
-
SHRiMP: Accurate mapping of short color-space reads
-
Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. 2009. SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol 5: e1000386.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Rumble, S.M.1
Lacroute, P.2
Dalca, A.V.3
Fiume, M.4
Sidow, A.5
Brudno, M.6
-
31
-
-
10744225153
-
Asymmetry in the assembly of the RNAi enzyme complex
-
Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, Zamore PD. 2003. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208.
-
(2003)
Cell
, vol.115
, pp. 199-208
-
-
Schwarz, D.S.1
Hutvágner, G.2
Du, T.3
Xu, Z.4
Aronin, N.5
Zamore, P.D.6
-
32
-
-
34548480185
-
Crystal structure of human DGCR8 core
-
Sohn SY, Bae WJ, Kim JJ, Yeom K, Kim VN, Cho Y. 2007. Crystal structure of human DGCR8 core. Nat Struct Mol Biol 14: 847-853.
-
(2007)
Nat Struct Mol Biol
, vol.14
, pp. 847-853
-
-
Sohn, S.Y.1
Bae, W.J.2
Kim, J.J.3
Yeom, K.4
Kim, V.N.5
Cho, Y.6
-
33
-
-
20444446357
-
SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells
-
Sullivan CS, Grundhoff AT, Tevethia S, Pipas JM, Ganem D. 2005. SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 435: 682-686.
-
(2005)
Nature
, vol.435
, pp. 682-686
-
-
Sullivan, C.S.1
Grundhoff, A.T.2
Tevethia, S.3
Pipas, J.M.4
Ganem, D.5
-
34
-
-
67649277689
-
The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs
-
Trabucchi M, Briata P, Garcia-Mayoral MF, Haase AD, Filipowicz W, Ramos A, Gherzi R, Rosenfeld MG. 2009. The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs. Nature 459: 1010-1014.
-
(2009)
Nature
, vol.459
, pp. 1010-1014
-
-
Trabucchi, M.1
Briata, P.2
Garcia-Mayoral, M.F.3
Haase, A.D.4
Filipowicz, W.5
Ramos, A.6
Gherzi, R.7
Rosenfeld, M.G.8
-
35
-
-
17844363243
-
The contributions of dsRNA structure to Dicer specificity and efficiency
-
Vermeulen A, Behlen L, Reynolds A, Wolfson A, Marshall WS, Karpilow J, Khvorova A. 2005. The contributions of dsRNA structure to Dicer specificity and efficiency. RNA 11: 674-682.
-
(2005)
RNA
, vol.11
, pp. 674-682
-
-
Vermeulen, A.1
Behlen, L.2
Reynolds, A.3
Wolfson, A.4
Marshall, W.S.5
Karpilow, J.6
Khvorova, A.7
-
36
-
-
0031867449
-
PIG-B: A homemade monophasic cocktail for the extraction of RNA
-
Weber K, Bolander ME, Sarkar G. 1998. PIG-B: a homemade monophasic cocktail for the extraction of RNA. Mol Biotechnol 9: 73-77.
-
(1998)
Mol Biotechnol
, vol.9
, pp. 73-77
-
-
Weber, K.1
Bolander, M.E.2
Sarkar, G.3
-
37
-
-
23044502585
-
Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences
-
Zeng Y, Cullen BR. 2005. Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. J Biol Chem 280: 27595-27603.
-
(2005)
J Biol Chem
, vol.280
, pp. 27595-27603
-
-
Zeng, Y.1
Cullen, B.R.2
-
38
-
-
12544255565
-
Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha
-
Zeng Y, Yi R, Cullen BR. 2005. Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J 24: 138-148.
-
(2005)
EMBO J
, vol.24
, pp. 138-148
-
-
Zeng, Y.1
Yi, R.2
Cullen, B.R.3
-
39
-
-
78649870594
-
The terminal loop region controls micro-RNA processing by Drosha and Dicer
-
Zhang Z, Zeng Y. 2010. The terminal loop region controls micro-RNA processing by Drosha and Dicer. Nucleic Acids Res 38: 7689-7697.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 7689-7697
-
-
Zhang, Z.1
Zeng, Y.2
-
40
-
-
0036845374
-
Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP
-
Zhang H, Kolb FA, Brondani V, Billy E, Filipowicz W. 2002. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J 21: 5875-5885.
-
(2002)
EMBO J
, vol.21
, pp. 5875-5885
-
-
Zhang, H.1
Kolb, F.A.2
Brondani, V.3
Billy, E.4
Filipowicz, W.5
-
41
-
-
3142613181
-
Single processing center models for human Dicer and bacterial RNase III
-
Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W. 2004. Single processing center models for human Dicer and bacterial RNase III. Cell 118: 57 -68.
-
(2004)
Cell
, vol.118
, pp. 57-68
-
-
Zhang, H.1
Kolb, F.A.2
Jaskiewicz, L.3
Westhof, E.4
Filipowicz, W.5
-
42
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3406-3415
-
-
Zuker, M.1
|