-
1
-
-
84877310529
-
Structures of the human and Drosophila 80S ribosome
-
Anger A.M., Armache J.P., Berninghausen O., Habeck M., Subklewe M., Wilson D.N., Beckmann R. Structures of the human and Drosophila 80S ribosome. Nature 2013, 497:80-85.
-
(2013)
Nature
, vol.497
, pp. 80-85
-
-
Anger, A.M.1
Armache, J.P.2
Berninghausen, O.3
Habeck, M.4
Subklewe, M.5
Wilson, D.N.6
Beckmann, R.7
-
2
-
-
58249088751
-
MicroRNAs: target recognition and regulatory functions
-
Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
-
(2009)
Cell
, vol.136
, pp. 215-233
-
-
Bartel, D.P.1
-
3
-
-
84922469439
-
Genomic variation. Impact of regulatory variation from RNA to protein
-
Battle A., Khan Z., Wang S.H., Mitrano A., Ford M.J., Pritchard J.K., Gilad Y. Genomic variation. Impact of regulatory variation from RNA to protein. Science 2015, 347:664-667.
-
(2015)
Science
, vol.347
, pp. 664-667
-
-
Battle, A.1
Khan, Z.2
Wang, S.H.3
Mitrano, A.4
Ford, M.J.5
Pritchard, J.K.6
Gilad, Y.7
-
4
-
-
70449686545
-
Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis
-
Bohnsack M.T., Martin R., Granneman S., Ruprecht M., Schleiff E., Tollervey D. Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis. Mol. Cell 2009, 36:583-592.
-
(2009)
Mol. Cell
, vol.36
, pp. 583-592
-
-
Bohnsack, M.T.1
Martin, R.2
Granneman, S.3
Ruprecht, M.4
Schleiff, E.5
Tollervey, D.6
-
5
-
-
0036792048
-
MRNA decay enzymes: decappers conserved between yeast and mammals
-
Decker C.J., Parker R. mRNA decay enzymes: decappers conserved between yeast and mammals. Proc. Natl. Acad. Sci. USA 2002, 99:12512-12514.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12512-12514
-
-
Decker, C.J.1
Parker, R.2
-
6
-
-
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
-
7
-
-
84871809302
-
STAR: ultrafast universal RNA-seq aligner
-
Dobin A., Davis C.A., Schlesinger F., Drenkow J., Zaleski C., Jha S., Batut P., Chaisson M., Gingeras T.R. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29:15-21.
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
Davis, C.A.2
Schlesinger, F.3
Drenkow, J.4
Zaleski, C.5
Jha, S.6
Batut, P.7
Chaisson, M.8
Gingeras, T.R.9
-
8
-
-
84907536806
-
RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites
-
Engreitz J.M., Sirokman K., McDonel P., Shishkin A.A., Surka C., Russell P., Grossman S.R., Chow A.Y., Guttman M., Lander E.S. RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites. Cell 2014, 159:188-199.
-
(2014)
Cell
, vol.159
, pp. 188-199
-
-
Engreitz, J.M.1
Sirokman, K.2
McDonel, P.3
Shishkin, A.A.4
Surka, C.5
Russell, P.6
Grossman, S.R.7
Chow, A.Y.8
Guttman, M.9
Lander, E.S.10
-
10
-
-
79951495822
-
LncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements
-
Gong C., Maquat L.E. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature 2011, 470:284-288.
-
(2011)
Nature
, vol.470
, pp. 284-288
-
-
Gong, C.1
Maquat, L.E.2
-
11
-
-
79957610306
-
Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA
-
Greenfeld M., Solomatin S.V., Herschlag D. Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA. J. Biol. Chem. 2011, 286:19872-19879.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 19872-19879
-
-
Greenfeld, M.1
Solomatin, S.V.2
Herschlag, D.3
-
13
-
-
0019839745
-
Psoralen photochemistry and nucleic acid structure
-
Hearst J.E. Psoralen photochemistry and nucleic acid structure. J. Invest. Dermatol. 1981, 77:39-44.
-
(1981)
J. Invest. Dermatol.
, vol.77
, pp. 39-44
-
-
Hearst, J.E.1
-
14
-
-
0018040673
-
Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent
-
Jackson V. Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent. Cell 1978, 15:945-954.
-
(1978)
Cell
, vol.15
, pp. 945-954
-
-
Jackson, V.1
-
15
-
-
78651416809
-
PLEXY: efficient target prediction for box C/D snoRNAs
-
Kehr S., Bartschat S., Stadler P.F., Tafer H. PLEXY: efficient target prediction for box C/D snoRNAs. Bioinformatics 2011, 27:279-280.
-
(2011)
Bioinformatics
, vol.27
, pp. 279-280
-
-
Kehr, S.1
Bartschat, S.2
Stadler, P.F.3
Tafer, H.4
-
16
-
-
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
-
17
-
-
82055176702
-
A two-dimensional mutate-and-map strategy for non-coding RNA structure
-
Kladwang W., VanLang C.C., Cordero P., Das R. A two-dimensional mutate-and-map strategy for non-coding RNA structure. Nat. Chem. 2011, 3:954-962.
-
(2011)
Nat. Chem.
, vol.3
, pp. 954-962
-
-
Kladwang, W.1
VanLang, C.C.2
Cordero, P.3
Das, R.4
-
18
-
-
25844432236
-
The putative RNA helicase Dbp4p is required for release of the U14 snoRNA from Preribosomes in Saccharomyces cerevisiae
-
Kos M., Tollervey D. The putative RNA helicase Dbp4p is required for release of the U14 snoRNA from Preribosomes in Saccharomyces cerevisiae. Mol. Cell 2005, 20:53-64.
-
(2005)
Mol. Cell
, vol.20
, pp. 53-64
-
-
Kos, M.1
Tollervey, D.2
-
19
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
Kudla G., Murray A.W., Tollervey D., Plotkin J.B. Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324:255-258.
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
Murray, A.W.2
Tollervey, D.3
Plotkin, J.B.4
-
20
-
-
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. USA 2011, 108:10010-10015.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 10010-10015
-
-
Kudla, G.1
Granneman, S.2
Hahn, D.3
Beggs, J.D.4
Tollervey, D.5
-
21
-
-
33644875300
-
SnoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
-
Lestrade L., Weber M.J. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res. 2006, 34:D158-D162.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D158-D162
-
-
Lestrade, L.1
Weber, M.J.2
-
22
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li H., Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26:589-595.
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
23
-
-
33749588453
-
The helicase Has1p is required for snoRNA release from pre-rRNA
-
Liang X.H., Fournier M.J. The helicase Has1p is required for snoRNA release from pre-rRNA. Mol. Cell. Biol. 2006, 26:7437-7450.
-
(2006)
Mol. Cell. Biol.
, vol.26
, pp. 7437-7450
-
-
Liang, X.H.1
Fournier, M.J.2
-
24
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie B.R., Sabo P.J., Dorschner M.O., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
-
26
-
-
0037124096
-
Prp43 is an essential RNA-dependent ATPase required for release of lariat-intron from the spliceosome
-
Martin A., Schneider S., Schwer B. Prp43 is an essential RNA-dependent ATPase required for release of lariat-intron from the spliceosome. J. Biol. Chem. 2002, 277:17743-17750.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 17743-17750
-
-
Martin, A.1
Schneider, S.2
Schwer, B.3
-
27
-
-
84904472965
-
A pre-ribosomal RNA interaction network involving snoRNAs and the Rok1 helicase
-
Martin R., Hackert P., Ruprecht M., Simm S., Brüning L., Mirus O., Sloan K.E., Kudla G., Schleiff E., Bohnsack M.T. A pre-ribosomal RNA interaction network involving snoRNAs and the Rok1 helicase. RNA 2014, 20:1173-1182.
-
(2014)
RNA
, vol.20
, pp. 1173-1182
-
-
Martin, R.1
Hackert, P.2
Ruprecht, M.3
Simm, S.4
Brüning, L.5
Mirus, O.6
Sloan, K.E.7
Kudla, G.8
Schleiff, E.9
Bohnsack, M.T.10
-
28
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi U., Wang Z., Waern K., Shou C., Raha D., Gerstein M., Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320:1344-1349.
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
Gerstein, M.6
Snyder, M.7
-
29
-
-
84868154284
-
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels
-
Pai A.A., Cain C.E., Mizrahi-Man O., De Leon S., Lewellen N., Veyrieras J.B., Degner J.F., Gaffney D.J., Pickrell J.K., Stephens M., et al. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet. 2012, 8:e1003000.
-
(2012)
PLoS Genet.
, vol.8
, pp. e1003000
-
-
Pai, A.A.1
Cain, C.E.2
Mizrahi-Man, O.3
De Leon, S.4
Lewellen, N.5
Veyrieras, J.B.6
Degner, J.F.7
Gaffney, D.J.8
Pickrell, J.K.9
Stephens, M.10
-
30
-
-
33847270751
-
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA
-
Piekna-Przybylska D., Decatur W.A., Fournier M.J. New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 2007, 13:305-312.
-
(2007)
RNA
, vol.13
, pp. 305-312
-
-
Piekna-Przybylska, D.1
Decatur, W.A.2
Fournier, M.J.3
-
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
-
-
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
-
33
-
-
84869203467
-
HMGA1 reprograms somatic cells into pluripotent stem cells by inducing stem cell transcriptional networks
-
Shah S.N., Kerr C., Cope L., Zambidis E., Liu C., Hillion J., Belton A., Huso D.L., Resar L.M. HMGA1 reprograms somatic cells into pluripotent stem cells by inducing stem cell transcriptional networks. PLoS ONE 2012, 7:e48533.
-
(2012)
PLoS ONE
, vol.7
, pp. e48533
-
-
Shah, S.N.1
Kerr, C.2
Cope, L.3
Zambidis, E.4
Liu, C.5
Hillion, J.6
Belton, A.7
Huso, D.L.8
Resar, L.M.9
-
34
-
-
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., Chang H.Y. 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
Chang, H.Y.11
-
35
-
-
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
-
36
-
-
55749083578
-
RNAplex: a fast tool for RNA-RNA interaction search
-
Tafer H., Hofacker I.L. RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics 2008, 24:2657-2663.
-
(2008)
Bioinformatics
, vol.24
, pp. 2657-2663
-
-
Tafer, H.1
Hofacker, I.L.2
-
37
-
-
77954572735
-
Long noncoding RNA as modular scaffold of histone modification complexes
-
Tsai M.C., Manor O., Wan Y., Mosammaparast N., Wang J.K., Lan F., Shi Y., Segal E., Chang H.Y. 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
-
38
-
-
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
-
39
-
-
84868009378
-
Genome-wide measurement of RNA folding energies
-
Wan Y., Qu K., Ouyang Z., Kertesz M., Li J., Tibshirani R., Makino D.L., Nutter R.C., Segal E., Chang H.Y. Genome-wide measurement of RNA folding energies. Mol. Cell 2012, 48:169-181.
-
(2012)
Mol. Cell
, vol.48
, pp. 169-181
-
-
Wan, Y.1
Qu, K.2
Ouyang, Z.3
Kertesz, M.4
Li, J.5
Tibshirani, R.6
Makino, D.L.7
Nutter, R.C.8
Segal, E.9
Chang, H.Y.10
-
40
-
-
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. Nat. Protoc. 2013, 8:849-869.
-
(2013)
Nat. Protoc.
, vol.8
, pp. 849-869
-
-
Wan, Y.1
Qu, K.2
Ouyang, Z.3
Chang, H.Y.4
-
41
-
-
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., Chang H.Y. 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
Chang, H.Y.11
-
42
-
-
0032112017
-
Circularization of mRNA by eukaryotic translation initiation factors
-
Wells S.E., Hillner P.E., Vale R.D., Sachs A.B. Circularization of mRNA by eukaryotic translation initiation factors. Mol. Cell 1998, 2:135-140.
-
(1998)
Mol. Cell
, vol.2
, pp. 135-140
-
-
Wells, S.E.1
Hillner, P.E.2
Vale, R.D.3
Sachs, A.B.4
-
43
-
-
33846056836
-
Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs
-
Xie J., Zhang M., Zhou T., Hua X., Tang L., Wu W. Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs. Nucleic Acids Res. 2007, 35:D183-D187.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D183-D187
-
-
Xie, J.1
Zhang, M.2
Zhou, T.3
Hua, X.4
Tang, L.5
Wu, W.6
|