-
1
-
-
4944266319
-
Epstein-Barr virus: 40 years on
-
Young LS, Rickinson AB. 2004. Epstein-Barr virus: 40 years on. Nat Rev Cancer 4:757-768. http://dx.doi.org/10.1038/nrc1452.
-
(2004)
Nat Rev Cancer
, vol.4
, pp. 757-768
-
-
Young, L.S.1
Rickinson, A.B.2
-
2
-
-
84894429078
-
RNA families in Epstein-Barr virus
-
Moss WN, Lee N, Pimienta G, Steitz JA. 2014. RNA families in Epstein-Barr virus. RNA Biol 11:10-17. http://dx.doi.org/10.4161/rna.27488.
-
(2014)
RNA Biol
, vol.11
, pp. 10-17
-
-
Moss, W.N.1
Lee, N.2
Pimienta, G.3
Steitz, J.A.4
-
3
-
-
84922755348
-
EBV noncoding RNA binds nascent RNA to drive host PAX5 to viral DNA
-
Lee N, Moss WN, Yario TA, Steitz JA. 2015. EBV noncoding RNA binds nascent RNA to drive host PAX5 to viral DNA. Cell 160:607-618. http://dx.doi.org/10.1016/j.cell.2015.01.015.
-
(2015)
Cell
, vol.160
, pp. 607-618
-
-
Lee, N.1
Moss, W.N.2
Yario, T.A.3
Steitz, J.A.4
-
4
-
-
83655183273
-
Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes
-
Dresang LR, Teuton JR, Feng H, Jacobs JM, Camp DG, II, Purvine SO, Gritsenko MA, Li Z, Smith RD, Sugden B, Moore PS, Chang Y. 2011. Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes. BMC Genomics 12:625. http://dx.doi.org/10.1186/1471-2164-12-625.
-
(2011)
BMC Genomics
, vol.12
, pp. 625
-
-
Dresang, L.R.1
Teuton, J.R.2
Feng, H.3
Jacobs, J.M.4
Camp, D.G.5
Purvine, S.O.6
Gritsenko, M.A.7
Li, Z.8
Smith, R.D.9
Sugden, B.10
Moore, P.S.11
Chang, Y.12
-
5
-
-
77951996351
-
Array-based transcript profiling and limiting-dilution reverse transcription-PCR analysis identify additional latent genes in Kaposi's sarcoma-associated herpesvirus
-
Chandriani S, Ganem D. 2010. Array-based transcript profiling and limiting-dilution reverse transcription-PCR analysis identify additional latent genes in Kaposi's sarcoma-associated herpesvirus. J Virol 84:5565-5573. http://dx.doi.org/10.1128/JVI.02723-09.
-
(2010)
J Virol
, vol.84
, pp. 5565-5573
-
-
Chandriani, S.1
Ganem, D.2
-
6
-
-
77956548303
-
Redefining the genetics of murine gammaherpesvirus 68 via transcriptome-based annotation
-
Johnson LS, Willert EK, Virgin HW. 2010. Redefining the genetics of murine gammaherpesvirus 68 via transcriptome-based annotation. Cell Host Microbe 7:516-526. http://dx.doi.org/10.1016/j.chom.2010.05.005.
-
(2010)
Cell Host Microbe
, vol.7
, pp. 516-526
-
-
Johnson, L.S.1
Willert, E.K.2
Virgin, H.W.3
-
7
-
-
0036100266
-
Charting latency transcripts in Kaposi's sarcoma-associated herpesvirus by whole-genome real-time quantitative PCR
-
Fakhari FD, Dittmer DP. 2002. Charting latency transcripts in Kaposi's sarcoma-associated herpesvirus by whole-genome real-time quantitative PCR. J Virol 76:6213-6223. http://dx.doi.org/10.1128/JVI.76.12.6213-6223.2002.
-
(2002)
J Virol
, vol.76
, pp. 6213-6223
-
-
Fakhari, F.D.1
Dittmer, D.P.2
-
8
-
-
84866164089
-
Negative elongation factor-mediated suppression of RNA polymerase II elongation of Kaposi's sarcoma-associated herpesvirus lytic gene expression
-
Toth Z, Brulois KF, Wong LY, Lee HR, Chung B, Jung JU. 2012. Negative elongation factor-mediated suppression of RNA polymerase II elongation of Kaposi's sarcoma-associated herpesvirus lytic gene expression. J Virol 86:9696-9707. http://dx.doi.org/10.1128/JVI.01012-12.
-
(2012)
J Virol
, vol.86
, pp. 9696-9707
-
-
Toth, Z.1
Brulois, K.F.2
Wong, L.Y.3
Lee, H.R.4
Chung, B.5
Jung, J.U.6
-
9
-
-
84892455590
-
Global bidirectional transcription of the Epstein-Barr virus genome during reactivation
-
O'Grady T, Cao S, Strong MJ, Concha M, Wang X, Splinter Bondurant S, Adams M, Baddoo M, Srivastav SK, Lin Z, Fewell C, Yin Q, Flemington EK. 2014. Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. J Virol 88:1604-1616. http://dx.doi.org/10.1128/JVI.02989-13.
-
(2014)
J Virol
, vol.88
, pp. 1604-1616
-
-
O'Grady, T.1
Cao, S.2
Strong, M.J.3
Concha, M.4
Wang, X.5
Splinter Bondurant, S.6
Adams, M.7
Baddoo, M.8
Srivastav, S.K.9
Lin, Z.10
Fewell, C.11
Yin, Q.12
Flemington, E.K.13
-
10
-
-
84863159498
-
Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq
-
Concha M, Wang X, Cao S, Baddoo M, Fewell C, Lin Z, Hulme W, Hedges D, McBride J, Flemington EK. 2012. Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq. J Virol 86:1458-1467. http://dx.doi.org/10.1128/JVI.06537-11.
-
(2012)
J Virol
, vol.86
, pp. 1458-1467
-
-
Concha, M.1
Wang, X.2
Cao, S.3
Baddoo, M.4
Fewell, C.5
Lin, Z.6
Hulme, W.7
Hedges, D.8
McBride, J.9
Flemington, E.K.10
-
11
-
-
84871949044
-
Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains
-
Lin Z, Wang X, Strong MJ, Concha M, Baddoo M, Xu G, Baribault C, Fewell C, Hulme W, Hedges D, Taylor CM, Flemington EK. 2013. Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains. J Virol 87:1172-1182. http://dx.doi.org/10.1128/JVI.02517-12.
-
(2013)
J Virol
, vol.87
, pp. 1172-1182
-
-
Lin, Z.1
Wang, X.2
Strong, M.J.3
Concha, M.4
Baddoo, M.5
Xu, G.6
Baribault, C.7
Fewell, C.8
Hulme, W.9
Hedges, D.10
Taylor, C.M.11
Flemington, E.K.12
-
12
-
-
84859467162
-
Technique for strand-specific gene-expression analysis and monitoring of primerindependent cDNA synthesis in reverse transcription
-
Feng L, Lintula S, Ho TH, Anastasina M, Paju A, Haglund C, Stenman UH, Hotakainen K, Orpana A, Kainov D, Stenman J. 2012. Technique for strand-specific gene-expression analysis and monitoring of primerindependent cDNA synthesis in reverse transcription. Biotechniques 52: 263-270. http://dx.doi.org/10.2144/0000113842.
-
(2012)
Biotechniques
, vol.52
, pp. 263-270
-
-
Feng, L.1
Lintula, S.2
Ho, T.H.3
Anastasina, M.4
Paju, A.5
Haglund, C.6
Stenman, U.H.7
Hotakainen, K.8
Orpana, A.9
Kainov, D.10
Stenman, J.11
-
13
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079. http://dx.doi.org/10.1093/bioinformatics/btp352.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
14
-
-
84863229597
-
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing
-
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. 2012. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22:568-576. http://dx.doi.org/10.1101/gr.129684.111.
-
(2012)
Genome Res
, vol.22
, pp. 568-576
-
-
Koboldt, D.C.1
Zhang, Q.2
Larson, D.E.3
Shen, D.4
McLellan, M.D.5
Lin, L.6
Miller, C.A.7
Mardis, E.R.8
Ding, L.9
Wilson, R.K.10
-
15
-
-
58249121729
-
RNAalifold: improved consensus structure prediction for RNA alignments
-
Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF. 2008. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 9:474. http://dx.doi.org/10.1186/1471-2105-9-474.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 474
-
-
Bernhart, S.H.1
Hofacker, I.L.2
Will, S.3
Gruber, A.R.4
Stadler, P.F.5
-
16
-
-
84890037468
-
Infernal 1.1: 100-fold faster RNA homology searches
-
Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29:2933-2935. http://dx.doi.org/10.1093/bioinformatics/btt509.
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
17
-
-
0036081355
-
Gene Expr. Omnibus: NCBI gene expression and hybridization array data repository
-
Edgar R, Domrachev M, Lash AE. 2002. Gene Expr. Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
18
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111. http://dx.doi.org/10.1093/bioinformatics/btp120.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
19
-
-
78651271733
-
Integrative genomics viewer
-
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nat Biotechnol 29:24-26. http://dx.doi.org/10.1038/nbt.1754.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
Thorvaldsdottir, H.2
Winckler, W.3
Guttman, M.4
Lander, E.S.5
Getz, G.6
Mesirov, J.P.7
-
20
-
-
84875634162
-
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
-
Thorvaldsdottir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178-192. http://dx.doi.org/10.1093/bib/bbs017.
-
(2013)
Brief Bioinform
, vol.14
, pp. 178-192
-
-
Thorvaldsdottir, H.1
Robinson, J.T.2
Mesirov, J.P.3
-
21
-
-
78651289575
-
SAMMate: a GUI tool for processing short read alignments in SAM/BAM format
-
Xu G, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D. 2011. SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. Source Code Biol Med 6:2. http://dx.doi.org/10.1186/1751-0473-6-2.
-
(2011)
Source Code Biol Med
, vol.6
, pp. 2
-
-
Xu, G.1
Deng, N.2
Zhao, Z.3
Judeh, T.4
Flemington, E.5
Zhu, D.6
-
22
-
-
0029884311
-
Transcriptional analysis of the Epstein-Barr virus interleukin-10 homologue during the lytic cycle
-
Touitou R, Cochet C, Joab I. 1996. Transcriptional analysis of the Epstein-Barr virus interleukin-10 homologue during the lytic cycle. J Gen Virol 77(Pt 6):1163-1168.
-
(1996)
J Gen Virol
, vol.77
, pp. 1163-1168
-
-
Touitou, R.1
Cochet, C.2
Joab, I.3
-
23
-
-
0027265976
-
Epstein-Barr virus gene expression in oral hairy leukoplakia
-
Lau R, Middeldorp J, Farrell PJ. 1993. Epstein-Barr virus gene expression in oral hairy leukoplakia. Virology 195:463-474. http://dx.doi.org/10.1006/viro.1993.1397.
-
(1993)
Virology
, vol.195
, pp. 463-474
-
-
Lau, R.1
Middeldorp, J.2
Farrell, P.J.3
-
24
-
-
0022375089
-
The short unique region of the B95-8 Epstein-Barr virus genome
-
Hudson GS, Bankier AT, Satchwell SC, Barrell BG. 1985. The short unique region of the B95-8 Epstein-Barr virus genome. Virology 147:81-98. http://dx.doi.org/10.1016/0042-6822(85)90229-6.
-
(1985)
Virology
, vol.147
, pp. 81-98
-
-
Hudson, G.S.1
Bankier, A.T.2
Satchwell, S.C.3
Barrell, B.G.4
-
25
-
-
34547582418
-
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
-
Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, Gao G. 2007. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35:W345-W349. http://dx.doi.org/10.1093/nar/gkm391.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. W345-W349
-
-
Kong, L.1
Zhang, Y.2
Ye, Z.Q.3
Liu, X.Q.4
Zhao, S.Q.5
Wei, L.6
Gao, G.7
-
26
-
-
77958483268
-
Editing of Epstein-Barr virus-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency
-
Iizasa H, Wulff BE, Alla NR, Maragkakis M, Megraw M, Hatzigeorgiou A, Iwakiri D, Takada K, Wiedmer A, Showe L, Lieberman P, Nishikura K. 2010. Editing of Epstein-Barr virus-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency. J Biol Chem 285:33358-33370. http://dx.doi.org/10.1074/jbc.M110.138362.
-
(2010)
J Biol Chem
, vol.285
, pp. 33358-33370
-
-
Iizasa, H.1
Wulff, B.E.2
Alla, N.R.3
Maragkakis, M.4
Megraw, M.5
Hatzigeorgiou, A.6
Iwakiri, D.7
Takada, K.8
Wiedmer, A.9
Showe, L.10
Lieberman, P.11
Nishikura, K.12
-
27
-
-
84887536769
-
Perturbation of biogenesis and targeting of Epstein-Barr virus-encoded miR-BART3 microRNA by adenosine-to-inosine editing
-
Lei T, Yuen KS, Tsao SW, Chen H, Kok KH, Jin DY. 2013. Perturbation of biogenesis and targeting of Epstein-Barr virus-encoded miR-BART3 microRNA by adenosine-to-inosine editing. J Gen Virol 94:2739-2744. http://dx.doi.org/10.1099/vir.0.056226-0.
-
(2013)
J Gen Virol
, vol.94
, pp. 2739-2744
-
-
Lei, T.1
Yuen, K.S.2
Tsao, S.W.3
Chen, H.4
Kok, K.H.5
Jin, D.Y.6
-
28
-
-
0027967784
-
Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase
-
Polson AG, Bass BL. 1994. Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J 13: 5701-5711.
-
(1994)
EMBO J
, vol.13
, pp. 5701-5711
-
-
Polson, A.G.1
Bass, B.L.2
-
29
-
-
0025943830
-
Substrate specificity of the dsRNA unwinding/modifying activity
-
Nishikura K, Yoo C, Kim U, Murray JM, Estes PA, Cash FE, Liebhaber SA. 1991. Substrate specificity of the dsRNA unwinding/modifying activity. EMBO J 10:3523-3532.
-
(1991)
EMBO J
, vol.10
, pp. 3523-3532
-
-
Nishikura, K.1
Yoo, C.2
Kim, U.3
Murray, J.M.4
Estes, P.A.5
Cash, F.E.6
Liebhaber, S.A.7
-
30
-
-
79956271523
-
Predicting sites of ADAR editing in double-stranded RNA
-
Eggington JM, Greene T, Bass BL. 2011. Predicting sites of ADAR editing in double-stranded RNA. Nat Commun 2:319. http://dx.doi.org/10.1038/ncomms1324.
-
(2011)
Nat Commun
, vol.2
, pp. 319
-
-
Eggington, J.M.1
Greene, T.2
Bass, B.L.3
-
31
-
-
0037062438
-
RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA
-
Morse DP, Aruscavage PJ, Bass BL. 2002. RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Proc Natl Acad Sci USA 99:7906-7911. http://dx.doi.org/10.1073/pnas.112704299.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 7906-7911
-
-
Morse, D.P.1
Aruscavage, P.J.2
Bass, B.L.3
-
33
-
-
84881175425
-
Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA
-
Moss WN, Steitz JA. 2013. Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. BMC Genomics 14:543. http://dx.doi.org/10.1186/1471-2164-14-543.
-
(2013)
BMC Genomics
, vol.14
, pp. 543
-
-
Moss, W.N.1
Steitz, J.A.2
-
34
-
-
17844391015
-
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency
-
Clote P, Ferre F, Kranakis E, Krizanc D. 2005. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA 11:578-591. http://dx.doi.org/10.1261/rna.7220505.
-
(2005)
RNA
, vol.11
, pp. 578-591
-
-
Clote, P.1
Ferre, F.2
Kranakis, E.3
Krizanc, D.4
-
35
-
-
65549111754
-
Infernal 1.0: inference of RNA alignments
-
Nawrocki EP, Kolbe DL, Eddy SR. 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics 25:1335-1337. http://dx.doi.org/10.1093/bioinformatics/btp157.
-
(2009)
Bioinformatics
, vol.25
, pp. 1335-1337
-
-
Nawrocki, E.P.1
Kolbe, D.L.2
Eddy, S.R.3
-
36
-
-
77954313452
-
ADAR editing in double-stranded UTRs and other noncoding RNA sequences
-
Hundley HA, Bass BL. 2010. ADAR editing in double-stranded UTRs and other noncoding RNA sequences. Trends Biochem Sci 35:377-383. http://dx.doi.org/10.1016/j.tibs.2010.02.008.
-
(2010)
Trends Biochem Sci
, vol.35
, pp. 377-383
-
-
Hundley, H.A.1
Bass, B.L.2
-
37
-
-
0034711082
-
Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities
-
Lehmann KA, Bass BL. 2000. Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities. Biochemistry 39:12875-12884. http://dx.doi.org/10.1021/bi001383g.
-
(2000)
Biochemistry
, vol.39
, pp. 12875-12884
-
-
Lehmann, K.A.1
Bass, B.L.2
-
38
-
-
84874965439
-
Paraspeckle formation during the biogenesis of long non-coding RNAs
-
Naganuma T, Hirose T. 2013. Paraspeckle formation during the biogenesis of long non-coding RNAs. RNA Biol 10:456-461. http://dx.doi.org/10.4161/rna.23547.
-
(2013)
RNA Biol
, vol.10
, pp. 456-461
-
-
Naganuma, T.1
Hirose, T.2
-
39
-
-
84865628181
-
Paraspeckle nuclear bodies-useful uselessness?
-
Nakagawa S, Hirose T. 2012. Paraspeckle nuclear bodies-useful uselessness? Cell Mol Life Sci 69:3027-3036. http://dx.doi.org/10.1007/s00018-012-0973-x.
-
(2012)
Cell Mol Life Sci
, vol.69
, pp. 3027-3036
-
-
Nakagawa, S.1
Hirose, T.2
-
40
-
-
84893452948
-
Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL-8 expression upon immune stimuli
-
Imamura K, Imamachi N, Akizuki G, Kumakura M, Kawaguchi A, Nagata K, Kato A, Kawaguchi Y, Sato H, Yoneda M, Kai C, Yada T, Suzuki Y, Yamada T, Ozawa T, Kaneki K, Inoue T, Kobayashi M, Kodama T, Wada Y, Sekimizu K, Akimitsu N. 2014. Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL-8 expression upon immune stimuli. Mol Cell 53:393-406. http://dx.doi.org/10.1016/j.molcel.2014.01.009.
-
(2014)
Mol Cell
, vol.53
, pp. 393-406
-
-
Imamura, K.1
Imamachi, N.2
Akizuki, G.3
Kumakura, M.4
Kawaguchi, A.5
Nagata, K.6
Kato, A.7
Kawaguchi, Y.8
Sato, H.9
Yoneda, M.10
Kai, C.11
Yada, T.12
Suzuki, Y.13
Yamada, T.14
Ozawa, T.15
Kaneki, K.16
Inoue, T.17
Kobayashi, M.18
Kodama, T.19
Wada, Y.20
Sekimizu, K.21
Akimitsu, N.22
more..
-
41
-
-
33745595582
-
Identification and characterization of a virus-inducible noncoding RNA in mouse brain
-
Saha S, Murthy S, Rangarajan PN. 2006. Identification and characterization of a virus-inducible noncoding RNA in mouse brain. J Gen Virol 87:1991-1995. http://dx.doi.org/10.1099/vir.0.81768-0.
-
(2006)
J Gen Virol
, vol.87
, pp. 1991-1995
-
-
Saha, S.1
Murthy, S.2
Rangarajan, P.N.3
-
42
-
-
84874614275
-
NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression
-
Zhang Q, Chen CY, Yedavalli VS, Jeang KT. 2013. NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression. mBio 4:e00596-12. http://dx.doi.org/10.1128/mBio.00596-12.
-
(2013)
mBio
, vol.4
-
-
Zhang, Q.1
Chen, C.Y.2
Yedavalli, V.S.3
Jeang, K.T.4
-
43
-
-
0038578021
-
Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2'-O-methyl RNA, phosphorothioates, and small interfering RNA
-
Grunweller A, Wyszko E, Bieber B, Jahnel R, Erdmann VA, Kurreck J. 2003. Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2'-O-methyl RNA, phosphorothioates, and small interfering RNA. Nucleic Acids Res 31:3185-3193. http://dx.doi.org/10.1093/nar/gkg409.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3185-3193
-
-
Grunweller, A.1
Wyszko, E.2
Bieber, B.3
Jahnel, R.4
Erdmann, V.A.5
Kurreck, J.6
-
44
-
-
84876263777
-
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments
-
Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, Haag JD, Gould MN, Stewart RM, Kendziorski C. 2013. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics 29:1035-1043. http://dx.doi.org/10.1093/bioinformatics/btt087.
-
(2013)
Bioinformatics
, vol.29
, pp. 1035-1043
-
-
Leng, N.1
Dawson, J.A.2
Thomson, J.A.3
Ruotti, V.4
Rissman, A.I.5
Smits, B.M.6
Haag, J.D.7
Gould, M.N.8
Stewart, R.M.9
Kendziorski, C.10
-
45
-
-
84919431442
-
High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia Project
-
Cao S, Strong MJ, Wang X, Moss WN, Concha M, Lin Z, O'Grady T, Baddoo M, Fewell C, Renne R, Flemington EK. 2015. High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia Project. J Virol 89:713-729. http://dx.doi.org/10.1128/JVI.02570-14.
-
(2015)
J Virol
, vol.89
, pp. 713-729
-
-
Cao, S.1
Strong, M.J.2
Wang, X.3
Moss, W.N.4
Concha, M.5
Lin, Z.6
O'Grady, T.7
Baddoo, M.8
Fewell, C.9
Renne, R.10
Flemington, E.K.11
-
46
-
-
0024424127
-
Epstein-Barr virus bicistronic mRNAs generated by facultative splicing code for two transcriptional trans-activators
-
Manet E, Gruffat H, Trescol-Biemont MC, Moreno N, Chambard P, Giot JF, Sergeant A. 1989. Epstein-Barr virus bicistronic mRNAs generated by facultative splicing code for two transcriptional trans-activators. EMBO J 8:1819-1826.
-
(1989)
EMBO J
, vol.8
, pp. 1819-1826
-
-
Manet, E.1
Gruffat, H.2
Trescol-Biemont, M.C.3
Moreno, N.4
Chambard, P.5
Giot, J.F.6
Sergeant, A.7
-
47
-
-
80054756754
-
Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions
-
Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. 2011. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 44:667-678.
-
(2011)
Mol Cell
, vol.44
, pp. 667-678
-
-
Chu, C.1
Qu, K.2
Zhong, F.L.3
Artandi, S.E.4
Chang, H.Y.5
-
48
-
-
0037032415
-
PSF and p54(nrb)/NonO-multi-functional nuclear proteins
-
Shav-Tal Y, Zipori D. 2002. PSF and p54(nrb)/NonO-multi-functional nuclear proteins. FEBS Lett 531:109-114. http://dx.doi.org/10.1016/S0014-5793(02)03447-6.
-
(2002)
FEBS Lett
, vol.531
, pp. 109-114
-
-
Shav-Tal, Y.1
Zipori, D.2
-
49
-
-
0031039425
-
The intracisternal A-particle proximal enhancer-binding protein activates transcription and is identical to the RNA-and DNA-binding protein p54nrb/NonO
-
Basu A, Dong B, Krainer AR, Howe CC. 1997. The intracisternal A-particle proximal enhancer-binding protein activates transcription and is identical to the RNA-and DNA-binding protein p54nrb/NonO. Mol Cell Biol 17:677-686.
-
(1997)
Mol Cell Biol
, vol.17
, pp. 677-686
-
-
Basu, A.1
Dong, B.2
Krainer, A.R.3
Howe, C.C.4
-
50
-
-
84897911847
-
The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression
-
Yadav SP, Hao H, Yang HJ, Kautzmann MA, Brooks M, Nellissery J, Klocke B, Seifert M, Swaroop A. 2014. The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression. Hum Mol Genet 23: 2132-2144. http://dx.doi.org/10.1093/hmg/ddt609.
-
(2014)
Hum Mol Genet
, vol.23
, pp. 2132-2144
-
-
Yadav, S.P.1
Hao, H.2
Yang, H.J.3
Kautzmann, M.A.4
Brooks, M.5
Nellissery, J.6
Klocke, B.7
Seifert, M.8
Swaroop, A.9
-
51
-
-
79959849578
-
Consensus PP1 binding motifs regulate transcriptional corepression and alternative RNA splicing activities of the steroid receptor coregulators, p54nrb and PSF
-
Liu L, Xie N, Rennie P, Challis JR, Gleave M, Lye SJ, Dong X. 2011. Consensus PP1 binding motifs regulate transcriptional corepression and alternative RNA splicing activities of the steroid receptor coregulators, p54nrb and PSF. Mol Endocrinol 25:1197-1210. http://dx.doi.org/10.1210/me.2010-0517.
-
(2011)
Mol Endocrinol
, vol.25
, pp. 1197-1210
-
-
Liu, L.1
Xie, N.2
Rennie, P.3
Challis, J.R.4
Gleave, M.5
Lye, S.J.6
Dong, X.7
-
52
-
-
0036715543
-
Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD
-
Emili A, Shales M, McCracken S, Xie W, Tucker PW, Kobayashi R, Blencowe BJ, Ingles CJ. 2002. Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD. RNA 8:1102-1111. http://dx.doi.org/10.1017/S1355838202025037.
-
(2002)
RNA
, vol.8
, pp. 1102-1111
-
-
Emili, A.1
Shales, M.2
McCracken, S.3
Xie, W.4
Tucker, P.W.5
Kobayashi, R.6
Blencowe, B.J.7
Ingles, C.J.8
-
53
-
-
34347332370
-
Transcriptional activity of androgen receptor is modulated by two RNA splicing factors, PSF and p54nrb
-
Dong X, Sweet J, Challis JR, Brown T, Lye SJ. 2007. Transcriptional activity of androgen receptor is modulated by two RNA splicing factors, PSF and p54nrb. Mol Cell Biol 27:4863-4875. http://dx.doi.org/10.1128/MCB.02144-06.
-
(2007)
Mol Cell Biol
, vol.27
, pp. 4863-4875
-
-
Dong, X.1
Sweet, J.2
Challis, J.R.3
Brown, T.4
Lye, S.J.5
-
54
-
-
0027328533
-
NonO, a non-POU-domain-containing, octamer-binding protein, is the mammalian homolog of Drosophila nonAdiss
-
Yang YS, Hanke JH, Carayannopoulos L, Craft CM, Capra JD, Tucker PW. 1993. NonO, a non-POU-domain-containing, octamer-binding protein, is the mammalian homolog of Drosophila nonAdiss. Mol Cell Biol 13:5593-5603.
-
(1993)
Mol Cell Biol
, vol.13
, pp. 5593-5603
-
-
Yang, Y.S.1
Hanke, J.H.2
Carayannopoulos, L.3
Craft, C.M.4
Capra, J.D.5
Tucker, P.W.6
-
55
-
-
22544472117
-
Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo
-
Rosonina E, Ip JY, Calarco JA, Bakowski MA, Emili A, McCracken S, Tucker P, Ingles CJ, Blencowe BJ. 2005. Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol Cell Biol 25:6734-6746. http://dx.doi.org/10.1128/MCB.25.15.6734-6746.2005.
-
(2005)
Mol Cell Biol
, vol.25
, pp. 6734-6746
-
-
Rosonina, E.1
Ip, J.Y.2
Calarco, J.A.3
Bakowski, M.A.4
Emili, A.5
McCracken, S.6
Tucker, P.7
Ingles, C.J.8
Blencowe, B.J.9
-
56
-
-
29844444075
-
p54nrb is a component of the snRNP-free U1A (SF-A) complex that promotes pre-mRNA cleavage during polyadenylation
-
Liang S, Lutz CS. 2006. p54nrb is a component of the snRNP-free U1A (SF-A) complex that promotes pre-mRNA cleavage during polyadenylation. RNA 12:111-121. http://dx.doi.org/10.1261/rna.2213506.
-
(2006)
RNA
, vol.12
, pp. 111-121
-
-
Liang, S.1
Lutz, C.S.2
-
57
-
-
0032500516
-
The RNA-splicing factor PSF/p54 controls DNAtopoisomerase I activity by a direct interaction
-
Straub T, Grue P, Uhse A, Lisby M, Knudsen BR, Tange TO, Westergaard O, Boege F. 1998. The RNA-splicing factor PSF/p54 controls DNAtopoisomerase I activity by a direct interaction. J Biol Chem 273:26261-26264. http://dx.doi.org/10.1074/jbc.273.41.26261.
-
(1998)
J Biol Chem
, vol.273
, pp. 26261-26264
-
-
Straub, T.1
Grue, P.2
Uhse, A.3
Lisby, M.4
Knudsen, B.R.5
Tange, T.O.6
Westergaard, O.7
Boege, F.8
-
58
-
-
0034720780
-
PSF/p54(nrb) stimulates "jumping" of DNA topoisomerase I between separate DNA helices
-
Straub T, Knudsen BR, Boege F. 2000. PSF/p54(nrb) stimulates "jumping" of DNA topoisomerase I between separate DNA helices. Biochemistry 39:7552-7558. http://dx.doi.org/10.1021/bi992898e.
-
(2000)
Biochemistry
, vol.39
, pp. 7552-7558
-
-
Straub, T.1
Knudsen, B.R.2
Boege, F.3
-
59
-
-
0034779253
-
CRM1 mediates the export of ADAR1 through a nuclear export signal within the Z-DNA binding domain
-
Poulsen H, Nilsson J, Damgaard CK, Egebjerg J, Kjems J. 2001. CRM1 mediates the export of ADAR1 through a nuclear export signal within the Z-DNA binding domain. Mol Cell Biol 21:7862-7871. http://dx.doi.org/10.1128/MCB.21.22.7862-7871.2001.
-
(2001)
Mol Cell Biol
, vol.21
, pp. 7862-7871
-
-
Poulsen, H.1
Nilsson, J.2
Damgaard, C.K.3
Egebjerg, J.4
Kjems, J.5
-
60
-
-
62849103689
-
RNA-regulated interaction of transportin-1 and exportin-5 with the double-stranded RNA-binding domain regulates nucleocytoplasmic shuttling of ADAR1
-
Fritz J, Strehblow A, Taschner A, Schopoff S, Pasierbek P, Jantsch MF. 2009. RNA-regulated interaction of transportin-1 and exportin-5 with the double-stranded RNA-binding domain regulates nucleocytoplasmic shuttling of ADAR1. Mol Cell Biol 29:1487-1497. http://dx.doi.org/10.1128/MCB.01519-08.
-
(2009)
Mol Cell Biol
, vol.29
, pp. 1487-1497
-
-
Fritz, J.1
Strehblow, A.2
Taschner, A.3
Schopoff, S.4
Pasierbek, P.5
Jantsch, M.F.6
-
61
-
-
0036856310
-
Nucleocytoplasmic distribution of human RNA-editing enzyme ADAR1 is modulated by doublestranded RNA-binding domains, a leucine-rich export signal, and a putative dimerization domain
-
Strehblow A, Hallegger M, Jantsch MF. 2002. Nucleocytoplasmic distribution of human RNA-editing enzyme ADAR1 is modulated by doublestranded RNA-binding domains, a leucine-rich export signal, and a putative dimerization domain. Mol Biol Cell 13:3822-3835. http://dx.doi.org/10.1091/mbc.E02-03-0161.
-
(2002)
Mol Biol Cell
, vol.13
, pp. 3822-3835
-
-
Strehblow, A.1
Hallegger, M.2
Jantsch, M.F.3
-
62
-
-
3543004084
-
Systematic identification of abundant A-to-I editing sites in the human transcriptome
-
Levanon EY, Eisenberg E, Yelin R, Nemzer S, Hallegger M, Shemesh R, Fligelman ZY, Shoshan A, Pollock SR, Sztybel D, Olshansky M, Rechavi G, Jantsch MF. 2004. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol 22:1001-1005. http://dx.doi.org/10.1038/nbt996.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 1001-1005
-
-
Levanon, E.Y.1
Eisenberg, E.2
Yelin, R.3
Nemzer, S.4
Hallegger, M.5
Shemesh, R.6
Fligelman, Z.Y.7
Shoshan, A.8
Pollock, S.R.9
Sztybel, D.10
Olshansky, M.11
Rechavi, G.12
Jantsch, M.F.13
-
63
-
-
0035512727
-
The many roles of an RNA editor
-
Keegan LP, Gallo A, O'Connell MA. 2001. The many roles of an RNA editor. Nat Rev Genet 2:869-878. http://dx.doi.org/10.1038/35098584.
-
(2001)
Nat Rev Genet
, vol.2
, pp. 869-878
-
-
Keegan, L.P.1
Gallo, A.2
O'Connell, M.A.3
-
64
-
-
30044443191
-
Modulation of microRNA processing and expression through RNA editing by ADAR deaminases
-
Yang W, Chendrimada TP, Wang Q, Higuchi M, Seeburg PH, Shiekhattar R, Nishikura K. 2006. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol 13:13-21. http://dx.doi.org/10.1038/nsmb1041.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 13-21
-
-
Yang, W.1
Chendrimada, T.P.2
Wang, Q.3
Higuchi, M.4
Seeburg, P.H.5
Shiekhattar, R.6
Nishikura, K.7
-
65
-
-
33847317017
-
Redirection of silencing targets by adenosine-toinosine editing of miRNAs
-
Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K. 2007. Redirection of silencing targets by adenosine-toinosine editing of miRNAs. Science 315:1137-1140. http://dx.doi.org/10.1126/science.1138050.
-
(2007)
Science
, vol.315
, pp. 1137-1140
-
-
Kawahara, Y.1
Zinshteyn, B.2
Sethupathy, P.3
Iizasa, H.4
Hatzigeorgiou, A.G.5
Nishikura, K.6
-
66
-
-
84921463352
-
A-to-I editing in the miRNA seed region regulates target mRNA selection and silencing efficiency
-
Kume H, Hino K, Galipon J, Ui-Tei K. 2014. A-to-I editing in the miRNA seed region regulates target mRNA selection and silencing efficiency. Nucleic Acids Res 42:10050-10060. http://dx.doi.org/10.1093/nar/gku662.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 10050-10060
-
-
Kume, H.1
Hino, K.2
Galipon, J.3
Ui-Tei, K.4
-
67
-
-
33645765165
-
RNA editing and alternative splicing: the importance of cotranscriptional coordination
-
Laurencikiene J, Kallman AM, Fong N, Bentley DL, Ohman M. 2006. RNA editing and alternative splicing: the importance of cotranscriptional coordination. EMBO Rep 7:303-307. http://dx.doi.org/10.1038/sj.embor.7400621.
-
(2006)
EMBO Rep
, vol.7
, pp. 303-307
-
-
Laurencikiene, J.1
Kallman, A.M.2
Fong, N.3
Bentley, D.L.4
Ohman, M.5
|