-
1
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57: 289-300.
-
(1995)
J R Stat Soc ser B Methodol
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
2
-
-
0034687740
-
Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization
-
DOI 10.1073/pnas.250426397
-
Cavaille J, Buiting K, Kiefmann M, Lalande M, Brannan CI, Horsthemke B, Bachellerie JP, Brosius J, Huttenhofer A. 2000. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc Natl Acad Sci 97: 14311-14316. (Pubitemid 32016572)
-
(2000)
Proceedings of the National Academy of Sciences of the United States of America
, vol.97
, Issue.26
, pp. 14311-14316
-
-
Cavaille, J.1
Buiting, K.2
Kiefmann, M.3
Lalande, M.4
Brannan, C.I.5
Horsthemke, B.6
Bachellerie, J.-P.7
Brosius, J.8
Huttenhofer, A.9
-
3
-
-
77953798171
-
Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA
-
Cazalla D, Yario T, Steitz JA. 2010. Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA. Science 328: 1563-1566.
-
(2010)
Science
, vol.328
, pp. 1563-1566
-
-
Cazalla, D.1
Yario, T.2
Steitz, J.A.3
-
4
-
-
0029461958
-
Modification of the TRI ReagentT procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources
-
Chomczynski P, Mackey K. 1995. Short technical reports. Modification of the TRI reagent procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources. Biotechniques 19: 942-945. (Pubitemid 3021405)
-
(1995)
BioTechniques
, vol.19
, Issue.6
, pp. 942-945
-
-
Chomczynski, P.1
Mackey, K.2
-
5
-
-
13844281888
-
Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay
-
DOI 10.1038/nbt1061
-
Cleary MD, Meiering CD, Jan E, Guymon R, Boothroyd JC. 2005. Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay. Nat Biotechnol 23: 232-237. (Pubitemid 40255335)
-
(2005)
Nature Biotechnology
, vol.23
, Issue.2
, pp. 232-237
-
-
Cleary, M.D.1
Meiering, C.D.2
Jan, E.3
Guymon, R.4
Boothroyd, J.C.5
-
6
-
-
0033064680
-
The stability and fate of a spliced intron from vertebrate cells
-
DOI 10.1017/S1355838299981190
-
Clement JQ, Qian L, Kaplinsky N, Wilkinson MF. 1999. The stability and fate of a spliced intron from vertebrate cells. RNA 5: 206-220. (Pubitemid 29079281)
-
(1999)
RNA
, vol.5
, Issue.2
, pp. 206-220
-
-
Clement, J.Q.1
Qian, L.2
Kaplinsky, N.3
Wilkinson, M.F.4
-
7
-
-
67649933366
-
Eukaryotic snoRNAs: A paradigm for gene expression flexibility
-
Dieci G, Preti M, Montanini B. 2009. Eukaryotic snoRNAs: A paradigm for gene expression flexibility. Genomics 94: 83-88.
-
(2009)
Genomics
, vol.94
, pp. 83-88
-
-
Dieci, G.1
Preti, M.2
Montanini, B.3
-
8
-
-
50649118115
-
High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay
-
Dölken L, Ruzsics Z, Rädle B, Friedel CC, Zimmer R, Mages J, Hoffmann R, Dickinson P, Forster T, Ghazal P, et al. 2008. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 14: 1959-1972.
-
(2008)
RNA
, vol.14
, pp. 1959-1972
-
-
Dölken, L.1
Ruzsics, Z.2
Rädle, B.3
Friedel, C.C.4
Zimmer, R.5
Mages, J.6
Hoffmann, R.7
Dickinson, P.8
Forster, T.9
Ghazal, P.10
-
9
-
-
77954573536
-
Systematic analysis of viral and cellular microRNA targets in cells latently infected with human γ-herpesviruses by RISC immunoprecipitation assay
-
Dölken L, Malterer G, Erhard F, Kothe S, Friedel CC, Suffert G, Marcinowski L, Motsch N, Barth S, Beitzinger M, et al. 2010. Systematic analysis of viral and cellular microRNA targets in cells latently infected with human γ-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe 7: 324-334.
-
(2010)
Cell Host Microbe
, vol.7
, pp. 324-334
-
-
Dölken, L.1
Malterer, G.2
Erhard, F.3
Kothe, S.4
Friedel, C.C.5
Suffert, G.6
Marcinowski, L.7
Motsch, N.8
Barth, S.9
Beitzinger, M.10
-
10
-
-
33644856084
-
Exon tethering in transcription by RNA polymerase II
-
DOI 10.1016/j.molcel.2006.01.032, PII S1097276506000803
-
Dye MJ, Gromak N, Proudfoot NJ. 2006. Exon tethering in transcription by RNA polymerase II. Mol Cell 21: 849-859. (Pubitemid 43376134)
-
(2006)
Molecular Cell
, vol.21
, Issue.6
, pp. 849-859
-
-
Dye, M.J.1
Gromak, N.2
Proudfoot, N.J.3
-
11
-
-
70350035567
-
Metabolic tagging and purification of nascent RNA: Implications for transcriptomics
-
Friedel CC, Dölken L. 2009. Metabolic tagging and purification of nascent RNA: Implications for transcriptomics. Mol Biosyst 5: 1271-1278.
-
(2009)
Mol Biosyst
, vol.5
, pp. 1271-1278
-
-
Friedel, C.C.1
Dölken, L.2
-
12
-
-
73049097101
-
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
-
doi: 10.1093/nar/gkp542
-
Friedel CC, Dölken L, Ruzsics Z, Koszinowski UH, Zimmer R. 2009. Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res 37: e115. doi: 10.1093/nar/gkp542.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Friedel, C.C.1
Dölken, L.2
Ruzsics, Z.3
Koszinowski, U.H.4
Zimmer, R.5
-
13
-
-
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 Jr, Jungkamp AC, Munschauer M, et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 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 Jr., M.8
Jungkamp, A.C.9
Munschauer, M.10
-
14
-
-
0043172414
-
Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells
-
DOI 10.1016/S1097-2765(03)00267-3
-
Hirose T, Shu MD, Steitz JA. 2003. Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol Cell 12: 113-123. (Pubitemid 36945040)
-
(2003)
Molecular Cell
, vol.12
, Issue.1
, pp. 113-123
-
-
Hirose, T.1
Shu, M.-D.2
Steitz, J.A.3
-
15
-
-
20044388720
-
Involvement of MicroRNA in AU-Rich Element-Mediated mRNA Instability
-
DOI 10.1016/j.cell.2004.12.038
-
Jing Q, Huang S, Guth S, Zarubin T, Motoyama A, Chen J, Di Padova F, Lin SC, Gram H, Han J. 2005. Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 120: 623-634. (Pubitemid 40343075)
-
(2005)
Cell
, vol.120
, Issue.5
, pp. 623-634
-
-
Jing, Q.1
Huang, S.2
Guth, S.3
Zarubin, T.4
Motoyama, A.5
Chen, J.6
Di, P.F.7
Lin, S.-C.8
Gram, H.9
Han, J.10
-
16
-
-
0036079158
-
The human genome browser at UCSC
-
DOI 10.1101/gr.229102. Article published online before print in May 2002
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12: 996-1006. (Pubitemid 34662293)
-
(2002)
Genome Research
, vol.12
, Issue.6
, pp. 996-1006
-
-
James, K.W.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
17
-
-
34547495201
-
Microarray analysis of newly synthesized RNA in cells and animals
-
DOI 10.1073/pnas.0610439104
-
Kenzelmann M, Maertens S, Hergenhahn M, Kueffer S, Hotz-Wagenblatt A, Li L, Wang S, Ittrich C, Lemberger T, Arribas R, et al. 2007. Microarray analysis of newly synthesized RNA in cells and animals. Proc Natl Acad Sci 104: 6164-6169. (Pubitemid 47186066)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.15
, pp. 6164-6169
-
-
Kenzelmann, M.1
Maertens, S.2
Hergenhahn, M.3
Kueffer, S.4
Hotz-Wagenblatt, A.5
Li, L.6
Wang, S.7
Ittrich, C.8
Lemberger, T.9
Arribas, R.10
Jonnakuty, S.11
Hollstein, M.C.12
Schmid, W.13
Gretz, N.14
Grone, H.J.15
Schutz, G.16
-
18
-
-
67749113808
-
Transcriptional regulatory circuits: Predicting numbers from alphabets
-
Kim HD, Shay T, O'Shea EK, Regev A. 2009. Transcriptional regulatory circuits: Predicting numbers from alphabets. Science 325: 429-432.
-
(2009)
Science
, vol.325
, pp. 429-432
-
-
Kim, H.D.1
Shay, T.2
O'Shea, E.K.3
Regev, A.4
-
19
-
-
0037133942
-
Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions
-
DOI 10.1016/S0092-8674(02)00718-3
-
Kiss T. 2002. Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions. Cell 109: 145-148. (Pubitemid 34518252)
-
(2002)
Cell
, vol.109
, Issue.2
, pp. 145-148
-
-
Kiss, T.1
-
20
-
-
0023672447
-
Spliceosome assembly involves the binding and release of U4 small nuclear ribonucleoprotein
-
Lamond AI, Konarska MM, Grabowski PJ, Sharp PA. 1988. Spliceosome assembly involves the binding and release of U4 small nuclear ribonucleoprotein. Proc Natl Acad Sci 85: 411-415.
-
(1988)
Proc Natl Acad Sci
, vol.85
, pp. 411-415
-
-
Lamond, A.I.1
Konarska, M.M.2
Grabowski, P.J.3
Sharp, P.A.4
-
21
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
doi: 10.1186/gb-2009-10-3-r25
-
Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
22
-
-
0018063623
-
Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography
-
Melvin WT, Milne HB, Slater AA, Allen HJ, Keir HM. 1978. Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography. Eur J Biochem 92: 373-379.
-
(1978)
Eur J Biochem
, vol.92
, pp. 373-379
-
-
Melvin, W.T.1
Milne, H.B.2
Slater, A.A.3
Allen, H.J.4
Keir, H.M.5
-
23
-
-
67349288523
-
TU-tagging: Cell type-specific RNA isolation from intact complex tissues
-
Miller MR, Robinson KJ, Cleary MD, Doe CQ. 2009. TU-tagging: Cell type-specific RNA isolation from intact complex tissues. Nat Methods 6: 439-441.
-
(2009)
Nat Methods
, vol.6
, pp. 439-441
-
-
Miller, M.R.1
Robinson, K.J.2
Cleary, M.D.3
Doe, C.Q.4
-
24
-
-
78650930357
-
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast
-
doi: 10.1038/msb.2010.112
-
Miller C, Schwalb B, Maier K, Schulz D, Dümcke S, Zacher B, Mayer A, Sydow J, Marcinowski L, Dölken L, et al. 2011. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7: 458. doi: 10.1038/msb.2010.112.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 458
-
-
Miller, C.1
Schwalb, B.2
Maier, K.3
Schulz, D.4
Dümcke, S.5
Zacher, B.6
Mayer, A.7
Sydow, J.8
Marcinowski, L.9
Dölken, L.10
-
25
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
DOI 10.1038/nmeth.1226, PII NMETH.1226
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. (Pubitemid 351911867)
-
(2008)
Nature Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
26
-
-
0031053705
-
Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation
-
Nam K, Lee G, Trambley J, Devine SE, Boeke JD. 1997. Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation. Mol Cell Biol 17: 809-818. (Pubitemid 27044380)
-
(1997)
Molecular and Cellular Biology
, vol.17
, Issue.2
, pp. 809-818
-
-
Nam, K.1
Lee, G.2
Trambley, J.3
Devine, S.E.4
Boeke, J.D.5
-
27
-
-
75849145292
-
Expansion of the eukaryotic proteome by alternative splicing
-
Nilsen TW, Graveley BR. 2010. Expansion of the eukaryotic proteome by alternative splicing. Nature 463: 457-463.
-
(2010)
Nature
, vol.463
, pp. 457-463
-
-
Nilsen, T.W.1
Graveley, B.R.2
-
28
-
-
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. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 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
-
29
-
-
79955768436
-
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
-
Rabani M, Levin JZ, Fan L, Adiconis X, Raychowdhury R, Garber M, Gnirke A, Nusbaum C, Hacohen N, Friedman N, et al. 2011. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol 29: 436-442.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 436-442
-
-
Rabani, M.1
Levin, J.Z.2
Fan, L.3
Adiconis, X.4
Raychowdhury, R.5
Garber, M.6
Gnirke, A.7
Nusbaum, C.8
Hacohen, N.9
Friedman, N.10
-
30
-
-
40649106258
-
Non-coding RNAs in imprinted gene clusters
-
DOI 10.1042/BC20070126
-
Royo H, Cavaille J. 2008. Non-coding RNAs in imprinted gene clusters. Biol Cell 100: 149-166. (Pubitemid 351372674)
-
(2008)
Biology of the Cell
, vol.100
, Issue.3
, pp. 149-166
-
-
Royo, H.1
Cavaille, J.2
-
31
-
-
0035509699
-
The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A
-
Runte M, Huttenhofer A, Gross S, Kiefmann M, Horsthemke B, Buiting K. 2001. The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum Mol Genet 10: 2687-2700. (Pubitemid 33133410)
-
(2001)
Human Molecular Genetics
, vol.10
, Issue.23
, pp. 2687-2700
-
-
Runte, M.1
Huttenhofer, A.2
Gross, S.3
Kiefmann, M.4
Horsthemke, B.5
Buiting, K.6
-
32
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M. 2011. Global quantification of mammalian gene expression control. Nature 473: 337-342.
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwanhäusser, B.1
Busse, D.2
Li, N.3
Dittmar, G.4
Schuchhardt, J.5
Wolf, J.6
Chen, W.7
Selbach, M.8
-
33
-
-
53949098609
-
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
-
doi: 10.1038/msb.2008.59
-
Shalem O, Dahan O, Levo M, Martinez MR, Furman I, Segal E, Pilpel Y. 2008. Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol 4: 223. doi: 10.1038/msb.2008.59.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 223
-
-
Shalem, O.1
Dahan, O.2
Levo, M.3
Martinez, M.R.4
Furman, I.5
Segal, E.6
Pilpel, Y.7
-
34
-
-
79953288782
-
The C-terminal domain of RNA polymerase II is modified by site-specific methylation
-
Sims RJ III, Rojas LA, Beck D, Bonasio R, Schuller R, Drury WJ III, Eick D, Reinberg D. 2011. The C-terminal domain of RNA polymerase II is modified by site-specific methylation. Science 332: 99-103.
-
(2011)
Science
, vol.332
, pp. 99-103
-
-
Sims III, R.J.1
Rojas, L.A.2
Beck, D.3
Bonasio, R.4
Schuller, R.5
Drury III, W.J.6
Eick, D.7
Reinberg, D.8
-
36
-
-
0242497663
-
CLIP Identifies Nova-Regulated RNA Networks in the Brain
-
DOI 10.1126/science.1090095
-
Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB. 2003. CLIP identifies Nova-regulated RNA networks in the brain. Science 302: 1212-1215. (Pubitemid 37421026)
-
(2003)
Science
, vol.302
, Issue.5648
, pp. 1212-1215
-
-
Ule, J.1
Jensen, K.B.2
Ruggiu, M.3
Mele, A.4
Ule, A.5
Darnell, R.B.6
-
37
-
-
33749056769
-
An RNA map predicting Nova-dependent splicing regulation
-
DOI 10.1038/nature05304, PII NATURE05304
-
Ule J, Stefani G, Mele A, Ruggiu M, Wang X, Taneri B, Gaasterland T, Blencowe BJ, Darnell RB. 2006. An RNA map predicting Nova-dependent splicing regulation. Nature 444: 580-586. (Pubitemid 44864431)
-
(2006)
Nature
, vol.444
, Issue.7119
, pp. 580-586
-
-
Ule, J.1
Stefani, G.2
Mele, A.3
Ruggiu, M.4
Wang, X.5
Taneri, B.6
Gaasterland, T.7
Blencowe, B.J.8
Darnell, R.B.9
-
38
-
-
72449205602
-
Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays
-
Vitali P, Royo H, Marty V, Bortolin-Cavaille ML, Cavaille J. 2010. Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays. J Cell Sci 123: 70-83.
-
(2010)
J Cell Sci
, vol.123
, pp. 70-83
-
-
Vitali, P.1
Royo, H.2
Marty, V.3
Bortolin-Cavaille, M.L.4
Cavaille, J.5
-
39
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
DOI 10.1038/nature07509, PII NATURE07509
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476. (Pubitemid 352759009)
-
(2008)
Nature
, vol.456
, Issue.7221
, 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
-
40
-
-
77953262646
-
The phosphoproteome of toll-like receptor-activated macrophages
-
doi: 10.1038/msb.2010.29
-
Weintz G, Olsen JV, Frühauf K, Niedzielska M, Amit I, Jantsch J, Mages J, Frech C, Dölken L, Mann M, et al. 2010. The phosphoproteome of toll-like receptor-activated macrophages. Mol Syst Biol 6: 371. doi: 10.1038/msb.2010.29.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 371
-
-
Weintz, G.1
Olsen, J.V.2
Frühauf, K.3
Niedzielska, M.4
Amit, I.5
Jantsch, J.6
Mages, J.7
Frech, C.8
Dölken, L.9
Mann, M.10
-
41
-
-
2442441507
-
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
-
DOI 10.1089/1066527041410418
-
Yeo G, Burge CB. 2004. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11: 377-394. (Pubitemid 38901668)
-
(2004)
Journal of Computational Biology
, vol.11
, Issue.2-3
, pp. 377-394
-
-
Yeo, G.1
Burge, C.B.2
|