-
1
-
-
78651325932
-
LncRNAdb: A reference database for long noncoding RNAs
-
Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. 2011. lncRNAdb: A reference database for long noncoding RNAs. Nucleic Acids Res 39: D146-D151.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Amaral, P.P.1
Clark, M.B.2
Gascoigne, D.K.3
Dinger, M.E.4
Mattick, J.S.5
-
2
-
-
0037039159
-
Directed proteomic analysis of the human nucleolus
-
Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI. 2002. Directed proteomic analysis of the human nucleolus. Curr Biol 12: 1-11.
-
(2002)
Curr Biol
, vol.12
, pp. 1-11
-
-
Andersen, J.S.1
Lyon, C.E.2
Fox, A.H.3
Leung, A.K.4
Lam, Y.W.5
Steen, H.6
Mann, M.7
Lamond, A.I.8
-
3
-
-
79955005458
-
SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer
-
Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru K, Mercer TR, Thompson ER, Lakhani SR, et al. 2011. SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA 17: 878-891.
-
(2011)
RNA
, vol.17
, pp. 878-891
-
-
Askarian-Amiri, M.E.1
Crawford, J.2
French, J.D.3
Smart, C.E.4
Smith, M.A.5
Clark, M.B.6
Ru, K.7
Mercer, T.R.8
Thompson, E.R.9
Lakhani, S.R.10
-
4
-
-
0035162672
-
ARED: Human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins
-
Bakheet T, Frevel M, Williams BR, Greer W, Khabar KS. 2001. ARED: Human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins. Nucleic Acids Res 29: 246-254. (Pubitemid 32054460)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.1
, pp. 246-254
-
-
Bakheet, T.1
Frevel, M.2
Williams, B.R.G.3
Greer, W.4
Khabar, K.S.A.5
-
5
-
-
77956882723
-
A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression
-
Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z, Zhang MQ, Sedel F, Jourdren L, Coulpier F, et al. 2010. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J 29: 3082-3093.
-
(2010)
EMBO J
, vol.29
, pp. 3082-3093
-
-
Bernard, D.1
Prasanth, K.V.2
Tripathi, V.3
Colasse, S.4
Nakamura, T.5
Xuan, Z.6
Zhang, M.Q.7
Sedel, F.8
Jourdren, L.9
Coulpier, F.10
-
6
-
-
40349116304
-
A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae
-
DOI 10.1101/gad.458008
-
Berretta J, Pinskaya M, Morillon A. 2008. A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev 22: 615-626. (Pubitemid 351342434)
-
(2008)
Genes and Development
, vol.22
, Issue.5
, pp. 615-626
-
-
Berretta, J.1
Pinskaya, M.2
Morillon, A.3
-
7
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
Margulies, E.H.6
Weng, Z.7
Snyder, M.8
Dermitzakis, E.T.9
Thurman, R.E.10
-
8
-
-
0034053967
-
UV-induced stabilization of c-fos and other short-lived mRNAs
-
DOI 10.1128/MCB.20.10.3616-3625.2000
-
Blattner C, Kannouche P, Litfin M, Bender K, Rahmsdorf HJ, Angulo JF, Herrlich P. 2000. UV-Induced stabilization of c-fos and other short-lived mRNAs. Mol Cell Biol 20: 3616-3625. (Pubitemid 30243907)
-
(2000)
Molecular and Cellular Biology
, vol.20
, Issue.10
, pp. 3616-3625
-
-
Blattner, C.1
Kannouche, P.2
Litfin, M.3
Bender, K.4
Rahmsdorf, H.J.5
Angulo, J.F.6
Herrlich, P.7
-
9
-
-
69949132008
-
Paraspeckles: Nuclear bodies built on long noncoding RNA
-
Bond CS, Fox AH. 2009. Paraspeckles: Nuclear bodies built on long noncoding RNA. J Cell Biol 186: 637-644.
-
(2009)
J Cell Biol
, vol.186
, pp. 637-644
-
-
Bond, C.S.1
Fox, A.H.2
-
10
-
-
0031922811
-
Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding
-
Bortolin ML, Kiss T. 1998. Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding. RNA 4: 445-454. (Pubitemid 28160785)
-
(1998)
RNA
, vol.4
, Issue.4
, pp. 445-454
-
-
Bortolin, M.-L.1
Kiss, T.2
-
11
-
-
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. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 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
-
12
-
-
36048951040
-
Antisense RNA Stabilization Induces Transcriptional Gene Silencing via Histone Deacetylation in S. cerevisiae
-
DOI 10.1016/j.cell.2007.09.014, PII S0092867407012019
-
Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F. 2007. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 131: 706-717. (Pubitemid 350087198)
-
(2007)
Cell
, vol.131
, Issue.4
, pp. 706-717
-
-
Camblong, J.1
Iglesias, N.2
Fickentscher, C.3
Dieppois, G.4
Stutz, F.5
-
13
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
Maeda, N.6
Oyama, R.7
Ravasi, T.8
Lenhard, B.9
Wells, C.10
-
14
-
-
33751384465
-
GATHER: A systems approach to interpreting genomic signatures
-
DOI 10.1093/bioinformatics/btl483
-
Chang JT, Nevins JR. 2006. GATHER: A systems approach to interpreting genomic signatures. Bioinformatics 22: 2926-2933. (Pubitemid 44811565)
-
(2006)
Bioinformatics
, vol.22
, Issue.23
, pp. 2926-2933
-
-
Chang, J.T.1
Nevins, J.R.2
-
15
-
-
37349038984
-
Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome
-
DOI 10.1016/j.cell.2007.10.056, PII S0092867407014766
-
Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, et al. 2007. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131: 1340-1353. (Pubitemid 350297418)
-
(2007)
Cell
, vol.131
, Issue.7
, pp. 1340-1353
-
-
Chekanova, J.A.1
Gregory, B.D.2
Reverdatto, S.V.3
Chen, H.4
Kumar, R.5
Hooker, T.6
Yazaki, J.7
Li, P.8
Skiba, N.9
Peng, Q.10
Alonso, J.11
Brukhin, V.12
Grossniklaus, U.13
Ecker, J.R.14
Belostotsky, D.A.15
-
16
-
-
68949212914
-
Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: Functional role of a nuclear noncoding RNA
-
Chen LL, Carmichael GG. 2009. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: Functional role of a nuclear noncoding RNA. Mol Cell 35: 467-478.
-
(2009)
Mol Cell
, vol.35
, pp. 467-478
-
-
Chen, L.L.1
Carmichael, G.G.2
-
17
-
-
0001087931
-
Extreme instability of myc mRNA in normal and transformed human cells
-
DOI 10.1073/pnas.81.22.7046
-
Dani C, Blanchard JM, Piechaczyk M, El Sabouty S, Marty L, Jeanteur P. 1984. Extreme instability of myc mRNA in normal and transformed human cells. Proc Natl Acad Sci 81: 7046-7050. (Pubitemid 15216694)
-
(1984)
Proceedings of the National Academy of Sciences of the United States of America
, vol.81
, Issue.22 I
, pp. 7046-7050
-
-
Dani, C..1
Blanchard, J.M.2
Piechaczyk, M.3
-
18
-
-
3142756502
-
Open source clustering software
-
DOI 10.1093/bioinformatics/bth078
-
de Hoon MJ, Imoto S, Nolan J, Miyano S. 2004. Open source clustering software. Bioinformatics 20: 1453-1454. (Pubitemid 38931415)
-
(2004)
Bioinformatics
, vol.20
, Issue.9
, pp. 1453-1454
-
-
De Hoon, M.J.L.1
Imoto, S.2
Nolan, J.3
Miyano, S.4
-
19
-
-
50649118350
-
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
-
Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian- Amiri ME, Ru K, Solda G, Simons C, et al. 2008. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18: 1433-1445.
-
(2008)
Genome Res
, vol.18
, pp. 1433-1445
-
-
Dinger, M.E.1
Amaral, P.P.2
Mercer, T.R.3
Pang, K.C.4
Bruce, S.J.5
Gardiner, B.B.6
Askarian- Amiri, M.E.7
Ru, K.8
Solda, G.9
Simons, C.10
-
20
-
-
70449707787
-
Pervasive transcription of the eukaryotic genome: Functional indices and conceptual implications
-
Dinger ME, Amaral PP, Mercer TR, Mattick JS. 2009a. Pervasive transcription of the eukaryotic genome: Functional indices and conceptual implications. Brief Funct Genomics Proteomics 8: 407-423.
-
(2009)
Brief Funct Genomics Proteomics
, vol.8
, pp. 407-423
-
-
Dinger, M.E.1
Amaral, P.P.2
Mercer, T.R.3
Mattick, J.S.4
-
21
-
-
58149177177
-
NRED: A database of long noncoding RNA expression
-
Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS. 2009b. NRED: A database of long noncoding RNA expression. Nucleic Acids Res 37: D122-D126.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Dinger, M.E.1
Pang, K.C.2
Mercer, T.R.3
Crowe, M.L.4
Grimmond, S.M.5
Mattick, J.S.6
-
22
-
-
50649118115
-
High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay
-
Dolken L, Ruzsics Z, Radle 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
-
-
Dolken, L.1
Ruzsics, Z.2
Radle, B.3
Friedel, C.C.4
Zimmer, R.5
Mages, J.6
Hoffmann, R.7
Dickinson, P.8
Forster, T.9
Ghazal, P.10
-
23
-
-
77951083459
-
Major role for mRNA stability in shaping the kinetics of gene induction
-
doi: 10.1186/1471-2164-11-259
-
Elkon R, Zlotorynski E, Zeller KI, Agami R. 2010. Major role for mRNA stability in shaping the kinetics of gene induction. BMC Genomics 11: 259. doi: 10.1186/1471-2164-11-259.
-
(2010)
BMC Genomics
, vol.11
, pp. 259
-
-
Elkon, R.1
Zlotorynski, E.2
Zeller, K.I.3
Agami, R.4
-
24
-
-
33646473694
-
Complex loci in human and mouse genomes
-
doi: 10.1371/journal.pgen.0020047
-
Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, et al. 2006. Complex loci in human and mouse genomes. PLoS Genet 2: e47. doi: 10.1371/journal.pgen.0020047.
-
(2006)
PLoS Genet
, vol.2
-
-
Engstrom, P.G.1
Suzuki, H.2
Ninomiya, N.3
Akalin, A.4
Sessa, L.5
Lavorgna, G.6
Brozzi, A.7
Luzi, L.8
Tan, S.L.9
Yang, L.10
-
25
-
-
73049097101
-
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
-
doi: 10.1093/nar/gkp542
-
Friedel CC, Dolken 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
Dolken, L.2
Ruzsics, Z.3
Koszinowski, U.H.4
Zimmer, R.5
-
26
-
-
78651320424
-
The UCSC Genome Browser database: Update 2011
-
Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, et al. 2011. The UCSC Genome Browser database: Update 2011. Nucleic Acids Res 39: D876-D882.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Fujita, P.A.1
Rhead, B.2
Zweig, A.S.3
Hinrichs, A.S.4
Karolchik, D.5
Cline, M.S.6
Goldman, M.7
Barber, G.P.8
Clawson, H.9
Coelho, A.10
-
27
-
-
0030762226
-
A transcript map for the 2.8-Mb region containing the multiple endocrine neoplasia type 1 locus
-
Guru SC, Agarwal SK, Manickam P, Olufemi SE, Crabtree JS, Weisemann JM, Kester MB, Kim YS, Wang Y, Emmert-Buck MR, et al. 1997. A transcript map for the 2.8-Mb region containing the multiple endocrine neoplasia type 1 locus. Genome Res 7: 725-735. (Pubitemid 27373024)
-
(1997)
Genome Research
, vol.7
, Issue.7
, pp. 725-735
-
-
Guru, S.C.1
Agarwal, S.K.2
Manickam, P.3
Olufemi, S.-E.4
Crabtree, J.S.5
Weisemann, J.M.6
Kester, M.B.7
Kim, Y.S.8
Wang, Y.9
Emmert-Buck, M.R.10
Liotta, L.A.11
Spiegel, A.M.12
Boguski, M.S.13
Roe, B.A.14
Collins, F.S.15
Marx, S.J.16
Burns, L.17
Chandrasekharappa, S.C.18
-
28
-
-
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, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 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
-
29
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multiexonic structure of lincRNAs
-
GuttmanM, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, et al. 2010. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multiexonic structure of lincRNAs. Nat Biotechnol 28: 503-510.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 503-510
-
-
Guttman, M.1
Garber, M.2
Levin, J.Z.3
Donaghey, J.4
Robinson, J.5
Adiconis, X.6
Fan, L.7
Koziol, M.J.8
Gnirke, A.9
Nusbaum, C.10
-
30
-
-
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, et al. 2011. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 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
-
31
-
-
80455143733
-
miRNA-dependent gene silencing involving Ago2- mediated cleavage of a circular antisense RNA
-
Hansen TB, Wiklund ED, Bramsen JB, Villadsen SB, Statham AL, Clark SJ, Kjems J. 2011. miRNA-dependent gene silencing involving Ago2- mediated cleavage of a circular antisense RNA. EMBO J 30: 4414-4422.
-
(2011)
EMBO J
, vol.30
, pp. 4414-4422
-
-
Hansen, T.B.1
Wiklund, E.D.2
Bramsen, J.B.3
Villadsen, S.B.4
Statham, A.L.5
Clark, S.J.6
Kjems, J.7
-
32
-
-
60149090021
-
The many pathways of RNA degradation
-
Houseley J, Tollervey D. 2009. The many pathways of RNA degradation. Cell 136: 763-776.
-
(2009)
Cell
, vol.136
, pp. 763-776
-
-
Houseley, J.1
Tollervey, D.2
-
33
-
-
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, et al. 2010. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 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
-
34
-
-
0011731390
-
The role of deoxyribonucleic acid in ribonucleic acid synthesis. III. The inhibition of the enzymatic synthesis of ribonucleic acid and deoxyribonucleic acid by actinomycin D and proflavin
-
Hurwitz J, Furth JJ, Malamy M, Alexander M. 1962. The role of deoxyribonucleic acid in ribonucleic acid synthesis. III. The inhibition of the enzymatic synthesis of ribonucleic acid and deoxyribonucleic acid by actinomycin D and proflavin. Proc Natl Acad Sci 48: 1222-1230.
-
(1962)
Proc Natl Acad Sci
, vol.48
, pp. 1222-1230
-
-
Hurwitz, J.1
Furth, J.J.2
Malamy, M.3
Alexander, M.4
-
35
-
-
79251570254
-
QAPgrid: A two level QAP-based approach for large-scale data analysis and visualization
-
doi: 10.1371/journal.pone.0014468
-
Inostroza-Ponta M, Berretta R, Moscato P. 2011. QAPgrid: A two level QAP-based approach for large-scale data analysis and visualization. PLoS ONE 6: e14468. doi: 10.1371/journal.pone.0014468.
-
(2011)
PLoS ONE
, vol.6
-
-
Inostroza-Ponta, M.1
Berretta, R.2
Moscato, P.3
-
36
-
-
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, et al. 2009. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci 106: 11667-11672.
-
(2009)
Proc Natl Acad Sci
, 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
-
37
-
-
60549106018
-
Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis
-
Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, Morosawa T, Tanaka M, Kaminuma E, Mochizuki Y, Matsushima A, et al. 2009. Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc Natl Acad Sci 106: 2453-2458.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 2453-2458
-
-
Kurihara, Y.1
Matsui, A.2
Hanada, K.3
Kawashima, M.4
Ishida, J.5
Morosawa, T.6
Tanaka, M.7
Kaminuma, E.8
Mochizuki, Y.9
Matsushima, A.10
-
38
-
-
79959446962
-
PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions
-
Lin MF, Jungreis I, Kellis M. 2011. PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 27: i275-i282.
-
(2011)
Bioinformatics
, vol.27
-
-
Lin, M.F.1
Jungreis, I.2
Kellis, M.3
-
39
-
-
78650511795
-
Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs
-
Mao YS, Sunwoo H, Zhang B, Spector DL. 2011. Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol 13: 95-101.
-
(2011)
Nat Cell Biol
, vol.13
, pp. 95-101
-
-
Mao, Y.S.1
Sunwoo, H.2
Zhang, B.3
Spector, D.L.4
-
40
-
-
77955326776
-
The pioneer round of translation: Features and functions
-
Maquat LE, Tarn WY, Isken O. 2010. The pioneer round of translation: Features and functions. Cell 142: 368-374.
-
(2010)
Cell
, vol.142
, pp. 368-374
-
-
Maquat, L.E.1
Tarn, W.Y.2
Isken, O.3
-
41
-
-
77954339096
-
Babelomics: An integrative platform for the analysis of transcriptomics, proteomics, and genomic data with advanced functional profiling
-
Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tarraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, et al. 2010. Babelomics: An integrative platform for the analysis of transcriptomics, proteomics, and genomic data with advanced functional profiling. Nucleic Acids Res 38: W210-W213.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Medina, I.1
Carbonell, J.2
Pulido, L.3
Madeira, S.C.4
Goetz, S.5
Conesa, A.6
Tarraga, J.7
Pascual-Montano, A.8
Nogales-Cadenas, R.9
Santoyo, J.10
-
43
-
-
79953673245
-
Expression of distinct RNAs from 3′ untranslated regions
-
Mercer TR, Wilhelm D, Dinger ME, Solda G, Korbie DJ, Glazov EA, Truong V, Schwenke M, Simons C, Matthaei KI, et al. 2011. Expression of distinct RNAs from 3′ untranslated regions. Nucleic Acids Res 39: 2393-2403.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 2393-2403
-
-
Mercer, T.R.1
Wilhelm, D.2
Dinger, M.E.3
Solda, G.4
Korbie, D.J.5
Glazov, E.A.6
Truong, V.7
Schwenke, M.8
Simons, C.9
Matthaei, K.I.10
-
44
-
-
34247863985
-
Beyond the 3′ end: Experimental validation of extended transcript isoforms
-
DOI 10.1093/nar/gkm062
-
Moucadel V, Lopez F, Ara T, Benech P, Gautheret D. 2007. Beyond the 3′ end: Experimental validation of extended transcript isoforms. Nucleic Acids Res 35: 1947-1957. (Pubitemid 47061661)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.6
, pp. 1947-1957
-
-
Moucadel, V.1
Lopez, F.2
Ara, T.3
Benech, P.4
Gautheret, D.5
-
45
-
-
79955506825
-
Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice
-
Nakagawa S, Naganuma T, Shioi G, Hirose T. 2011. Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J Cell Biol 193: 31-39.
-
(2011)
J Cell Biol
, vol.193
, pp. 31-39
-
-
Nakagawa, S.1
Naganuma, T.2
Shioi, G.3
Hirose, T.4
-
46
-
-
37849034683
-
Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana
-
Narsai R, Howell KA, Millar AH, O'Toole N, Small I, Whelan J. 2007. Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. Plant Cell 19: 3418-3436.
-
(2007)
Plant Cell
, vol.19
, pp. 3418-3436
-
-
Narsai, R.1
Howell, K.A.2
Millar, A.H.3
O'Toole, N.4
Small, I.5
Whelan, J.6
-
47
-
-
57849123049
-
RNA exosome depletion reveals transcription upstream of active human promoters
-
Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH. 2008. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322: 1851-1854.
-
(2008)
Science
, vol.322
, pp. 1851-1854
-
-
Preker, P.1
Nielsen, J.2
Kammler, S.3
Lykke-Andersen, S.4
Christensen, M.S.5
Mapendano, C.K.6
Schierup, M.H.7
Jensen, T.H.8
-
48
-
-
58149178579
-
NCBI Reference Sequences: Current status, policy, and new initiatives
-
Pruitt KD, Tatusova T, Klimke W, Maglott DR. 2009. NCBI Reference Sequences: Current status, policy, and new initiatives. Nucleic Acids Res 37: D32-D36.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Pruitt, K.D.1
Tatusova, T.2
Klimke, W.3
Maglott, D.R.4
-
49
-
-
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
-
50
-
-
0037115826
-
Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes
-
DOI 10.1093/nar/gkf682
-
Raghavan A, Ogilvie RL, Reilly C, Abelson ML, Raghavan S, Vasdewani J, Krathwohl M, Bohjanen PR. 2002. Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res 30: 5529-5538. (Pubitemid 36113930)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.24
, pp. 5529-5538
-
-
Raghavan, A.1
Ogilvie, R.L.2
Reilly, C.3
Abelson, M.L.4
Raghavan, S.5
Vasdewani, J.6
Krathwohl, M.7
Bohjanen, P.R.8
-
51
-
-
79959923522
-
g:Profiler - A web server for functional interpretation of gene lists (2011 update)
-
Reimand J, Arak T, Vilo J. 2011. g:Profiler - a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res 39: W307-W315.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Reimand, J.1
Arak, T.2
Vilo, J.3
-
52
-
-
35748949257
-
A comparison of background correction methods for two-colour microarrays
-
DOI 10.1093/bioinformatics/btm412
-
Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK. 2007. A comparison of background correction methods for twocolour microarrays. Bioinformatics 23: 2700-2707. (Pubitemid 350048334)
-
(2007)
Bioinformatics
, vol.23
, Issue.20
, pp. 2700-2707
-
-
Ritchie, M.E.1
Silver, J.2
Oshlack, A.3
Holmes, M.4
Diyagama, D.5
Holloway, A.6
Smyth, G.K.7
-
53
-
-
9444225935
-
Java Treeview - Extensible visualization of microarray data
-
DOI 10.1093/bioinformatics/bth349
-
Saldanha AJ. 2004. Java Treeview - extensible visualization of microarray data. Bioinformatics 20: 3246-3248. (Pubitemid 39619217)
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 3246-3248
-
-
Saldanha, A.J.1
-
54
-
-
62449319486
-
MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles
-
Sasaki YT, Ideue T, Sano M, Mituyama T, Hirose T. 2009. MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci 106: 2525-2530.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 2525-2530
-
-
Sasaki, Y.T.1
Ideue, T.2
Sano, M.3
Mituyama, T.4
Hirose, T.5
-
55
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwanhausser 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
-
-
Schwanhausser, B.1
Busse, D.2
Li, N.3
Dittmar, G.4
Schuchhardt, J.5
Wolf, J.6
Chen, W.7
Selbach, M.8
-
56
-
-
33747603960
-
The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export
-
DOI 10.1038/sj.emboj.7601245, PII 7601245
-
Seidl CI, Stricker SH, Barlow DP. 2006. The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. EMBO J 25: 3565-3575. (Pubitemid 44264867)
-
(2006)
EMBO Journal
, vol.25
, Issue.15
, pp. 3565-3575
-
-
Seidl, C.I.M.1
Stricker, S.H.2
Barlow, D.P.3
-
57
-
-
65249141709
-
Database for mRNA half-life of 19,977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells
-
Sharova LV, Sharov AA, Nedorezov T, Piao Y, Shaik N, Ko MS. 2009. Database for mRNA half-life of 19,977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res 16: 45-58.
-
(2009)
DNA Res
, vol.16
, pp. 45-58
-
-
Sharova, L.V.1
Sharov, A.A.2
Nedorezov, T.3
Piao, Y.4
Shaik, N.5
Ko, M.S.6
-
58
-
-
18844472627
-
Stabilization of Xist RNA mediates initiation of X chromosome inactivation
-
DOI 10.1016/S0092-8674(01)80012-X
-
Sheardown SA, Duthie SM, Johnston CM, Newall AE, Formstone EJ, Arkell RM, Nesterova TB, Alghisi GC, Rastan S, Brockdorff N. 1997. Stabilization of Xist RNA mediates initiation of X chromosome inactivation. Cell 91: 99-107. (Pubitemid 27431316)
-
(1997)
Cell
, vol.91
, Issue.1
, pp. 99-107
-
-
Sheardown, S.A.1
Duthie, S.M.2
Johnston, C.M.3
Newall, A.E.T.4
Formstone, E.J.5
Arkell, R.M.6
Nesterova, T.B.7
Alghisi, G.-C.8
Rastan, S.9
Brockdorff, N.10
-
59
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
-
Smyth GK. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: 1-25.
-
(2004)
Stat Appl Genet Mol Biol
, vol.3
, pp. 1-25
-
-
Smyth, G.K.1
-
60
-
-
0242333835
-
Normalization of cDNA microarray data
-
DOI 10.1016/S1046-2023(03)00155-5
-
Smyth GK, Speed T. 2003. Normalization of cDNA microarray data. Methods 31: 265-273. (Pubitemid 37338763)
-
(2003)
Methods
, vol.31
, Issue.4
, pp. 265-273
-
-
Smyth, G.K.1
Speed, T.2
-
61
-
-
34548291568
-
The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons
-
DOI 10.1242/jcs.009357
-
Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S. 2007. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 120: 2498-2506. (Pubitemid 47323859)
-
(2007)
Journal of Cell Science
, vol.120
, Issue.15
, pp. 2498-2506
-
-
Sone, M.1
Hayashi, T.2
Tarui, H.3
Agata, K.4
Takeichi, M.5
Nakagawa, S.6
-
62
-
-
78649637489
-
Highly ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies
-
Souquere S, Beauclair G, Harper F, Fox A, Pierron G. 2010. Highly ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies. Mol Biol Cell 21: 4020-4027.
-
(2010)
Mol Biol Cell
, vol.21
, pp. 4020-4027
-
-
Souquere, S.1
Beauclair, G.2
Harper, F.3
Fox, A.4
Pierron, G.5
-
63
-
-
61849113891
-
MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles
-
Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL. 2009. MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19: 347-359.
-
(2009)
Genome Res
, vol.19
, pp. 347-359
-
-
Sunwoo, H.1
Dinger, M.E.2
Wilusz, J.E.3
Amaral, P.P.4
Mattick, J.S.5
Spector, D.L.6
-
64
-
-
77956927823
-
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation
-
Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q,Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, et al. 2010. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39: 925-938.
-
(2010)
Mol Cell
, vol.39
, pp. 925-938
-
-
Tripathi, V.1
Ellis, J.D.2
Shen, Z.3
Song, D.Y.4
Pan, Q.5
Watt, A.T.6
Freier, S.M.7
Bennett, C.F.8
Sharma, A.9
Bubulya, P.A.10
-
65
-
-
0030033546
-
A mammalian gene with introns instead of exons generating stable RNA products
-
DOI 10.1038/379464a0
-
Tycowski KT, Shu MD, Steitz JA. 1996. A mammalian gene with introns instead of exons generating stable RNA products. Nature 379: 464-466. (Pubitemid 26039529)
-
(1996)
Nature
, vol.379
, Issue.6564
, pp. 464-466
-
-
Tycowski, K.T.1
Shu, M.-D.2
Steitz, J.A.3
-
66
-
-
79960065233
-
XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast
-
van Dijk EL, Chen CL, d'Aubenton-Carafa Y, Gourvennec S, Kwapisz M, Roche V, Bertrand C, Silvain M, Legoix-Ne P, Loeillet S, et al. 2011. XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature 475: 114-117.
-
(2011)
Nature
, vol.475
, pp. 114-117
-
-
Van Dijk, E.L.1
Chen, C.L.2
D'Aubenton-Carafa, Y.3
Gourvennec, S.4
Kwapisz, M.5
Roche, V.6
Bertrand, C.7
Silvain, M.8
Legoix-Ne, P.9
Loeillet, S.10
-
67
-
-
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, et al. 2011. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 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
-
68
-
-
20444368036
-
Cryptic Pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase
-
DOI 10.1016/j.cell.2005.04.030, PII S0092867405004435
-
Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Regnault B, Devaux F, Namane A, Seraphin B, et al. 2005. Cryptic Pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121: 725-737. (Pubitemid 40797595)
-
(2005)
Cell
, vol.121
, Issue.5
, pp. 725-737
-
-
Wyers, F.1
Rougemaille, M.2
Badis, G.3
Rousselle, J.-C.4
Dufour, M.-E.5
Boulay, J.6
Regnault, B.7
Devaux, F.8
Namane, A.9
Seraphin, B.10
Libri, D.11
Jacquier, A.12
-
69
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 39 UTRs by comparison of several mammals
-
DOI 10.1038/nature03441
-
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. 2005. Systematic discovery of regulatory motifs in human promoters and 39 UTRs by comparison of several mammals. Nature 434: 338-345. (Pubitemid 40469170)
-
(2005)
Nature
, vol.434
, Issue.7031
, pp. 338-345
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
Golub, T.R.4
Mootha, V.5
Lindblad-Toh, K.6
Lander, E.S.7
Kellis, M.8
-
70
-
-
0041523923
-
Decay rates of human mRNAs: Correlation with functional characteristics and sequence attributes
-
Yang E, van Nimwegen E, Zavolan M, Rajewsky N, Schroeder M, Magnasco M, Darnell JE Jr. 2003. Decay rates of human mRNAs: Correlation with functional characteristics and sequence attributes. Genome Res 13: 1863-1872. (Pubitemid 36987192)
-
(2003)
Genome Research
, vol.13
, Issue.8
, pp. 1863-1872
-
-
Yang, E.1
Van Nimwegen, E.2
Zavolan, M.3
Rajewsky, N.4
Schroeder, M.5
Magnasco, M.6
Darnell Jr., J.E.7
-
71
-
-
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. 2010. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 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
|