-
1
-
-
34250305146
-
Identification and analysis of functional elements in % of the human genome by the encode pilot project
-
ENCODE Project Consortium
-
ENCODE Project Consortium, Birney, E., Stamatoyannopoulos, J.A., Dutta, A., Guigó, R., Gingeras, T.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T. et al. (2007) Identification and analysis of functional elements in % 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
Guigó, R.4
Gingeras, T.R.5
Margulies, E.H.6
Weng, Z.7
Snyder, M.8
Dermitzakis, E.T.9
-
2
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A.S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S. et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15, 1034-1050.
-
(2005)
Genome Res.
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
-
3
-
-
34250365369
-
Analyses of deep mammalian sequence alignments and constraint predictions for % of the human genome
-
Margulies, E.H., Cooper, G.M., Asimenos, G., Thomas, D.J., Dewey, C.N., Siepel, A., Birney, E., Keefe, D., Schwartz, A.S., Hou, M. et al. (2007) Analyses of deep mammalian sequence alignments and constraint predictions for % of the human genome. Genome Res., 17, 760-774.
-
(2007)
Genome Res.
, vol.17
, pp. 760-774
-
-
Margulies, E.H.1
Cooper, G.M.2
Asimenos, G.3
Thomas, D.J.4
Dewey, C.N.5
Siepel, A.6
Birney, E.7
Keefe, D.8
Schwartz, A.S.9
Hou, M.10
-
4
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio, L.A., Ahituv, N., Moses, A.M., Prabhakar, S., Nobrega, M.A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K.D. et al. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature, 444, 499-502.
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
Ahituv, N.2
Moses, A.M.3
Prabhakar, S.4
Nobrega, M.A.5
Shoukry, M.6
Minovitsky, S.7
Dubchak, I.8
Holt, A.9
Lewis, K.D.10
-
5
-
-
65549104157
-
Histone modifications at human enhancers reflect global cell-type-specific gene expression
-
Heintzman, N.D., Hon, G.C., Hawkins, R.D., Kheradpour, P., Stark, A., Harp, L.F., Ye, Z., Lee, L.K., Stuart, R.K., Ching, C.W. et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature, 459, 108-112.
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
Hon, G.C.2
Hawkins, R.D.3
Kheradpour, P.4
Stark, A.5
Harp, L.F.6
Ye, Z.7
Lee, L.K.8
Stuart, R.K.9
Ching, C.W.10
-
6
-
-
60149091656
-
Chip-seq accurately predicts tissue-specific activity of enhancers
-
Visel, A., Blow, M.J., Li, Z., Zhang, T., Akiyama, J.A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F. et al. (2009) Chip-seq accurately predicts tissue-specific activity of enhancers. Nature, 457, 854-858.
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
Blow, M.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
Holt, A.6
Plajzer-Frick, I.7
Shoukry, M.8
Wright, C.9
Chen, F.10
-
7
-
-
79959198166
-
Reprogramming transcription by distinct classes of enhancers functionally defined by erna
-
Wang, D., Garcia-Bassets, I., Benner, C., Li, W., Su, X., Zhou, Y., Qiu, J., Liu, W., Kaikkonen, M.U., Ohgi, K.A. et al. (2011) Reprogramming transcription by distinct classes of enhancers functionally defined by erna. Nature, 474, 390-394.
-
(2011)
Nature
, vol.474
, pp. 390-394
-
-
Wang, D.1
Garcia-Bassets, I.2
Benner, C.3
Li, W.4
Su, X.5
Zhou, Y.6
Qiu, J.7
Liu, W.8
Kaikkonen, M.U.9
Ohgi, K.A.10
-
8
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman, N.D., Stuart, R.K., Hon, G., Fu, Y., Ching, C.W., Hawkins, R.D., Barrera, L.O., Van Calcar, S., Qu, C., Ching, K.A. et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet., 39, 311-318.
-
(2007)
Nat. Genet.
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.4
Ching, C.W.5
Hawkins, R.D.6
Barrera, L.O.7
Van Calcar, S.8
Qu, C.9
Ching, K.A.10
-
9
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., 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
-
10
-
-
34248162440
-
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
-
Ponjavic, J., Ponting, C.P. and Lunter, G. (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res., 17, 556-565.
-
(2007)
Genome Res.
, vol.17
, pp. 556-565
-
-
Ponjavic, J.1
Ponting, C.P.2
Lunter, G.3
-
11
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman, M., Amit, I., Garber, M., French, C., Lin, M., Feldser, D., Huarte, M., Zuk, O., Carey, B., Cassady, J. 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.5
Feldser, D.6
Huarte, M.7
Zuk, O.8
Carey, B.9
Cassady, J.10
-
12
-
-
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, M.J., Kenzelmann-Broz, D., Khalil, A.M., 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
-
13
-
-
77951118936
-
Long non-coding RNA hotair reprograms chromatin state to promote cancer metastasis
-
Gupta, R.A., Shah, N., Wang, K.C., Kim, J., Horlings, H.M., Wong, D.J., Tsai, M.-C., Hung, T., Argani, P., Rinn, J.L. et al. (2010) Long non-coding RNA hotair reprograms chromatin state to promote cancer metastasis. Nature, 464, 1071-1076.
-
(2010)
Nature
, vol.464
, pp. 1071-1076
-
-
Gupta, R.A.1
Shah, N.2
Wang, K.C.3
Kim, J.4
Horlings, H.M.5
Wong, D.J.6
Tsai, M.-C.7
Hung, T.8
Argani, P.9
Rinn, J.L.10
-
14
-
-
79953748673
-
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
-
Wang, K.C., Yang, Y.W., Liu, B., Sanyal, A., Corces-Zimmerman, R., Chen, Y., Lajoie, B.R., Protacio, A., Flynn, R.A., Gupta, R.A. et al. (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature.
-
(2011)
Nature
-
-
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
-
15
-
-
77957243921
-
Long noncoding RNAs with enhancer-like function in human cells
-
Andersson Ørom, U., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q. et al. (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell, 143, 46-58.
-
(2010)
Cell
, vol.143
, pp. 46-58
-
-
Anderssonørom, U.1
Derrien, T.2
Beringer, M.3
Gumireddy, K.4
Gardini, A.5
Bussotti, G.6
Lai, F.7
Zytnicki, M.8
Notredame, C.9
Huang, Q.10
-
16
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman, M., Garber, M., Levin, J.Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M.J., Gnirke, A., Nusbaum, C. et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotech., 28, 503-510.
-
(2010)
Nat. Biotech.
, 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
-
17
-
-
0036978961
-
Definition of transcriptional promoters in the human beta globin locus control region
-
Routledge, S.J.E. and Proudfoot, N.J. (2002) Definition of transcriptional promoters in the human beta globin locus control region. J. Mol. Biol., 323, 601-611.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 601-611
-
-
Routledge, S.J.E.1
Proudfoot, N.J.2
-
18
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim, T.-K., Hemberg, M., Gray, J.M., Costa, A.M., Bear, D.M., Wu, J., Harmin, D.A., Laptewicz, M., Barbara-Haley, K., Kuersten, S. et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature, 465, 182-187.
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.-K.1
Hemberg, M.2
Gray, J.M.3
Costa, A.M.4
Bear, D.M.5
Wu, J.6
Harmin, D.A.7
Laptewicz, M.8
Barbara-Haley, K.9
Kuersten, S.10
-
19
-
-
77952908743
-
A large fraction of extragenic RNA pol II transcription sites overlap enhancers
-
De Santa, F., Barozzi, I., Mietton, F., Ghisletti, S., Polletti, S., Tusi, B.K., Muller, H., Ragoussis, J., Wei, C.-L. and Natoli, G. (2010) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol., 8, e1000384.
-
(2010)
PLoS Biol.
, vol.8
-
-
De Santa, F.1
Barozzi, I.2
Mietton, F.3
Ghisletti, S.4
Polletti, S.5
Tusi, B.K.6
Muller, H.7
Ragoussis, J.8
Wei, C.-L.9
Natoli, G.10
-
20
-
-
79955836460
-
A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells
-
Hah, N., Danko, C.G., Core, L., Waterfall, J.J., Siepel, A., Lis, J.T. and Kraus, W.L. (2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell, 145, 622-634.
-
(2011)
Cell
, vol.145
, pp. 622-634
-
-
Hah, N.1
Danko, C.G.2
Core, L.3
Waterfall, J.J.4
Siepel, A.5
Lis, J.T.6
Kraus, W.L.7
-
21
-
-
0032479079
-
Going the distance: A current view of enhancer action
-
Blackwood, E.M. and Kadonaga, J.T. (1998) Going the distance: a current view of enhancer action. Science, 281, 60-63.
-
(1998)
Science
, vol.281
, pp. 60-63
-
-
Blackwood, E.M.1
Kadonaga, J.T.2
-
22
-
-
33645887244
-
Chromatin looping and the probability of transcription
-
Li, Q., Barkess, G. and Qian, H. (2006) Chromatin looping and the probability of transcription. Trends Genet., 22, 197-202.
-
(2006)
Trends Genet.
, vol.22
, pp. 197-202
-
-
Li, Q.1
Barkess, G.2
Qian, H.3
-
23
-
-
29444448047
-
On a chromosome far, far away: LCRs and gene expression
-
Dean, A. (2006) On a chromosome far, far away: LCRs and gene expression. Trends Genet., 22, 38-45.
-
(2006)
Trends Genet.
, vol.22
, pp. 38-45
-
-
Dean, A.1
-
24
-
-
63849308888
-
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
-
Hesselberth, J.R., Chen, X., Zhang, Z., Sabo, P.J., Sandstrom, R., Reynolds, A.P., Thurman, R.E., Neph, S., Kuehn, M.S., Noble, W.S. et al. (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat. Methods, 6, 283-289.
-
(2009)
Nat. Methods
, vol.6
, pp. 283-289
-
-
Hesselberth, J.R.1
Chen, X.2
Zhang, Z.3
Sabo, P.J.4
Sandstrom, R.5
Reynolds, A.P.6
Thurman, R.E.7
Neph, S.8
Kuehn, M.S.9
Noble, W.S.10
-
25
-
-
33744783407
-
Histone modification patterns associated with the human X chromosome
-
Brinkman, A.B., Roelofsen, T., Pennings, S.W.C., Martens, J.H.A., Jenuwein, T. and Stunnenberg, H.G. (2006) Histone modification patterns associated with the human X chromosome. EMBO Rep., 7, 628-634.
-
(2006)
EMBO Rep.
, vol.7
, pp. 628-634
-
-
Brinkman, A.B.1
Roelofsen, T.2
Pennings, S.W.C.3
Martens, J.H.A.4
Jenuwein, T.5
Stunnenberg, H.G.6
-
26
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I. and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.-Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
27
-
-
57149096220
-
Genome-wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding
-
Robertson, A.G., Bilenky, M., Tam, A., Zhao, Y., Zeng, T., Thiessen, N., Cezard, T., Fejes, A.P., Wederell, E.D., Cullum, R. et al. (2008) Genome-wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding. Genome Res., 18, 1906-1917.
-
(2008)
Genome Res.
, vol.18
, pp. 1906-1917
-
-
Robertson, A.G.1
Bilenky, M.2
Tam, A.3
Zhao, Y.4
Zeng, T.5
Thiessen, N.6
Cezard, T.7
Fejes, A.P.8
Wederell, E.D.9
Cullum, R.10
-
28
-
-
77952905505
-
Most ''dark matter'' transcripts are associated with known genes
-
van Bakel, H., Nislow, C., Blencowe, B.J. and Hughes, T.R. (2010) Most ''dark matter'' transcripts are associated with known genes. PLoS Biol., 8, e1000371.
-
(2010)
PLoS Biol.
, vol.8
-
-
Van Bakel, H.1
Nislow, C.2
Blencowe, B.J.3
Hughes, T.R.4
-
29
-
-
57849140661
-
Divergent transcription from active promoters
-
Seila, A.C., Calabrese, J.M., Levine, S.S., Yeo, G.W., Rahl, P.B., Flynn, R.A., Young, R.A. and Sharp, P.A. (2008) Divergent transcription from active promoters. Science, 322, 1849-1851.
-
(2008)
Science
, vol.322
, pp. 1849-1851
-
-
Seila, A.C.1
Calabrese, J.M.2
Levine, S.S.3
Yeo, G.W.4
Rahl, P.B.5
Flynn, R.A.6
Young, R.A.7
Sharp, P.A.8
-
30
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
Core, L.J., Waterfall, J.J. and Lis, J.T. (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 322, 1845-1848.
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
31
-
-
62549126083
-
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing
-
Yassour, M., Kaplan, T., Fraser, H.B., Levin, J.Z., Pfiffner, J., Adiconis, X., Schroth, G., Luo, S., Khrebtukova, I., Gnirke, A. et al. (2009) Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc. Natl Acad. Sci. USA, 106, 3264-3269.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 3264-3269
-
-
Yassour, M.1
Kaplan, T.2
Fraser, H.B.3
Levin, J.Z.4
Pfiffner, J.5
Adiconis, X.6
Schroth, G.7
Luo, S.8
Khrebtukova, I.9
Gnirke, A.10
-
32
-
-
77952123055
-
Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J. and Pachter, L. (2010) Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotech., 28, 511-515.
-
(2010)
Nat. Biotech.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
33
-
-
50949090496
-
Poly A-Transcripts expressed in hela cells
-
Wu, Q., Kim, Y.C., Lu, J., Xuan, Z., Chen, J., Zheng, Y., Zhou, T., Zhang, M.Q., Wu, C.-I. and Wang, S.M. (2008) Poly A-Transcripts expressed in hela cells. PLoS One, 3, e2803.
-
(2008)
PLoS One
, vol.3
-
-
Wu, Q.1
Kim, Y.C.2
Lu, J.3
Xuan, Z.4
Chen, J.5
Zheng, Y.6
Zhou, T.7
Zhang, M.Q.8
Wu, C.-I.9
Wang, S.M.10
-
34
-
-
57849105533
-
The antisense transcriptomes of human cells
-
He, Y., Vogelstein, B., Velculescu, V.E., Papadopoulos, N. and Kinzler, K.W. (2008) The antisense transcriptomes of human cells. Science, 322, 1855-1857.
-
(2008)
Science
, vol.322
, pp. 1855-1857
-
-
He, Y.1
Vogelstein, B.2
Velculescu, V.E.3
Papadopoulos, N.4
Kinzler, K.W.5
-
35
-
-
49549085311
-
A fast and flexible method for the segmentation of aCGH data
-
Ben-Yaacov, E. and Eldar, Y. (2008) A fast and flexible method for the segmentation of aCGH data. Bioinformatics., 24, 139-145.
-
(2008)
Bioinformatics.
, vol.24
, pp. 139-145
-
-
Ben-Yaacov, E.1
Eldar, Y.2
-
36
-
-
33846057724
-
NCBI reference sequences (refseq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2007) NCBI reference sequences (refseq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
37
-
-
75549089967
-
The UCSC Genome Browser database: Update 2010
-
Rhead, B., Karolchik, D., Kuhn, R.M., Hinrichs, A.S., Zweig, A.S., Fujita, P.A., Diekhans, M., Smith, K.E., Rosenbloom, K.R., Raney, B.J. et al. (2010) The UCSC Genome Browser database: update 2010. Nucleic Acids Res., 38, D613-D619.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Rhead, B.1
Karolchik, D.2
Kuhn, R.M.3
Hinrichs, A.S.4
Zweig, A.S.5
Fujita, P.A.6
Diekhans, M.7
Smith, K.E.8
Rosenbloom, K.R.9
Raney, B.J.10
-
38
-
-
75549089335
-
Ensembl's 10th year
-
Flicek, P., Aken, B.L., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S. et al. (2010) Ensembl's 10th year. Nucleic Acids Res., 38, D557-D562.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Flicek, P.1
Aken, B.L.2
Ballester, B.3
Beal, K.4
Bragin, E.5
Brent, S.6
Chen, Y.7
Clapham, P.8
Coates, G.9
Fairley, S.10
-
39
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. and Rinn, J.L. (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
-
40
-
-
44349104241
-
An endogenous small interfering RNA pathway in drosophila
-
Czech, B., Malone, C.D., Zhou, R., Stark, A., Schlingeheyde, C., Dus, M., Perrimon, N., Kellis, M., Wohlschlegel, J.A., Sachidanandam, R. et al. (2008) An endogenous small interfering RNA pathway in drosophila. Nature, 453, 798-802.
-
(2008)
Nature
, vol.453
, pp. 798-802
-
-
Czech, B.1
Malone, C.D.2
Zhou, R.3
Stark, A.4
Schlingeheyde, C.5
Dus, M.6
Perrimon, N.7
Kellis, M.8
Wohlschlegel, J.A.9
Sachidanandam, R.10
-
41
-
-
44349130233
-
Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes
-
Watanabe, T., Totoki, Y., Toyoda, A., Kaneda, M., Kuramochi-Miyagawa, S., Obata, Y., Chiba, H., Kohara, Y., Kono, T., Nakano, T. et al. (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature, 453, 539-543.
-
(2008)
Nature
, vol.453
, pp. 539-543
-
-
Watanabe, T.1
Totoki, Y.2
Toyoda, A.3
Kaneda, M.4
Kuramochi-Miyagawa, S.5
Obata, Y.6
Chiba, H.7
Kohara, Y.8
Kono, T.9
Nakano, T.10
-
42
-
-
61449191758
-
Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in oryza sativa
-
Zhou, X., Sunkar, R., Jin, H., Zhu, J. and Zhang, W. (2008) Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in oryza sativa. Genome Res., 19, 70-78.
-
(2008)
Genome Res.
, vol.19
, pp. 70-78
-
-
Zhou, X.1
Sunkar, R.2
Jin, H.3
Zhu, J.4
Zhang, W.5
-
43
-
-
60549107869
-
Wrap53 a natural p53 antisense transcript required for p53 induction upon DNA damage
-
Mahmoudi, S., Henriksson, S., Corcoran, M., Méndez-Vidal, C., Wiman, K.G. and Farnebo, M. (2009) Wrap53, a natural p53 antisense transcript required for p53 induction upon DNA damage. Mol. Cell, 33, 462-471.
-
(2009)
Mol. Cell
, vol.33
, pp. 462-471
-
-
Mahmoudi, S.1
Henriksson, S.2
Corcoran, M.3
Méndez-Vidal, C.4
Wiman, K.G.5
Farnebo, M.6
-
44
-
-
60549114880
-
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
-
Neil, H., Malabat, C., d'Aubenton Carafa, Y., Xu, Z., Steinmetz, L. and Jacquier, A. (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature., 457, 1038-1042.
-
(2009)
Nature
, vol.457
, pp. 1038-1042
-
-
Neil, H.1
Malabat, C.2
D'aubenton Carafa, Y.3
Xu, Z.4
Steinmetz, L.5
Jacquier, A.6
-
45
-
-
60549108380
-
Bidirectional promoters generate pervasive transcription in yeast
-
Xu, Z., Wei, W., Gagneur, J., Perocchi, F., Clauder-Münster, S., Camblong, J., Guffanti, E., Stutz, F., Huber, W. and Steinmetz, L. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature., 457, 1033-1037.
-
(2009)
Nature.
, vol.457
, pp. 1033-1037
-
-
Xu, Z.1
Wei, W.2
Gagneur, J.3
Perocchi, F.4
Clauder-Münster, S.5
Camblong, J.6
Guffanti, E.7
Stutz, F.8
Huber, W.9
Steinmetz, L.10
-
46
-
-
24644472515
-
Antisense transcription in the mammalian transcriptome
-
Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nishida, H., Yap, C.C., Suzuki, M., Kawai, J. et al. (2005) Antisense transcription in the mammalian transcriptome. Science, 309, 1564-1566.
-
(2005)
Science
, vol.309
, pp. 1564-1566
-
-
Katayama, S.1
Tomaru, Y.2
Kasukawa, T.3
Waki, K.4
Nakanishi, M.5
Nakamura, M.6
Nishida, H.7
Yap, C.C.8
Suzuki, M.9
Kawai, J.10
-
47
-
-
79959403670
-
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
-
Islam, S., Kjällquist, U., Moliner, A., Zajac, P., Fan, J.-B., Lönnerberg, P. and Linnarsson, S. (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res., 21, 1160-1167.
-
(2011)
Genome Res.
, vol.21
, pp. 1160-1167
-
-
Islam, S.1
Kjällquist, U.2
Moliner, A.3
Zajac, P.4
Fan, J.-B.5
Lönnerberg, P.6
Linnarsson, S.7
-
48
-
-
79958724665
-
RNA sequencing reveals two major classes of gene expression levels in metazoan cells
-
Hebenstreit, D., Fang, M., Gu, M., Charoensawan, V., van Oudenaarden, A. and Teichmann, S.A. (2011) RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol. Syst. Biol., 7, 497.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 497
-
-
Hebenstreit, D.1
Fang, M.2
Gu, M.3
Charoensawan, V.4
Van Oudenaarden, A.5
Teichmann, S.A.6
-
49
-
-
33846984935
-
Transcriptional noise and the fidelity of initiation by RNA polymerase II
-
Struhl, K. (2007) Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat. Struct. Mol. Biol., 14, 103-105.
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 103-105
-
-
Struhl, K.1
-
50
-
-
33750352462
-
Transcriptional regulatory elements in the human genome
-
Maston, G.A., Evans, S.K. and Green, M.R. (2006) Transcriptional regulatory elements in the human genome. Annu. Rev. Genom. Hum. Genet., 7, 29-59.
-
(2006)
Annu. Rev. Genom. Hum. Genet.
, vol.7
, pp. 29-59
-
-
Maston, G.A.1
Evans, S.K.2
Green, M.R.3
-
51
-
-
0023899769
-
Nuclease hypersensitive sites in chromatin
-
Gross, D.S. and Garrard, W.T. (1988) Nuclease hypersensitive sites in chromatin. Ann. Rev. Biochem., 57, 159-197.
-
(1988)
Ann. Rev. Biochem.
, vol.57
, pp. 159-197
-
-
Gross, D.S.1
Garrard, W.T.2
-
52
-
-
0018458970
-
The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence
-
Wu, C., Bingham, P.M., Livak, K.J., Holmgren, R. and Elgin, S.C. (1979) The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence. Cell, 16, 797-806.
-
(1979)
Cell
, vol.16
, pp. 797-806
-
-
Wu, C.1
Bingham, P.M.2
Livak, K.J.3
Holmgren, R.4
Elgin, S.C.5
-
53
-
-
17444402501
-
Drosophila DNase i footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, drosophila melanogaster
-
Bergman, C.M., Carlson, J.W. and Celniker, S.E. (2005) Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, drosophila melanogaster. Bioinformatics, 21, 1747-1749.
-
(2005)
Bioinformatics
, vol.21
, pp. 1747-1749
-
-
Bergman, C.M.1
Carlson, J.W.2
Celniker, S.E.3
-
54
-
-
33947201809
-
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
-
Kim, T.H., Abdullaev, Z.K., Smith, A.D., Ching, K.A., Loukinov, D.I., Green, R.D., Zhang, M.Q., Lobanenkov, V.V. and Ren, B. (2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell, 128, 1231-1245.
-
(2007)
Cell
, vol.128
, pp. 1231-1245
-
-
Kim, T.H.1
Abdullaev, Z.K.2
Smith, A.D.3
Ching, K.A.4
Loukinov, D.I.5
Green, R.D.6
Zhang, M.Q.7
Lobanenkov, V.V.8
Ren, B.9
-
55
-
-
33746211341
-
Human cell type diversity, evolution, development, and classification with special reference to cells derived from the neural crest
-
Vickaryous, M.K. and Hall, B.K. (2006) Human cell type diversity, evolution, development, and classification with special reference to cells derived from the neural crest. Biol. Rev. Camb. Philos. Soc., 81, 425-455.
-
(2006)
Biol. Rev. Camb. Philos. Soc.
, vol.81
, pp. 425-455
-
-
Vickaryous, M.K.1
Hall, B.K.2
-
56
-
-
34147175089
-
A comparative study of S/MAR prediction tools
-
Evans, K., Ott, S., Hansen, A., Koentges, G. and Wernisch, L. A comparative study of S/MAR prediction tools. BMC Bioinformatics, 8, 71.
-
BMC Bioinformatics
, vol.8
, pp. 71
-
-
Evans, K.1
Ott, S.2
Hansen, A.3
Koentges, G.4
Wernisch, L.5
-
57
-
-
0037372327
-
A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions
-
Glazko, G.V., Koonin, E.V., Rogozin, I.B. and Shabalina, S.A. (2003) A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet., 19, 119-124.
-
(2003)
Trends Genet.
, vol.19
, pp. 119-124
-
-
Glazko, G.V.1
Koonin, E.V.2
Rogozin, I.B.3
Shabalina, S.A.4
-
58
-
-
84858797002
-
Targeted RNA sequencing reveals the deep complexity of the human transcriptome
-
Mercer, T., Gerhardt, D.J., Dinger, M.E., Crawford, J., Trapnell, C., Jeddeloh, J.A., Mattick, J.S. and Rinn, J.L. (2011) Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol.
-
(2011)
Nat. Biotechnol
-
-
Mercer, T.1
Gerhardt, D.J.2
Dinger, M.E.3
Crawford, J.4
Trapnell, C.5
Jeddeloh, J.A.6
Mattick, J.S.7
Rinn, J.L.8
-
59
-
-
79960911703
-
The reality of pervasive transcription
-
Clark, M.B., Amaral, P.P., Schlesinger, F.J., Dinger, M.E., Taft, R.J., Rinn, J.L., Ponting, C.P., Stadler, P.F., Morris, K.V., Morillon, A. et al. (2011) The reality of pervasive transcription. PLoS Biol., 9, e1000625.
-
(2011)
PLoS Biol.
, vol.9
-
-
Clark, M.B.1
Amaral, P.P.2
Schlesinger, F.J.3
Dinger, M.E.4
Taft, R.J.5
Rinn, J.L.6
Ponting, C.P.7
Stadler, P.F.8
Morris, K.V.9
Morillon, A.10
-
60
-
-
84858798657
-
Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs
-
Managadze, D., Rogozin, I.B., Chernikova, D., Shabalina, S.A. and Koonin, E.V. (2011) Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. GB, 3, 1390-1404.
-
(2011)
GB
, vol.3
, pp. 1390-1404
-
-
Managadze, D.1
Rogozin, I.B.2
Chernikova, D.3
Shabalina, S.A.4
Koonin, E.V.5
-
61
-
-
0037524702
-
The Paf1 complex is required for histone H3 methylation by compass and Dot1p: Linking transcriptional elongation to histone methylation
-
Krogan, N.J., Dover, J., Wood, A., Schneider, J., Heidt, J., Boateng, M.A., Dean, K., Ryan, O.W., Golshani, A., Johnston, M. et al. (2003) The Paf1 complex is required for histone H3 methylation by compass and Dot1p: linking transcriptional elongation to histone methylation. Mol. Cell, 11, 721-729.
-
(2003)
Mol. Cell
, vol.11
, pp. 721-729
-
-
Krogan, N.J.1
Dover, J.2
Wood, A.3
Schneider, J.4
Heidt, J.5
Boateng, M.A.6
Dean, K.7
Ryan, O.W.8
Golshani, A.9
Johnston, M.10
-
62
-
-
0344022572
-
Targeted recruitment of set1 histone methylase by elongating pol II provides a localized mark and memory of recent transcriptional activity
-
Ng, H.H., Robert, F., Young, R.A. and Struhl, K. (2003) Targeted recruitment of set1 histone methylase by elongating pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell, 11, 709-719.
-
(2003)
Mol. Cell
, vol.11
, pp. 709-719
-
-
Ng, H.H.1
Robert, F.2
Young, R.A.3
Struhl, K.4
-
63
-
-
77953062527
-
Five-vertebrate chip-seq reveals the evolutionary dynamics of transcription factor binding
-
Schmidt, D., Wilson, M.D., Ballester, B., Schwalie, P.C., Brown, G.D., Marshall, A., Kutter, C., Watt, S., Martinez-Jimenez, C.P., Mackay, S. et al. (2010) Five-vertebrate chip-seq reveals the evolutionary dynamics of transcription factor binding. Science, 328, 1036-1040.
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
Wilson, M.D.2
Ballester, B.3
Schwalie, P.C.4
Brown, G.D.5
Marshall, A.6
Kutter, C.7
Watt, S.8
Martinez-Jimenez, C.P.9
MacKay, S.10
-
64
-
-
80052461299
-
Conservation of transcription factor binding events predicts gene expression across species
-
Hemberg, M. and Kreiman, G. (2011) Conservation of transcription factor binding events predicts gene expression across species. Nucleic Acids Res., 39, 7092-7102.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 7092-7102
-
-
Hemberg, M.1
Kreiman, G.2
-
65
-
-
79955471381
-
High conservation of transcription factor binding and evidence for combinatorial regulation across six drosophila species
-
He, Q., Bardet, A.F., Patton, B., Purvis, J., Johnston, J., Paulson, A., Gogol, M., Stark, A. and Zeitlinger, J. (2011) High conservation of transcription factor binding and evidence for combinatorial regulation across six drosophila species. Nat. Genet., 43, 414-420.
-
(2011)
Nat. Genet.
, vol.43
, pp. 414-420
-
-
He, Q.1
Bardet, A.F.2
Patton, B.3
Purvis, J.4
Johnston, J.5
Paulson, A.6
Gogol, M.7
Stark, A.8
Zeitlinger, J.9
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