-
1
-
-
25444475788
-
Functional coupling of cleavage and polyadenylation with transcription of mRNA
-
Adamson T.E., Shutt D.C., Price D.H. Functional coupling of cleavage and polyadenylation with transcription of mRNA. J. Biol. Chem. 2005, 280:32262-32271.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 32262-32271
-
-
Adamson, T.E.1
Shutt, D.C.2
Price, D.H.3
-
2
-
-
44449158814
-
Splicing, transcription, and chromatin: a menage a trois
-
Allemand E., Batsche E., Muchardt C. Splicing, transcription, and chromatin: a menage a trois. Curr. Opin. Genet. Dev. 2008, 18:145-151.
-
(2008)
Curr. Opin. Genet. Dev.
, vol.18
, pp. 145-151
-
-
Allemand, E.1
Batsche, E.2
Muchardt, C.3
-
3
-
-
70349333201
-
Nucleosomes are well positioned in exons and carry characteristic histone modifications
-
Andersson R., Enroth S., Rada-Iglesias A., Wadelius C., Komorowski J. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res. 2009, 19:1732-1741.
-
(2009)
Genome Res.
, vol.19
, pp. 1732-1741
-
-
Andersson, R.1
Enroth, S.2
Rada-Iglesias, A.3
Wadelius, C.4
Komorowski, J.5
-
4
-
-
50949091488
-
Identify alternative splicing events based on position-specific evolutionary conservation
-
Chen L., Zheng S. Identify alternative splicing events based on position-specific evolutionary conservation. PLoS ONE 2008, 3:e2806.
-
(2008)
PLoS ONE
, vol.3
-
-
Chen, L.1
Zheng, S.2
-
5
-
-
77952581343
-
The organization of nucleosomes around splice sites
-
Chen W., Luo L., Zhang L. The organization of nucleosomes around splice sites. Nucleic Acids Res. 2010, 38:2788-2798.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 2788-2798
-
-
Chen, W.1
Luo, L.2
Zhang, L.3
-
6
-
-
34547599504
-
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets
-
Foissac S., Sammeth M. ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res. 2007, 35:W297-W299.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Foissac, S.1
Sammeth, M.2
-
7
-
-
2442441507
-
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
-
Gene Yeo C.B.B. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol. 2004, 11:377-394.
-
(2004)
J. Comput. Biol.
, vol.11
, pp. 377-394
-
-
Gene Yeo, C.B.B.1
-
8
-
-
38449094616
-
Cross-talks between transcription and post-transcriptional events within a 'mRNA factory'
-
Hagiwara M., Nojima T. Cross-talks between transcription and post-transcriptional events within a 'mRNA factory'. J. Biochem. 2007, 142:11-15.
-
(2007)
J. Biochem.
, vol.142
, pp. 11-15
-
-
Hagiwara, M.1
Nojima, T.2
-
9
-
-
37249012276
-
Nucleosome destabilization in the epigenetic regulation of gene expression
-
Henikoff S. Nucleosome destabilization in the epigenetic regulation of gene expression. Nat. Rev. Genet. 2008, 9:15-26.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 15-26
-
-
Henikoff, S.1
-
11
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan N., Moore I.K., Fondufe-Mittendorf Y., Gossett A.J., Tillo D., Field Y., LeProust E.M., Hughes T.R., Lieb J.D., Widom J., Segal E. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 2009, 458:362-366.
-
(2009)
Nature
, vol.458
, pp. 362-366
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
Field, Y.6
LeProust, E.M.7
Hughes, T.R.8
Lieb, J.D.9
Widom, J.10
Segal, E.11
-
12
-
-
20444429051
-
Gene splice sites correlate with nucleosome positions
-
Kogan S., Trifonov E.N. Gene splice sites correlate with nucleosome positions. Gene 2005, 352:57-62.
-
(2005)
Gene
, vol.352
, pp. 57-62
-
-
Kogan, S.1
Trifonov, E.N.2
-
13
-
-
34249703972
-
The emergence of alternative 3' and 5' splice site exons from constitutive exons
-
Koren E., Lev-Maor G., Ast G. The emergence of alternative 3' and 5' splice site exons from constitutive exons. PLoS Comput. Biol. 2007, 3:e95.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Koren, E.1
Lev-Maor, G.2
Ast, G.3
-
14
-
-
37349077216
-
The alternative choice of constitutive exons throughout evolution
-
Lev-Maor G., Goren A., Sela N., Kim E., Keren H., Doron-Faigenboim A., Leibman-Barak S., Pupko T., Ast G. The alternative choice of constitutive exons throughout evolution. PLoS Genet. 2007, 3:e203.
-
(2007)
PLoS Genet.
, vol.3
-
-
Lev-Maor, G.1
Goren, A.2
Sela, N.3
Kim, E.4
Keren, H.5
Doron-Faigenboim, A.6
Leibman-Barak, S.7
Pupko, T.8
Ast, G.9
-
15
-
-
78649575971
-
Nucleosomes are well positioned at both ends of exons
-
Springer, Berlin/Heidelberg
-
Liu H., Sun X. Nucleosomes are well positioned at both ends of exons. Life System Modeling and Intelligent Computing 2010, Springer, Berlin/Heidelberg, pp. 291-297.
-
(2010)
Life System Modeling and Intelligent Computing
, pp. 291-297
-
-
Liu, H.1
Sun, X.2
-
16
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Pan Q., Shai O., Lee L.J., Frey B.J., Blencowe B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 2008, 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
-
17
-
-
44649196386
-
Functional integration of transcriptional and RNA processing machineries
-
Pandit S., Wang D., Fu X.D. Functional integration of transcriptional and RNA processing machineries. Curr. Opin. Cell Biol. 2008, 20:260-265.
-
(2008)
Curr. Opin. Cell Biol.
, vol.20
, pp. 260-265
-
-
Pandit, S.1
Wang, D.2
Fu, X.D.3
-
18
-
-
70349125488
-
Co-transcriptional splicing of constitutive and alternative exons
-
Pandya-Jones A., Black D.L. Co-transcriptional splicing of constitutive and alternative exons. RNA 2009, 15:1896-1908.
-
(2009)
RNA
, vol.15
, pp. 1896-1908
-
-
Pandya-Jones, A.1
Black, D.L.2
-
19
-
-
70350005395
-
Cotranscriptionality: the transcription elongation complex as a nexus for nuclear transactions
-
Perales R., Bentley D. Cotranscriptionality: the transcription elongation complex as a nexus for nuclear transactions. Mol. Cell 2009, 36:178-191.
-
(2009)
Mol. Cell
, vol.36
, pp. 178-191
-
-
Perales, R.1
Bentley, D.2
-
20
-
-
76949093375
-
Nucleosome positioning: how is it established, and why does it matter?
-
Radman-Livaja M., Rando O.J. Nucleosome positioning: how is it established, and why does it matter?. Dev. Biol. 2010, 339:258-266.
-
(2010)
Dev. Biol.
, vol.339
, pp. 258-266
-
-
Radman-Livaja, M.1
Rando, O.J.2
-
21
-
-
50949105626
-
A general definition and nomenclature for alternative splicing events
-
Sammeth M., Foissac S., Guigo R. A general definition and nomenclature for alternative splicing events. PLoS Comput. Biol. 2008, 4:e1000147.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Sammeth, M.1
Foissac, S.2
Guigo, R.3
-
22
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Schones D.E., Cui K., Cuddapah S., Roh T.Y., Barski A., Wang Z., Wei G., Zhao K. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008, 132:887-898.
-
(2008)
Cell
, vol.132
, pp. 887-898
-
-
Schones, D.E.1
Cui, K.2
Cuddapah, S.3
Roh, T.Y.4
Barski, A.5
Wang, Z.6
Wei, G.7
Zhao, K.8
-
23
-
-
77952584374
-
Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing
-
Schwartz S., Ast G. Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing. EMBO J. 2010, 29:1629-1636.
-
(2010)
EMBO J.
, vol.29
, pp. 1629-1636
-
-
Schwartz, S.1
Ast, G.2
-
25
-
-
79959557189
-
Determinants of nucleosome organization in primary human cells
-
516-U148
-
Sidow A., Valouev A., Johnson S.M., Boyd S.D., Smith C.L., Fire A.Z. Determinants of nucleosome organization in primary human cells. Nature 2011, 474. 516-U148.
-
(2011)
Nature
, vol.474
-
-
Sidow, A.1
Valouev, A.2
Johnson, S.M.3
Boyd, S.D.4
Smith, C.L.5
Fire, A.Z.6
-
26
-
-
70350754211
-
Rates of in situ transcription and splicing in large human genes
-
Singh J., Padgett R.A. Rates of in situ transcription and splicing in large human genes. Nat. Struct. Mol. Biol. 2009, 16:1128-1133.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 1128-1133
-
-
Singh, J.1
Padgett, R.A.2
-
27
-
-
70350013550
-
Biased chromatin signatures around polyadenylation sites and exons
-
Spies N., Nielsen C.B., Padgett R.A., Burge C.B. Biased chromatin signatures around polyadenylation sites and exons. Mol. Cell 2009, 36:245-254.
-
(2009)
Mol. Cell
, vol.36
, pp. 245-254
-
-
Spies, N.1
Nielsen, C.B.2
Padgett, R.A.3
Burge, C.B.4
-
28
-
-
0037705467
-
Conservation of human alternative splice events in mouse
-
Thanaraj T.A., Clark F., Muilu J. Conservation of human alternative splice events in mouse. Nucleic Acids Res. 2003, 31:2544-2552.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 2544-2552
-
-
Thanaraj, T.A.1
Clark, F.2
Muilu, J.3
-
29
-
-
69949124307
-
Nucleosome positioning as a determinant of exon recognition
-
Tilgner H., Nikolaou C., Althammer S., Sammeth M., Beato M., Valcarcel J., Guigo R. Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol. 2009, 16:996-1001.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 996-1001
-
-
Tilgner, H.1
Nikolaou, C.2
Althammer, S.3
Sammeth, M.4
Beato, M.5
Valcarcel, J.6
Guigo, R.7
-
30
-
-
79952183494
-
Cracking the chromatin code: precise rule of nucleosome positioning
-
Trifonov E.N. Cracking the chromatin code: precise rule of nucleosome positioning. Phys. Life Rev. 2011, 8:39-50.
-
(2011)
Phys. Life Rev.
, vol.8
, pp. 39-50
-
-
Trifonov, E.N.1
-
31
-
-
70849129503
-
A wave of nascent transcription on activated human genes
-
Wada Y., Ohta Y., Xu M., Tsutsumi S., Minami T., Inoue K., Komura D., Kitakami J.I., Oshida N., Papantonis A., Izumi A., Kobayashi M., Meguro H., Kanki Y., Mimura I., Yamamoto K., Mataki C., Hamakubo T., Shirahige K., Aburatani H., Kimura H., Kodama T., Cook P.R., Ihara S. A wave of nascent transcription on activated human genes. Proc. Natl. Acad. Sci. 2009, 106:18357-18361.
-
(2009)
Proc. Natl. Acad. Sci.
, vol.106
, pp. 18357-18361
-
-
Wada, Y.1
Ohta, Y.2
Xu, M.3
Tsutsumi, S.4
Minami, T.5
Inoue, K.6
Komura, D.7
Kitakami, J.I.8
Oshida, N.9
Papantonis, A.10
Izumi, A.11
Kobayashi, M.12
Meguro, H.13
Kanki, Y.14
Mimura, I.15
Yamamoto, K.16
Mataki, C.17
Hamakubo, T.18
Shirahige, K.19
Aburatani, H.20
Kimura, H.21
Kodama, T.22
Cook, P.R.23
Ihara, S.24
more..
-
32
-
-
43249087733
-
Regulation of alternative polyadenylation by genomic imprinting
-
Wood A.J., Schulz R., Woodfine K., Koltowska K., Beechey C.V., Peters J., Bourc'his D., Oakey R.J. Regulation of alternative polyadenylation by genomic imprinting. Genes Dev. 2008, 22:1141-1146.
-
(2008)
Genes Dev.
, vol.22
, pp. 1141-1146
-
-
Wood, A.J.1
Schulz, R.2
Woodfine, K.3
Koltowska, K.4
Beechey, C.V.5
Peters, J.6
Bourc'his, D.7
Oakey, R.J.8
-
33
-
-
33744809531
-
The types and prevalence of alternative splice forms
-
Zavolan M., van Nimwegen E. The types and prevalence of alternative splice forms. Curr. Opin. Struct. Biol. 2006, 16:362-367.
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 362-367
-
-
Zavolan, M.1
van Nimwegen, E.2
|