-
1
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
10.1038/ng.259, 18978789
-
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40:1413-1415. 10.1038/ng.259, 18978789.
-
(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
-
2
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
10.1038/nature07509, 2593745, 18978772
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476. 10.1038/nature07509, 2593745, 18978772.
-
(2008)
Nature
, vol.456
, 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
-
3
-
-
34548758543
-
Splicing in disease: disruption of the splicing code and the decoding machinery
-
Wang ET, Cooper AT. Splicing in disease: disruption of the splicing code and the decoding machinery. Nature 2007, 8:749-761.
-
(2007)
Nature
, vol.8
, pp. 749-761
-
-
Wang, E.T.1
Cooper, A.T.2
-
4
-
-
42449098125
-
Splicing regulation: from a parts list of regulatory elements to an integrated splicing code
-
10.1261/rna.876308, 2327353, 18369186
-
Wang Z, Burge CB. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 2008, 14:802-813. 10.1261/rna.876308, 2327353, 18369186.
-
(2008)
RNA
, vol.14
, pp. 802-813
-
-
Wang, Z.1
Burge, C.B.2
-
5
-
-
77952029221
-
Deciphering the splicing code
-
10.1038/nature09000, 20445623
-
Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ. Deciphering the splicing code. Nature 2010, 465:53-59. 10.1038/nature09000, 20445623.
-
(2010)
Nature
, vol.465
, pp. 53-59
-
-
Barash, Y.1
Calarco, J.A.2
Gao, W.3
Pan, Q.4
Wang, X.5
Shai, O.6
Blencowe, B.J.7
Frey, B.J.8
-
6
-
-
84871410405
-
The evolutionary landscape of alternative splicing in vertebrate species
-
10.1126/science.1230612, 23258890
-
Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Çolak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ. The evolutionary landscape of alternative splicing in vertebrate species. Science 2012, 338:1587-1593. 10.1126/science.1230612, 23258890.
-
(2012)
Science
, vol.338
, pp. 1587-1593
-
-
Barbosa-Morais, N.L.1
Irimia, M.2
Pan, Q.3
Xiong, H.Y.4
Gueroussov, S.5
Lee, L.J.6
Slobodeniuc, V.7
Kutter, C.8
Watt, S.9
Çolak, R.10
Kim, T.11
Misquitta-Ali, C.M.12
Wilson, M.D.13
Kim, P.M.14
Odom, D.T.15
Frey, B.J.16
Blencowe, B.J.17
-
7
-
-
2442441507
-
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
-
10.1089/1066527041410418, 15285897
-
Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 2004, 11:377-394. 10.1089/1066527041410418, 15285897.
-
(2004)
J Comput Biol
, vol.11
, pp. 377-394
-
-
Yeo, G.1
Burge, C.B.2
-
8
-
-
34547559084
-
SplicePort--an interactive splice-site analysis tool
-
10.1093/nar/gkm407, 1933122, 17576680
-
Dogan RI, Getoor L, Wilbur WJ, Mount SM. SplicePort--an interactive splice-site analysis tool. Nucleic Acids Res 2007, 35:W285-W291. 10.1093/nar/gkm407, 1933122, 17576680.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Dogan, R.I.1
Getoor, L.2
Wilbur, W.J.3
Mount, S.M.4
-
9
-
-
0042242582
-
ESEfinder: a web resource to identify exonic splicing enhancers
-
10.1093/nar/gkg616, 169022, 12824367
-
Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR. ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res 2003, 31:3568-3571. 10.1093/nar/gkg616, 169022, 12824367.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3568-3571
-
-
Cartegni, L.1
Wang, J.2
Zhu, Z.3
Zhang, M.Q.4
Krainer, A.R.5
-
10
-
-
59649107040
-
An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells
-
10.1038/nsmb.1545, 2735254, 19136955
-
Yeo GW, Coufal NG, Liang TY, Peng GE, Fu X-D, Gage FH. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol 2009, 16:130-137. 10.1038/nsmb.1545, 2735254, 19136955.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 130-137
-
-
Yeo, G.W.1
Coufal, N.G.2
Liang, T.Y.3
Peng, G.E.4
Fu, X.-D.5
Gage, F.H.6
-
11
-
-
80052766045
-
Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context
-
Xiong HY, Barash Y, Frey BJ. Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context. Bioinformatics 2011, 27:2554-2562.
-
(2011)
Bioinformatics
, vol.27
, pp. 2554-2562
-
-
Xiong, H.Y.1
Barash, Y.2
Frey, B.J.3
-
12
-
-
69849097846
-
Affy exon tissues: exon levels in normal tissues in human, mouse and rat
-
10.1093/bioinformatics/btp414, 2735668, 19570805
-
Pohl AA, Sugnet CW, Clark TA, Smith K, Fujita PA, Cline MS. Affy exon tissues: exon levels in normal tissues in human, mouse and rat. Bioinformatics 2009, 25:2442-2443. 10.1093/bioinformatics/btp414, 2735668, 19570805.
-
(2009)
Bioinformatics
, vol.25
, pp. 2442-2443
-
-
Pohl, A.A.1
Sugnet, C.W.2
Clark, T.A.3
Smith, K.4
Fujita, P.A.5
Cline, M.S.6
-
13
-
-
77954616951
-
Predicting nucleosome positioning using a duration Hidden Markov Model
-
10.1186/1471-2105-11-346, 2900280, 20576140
-
Xi L, Fondufe-Mittendorf Y, Xia L, Flatow J, Widom J, Wang JP. Predicting nucleosome positioning using a duration Hidden Markov Model. BMC Bioinformatics 2010, 11:346. 10.1186/1471-2105-11-346, 2900280, 20576140.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 346
-
-
Xi, L.1
Fondufe-Mittendorf, Y.2
Xia, L.3
Flatow, J.4
Widom, J.5
Wang, J.P.6
-
14
-
-
84865201988
-
Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins
-
10.1016/j.cell.2012.06.041, 3428802, 22901804
-
Wang ET, Cody NAL, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB. Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 2012, 150:710-724. 10.1016/j.cell.2012.06.041, 3428802, 22901804.
-
(2012)
Cell
, vol.150
, pp. 710-724
-
-
Wang, E.T.1
Cody, N.A.L.2
Jog, S.3
Biancolella, M.4
Wang, T.T.5
Treacy, D.J.6
Luo, S.7
Schroth, G.P.8
Housman, D.E.9
Reddy, S.10
Lécuyer, E.11
Burge, C.B.12
-
15
-
-
69949132191
-
Chromatin organization marks exon-intron structure
-
10.1038/nsmb.1659, 19684600
-
Schwartz S, Meshorer E, Ast G. Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 2009, 16:990-995. 10.1038/nsmb.1659, 19684600.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 990-995
-
-
Schwartz, S.1
Meshorer, E.2
Ast, G.3
-
16
-
-
69949124307
-
Nucleosome positioning as a determinant of exon recognition
-
10.1038/nsmb.1658, 19684599
-
Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcárcel J, Guigó R. Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 2009, 16:996-1001. 10.1038/nsmb.1658, 19684599.
-
(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
Valcárcel, J.6
Guigó, R.7
-
17
-
-
54549123309
-
VEGF-A splicing: the key to anti-angiogenic therapeutics?
-
10.1038/nrc2505, 2613352, 18923433
-
Harper SJ, Bates DO. VEGF-A splicing: the key to anti-angiogenic therapeutics?. Nat Rev Cancer 2008, 8:880-887. 10.1038/nrc2505, 2613352, 18923433.
-
(2008)
Nat Rev Cancer
, vol.8
, pp. 880-887
-
-
Harper, S.J.1
Bates, D.O.2
-
18
-
-
58149492467
-
A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart
-
10.1073/pnas.0809045105, 2629332, 19075228
-
Kalsotra A, Xiao X, Ward AJ, Castle JC, Johnson JM, Burge CB, Cooper TA. A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart. Proc Natl Acad Sci USA 2008, 105:20333-20338. 10.1073/pnas.0809045105, 2629332, 19075228.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 20333-20338
-
-
Kalsotra, A.1
Xiao, X.2
Ward, A.J.3
Castle, J.C.4
Johnson, J.M.5
Burge, C.B.6
Cooper, T.A.7
-
19
-
-
77949318969
-
Regulation of Vascular Endothelial Growth Factor (VEGF) Splicing from Pro-angiogenic to Anti-angiogenic Isoforms: a Novel Therapeutic Strategy for Angiogenesis
-
2820781, 19906640
-
Nowak DG, Amin EM, Rennel ES, Hoareau-Aveilla C, Gammons M, Damodoran G, Hagiwara M, Harper SJ, Woolard J, Ladomery MR, Bates DO. Regulation of Vascular Endothelial Growth Factor (VEGF) Splicing from Pro-angiogenic to Anti-angiogenic Isoforms: a Novel Therapeutic Strategy for Angiogenesis. J Biol Chem 2009, 285:5532-5540. 2820781, 19906640.
-
(2009)
J Biol Chem
, vol.285
, pp. 5532-5540
-
-
Nowak, D.G.1
Amin, E.M.2
Rennel, E.S.3
Hoareau-Aveilla, C.4
Gammons, M.5
Damodoran, G.6
Hagiwara, M.7
Harper, S.J.8
Woolard, J.9
Ladomery, M.R.10
Bates, D.O.11
-
20
-
-
84876512920
-
Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation
-
10.1261/rna.038422.113, 23525800
-
Hall MP, Nagel RJ, Fagg WS, Shiue L, Cline MS, Perriman RJ, Donohue JP, Ares M. Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation. RNA 2013, 19:627-638. 10.1261/rna.038422.113, 23525800.
-
(2013)
RNA
, vol.19
, pp. 627-638
-
-
Hall, M.P.1
Nagel, R.J.2
Fagg, W.S.3
Shiue, L.4
Cline, M.S.5
Perriman, R.J.6
Donohue, J.P.7
Ares, M.8
-
21
-
-
33749056769
-
An RNA map predicting Nova-dependent splicing regulation
-
10.1038/nature05304, 17065982
-
Ule J, Stefani G, Mele A, Ruggiu M, Wang X, Taneri B, Gaasterland T, Blencowe BJ, Darnell RB. An RNA map predicting Nova-dependent splicing regulation. Nature 2006, 444:580-586. 10.1038/nature05304, 17065982.
-
(2006)
Nature
, vol.444
, 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
-
22
-
-
0029952557
-
Neuron-specific alternative splicing of nonmuscle myosin II heavy chain-B pre-mRNA requires a cis-acting intron sequence
-
Kawamoto S. Neuron-specific alternative splicing of nonmuscle myosin II heavy chain-B pre-mRNA requires a cis-acting intron sequence. J Biol Chem 1996, 271:17613-17616.
-
(1996)
J Biol Chem
, vol.271
, pp. 17613-17616
-
-
Kawamoto, S.1
-
23
-
-
48949103996
-
A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation
-
10.1101/gr.073155.107, 2493427, 18456862
-
Aznarez I, Barash Y, Shai O, He D, Zielenski J, Tsui LC, Parkinson J, Frey BJ, Rommens JM, Blencowe BJ. A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. Genome Res 2008, 18:1247-1258. 10.1101/gr.073155.107, 2493427, 18456862.
-
(2008)
Genome Res
, vol.18
, pp. 1247-1258
-
-
Aznarez, I.1
Barash, Y.2
Shai, O.3
He, D.4
Zielenski, J.5
Tsui, L.C.6
Parkinson, J.7
Frey, B.J.8
Rommens, J.M.9
Blencowe, B.J.10
-
24
-
-
70350569286
-
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches
-
2958924, 19773805
-
Chen M, Manley JL. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 2009, 10:741-754. 2958924, 19773805.
-
(2009)
Nat Rev Mol Cell Biol
, vol.10
, pp. 741-754
-
-
Chen, M.1
Manley, J.L.2
-
25
-
-
84880845397
-
Alternative Splicing Regulates Biogenesis of miRNAs Located across Exon-Intron Junctions
-
10.1016/j.molcel.2013.05.007, 23747012
-
Melamed Z, Levy A, Ashwal-Fluss R, Lev-Maor G, Mekahel K, Atias N, Gilad S, Sharan R, Levy C, Kadener S, Ast G. Alternative Splicing Regulates Biogenesis of miRNAs Located across Exon-Intron Junctions. Mol Cell 2013, 50:869-881. 10.1016/j.molcel.2013.05.007, 23747012.
-
(2013)
Mol Cell
, vol.50
, pp. 869-881
-
-
Melamed, Z.1
Levy, A.2
Ashwal-Fluss, R.3
Lev-Maor, G.4
Mekahel, K.5
Atias, N.6
Gilad, S.7
Sharan, R.8
Levy, C.9
Kadener, S.10
Ast, G.11
-
26
-
-
84859436530
-
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
-
10.1093/nar/gkr1079, 3245008, 22121212
-
Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 2012, 40:D130-D135. 10.1093/nar/gkr1079, 3245008, 22121212.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Pruitt, K.D.1
Tatusova, T.2
Brown, G.R.3
Maglott, D.R.4
-
27
-
-
84859865967
-
The UCSC Genome Browser database: extensions and updates 2011
-
10.1093/nar/gkr1055, 3245018, 22086951
-
Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res 2012, 40:D918-D923. 10.1093/nar/gkr1055, 3245018, 22086951.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Dreszer, T.R.1
Karolchik, D.2
Zweig, A.S.3
Hinrichs, A.S.4
Raney, B.J.5
Kuhn, R.M.6
Meyer, L.R.7
Wong, M.8
Sloan, C.A.9
Rosenbloom, K.R.10
|