-
1
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S., and Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biol. 11: R106.
-
(2010)
Genome Biol
, vol.11
-
-
Anders, S.1
Huber, W.2
-
2
-
-
33746597533
-
Potent induction of Arabidopsis thaliana flowering by elevated growth temperature
-
Balasubramanian, S., Sureshkumar, S., Lempe, J., and Weigel, D. (2006). Potent induction of Arabidopsis thaliana flowering by elevated growth temperature. PLoS Genet. 2: e106.
-
(2006)
PLoS Genet
, vol.2
-
-
Balasubramanian, S.1
Sureshkumar, S.2
Lempe, J.3
Weigel, D.4
-
3
-
-
51149118908
-
Plant SR proteins and their functions
-
Barta, A., Kalyna, M., and Lorkovic, Z.J. (2008). Plant SR proteins and their functions. Curr. Top. Microbiol. Immunol. 326: 83-102.
-
(2008)
Curr. Top. Microbiol. Immunol.
, vol.326
, pp. 83-102
-
-
Barta, A.1
Kalyna, M.2
Lorkovic, Z.J.3
-
4
-
-
0013394889
-
Mechanisms of alternative pre-messenger RNA splicing
-
Black, D.L. (2003). Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72: 291-336.
-
(2003)
Annu. Rev. Biochem
, vol.72
, pp. 291-336
-
-
Black, D.L.1
-
5
-
-
36248989143
-
Riboswitch-dependent gene regulation and its evolution in the plant kingdom
-
Bocobza, S., Adato, A., Mandel, T., Shapira, M., Nudler, E., and Aharoni, A. (2007). Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev. 21: 2874-2879.
-
(2007)
Genes Dev.
, vol.21
, pp. 2874-2879
-
-
Bocobza, S.1
Adato, A.2
Mandel, T.3
Shapira, M.4
Nudler, E.5
Aharoni, A.6
-
6
-
-
34347384211
-
A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons
-
Boutz, P.L., Stoilov, P., Li, Q., Lin, C.H., Chawla, G., Ostrow, K., Shiue, L., and Ares, M. Jr., and Black, D.L. (2007). A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev. 21: 1636-1652.
-
(2007)
Genes Dev.
, vol.21
, pp. 1636-1652
-
-
Boutz, P.L.1
Stoilov, P.2
Li, Q.3
Lin, C.H.4
Chawla, G.5
Ostrow, K.6
Shiue, L.7
Ares Jr., M.8
Black, D.L.9
-
7
-
-
77957725138
-
The plant-specific SR45 protein negatively regulates glucose and ABA signaling during early seedling development in Arabidopsis
-
Carvalho, R.F., Carvalho, S.D., and Duque, P. (2010). The plant-specific SR45 protein negatively regulates glucose and ABA signaling during early seedling development in Arabidopsis. Plant Physiol. 154: 772-783.
-
(2010)
Plant Physiol
, vol.154
, pp. 772-783
-
-
Carvalho, R.F.1
Carvalho, S.D.2
Duque, P.3
-
8
-
-
84870496060
-
XBAT35, a novel Arabidopsis RING E3 ligase exhibiting dual targeting of its splice isoforms, is involved in ethylene-mediated regulation of apical hook curvature
-
May 24
-
Carvalho, S.D., Saraiva, R., Maia, T.M., Abreu, I.A., and Duque, P. (May 24, 2012). XBAT35, a novel Arabidopsis RING E3 ligase exhibiting dual targeting of its splice isoforms, is involved in ethylene-mediated regulation of apical hook curvature. Mol. Plant http://dx.doi.org/10.1093/mp/sss048.
-
(2012)
Mol. Plant
-
-
Carvalho, S.D.1
Saraiva, R.2
Maia, T.M.3
Abreu, I.A.4
Duque, P.5
-
9
-
-
34247197937
-
The nonsense-mediated decay RNA surveillance pathway
-
Chang, Y.F., Imam, J.S., and Wilkinson, M.F. (2007). The nonsense-mediated decay RNA surveillance pathway. Annu. Rev. Biochem. 76: 51-74.
-
(2007)
Annu. Rev. Biochem
, vol.76
, pp. 51-74
-
-
Chang, Y.F.1
Imam, J.S.2
Wilkinson, M.F.3
-
10
-
-
70350569286
-
Mechanisms of alternative splicing regulation: Insights from molecular and genomics approaches
-
Chen, M., and Manley, J.L. (2009). Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol. 10: 741-754.
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 741-754
-
-
Chen, M.1
Manley, J.L.2
-
11
-
-
0032447801
-
Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana
-
Clough, S.J., and Bent, A.F. (1998). Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16: 735-743.
-
(1998)
Plant J
, vol.16
, pp. 735-743
-
-
Clough, S.J.1
Bent, A.F.2
-
12
-
-
78650488766
-
Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing
-
Deng, X., Gu, L., Liu, C, Lu, T., Lu, F., Lu, Z., Cui, P., Pei, Y., Wang, B., Hu, S., and Cao, X. (2010). Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing. Proc. Natl. Acad. Sci. USA 107: 19114-19119.
-
(2010)
Proc. Natl. Acad. Sci.
, vol.107
, pp. 19114-19119
-
-
Deng, X.1
Gu, L.2
Liu, C.3
Lu, T.4
Lu, F.5
Lu, Z.6
Cui, P.7
Pei, Y.8
Wang, B.9
Hu, S.10
Cao, X.11
-
13
-
-
79956213953
-
A role for SR proteins in plant stress responses
-
Duque, P. (2011). A role for SR proteins in plant stress responses. Plant Signal. Behav. 6: 49-54.
-
(2011)
Plant Signal. Behav.
, vol.6
, pp. 49-54
-
-
Duque, P.1
-
14
-
-
74949084336
-
Genome-wide mapping of alternative splicing in Arabidopsis thaliana
-
Filichkin, S.A., Priest, H.D., Givan, S.A., Shen, R., Bryant, D.W., Fox, S.E., Wong, W.K., and Mockler, T.C. (2010). Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 20: 45-58.
-
(2010)
Genome Res
, vol.20
, pp. 45-58
-
-
Filichkin, S.A.1
Priest, H.D.2
Givan, S.A.3
Shen, R.4
Bryant, D.W.5
Fox, S.E.6
Wong, W.K.7
Mockler, T.C.8
-
15
-
-
62549099549
-
A polypyrimidine tract binding protein, pumpkin RBP50, forms the basis of a phloem-mobile ri-bonucleoprotein complex
-
Ham, B.K., Brandom, J.L., Xoconostle-Cázares, B., Ringgold, V., Lough, T.J., and Lucas, W.J. (2009). A polypyrimidine tract binding protein, pumpkin RBP50, forms the basis of a phloem-mobile ri-bonucleoprotein complex. Plant Cell 21: 197-215.
-
(2009)
Plant Cell
, vol.21
, pp. 197-215
-
-
Ham, B.K.1
Brandom, J.L.2
Xoconostle-Cázares, B.3
Ringgold, V.4
Lough, T.J.5
Lucas, W.J.6
-
16
-
-
66149156302
-
A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs
-
Hammond, M.C., Wachter, A., and Breaker, R.R. (2009). A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs. Nat. Struct. Mol. Biol. 16: 541-549.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 541-549
-
-
Hammond, M.C.1
Wachter, A.2
Breaker, R.R.3
-
17
-
-
38249014803
-
Transgenic potato plants depleted for the major tuber protein patatin via expression of anti-sense RNA
-
Höfgen, R., and Willmitzer, L. (1992). Transgenic potato plants depleted for the major tuber protein patatin via expression of anti-sense RNA. Plant Sci. 87: 45-54.
-
(1992)
Plant Sci.
, vol.87
, pp. 45-54
-
-
Höfgen, R.1
Willmitzer, L.2
-
18
-
-
0346432008
-
Bacterial expression, purification and preliminary X-ray crystallographic characterization of the invertase inhibitor Nt-CIF from tobacco
-
Hothorn, M., Bonneau, F., Stier, G., Greiner, S., and Scheffzek, K. (2003). Bacterial expression, purification and preliminary X-ray crystallographic characterization of the invertase inhibitor Nt-CIF from tobacco. Acta Crystallogr. D Biol. Crystallogr. 59: 2279-2282.
-
(2003)
Acta Crystallogr. D Biol. Crystallogr
, vol.59
, pp. 2279-2282
-
-
Hothorn, M.1
Bonneau, F.2
Stier, G.3
Greiner, S.4
Scheffzek, K.5
-
19
-
-
33748753075
-
Structural basis for the redox control of plant glutamate cysteine ligase
-
Hothorn, M., Wachter, A., Gromes, R., Stuwe, T., Rausch, T., and Scheffzek, K. (2006). Structural basis for the redox control of plant glutamate cysteine ligase. J. Biol. Chem. 281: 27557-27565.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 27557-27565
-
-
Hothorn, M.1
Wachter, A.2
Gromes, R.3
Stuwe, T.4
Rausch, T.5
Scheffzek, K.6
-
20
-
-
84871913206
-
RNA regulatory elements and polyadenylation in plants
-
Hunt, A.G. (2011). RNA regulatory elements and polyadenylation in plants. Front. Plant Sci. 2: 109.
-
(2011)
Front. Plant Sci
, vol.2
, pp. 109
-
-
Hunt, A.G.1
-
21
-
-
23744492690
-
Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition
-
Izquierdo, J.M., Majós, N., Bonnal, S., Martínez, C., Castelo, R., Guigó, R., Bilbao, D., and Valcárcel, J. (2005). Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition. Mol. Cell 19: 475-484.
-
(2005)
Mol. Cell
, vol.19
, pp. 475-484
-
-
Izquierdo, J.M.1
Majós, N.2
Bonnal, S.3
Martínez, C.4
Castelo, R.5
Guigó, R.6
Bilbao, D.7
Valcárcel, J.8
-
22
-
-
84860128193
-
Alternative splicing mediates responses of the Arabidopsis circa-dian clock to temperature changes
-
James, A.B., Syed, N.H., Bordage, S., Marshall, J., Nimmo, G.A., Jenkins, G.I., Herzyk, P., Brown, J.W., and Nimmo, H.G. (2012). Alternative splicing mediates responses of the Arabidopsis circa-dian clock to temperature changes. Plant Cell 24: 961-981.
-
(2012)
Plant Cell
, vol.24
, pp. 961-981
-
-
James, A.B.1
Syed, N.H.2
Bordage, S.3
Marshall, J.4
Nimmo, G.A.5
Jenkins, G.I.6
Herzyk, P.7
Brown, J.W.8
Nimmo, H.G.9
-
23
-
-
79952360093
-
RNA-Seq read alignments with PALMapper
-
11.6.1-11.6.37
-
Jean, G., Kahles, A., Sreedharan, V.T., De Bona, F., and Ratsch, G. (2010). RNA-Seq read alignments with PALMapper. Curr. Protoc. Bioinformatics 32: 11.6.1-11.6.37.
-
(2010)
Curr. Protoc. Bioinformatics
, vol.32
-
-
Jean, G.1
Kahles, A.2
Sreedharan, V.T.3
de Bona, F.4
Ratsch, G.5
-
24
-
-
0141632822
-
Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development
-
Kalyna, M., Lopato, S., and Barta, A. (2003). Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development. Mol. Biol. Cell 14: 3565-3577.
-
(2003)
Mol. Biol. Cell.
, vol.14
, pp. 3565-3577
-
-
Kalyna, M.1
Lopato, S.2
Barta, A.3
-
25
-
-
84859293997
-
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabi-dopsis
-
Kalyna, M., et al. (2012). Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabi-dopsis. Nucleic Acids Res. 40: 2454-2469.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 2454-2469
-
-
Kalyna, M.1
-
26
-
-
0036581417
-
GATEWAY vectors for Agrobacterium-mediated plant transformation
-
Karimi, M., Inzé, D., and Depicker, A. (2002). GATEWAY vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci. 7: 193-195.
-
(2002)
Trends Plant Sci.
, vol.7
, pp. 193-195
-
-
Karimi, M.1
Inzé, D.2
Depicker, A.3
-
27
-
-
42449124624
-
The coupling of alternative splicing and nonsense-mediated mRNA decay
-
Lareau, L.F., Brooks, A.N., Soergel, D.A., Meng, Q., and Brenner, S.E. (2007). The coupling of alternative splicing and nonsense-mediated mRNA decay. Adv. Exp. Med. Biol. 623: 190-211.
-
(2007)
Adv. Exp. Med. Biol
, vol.623
, pp. 190-211
-
-
Lareau, L.F.1
Brooks, A.N.2
Soergel, D.A.3
Meng, Q.4
Brenner, S.E.5
-
28
-
-
47249089938
-
Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana
-
Laubinger, S., Sachsenberg, T., Zeller, G., Busch, W., Lohmann, J.U., Rätsch, G., and Weigel, D. (2008). Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 105: 8795-8800.
-
(2008)
Proc. Natl. Acad. Sci.
, vol.105
, pp. 8795-8800
-
-
Laubinger, S.1
Sachsenberg, T.2
Zeller, G.3
Busch, W.4
Lohmann, J.U.5
Rätsch, G.6
Weigel, D.7
-
29
-
-
0034665868
-
The AGAMOUS-LIKE 20 MADS domain protein integrates floral inductive pathways in Arabidopsis
-
Lee, H., Suh, S.S., Park, E., Cho, E., Ahn, J.H., Kim, S.G., Lee, J.S., Kwon, Y.M., and Lee, I. (2000). The AGAMOUS-LIKE 20 MADS domain protein integrates floral inductive pathways in Arabidopsis. Genes Dev. 14: 2366-2376.
-
(2000)
Genes Dev.
, vol.14
, pp. 2366-2376
-
-
Lee, H.1
Suh, S.S.2
Park, E.3
Cho, E.4
Ahn, J.H.5
Kim, S.G.6
Lee, J.S.7
Kwon, Y.M.8
Lee, I.9
-
30
-
-
79959557634
-
CmRBP50 protein phosphor-ylation is essential for assembly of a stable phloem-mobile high-affinity ribonucleoprotein complex
-
Li, P., Ham, B.K., and Lucas, W.J. (2011). CmRBP50 protein phosphor-ylation is essential for assembly of a stable phloem-mobile high-affinity ribonucleoprotein complex. J. Biol. Chem. 286: 23142-23149.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 23142-23149
-
-
Li, P.1
Ham, B.K.2
Lucas, W.J.3
-
31
-
-
12144286231
-
A new Arabi-dopsis gene, FLK, encodes an RNA binding protein with K homol-ogy motifs and regulates flowering time via FLOWERING LOCUS C
-
Lim, M.H., Kim, J., Kim, Y.S., Chung, K.S., Seo, Y.H., Lee, I., Kim, J., Hong, C.B., Kim, H.J., and Park, C.M. (2004). A new Arabi-dopsis gene, FLK, encodes an RNA binding protein with K homol-ogy motifs and regulates flowering time via FLOWERING LOCUS C. Plant Cell 16: 731-740.
-
(2004)
Plant Cell
, vol.16
, pp. 731-740
-
-
Lim, M.H.1
Kim, J.2
Kim, Y.S.3
Chung, K.S.4
Seo, Y.H.5
Lee, I.6
Kim, J.7
Hong, C.B.8
Kim, H.J.9
Park, C.M.10
-
32
-
-
77956342570
-
Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB
-
Llorian, M., Schwartz, S., Clark, T.A., Hollander, D., Tan, L.Y., Spellman, R., Gordon, A., Schweitzer, A.C., de la Grange, P., Ast, G., and Smith, C.W. (2010). Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB. Nat. Struct. Mol. Biol. 17: 1114-1123.
-
(2010)
Nat. Struct. Mol. Biol
, vol.17
, pp. 1114-1123
-
-
Llorian, M.1
Schwartz, S.2
Clark, T.A.3
Hollander, D.4
Tan, L.Y.5
Spellman, R.6
Gordon, A.7
Schweitzer, A.C.8
de la Grange, P.9
Ast, G.10
Smith, C.W.11
-
33
-
-
77956277181
-
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
-
Lu, T., Lu, G., Fan, D., Zhu, C., Li, W., Zhao, Q., Feng, Q., Zhao, Y., Guo, Y., Li, W., Huang, X., and Han, B. (2010). Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res. 20: 1238-1249.
-
(2010)
Genome Res
, vol.20
, pp. 1238-1249
-
-
Lu, T.1
Lu, G.2
Fan, D.3
Zhu, C.4
Li, W.5
Zhao, Q.6
Feng, Q.7
Zhao, Y.8
Guo, Y.9
Li, W.10
Huang, X.11
Han, B.12
-
34
-
-
34547212309
-
The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing
-
Makeyev, E.V., Zhang, J., Carrasco, M.A., and Maniatis, T. (2007). The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol. Cell 27: 435-448.
-
(2007)
Mol. Cell
, vol.27
, pp. 435-448
-
-
Makeyev, E.V.1
Zhang, J.2
Carrasco, M.A.3
Maniatis, T.4
-
35
-
-
77954847055
-
The landscape of C. elegans 3'UTRs
-
Mangone, M., et al. (2010). The landscape of C. elegans 3'UTRs. Science 329: 432-435.
-
(2010)
Science
, vol.329
, pp. 432-435
-
-
Mangone, M.1
-
36
-
-
84861890038
-
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
-
Marquez, Y., Brown, J.W., Simpson, C., Barta, A., and Kalyna, M. (2012). Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 22: 1184-1195.
-
(2012)
Genome Res
, vol.22
, pp. 1184-1195
-
-
Marquez, Y.1
Brown, J.W.2
Simpson, C.3
Barta, A.4
Kalyna, M.5
-
37
-
-
0033133554
-
FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering
-
Michaels, S.D., and Amasino, R.M. (1999). FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11: 949-956.
-
(1999)
Plant Cell
, vol.11
, pp. 949-956
-
-
Michaels, S.D.1
Amasino, R.M.2
-
38
-
-
4344596213
-
Regulation of flowering time in Arabidopsis by K homol-ogy domain proteins
-
Mockler, T.C., Yu, X., Shalitin, D., Parikh, D., Michael, T.P., Liou, J., Huang, J., Smith, Z., Alonso, J.M., Ecker, J.R., Chory, J., and Lin, C. (2004). Regulation of flowering time in Arabidopsis by K homol-ogy domain proteins. Proc. Natl. Acad. Sci. USA 101: 12759-12764.
-
(2004)
Proc. Natl. Acad. Sci.
, vol.101
, pp. 12759-12764
-
-
Mockler, T.C.1
Yu, X.2
Shalitin, D.3
Parikh, D.4
Michael, T.P.5
Liou, J.6
Huang, J.7
Smith, Z.8
Alonso, J.M.9
Ecker, J.R.10
Chory, J.11
Lin, C.12
-
39
-
-
77949904260
-
Nonsense-mediated mRNA decay in human cells: Mechanistic insights, functions beyond quality control and the double-life of NMD factors
-
Nicholson, P., Yepiskoposyan, H., Metze, S., Zamudio Orozco, R., Kleinschmidt, N., and Mühlemann, O. (2010). Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors. Cell. Mol. Life Sci. 67: 677-700.
-
(2010)
Cell. Mol. Life Sci.
, vol.67
, pp. 677-700
-
-
Nicholson, P.1
Yepiskoposyan, H.2
Metze, S.3
Zamudio Orozco, R.4
Kleinschmidt, N.5
Mühlemann, O.6
-
40
-
-
75849145292
-
Expansion of the eukaryotic proteome by alternative splicing
-
Nilsen, T.W., and Graveley, B.R. (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
-
41
-
-
38949151063
-
Gene silencing in plants using artificial microRNAs and other small RNAs
-
Ossowski, S., Schwab, R., and Weigel, D. (2008). Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J. 53: 674-690.
-
(2008)
Plant J
, vol.53
, pp. 674-690
-
-
Ossowski, S.1
Schwab, R.2
Weigel, D.3
-
42
-
-
33847343883
-
Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: Regulation by hormones and stresses
-
Palusa, S.G., Ali, G.S., and Reddy, A.S. (2007). Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses. Plant J. 49: 1091-1107.
-
(2007)
Plant J
, vol.49
, pp. 1091-1107
-
-
Palusa, S.G.1
Ali, G.S.2
Reddy, A.S.3
-
43
-
-
71249104734
-
Extensive coupling of alternative splicing of pre-mRNAs of serine/arginine (SR) genes with nonsense-mediated decay
-
Palusa, S.G., and Reddy, A.S. (2010). Extensive coupling of alternative splicing of pre-mRNAs of serine/arginine (SR) genes with nonsense-mediated decay. New Phytol. 185: 83-89.
-
(2010)
New Phytol
, vol.185
, pp. 83-89
-
-
Palusa, S.G.1
Reddy, A.S.2
-
44
-
-
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., and Blencowe, B.J. (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
-
45
-
-
77950492625
-
A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy
-
Penfield, S., Josse, E.M., and Halliday, K.J. (2010). A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy. Plant Mol. Biol. 73: 89-95.
-
(2010)
Plant Mol. Biol.
, vol.73
, pp. 89-95
-
-
Penfield, S.1
Josse, E.M.2
Halliday, K.J.3
-
46
-
-
27844432228
-
Cold and light control seed germination through the bHLH transcription factor SPATULA
-
Penfield, S., Josse, E.M., Kannangara, R., Gilday, A.D., Halliday, K.J., and Graham, I.A. (2005). Cold and light control seed germination through the bHLH transcription factor SPATULA. Curr. Biol. 15: 1998-2006.
-
(2005)
Curr. Biol.
, vol.15
, pp. 1998-2006
-
-
Penfield, S.1
Josse, E.M.2
Kannangara, R.3
Gilday, A.D.4
Halliday, K.J.5
Graham, I.A.6
-
47
-
-
75649123777
-
Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabi-dopsis thaliana
-
Raczynska, K.D., Simpson, C.G., Ciesiolka, A., Szewc, L., Lewandowska, D., McNicol, J., Szweykowska-Kulinska, Z., Brown, J.W., and Jarmolowski, A. (2010). Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabi-dopsis thaliana. Nucleic Acids Res. 38: 265-278.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 265-278
-
-
Raczynska, K.D.1
Simpson, C.G.2
Ciesiolka, A.3
Szewc, L.4
Lewandowska, D.5
McNicol, J.6
Szweykowska-Kulinska, Z.7
Brown, J.W.8
Jarmolowski, A.9
-
48
-
-
0034965534
-
Regulation of flowering in Arabidopsis by an FLC homo-logue
-
Ratcliffe, O.J., Nadzan, G.C., Reuber, T.L., and Riechmann, J.L. (2001). Regulation of flowering in Arabidopsis by an FLC homo-logue. Plant Physiol. 126: 122-132.
-
(2001)
Plant Physiol
, vol.126
, pp. 122-132
-
-
Ratcliffe, O.J.1
Nadzan, G.C.2
Reuber, T.L.3
Riechmann, J.L.4
-
49
-
-
34250813107
-
Alternative splicing of pre-messenger RNAs in plants in the genomic era
-
Reddy, A.S. (2007). Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu. Rev. Plant Biol. 58: 267-294.
-
(2007)
Annu. Rev. Plant Biol.
, vol.58
, pp. 267-294
-
-
Reddy, A.S.1
-
50
-
-
84865194709
-
Deciphering the plant splicing code: Experimental and computational approaches for predicting alternative splicing and splicing regulatory elements
-
Reddy, A.S., Rogers, M.F., Richardson, D.N., Hamilton, M., and Ben-Hur, A. (2012). Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Front. Plant Sci. 3: 18.
-
(2012)
Front. Plant Sci.
, vol.3
, pp. 18
-
-
Reddy, A.S.1
Rogers, M.F.2
Richardson, D.N.3
Hamilton, M.4
Ben-Hur, A.5
-
51
-
-
84857714524
-
Plant serine/arginine-rich proteins: Roles in precursor messenger RNA splicing, plant development, and stress responses
-
Reddy, A.S., and Shad Ali, G. (2011). Plant serine/arginine-rich proteins: Roles in precursor messenger RNA splicing, plant development, and stress responses. Wiley Interdiscip. Rev. RNA 2: 875-889.
-
(2011)
Wiley Interdiscip. Rev. RNA
, vol.2
, pp. 875-889
-
-
Reddy, A.S.1
Shad Ali, G.2
-
52
-
-
78149282260
-
A methyl transferase links the circadian clock to the regulation of alternative splicing
-
Sanchez, S.E., et al. (2010). A methyl transferase links the circadian clock to the regulation of alternative splicing. Nature 468: 112-116.
-
(2010)
Nature
, vol.468
, pp. 112-116
-
-
Sanchez, S.E.1
-
53
-
-
33845225902
-
The polypyrimidine tract binding protein (PTB) represses splicing of exon 6B from the beta-tropomyosin pre-mRNA by directly interfering with the binding of the U2AF65 subunit
-
Saulière, J., Sureau, A., Expert-Bezançon, A., and Marie, J. (2006). The polypyrimidine tract binding protein (PTB) represses splicing of exon 6B from the beta-tropomyosin pre-mRNA by directly interfering with the binding of the U2AF65 subunit. Mol. Cell. Biol. 26: 8755-8769.
-
(2006)
Mol. Cell. Biol.
, vol.26
, pp. 8755-8769
-
-
Saulière, J.1
Sureau, A.2
Expert-Bezançon, A.3
Marie, J.4
-
54
-
-
49349112872
-
Polypyrimidine-tract-binding protein: A multifunctional RNA-binding protein
-
Sawicka, K., Bushell, M., Spriggs, K.A., and Willis, A.E. (2008). Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein. Biochem. Soc. Trans. 36: 641-647.
-
(2008)
Biochem. Soc. Trans.
, vol.36
, pp. 641-647
-
-
Sawicka, K.1
Bushell, M.2
Spriggs, K.A.3
Willis, A.E.4
-
55
-
-
84863205849
-
NIH Image to ImageJ: 25 years of image analysis
-
Schneider, C.A., Rasband, W.S., and Eliceiri, K.W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9: 671-675.
-
(2012)
Nat. Methods
, vol.9
, pp. 671-675
-
-
Schneider, C.A.1
Rasband, W.S.2
Eliceiri, K.W.3
-
56
-
-
58749102066
-
Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis
-
Schöning, J.C., Streitner, C., Meyer, I.M., Gao, Y., and Staiger, D. (2008). Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis. Nucleic Acids Res. 36: 6977-6987.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 6977-6987
-
-
Schöning, J.C.1
Streitner, C.2
Meyer, I.M.3
Gao, Y.4
Staiger, D.5
-
57
-
-
84856283171
-
Predicting the impact of alternative splicing on plant MADS domain protein function
-
Severing, E.I., van Dijk, A.D., Morabito, G., Busscher-Lange, J., Immink, R.G., and van Ham, R.C. (2012). Predicting the impact of alternative splicing on plant MADS domain protein function. PLoS ONE 7: e30524.
-
(2012)
PLoS ONE
, vol.7
-
-
Severing, E.I.1
van Dijk, A.D.2
Morabito, G.3
Busscher-Lange, J.4
Immink, R.G.5
van Ham, R.C.6
-
58
-
-
65449181986
-
Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome
-
Severing, E.I., van Dijk, A.D., Stiekema, W.J., and van Ham, R.C. (2009). Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome. BMC Genomics 10: 154.
-
(2009)
BMC Genomics
, vol.10
, pp. 154
-
-
Severing, E.I.1
van Dijk, A.D.2
Stiekema, W.J.3
van Ham, R.C.4
-
59
-
-
23744484618
-
Polypyrimidine tract binding protein blocks the 59 splice site-dependent assembly of U2AF and the prespliceosomal E complex
-
Sharma, S., Falick, A.M., and Black, D.L. (2005). Polypyrimidine tract binding protein blocks the 59 splice site-dependent assembly of U2AF and the prespliceosomal E complex. Mol. Cell 19: 485-496.
-
(2005)
Mol. Cell
, vol.19
, pp. 485-496
-
-
Sharma, S.1
Falick, A.M.2
Black, D.L.3
-
60
-
-
0033101487
-
The FLF MADS box gene: A repressor of flowering in Arabidopsis regulated by vernalization and methylation
-
Sheldon, C.C., Burn, J.E., Perez, P.P., Metzger, J., Edwards, J.A., Peacock, W.J., and Dennis, E.S. (1999). The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11: 445-458.
-
(1999)
Plant Cell
, vol.11
, pp. 445-458
-
-
Sheldon, C.C.1
Burn, J.E.2
Perez, P.P.3
Metzger, J.4
Edwards, J.A.5
Peacock, W.J.6
Dennis, E.S.7
-
61
-
-
40549114298
-
Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts
-
Simpson, C.G., Fuller, J., Maronova, M., Kalyna, M., Davidson, D., McNicol, J., Barta, A., and Brown, J.W. (2008). Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts. Plant J. 53: 1035-1048.
-
(2008)
Plant J
, vol.53
, pp. 1035-1048
-
-
Simpson, C.G.1
Fuller, J.2
Maronova, M.3
Kalyna, M.4
Davidson, D.5
McNicol, J.6
Barta, A.7
Brown, J.W.8
-
62
-
-
34547205013
-
Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1
-
Spellman, R., Llorian, M., and Smith, C.W. (2007). Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol. Cell 27: 420-434.
-
(2007)
Mol. Cell
, vol.27
, pp. 420-434
-
-
Spellman, R.1
Llorian, M.2
Smith, C.W.3
-
63
-
-
32344437827
-
Novel modes of splicing repression by PTB
-
Spellman, R., and Smith, C.W. (2006). Novel modes of splicing repression by PTB. Trends Biochem. Sci. 31: 73-76.
-
(2006)
Trends Biochem. Sci.
, vol.31
, pp. 73-76
-
-
Spellman, R.1
Smith, C.W.2
-
64
-
-
80053318065
-
RNA-based regulation in the plant circadian clock
-
Staiger, D., and Green, R. (2011). RNA-based regulation in the plant circadian clock. Trends Plant Sci. 16: 517-523.
-
(2011)
Trends Plant Sci.
, vol.16
, pp. 517-523
-
-
Staiger, D.1
Green, R.2
-
65
-
-
0037266853
-
The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA
-
Staiger, D., Zecca, L., Wieczorek Kirk, D.A., Apel, K., and Eckstein, L. (2003). The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA. Plant J. 33: 361-371.
-
(2003)
Plant J
, vol.33
, pp. 361-371
-
-
Staiger, D.1
Zecca, L.2
Wieczorek Kirk, D.A.3
Apel, K.4
Eckstein, L.5
-
66
-
-
78649550144
-
Polypyrimidine tract-binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and downstream control
-
Stauffer, E., Westermann, A., Wagner, G., and Wachter, A. (2010). Polypyrimidine tract-binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and downstream control. Plant J. 64: 243-255.
-
(2010)
Plant J
, vol.64
, pp. 243-255
-
-
Stauffer, E.1
Westermann, A.2
Wagner, G.3
Wachter, A.4
-
67
-
-
78650552020
-
Statistical tests for detecting differential RNA-transcript expression from read counts
-
May 11, 10.1038/npre.2010.4437.1
-
Stegle, O., Drewe, P., Bohnert, R., Borgwardt, K.M., and Rätsch, G. (May 11, 2010). Statistical tests for detecting differential RNA-transcript expression from read counts. Nat. Preced. 10.1038/npre.2010.4437.1.
-
(2010)
Nat. Preced
-
-
Stegle, O.1
Drewe, P.2
Bohnert, R.3
Borgwardt, K.M.4
Rätsch, G.5
-
68
-
-
53549122472
-
The small glycine-rich RNA binding protein AtGRP7 promotes floral transition in Arabidopsis thaliana
-
Streitner, C., Danisman, S., Wehrle, F., Schöning, J.C., Alfano, J.R., and Staiger, D. (2008). The small glycine-rich RNA binding protein AtGRP7 promotes floral transition in Arabidopsis thaliana. Plant J. 56: 239-250.
-
(2008)
Plant J
, vol.56
, pp. 239-250
-
-
Streitner, C.1
Danisman, S.2
Wehrle, F.3
Schöning, J.C.4
Alfano, J.R.5
Staiger, D.6
-
69
-
-
77955900005
-
The conserved splicing factor SUA controls alternative splicing of the developmental regulator ABI3 in Arabidopsis
-
Sugliani, M., Brambilla, V., Clerkx, E.J., Koornneef, M., and Soppe, W.J. (2010). The conserved splicing factor SUA controls alternative splicing of the developmental regulator ABI3 in Arabidopsis. Plant Cell 22: 1936-1946.
-
(2010)
Plant Cell
, vol.22
, pp. 1936-1946
-
-
Sugliani, M.1
Brambilla, V.2
Clerkx, E.J.3
Koornneef, M.4
Soppe, W.J.5
-
70
-
-
72049133207
-
Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target
-
Swiezewski, S., Liu, F., Magusin, A., and Dean, C. (2009). Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462: 799-802.
-
(2009)
Nature
, vol.462
, pp. 799-802
-
-
Swiezewski, S.1
Liu, F.2
Magusin, A.3
Dean, C.4
-
71
-
-
84866843094
-
Alternative splicing in plants - Coming of age
-
Syed, N.H., Kalyna, M., Marquez, Y., Barta, A., and Brown, J.W. (2012). Alternative splicing in plants - Coming of age. Trends Plant Sci. 17: 616-623.
-
(2012)
Trends Plant Sci.
, vol.17
, pp. 616-623
-
-
Syed, N.H.1
Kalyna, M.2
Marquez, Y.3
Barta, A.4
Brown, J.W.5
-
72
-
-
51149118484
-
Regulation of flowering time by RNA processing
-
Terzi, L.C., and Simpson, G.G. (2008). Regulation of flowering time by RNA processing. Curr. Top. Microbiol. Immunol. 326: 201-218.
-
(2008)
Curr. Top. Microbiol. Immunol.
, vol.326
, pp. 201-218
-
-
Terzi, L.C.1
Simpson, G.G.2
-
73
-
-
12144291195
-
MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
-
Thimm, O., Bläsing, O., Gibon, Y., Nagel, A., Meyer, S., Krüger, P., Selbig, J., Müller, L.A., Rhee, S.Y., and Stitt, M. (2004). MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37: 914-939.
-
(2004)
Plant J
, vol.37
, pp. 914-939
-
-
Thimm, O.1
Bläsing, O.2
Gibon, Y.3
Nagel, A.4
Meyer, S.5
Krüger, P.6
Selbig, J.7
Müller, L.A.8
Rhee, S.Y.9
Stitt, M.10
-
74
-
-
85011940612
-
Riboswitch-mediated control of gene expression in eukaryotes
-
Wachter, A. (2010). Riboswitch-mediated control of gene expression in eukaryotes. RNA Biol. 7: 67-76.
-
(2010)
RNA Biol
, vol.7
, pp. 67-76
-
-
Wachter, A.1
-
75
-
-
84871188835
-
The role of poly-pyrimidine tract-binding proteins and other hnRNP proteins in plant splicing regulation
-
Wachter, A., Rühl, C., and Stauffer, E. (2012). The role of poly-pyrimidine tract-binding proteins and other hnRNP proteins in plant splicing regulation. Front. Plant Sci. 3: 81.
-
(2012)
Front. Plant Sci.
, vol.3
, pp. 81
-
-
Wachter, A.1
Rühl, C.2
Stauffer, E.3
-
76
-
-
37849045636
-
Riboswitch control of gene expression in plants by splicing and alternative 39 end processing of mRNAs
-
Wachter, A., Tunc-Ozdemir, M., Grove, B.C., Green, P.J., Shintani, D.K., and Breaker, R.R. (2007). Riboswitch control of gene expression in plants by splicing and alternative 39 end processing of mRNAs. Plant Cell 19: 3437-3450.
-
(2007)
Plant Cell
, vol.19
, pp. 3437-3450
-
-
Wachter, A.1
Tunc-Ozdemir, M.2
Grove, B.C.3
Green, P.J.4
Shintani, D.K.5
Breaker, R.R.6
-
77
-
-
33646484347
-
Genomewide comparative analysis of alternative splicing in plants
-
Wang, B.B., and Brendel, V. (2006). Genomewide comparative analysis of alternative splicing in plants. Proc. Natl. Acad. Sci. USA 103: 7175-7180.
-
(2006)
Proc. Natl. Acad. Sci.
, vol.103
, pp. 7175-7180
-
-
Wang, B.B.1
Brendel, V.2
-
78
-
-
60149092037
-
Involvement of polypyrimidine tract-binding protein (PTB)-related proteins in pollen germination in Arabidopsis
-
Wang, S., and Okamoto, T. (2009). Involvement of polypyrimidine tract-binding protein (PTB)-related proteins in pollen germination in Arabidopsis. Plant Cell Physiol. 50: 179-190.
-
(2009)
Plant Cell Physiol
, vol.50
, pp. 179-190
-
-
Wang, S.1
Okamoto, T.2
-
79
-
-
0346124413
-
Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay
-
Wollerton, M.C., Gooding, C., Wagner, E.J., Garcia-Blanco, M.A., and Smith, C.W. (2004). Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol. Cell 13: 91-100.
-
(2004)
Mol. Cell
, vol.13
, pp. 91-100
-
-
Wollerton, M.C.1
Gooding, C.2
Wagner, E.J.3
Garcia-Blanco, M.A.4
Smith, C.W.5
-
80
-
-
72149117411
-
Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping
-
Xue, Y., Zhou, Y., Wu, T., Zhu, T., Ji, X., Kwon, Y.S., Zhang, C., Yeo, G., Black, D.L., Sun, H., Fu, X.D., and Zhang, Y. (2009). Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol. Cell 36: 996-1006.
-
(2009)
Mol. Cell
, vol.36
, pp. 996-1006
-
-
Xue, Y.1
Zhou, Y.2
Wu, T.3
Zhu, T.4
Ji, X.5
Kwon, Y.S.6
Zhang, C.7
Yeo, G.8
Black, D.L.9
Sun, H.10
Fu, X.D.11
Zhang, Y.12
-
81
-
-
84861778204
-
Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention
-
Yap, K., Lim, Z.Q., Khandelia, P., Friedman, B., and Makeyev, E.V. (2012). Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention. Genes Dev. 26: 1209-1223.
-
(2012)
Genes Dev.
, vol.26
, pp. 1209-1223
-
-
Yap, K.1
Lim, Z.Q.2
Khandelia, P.3
Friedman, B.4
Makeyev, E.V.5
-
82
-
-
77950545365
-
Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq
-
Zenoni, S., Ferrarini, A., Giacomelli, E., Xumerle, L., Fasoli, M., Malerba, G., Bellin, D., Pezzotti, M., and Delledonne, M. (2010). Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol. 152: 1787-1795.
-
(2010)
Plant Physiol
, vol.152
, pp. 1787-1795
-
-
Zenoni, S.1
Ferrarini, A.2
Giacomelli, E.3
Xumerle, L.4
Fasoli, M.5
Malerba, G.6
Bellin, D.7
Pezzotti, M.8
Delledonne, M.9
-
83
-
-
77951871117
-
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
-
Zhang, G., et al. (2010). Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res. 20: 646-654.
-
(2010)
Genome Res
, vol.20
, pp. 646-654
-
-
Zhang, G.1
|