-
1
-
-
84900813109
-
Genomeview: Visualizing the next-generation of data
-
Abeel, T. (2011). Genomeview: visualizing the next-generation of data. J. Biomol. Tech. 22(Suppl.),:S19.
-
(2011)
J. Biomol. Tech.
, vol.22
, Issue.SUPPL.
-
-
Abeel, T.1
-
2
-
-
31544461505
-
Alternative splicing regulation at tandem 3' splice sites
-
Akerman, M., and Mandel-Gutfreund, Y. (2006). Alternative splicing regulation at tandem 3' splice sites. Nucleic Acids Res. 34, 23-31.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 23-31
-
-
Akerman, M.1
Mandel-Gutfreund, Y.2
-
3
-
-
67650299463
-
Control of alternative splicing through sirna-mediated transcriptional gene silencing
-
Allo, M., Buggiano, V., Fededa, J. P., Petrillo, E., Schor, I., de la Mata, M., Agirre, E., Plass, M., Eyras, E., Elela, S. A., Klinck, R., Chabot, B., and Kornblihtt, A. R. (2009). Control of alternative splicing through sirna-mediated transcriptional gene silencing. Nat. Struct. Mol. Biol. 16, 717-724.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 717-724
-
-
Allo, M.1
Buggiano, V.2
Fededa, J.P.3
Petrillo, E.4
Schor, I.5
de la Mata, M.6
Agirre, E.7
Plass, M.8
Eyras, E.9
Elela, S.A.10
Klinck, R.11
Chabot, B.12
Kornblihtt, A.R.13
-
4
-
-
33745817833
-
UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis
-
Arciga-Reyes, L., Wootton, L., Kieffer, M., and Davies, B. (2006). UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis. Plant J. 47, 480-489.
-
(2006)
Plant J.
, vol.47
, pp. 480-489
-
-
Arciga-Reyes, L.1
Wootton, L.2
Kieffer, M.3
Davies, B.4
-
5
-
-
77955443472
-
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
-
Au, K. F., Jiang, H., Lin, L., Xing, Y., and Wong, W. H. (2010). Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res. 38, 4570.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 4570
-
-
Au, K.F.1
Jiang, H.2
Lin, L.3
Xing, Y.4
Wong, W.H.5
-
6
-
-
45049087666
-
Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice
-
Baek, J. M., Han, P., Iandolino, A., and Cook, D. R. (2008). Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice. Plant Mol. Biol. 67, 499-510.
-
(2008)
Plant Mol. Biol.
, vol.67
, pp. 499-510
-
-
Baek, J.M.1
Han, P.2
Iandolino, A.3
Cook, D.R.4
-
7
-
-
77952029221
-
Deciphering the splicing code
-
Barash, Y., Calarco, J. A., Gao, W., Pan, Q., Wang, X., Shai, O., Blencowe, B. J., and Frey, B. J. (2010a). Deciphering the splicing code. Nature 465, 53-59.
-
(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
-
8
-
-
77954196300
-
Model-based detection of alternative splicing signals
-
Barash, Y., Blencowe, B. J., and Frey, B. J. (2010b). Model-based detection of alternative splicing signals. Bioinformatics 26, i325-i33.
-
(2010)
Bioinformatics
, vol.26
-
-
Barash, Y.1
Blencowe, B.J.2
Frey, B.J.3
-
9
-
-
77957317662
-
A conserved alternative splicing event in plants reveals an ancient exonization of 5s rRNA that regulates TFIIIA
-
Barbazuk, W. B. (2010). A conserved alternative splicing event in plants reveals an ancient exonization of 5s rRNA that regulates TFIIIA. RNA Biol. 7, 397-402.
-
(2010)
RNA Biol.
, vol.7
, pp. 397-402
-
-
Barbazuk, W.B.1
-
10
-
-
50649109231
-
Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
-
Barbazuk, W. B., Fu, Y., and McGinnis, K. M. (2008). Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res. 18, 1381-1392.
-
(2008)
Genome Res.
, vol.18
, pp. 1381-1392
-
-
Barbazuk, W.B.1
Fu, Y.2
McGinnis, K.M.3
-
11
-
-
73949131510
-
Genome-wide analysis of RNA-protein interactions in plants
-
Barkan, A. (2009). Genome-wide analysis of RNA-protein interactions in plants. Methods Mol. Biol. 553, 13-37.
-
(2009)
Methods Mol. Biol.
, vol.553
, pp. 13-37
-
-
Barkan, A.1
-
12
-
-
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
-
13
-
-
30044441988
-
The human SWI/SNF subunit Brm is a regulator of alternative splicing
-
Batsche, E., Yaniv, M., and Muchardt, C. (2006). The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat. Struct. Mol. Biol. 13, 22-29.
-
(2006)
Nat. Struct. Mol. Biol.
, vol.13
, pp. 22-29
-
-
Batsche, E.1
Yaniv, M.2
Muchardt, C.3
-
14
-
-
70350664649
-
De novo transcriptome assembly with ABySS
-
Birol, I., Jackman, S. D., Nielsen, C. B., Qian, J. Q., Varhol, R., Stazyk, G., Morin, R. D., Zhao, Y., Hirst, M., Schein, J. E., Horsman, D. E., Connors, J. M., Gascoyne, R. D., Marra, M. A., and Jones, S. J. (2009). De novo transcriptome assembly with ABySS. Bioinformatics 25, 2872.
-
(2009)
Bioinformatics
, vol.25
, pp. 2872
-
-
Birol, I.1
Jackman, S.D.2
Nielsen, C.B.3
Qian, J.Q.4
Varhol, R.5
Stazyk, G.6
Morin, R.D.7
Zhao, Y.8
Hirst, M.9
Schein, J.E.10
Horsman, D.E.11
Connors, J.M.12
Gascoyne, R.D.13
Marra, M.A.14
Jones, S.J.15
-
15
-
-
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
-
16
-
-
0034161419
-
Exonic splicing enhancers: Mechanism of action, diversity and role in human genetic diseases
-
Blencowe, B. J. (2000). Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem. Sci. 25, 106-110.
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 106-110
-
-
Blencowe, B.J.1
-
17
-
-
33745899048
-
Alternative splicing: New insights from global analyses
-
Blencowe, B. J. (2006). Alternative splicing: new insights from global analyses. Cell 126, 37-47.
-
(2006)
Cell
, vol.126
, pp. 37-47
-
-
Blencowe, B.J.1
-
18
-
-
67149098194
-
Current-generation high-throughput sequencing: Deepening insights into mammalian transcriptomes
-
Blencowe, B. J., Ahmad, S., and Lee, L. J. (2009). Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev. 23, 1379.
-
(2009)
Genes Dev.
, vol.23
, pp. 1379
-
-
Blencowe, B.J.1
Ahmad, S.2
Lee, L.J.3
-
19
-
-
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
-
20
-
-
53149095767
-
Switching the light on plant riboswitches
-
Bocobza, S. E., and Aharoni, A. (2008). Switching the light on plant riboswitches. Trends Plant Sci. 13, 526-533.
-
(2008)
Trends Plant Sci.
, vol.13
, pp. 526-533
-
-
Bocobza, S.E.1
Aharoni, A.2
-
21
-
-
58149216663
-
Detecting alternative gene structures from spliced ESTs: A computational approach
-
Bonizzoni, P., Mauri, G., Pesole, G., Picardi, E., Pirola, Y., and Rizzi, R. (2009). Detecting alternative gene structures from spliced ESTs: a computational approach. J. Comput. Biol. 16, 43-66.
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 43-66
-
-
Bonizzoni, P.1
Mauri, G.2
Pesole, G.3
Picardi, E.4
Pirola, Y.5
Rizzi, R.6
-
22
-
-
0030295312
-
Arabidopsis intron mutations and pre-mRNA splicing
-
Brown, J. W. (1996). Arabidopsis intron mutations and pre-mRNA splicing. Plant J. 10, 771-780.
-
(1996)
Plant J.
, vol.10
, pp. 771-780
-
-
Brown, J.W.1
-
23
-
-
18044379515
-
Microarray identification of fmrp-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome
-
Brown, V., Jin, P., Ceman, S., Darnell, J. C., O'Donnell, W. T., Tenenbaum, S. A., Jin, X., Feng, Y., Wilkinson, K. D., Keene, J. D., Darnell, R. B., and Warren, S. T. (2001). Microarray identification of fmrp-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 107, 477-487.
-
(2001)
Cell
, vol.107
, pp. 477-487
-
-
Brown, V.1
Jin, P.2
Ceman, S.3
Darnell, J.C.4
O'Donnell, W.T.5
Tenenbaum, S.A.6
Jin, X.7
Feng, Y.8
Wilkinson, K.D.9
Keene, J.D.10
Darnell, R.B.11
Warren, S.T.12
-
24
-
-
10044274340
-
Influence of RNA secondary structure on the pre-mRNA splicing process
-
Buratti, E., and Baralle, F. E. (2004). Influence of RNA secondary structure on the pre-mRNA splicing process. Mol. Cell Biol. 24, 10505-10514.
-
(2004)
Mol. Cell Biol.
, vol.24
, pp. 10505-10514
-
-
Buratti, E.1
Baralle, F.E.2
-
25
-
-
1642458353
-
RNA folding affects the recruitment of SR proteins by mouse and human polypurinic enhancer elements in the fibronectin EDA exon
-
Buratti, E., Muro, A. F., Giombi, M., Gherbassi, D., Iaconcig, A., and Baralle, F. E. (2004). RNA folding affects the recruitment of SR proteins by mouse and human polypurinic enhancer elements in the fibronectin EDA exon. Mol. Cell Biol. 24, 1387-1400.
-
(2004)
Mol. Cell Biol.
, vol.24
, pp. 1387-1400
-
-
Buratti, E.1
Muro, A.F.2
Giombi, M.3
Gherbassi, D.4
Iaconcig, A.5
Baralle, F.E.6
-
26
-
-
33846573830
-
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
-
doi:10.1186/1471-2164-7-327
-
Campbell, M. A., Haas, B. J., Hamilton, J. P., Mount, S. M., and Buell, C. R. (2006). Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7, 327. doi:10.1186/1471-2164-7-327
-
(2006)
BMC Genomics
, vol.7
, pp. 327
-
-
Campbell, M.A.1
Haas, B.J.2
Hamilton, J.P.3
Mount, S.M.4
Buell, C.R.5
-
27
-
-
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
-
28
-
-
42449129287
-
Searching for splicing motifs
-
Chasin, L. A. (2007). Searching for splicing motifs. Adv. Exp. Med. Biol. 623, 85-106.
-
(2007)
Adv. Exp. Med. Biol.
, vol.623
, pp. 85-106
-
-
Chasin, L.A.1
-
29
-
-
37849016921
-
Systematic analysis of alternative first exons in plant genomes
-
doi:10.1186/1471-2164-7-327
-
Chen, W. H., Lv, G., Lv, C., Zeng, C., and Hu, S. (2007). Systematic analysis of alternative first exons in plant genomes. BMC Plant Biol. 7, 55. doi:10.1186/1471-2164-7-327
-
(2007)
BMC Plant Biol.
, vol.7
, pp. 55
-
-
Chen, W.H.1
Lv, G.2
Lv, C.3
Zeng, C.4
Hu, S.5
-
30
-
-
70350227275
-
Small RNAs and their roles in plant development
-
Chen, X. (2009). Small RNAs and their roles in plant development. Annu. Rev. Cell Dev. Biol. 25, 21-44.
-
(2009)
Annu. Rev. Cell Dev. Biol.
, vol.25
, pp. 21-44
-
-
Chen, X.1
-
31
-
-
77954659099
-
Relationship between nucleosome positioning and DNA methylation
-
Chodavarapu, R. K., Feng, S., Bernatavichute, Y. V., Chen, P. Y., Stroud, H., Yu, Y., Hetzel, J. A., Kuo, F., Kim, J., Cokus, S. J., Casero, D., Bernal, M., Huijser, P., Clark, A. T., Kramer, U., Merchant, S. S., Zhang, X., Jacobsen, S. E., and Pellegrini, M. (2010). Relationship between nucleosome positioning and DNA methylation. Nature 466, 388-392.
-
(2010)
Nature
, vol.466
, pp. 388-392
-
-
Chodavarapu, R.K.1
Feng, S.2
Bernatavichute, Y.V.3
Chen, P.Y.4
Stroud, H.5
Yu, Y.6
Hetzel, J.A.7
Kuo, F.8
Kim, J.9
Cokus, S.J.10
Casero, D.11
Bernal, M.12
Huijser, P.13
Clark, A.T.14
Kramer, U.15
Merchant, S.S.16
Zhang, X.17
Jacobsen, S.E.18
Pellegrini, M.19
-
32
-
-
0037012922
-
Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays
-
Clark, T. A., Sugnet, C. W., and Ares, M. (2002). Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296, 907.
-
(2002)
Science
, vol.296
, pp. 907
-
-
Clark, T.A.1
Sugnet, C.W.2
Ares, M.3
-
33
-
-
77955393112
-
Uncovering the complexity of transcriptomes with RNA-seq
-
Costa, V., Angelini, C., De Feis, I., and Ciccodicola, A. (2010). Uncovering the complexity of transcriptomes with RNA-seq. J. Biomed. Biotechnol. 2010, 1-19.
-
(2010)
J. Biomed. Biotechnol.
, vol.2010
, pp. 1-19
-
-
Costa, V.1
Angelini, C.2
De Feis, I.3
Ciccodicola, A.4
-
34
-
-
38049169167
-
Thiamine biosynthesis in algae is regulated by riboswitches
-
Croft, M. T., Moulin, M., Webb, M. E., and Smith, A. G. (2007). Thiamine biosynthesis in algae is regulated by riboswitches. Proc. Natl. Acad. Sci. U.S.A. 104, 20770-20775.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 20770-20775
-
-
Croft, M.T.1
Moulin, M.2
Webb, M.E.3
Smith, A.G.4
-
35
-
-
33750062619
-
Data analysis of alternative splicing microarrays
-
Cuperlovic-Culf, M., Belacel, N., Culf, A. S., and Ouellette, R. J. (2006). Data analysis of alternative splicing microarrays. Drug Discov. Today 11, 983-990.
-
(2006)
Drug Discov. Today
, vol.11
, pp. 983-990
-
-
Cuperlovic-Culf, M.1
Belacel, N.2
Culf, A.S.3
Ouellette, R.J.4
-
36
-
-
77953928753
-
HITS-CLIP: Panoramice views of protein-RNA regulation in living cells
-
Darnell, R. B. (2010). HITS-CLIP: panoramice views of protein-RNA regulation in living cells. Wiley Interdiscip. Rev. RNA 1, 266-286.
-
(2010)
Wiley Interdiscip. Rev. RNA
, vol.1
, pp. 266-286
-
-
Darnell, R.B.1
-
37
-
-
16344396421
-
Accurate identification of alternatively spliced exons using support vector machine
-
Dror, G., Sorek, R., and Shamir, R. (2005). Accurate identification of alternatively spliced exons using support vector machine. Bioinformatics 21, 897-901.
-
(2005)
Bioinformatics
, vol.21
, pp. 897-901
-
-
Dror, G.1
Sorek, R.2
Shamir, R.3
-
38
-
-
84934439405
-
Pre-processing of microarray data and analysis of differential expression
-
Durinck, S. (2008). Pre-processing of microarray data and analysis of differential expression. Methods Mol. Biol. 452, 89.
-
(2008)
Methods Mol. Biol.
, vol.452
, pp. 89
-
-
Durinck, S.1
-
39
-
-
0031279984
-
Structural analysis of elements contributing to 5' splice site selection in plant pre-mRNA transcripts
-
Egoavil, C., Marton, H. A., Baynton, C. E., McCullough, A. J., and Schuler, M. A. (1997). Structural analysis of elements contributing to 5' splice site selection in plant pre-mRNA transcripts. Plant J. 12, 971-980.
-
(1997)
Plant J.
, vol.12
, pp. 971-980
-
-
Egoavil, C.1
Marton, H.A.2
Baynton, C.E.3
McCullough, A.J.4
Schuler, M.A.5
-
40
-
-
0037047644
-
Predictive identification of exonic splicing enhancers in human genes
-
Fairbrother, W. G., Yeh, R. F., Sharp, P. A., and Burge, C. B. (2002). Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007-1013.
-
(2002)
Science
, vol.297
, pp. 1007-1013
-
-
Fairbrother, W.G.1
Yeh, R.F.2
Sharp, P.A.3
Burge, C.B.4
-
41
-
-
79955756836
-
Design and validation issues in RNA-seq experiments
-
Fang, Z., and Cui, X. (2011). Design and validation issues in RNA-seq experiments. Brief. Bioinformatics 12, 280.
-
(2011)
Brief. Bioinformatics
, vol.12
, pp. 280
-
-
Fang, Z.1
Cui, X.2
-
42
-
-
79952389472
-
Inference of isoforms from short sequence reads
-
Feng, J., Li, W., and Jiang, T. (2011). Inference of isoforms from short sequence reads. J. Comput. Biol. 18, 305-321.
-
(2011)
J. Comput. Biol.
, vol.18
, pp. 305-321
-
-
Feng, J.1
Li, W.2
Jiang, T.3
-
43
-
-
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
-
44
-
-
0002976257
-
Pre-mRNA splicing in plants
-
Filipowicz, W., Gniadkowski, M., Klahre, U., and Liu, H.-X. (1995). Pre-mRNA splicing in plants. Trends Plant Sci. 4, 65-77.
-
(1995)
Trends Plant Sci.
, vol.4
, pp. 65-77
-
-
Filipowicz, W.1
Gniadkowski, M.2
Klahre, U.3
Liu, H.-X.4
-
45
-
-
77955433415
-
Savant: Genome browser for high-throughput sequencing data
-
Fiume, M., Williams, V., Brook, A., and Brudno, M. (2010). Savant: genome browser for high-throughput sequencing data. Bioinformatics 26, 1938-1944.
-
(2010)
Bioinformatics
, vol.26
, pp. 1938-1944
-
-
Fiume, M.1
Williams, V.2
Brook, A.3
Brudno, M.4
-
46
-
-
66049155420
-
Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA
-
Fu, Y., Bannach, O., Chen, H., Teune, J. H., Schmitz, A., Steger, G., Xiong, L., and Barbazuk, W. B. (2009). Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA. Genome Res. 19, 913-921.
-
(2009)
Genome Res.
, vol.19
, pp. 913-921
-
-
Fu, Y.1
Bannach, O.2
Chen, H.3
Teune, J.H.4
Schmitz, A.5
Steger, G.6
Xiong, L.7
Barbazuk, W.B.8
-
47
-
-
77249084320
-
Overestimation of alternative splicing caused by variable probe characteristics in exon arrays
-
Gaidatzis, D., Jacobeit, K., Oakeley, E. J., and Stadler, M. B. (2009). Overestimation of alternative splicing caused by variable probe characteristics in exon arrays. Nucleic Acids Res. 37, e107.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Gaidatzis, D.1
Jacobeit, K.2
Oakeley, E.J.3
Stadler, M.B.4
-
48
-
-
80053132716
-
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
-
Gan, X., Stegle, O., Behr, J., Steffen, J. G., Drewe, P., Hildebrand, K. L., Lyngsoe, R., Schultheiss, S. J., Osborne, E. J., Sreedharan, V. T., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E. J., Harberd, N. P., Kemen, E., Toomajian, C., Kover, P. X., Clark, R. M., Ratsch, G., and Mott, R. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477, 419-423.
-
(2011)
Nature
, vol.477
, pp. 419-423
-
-
Gan, X.1
Stegle, O.2
Behr, J.3
Steffen, J.G.4
Drewe, P.5
Hildebrand, K.L.6
Lyngsoe, R.7
Schultheiss, S.J.8
Osborne, E.J.9
Sreedharan, V.T.10
Kahles, A.11
Bohnert, R.12
Jean, G.13
Derwent, P.14
Kersey, P.15
Belfield, E.J.16
Harberd, N.P.17
Kemen, E.18
Toomajian, C.19
Kover, P.X.20
Clark, R.M.21
Ratsch, G.22
Mott, R.23
more..
-
49
-
-
0029664611
-
Characterization of intronic uridine-rich sequence elements acting as possible targets for nuclear proteins during pre-mRNA splicing in Nicotiana plumbaginifolia
-
Gniadkowski, M., Hemmings-Mieszczak, M., Klahre, U., Liu, H. X., and Filipowicz, W. (1996). Characterization of intronic uridine-rich sequence elements acting as possible targets for nuclear proteins during pre-mRNA splicing in Nicotiana plumbaginifolia. Nucleic Acids Res. 24, 619-627.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 619-627
-
-
Gniadkowski, M.1
Hemmings-Mieszczak, M.2
Klahre, U.3
Liu, H.X.4
Filipowicz, W.5
-
50
-
-
84858593012
-
The iPlant collaborative: Cyberinfrastructure for plant biology
-
doi:10.3389/fpls.2011.00034
-
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M., Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W. H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S.-J., Kvilekval, K., Manjunath, B. S., Tannen, V., Stamatakis, A., Sanderson, M., Welch, S. M., Cranston, K. A., Soltis, P., Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D. J., White, J. W., Leebens-Mack, J., Donoghue, M. J., Spalding, E. P., Vision, T. J., Myers, C. R., Lowenthal, D., Enquist, B. J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., and Stanzione, D. (2011). The iPlant collaborative: cyberinfrastructure for plant biology. Front. Plant Sci. 2:34. doi:10.3389/fpls.2011.00034
-
(2011)
Front. Plant Sci.
, vol.2
, pp. 34
-
-
Goff, S.A.1
Vaughn, M.2
McKay, S.3
Lyons, E.4
Stapleton, A.E.5
Gessler, D.6
Matasci, N.7
Wang, L.8
Hanlon, M.9
Lenards, A.10
Muir, A.11
Merchant, N.12
Lowry, S.13
Mock, S.14
Helmke, M.15
Kubach, A.16
Narro, M.17
Hopkins, N.18
Micklos, D.19
Hilgert, U.20
Gonzales, M.21
Jordan, C.22
Skidmore, E.23
Dooley, R.24
Cazes, J.25
McLay, R.26
Lu, Z.27
Pasternak, S.28
Koesterke, L.29
Piel, W.H.30
Grene, R.31
Noutsos, C.32
Gendler, K.33
Feng, X.34
Tang, C.35
Lent, M.36
Kim, S.-J.37
Kvilekval, K.38
Manjunath, B.S.39
Tannen, V.40
Stamatakis, A.41
Sanderson, M.42
Welch, S.M.43
Cranston, K.A.44
Soltis, P.45
Soltis, D.46
O'Meara, B.47
Ane, C.48
Brutnell, T.49
Kleibenstein, D.J.50
White, J.W.51
Leebens-Mack, J.52
Donoghue, M.J.53
Spalding, E.P.54
Vision, T.J.55
Myers, C.R.56
Lowenthal, D.57
Enquist, B.J.58
Boyle, B.59
Akoglu, A.60
Andrews, G.61
Ram, S.62
Ware, D.63
Stein, L.64
Stanzione, D.65
more..
-
51
-
-
0024967250
-
The au-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing
-
Goodall, G. J., and Filipowicz, W. (1989). The au-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell 58, 473-483.
-
(1989)
Cell
, vol.58
, pp. 473-483
-
-
Goodall, G.J.1
Filipowicz, W.2
-
52
-
-
79960264362
-
Full-length transcriptome assembly from RNA-seq data without a reference genome
-
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B. W., Nusbaum, C., Lindblad-Toh, K., Friedman, N., and Regev, A. (2011). Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644-652.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
Chen, Z.11
Mauceli, E.12
Hacohen, N.13
Gnirke, A.14
Rhind, N.15
di Palma, F.16
Birren, B.W.17
Nusbaum, C.18
Lindblad-Toh, K.19
Friedman, N.20
Regev, A.21
more..
-
53
-
-
53449084204
-
Analysis and management of microarray gene expression data
-
19.6.1-19.6.30
-
Grant, G. R., Manduchi, E., and Stoeckert, C. J. Jr. (2007). Analysis and management of microarray gene expression data. Curr. Protoc. Mol. Biol. 77, 19.6.1-19.6.30.
-
(2007)
Curr. Protoc. Mol. Biol.
, vol.77
-
-
Grant, G.R.1
Manduchi, E.2
Stoeckert Jr., C.J.3
-
54
-
-
34247850935
-
Genome-wide detection and analysis of alternative splicing for nucleotide binding site-leucine-rich repeats sequences in rice
-
Gu, L., and Guo, R. (2007). Genome-wide detection and analysis of alternative splicing for nucleotide binding site-leucine-rich repeats sequences in rice. J. Genet. Genomics 34, 247-257.
-
(2007)
J. Genet. Genomics
, vol.34
, pp. 247-257
-
-
Gu, L.1
Guo, R.2
-
55
-
-
73349116881
-
Acetylation by the transcriptional coactivator Gcn5 plays a novel role in co-transcriptional spliceosome assembly
-
doi:10.1371/journal.pgen.1000682
-
Gunderson, F. Q., and Johnson, T. L. (2009). Acetylation by the transcriptional coactivator Gcn5 plays a novel role in co-transcriptional spliceosome assembly. PLoS Genet. 5, e1000682. doi:10.1371/journal.pgen.1000682
-
(2009)
PLoS Genet.
, vol.5
-
-
Gunderson, F.Q.1
Johnson, T.L.2
-
56
-
-
77953600890
-
Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
-
doi:10.1186/1471-2164-11-384
-
Guo, S., Zheng, Y., Joung, J. G., Liu, S., Zhang, Z., Crasta, O. R., Sobral, B. W., Xu, Y., Huang, S., and Fei, Z. (2010). Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics 11, 384. doi:10.1186/1471-2164-11-384
-
(2010)
BMC Genomics
, vol.11
, pp. 384
-
-
Guo, S.1
Zheng, Y.2
Joung, J.G.3
Liu, S.4
Zhang, Z.5
Crasta, O.R.6
Sobral, B.W.7
Xu, Y.8
Huang, S.9
Fei, Z.10
-
57
-
-
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., Rinn, J. L., Lander, E. S., and Regev, A. (2010). Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic 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
Rinn, J.L.11
Lander, E.S.12
Regev, A.13
-
58
-
-
0141905891
-
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
-
Haas, B. J., Delcher, A. L., Mount, S. M., Wortman, J. R., Smith, R. K. Jr., Hannick, L. I., Maiti, R., Ronning, C. M., Rusch, D. B., Town, C. D., Salzberg, S. L., and White, O. (2003). Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5654
-
-
Haas, B.J.1
Delcher, A.L.2
Mount, S.M.3
Wortman, J.R.4
Smith Jr., R.K.5
Hannick, L.I.6
Maiti, R.7
Ronning, C.M.8
Rusch, D.B.9
Town, C.D.10
Salzberg, S.L.11
White, O.12
-
59
-
-
77950920903
-
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
-
Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A. Jr., Ascano, M., Jungkamp, A. C., Munschauer, M., Ulrich, A., Wardle, G. S., Dewell, S., Zavolan, M., and Tuschl, T. (2010a). Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129-141.
-
(2010)
Cell
, vol.141
, pp. 129-141
-
-
Hafner, M.1
Landthaler, M.2
Burger, L.3
Khorshid, M.4
Hausser, J.5
Berninger, P.6
Rothballer Jr., A.7
Ascano, M.8
Jungkamp, A.C.9
Munschauer, M.10
Ulrich, A.11
Wardle, G.S.12
Dewell, S.13
Zavolan, M.14
Tuschl, T.15
-
60
-
-
80055101895
-
PAR-CliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins
-
doi:10.3791/2034
-
Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M., Jungkamp, A. C., Munschauer, M., Ulrich, A., Wardle, G. S., Dewell, S., Zavolan, M., and Tuschl, T. (2010b). PAR-CliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins. J. Vis. Exp. doi:10.3791/2034.
-
(2010)
J. Vis. Exp.
-
-
Hafner, M.1
Landthaler, M.2
Burger, L.3
Khorshid, M.4
Hausser, J.5
Berninger, P.6
Rothballer, A.7
Ascano, M.8
Jungkamp, A.C.9
Munschauer, M.10
Ulrich, A.11
Wardle, G.S.12
Dewell, S.13
Zavolan, M.14
Tuschl, T.15
-
61
-
-
76149130971
-
Alternative splicing: Global insights
-
Hallegger, M., Llorian, M., and Smith, C. W. (2010). Alternative splicing: global insights. FEBS J. 277, 856-866.
-
(2010)
FEBS J.
, vol.277
, pp. 856-866
-
-
Hallegger, M.1
Llorian, M.2
Smith, C.W.3
-
62
-
-
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
-
63
-
-
50549085304
-
Sircah: A tool for the detection and visualization of alternative transcripts
-
Harrington, E. D., and Bork, P. (2008). Sircah: a tool for the detection and visualization of alternative transcripts. Bioinformatics 24, 1959.
-
(2008)
Bioinformatics
, vol.24
, pp. 1959
-
-
Harrington, E.D.1
Bork, P.2
-
64
-
-
62349089764
-
Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays
-
Hazen, S. P., Naef, F., Quisel, T., Gendron, J. M., Chen, H., Ecker, J. R., Borevitz, J. O., and Kay, S. A. (2009). Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol. 10, R17.
-
(2009)
Genome Biol.
, vol.10
-
-
Hazen, S.P.1
Naef, F.2
Quisel, T.3
Gendron, J.M.4
Chen, H.5
Ecker, J.R.6
Borevitz, J.O.7
Kay, S.A.8
-
65
-
-
46749127306
-
Maturation of the nodule-specific transcript MsHSF1c in Medicago sativa may involve interallelic trans-splicing
-
He, Z. S., Zou, H. S., Wang, Y. Z., Zhu, J. B., and Yu, G. Q. (2008). Maturation of the nodule-specific transcript MsHSF1c in Medicago sativa may involve interallelic trans-splicing. Genomics 92, 115-121.
-
(2008)
Genomics
, vol.92
, pp. 115-121
-
-
He, Z.S.1
Zou, H.S.2
Wang, Y.Z.3
Zhu, J.B.4
Yu, G.Q.5
-
66
-
-
0013159620
-
Splicing graphs and EST assembly problem
-
Heber, S., Alekseyev, M., Sze, S. H., Tang, H., and Pevzner, P. A. (2002). Splicing graphs and EST assembly problem. Bioinformatics 18, 181-188.
-
(2002)
Bioinformatics
, vol.18
, pp. 181-188
-
-
Heber, S.1
Alekseyev, M.2
Sze, S.H.3
Tang, H.4
Pevzner, P.A.5
-
67
-
-
33745442032
-
Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts
-
Hirsch, J., Lefort, V., Vankersschaver, M., Boualem, A., Lucas, A., Thermes, C., D'Aubenton Carafa, Y., and Crespi, M. (2006). Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiol. 140, 1192-1204.
-
(2006)
Plant Physiol.
, vol.140
, pp. 1192-1204
-
-
Hirsch, J.1
Lefort, V.2
Vankersschaver, M.3
Boualem, A.4
Lucas, A.5
Thermes, C.6
D'Aubenton Carafa, Y.7
Crespi, M.8
-
68
-
-
4844222571
-
Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences
-
Iida, K., Seki, M., Sakurai, T., Satou, M., Akiyama, K., Toyoda, T., Konagaya, A., and Shinozaki, K. (2004). Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res. 32, 5096-5103.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5096-5103
-
-
Iida, K.1
Seki, M.2
Sakurai, T.3
Satou, M.4
Akiyama, K.5
Toyoda, T.6
Konagaya, A.7
Shinozaki, K.8
-
69
-
-
40849086257
-
Alternative splicing at NAGNAG acceptor sites shares common properties in land plants and mammals
-
Iida, K., Shionyu, M., and Suso, Y. (2008). Alternative splicing at NAGNAG acceptor sites shares common properties in land plants and mammals. Mol. Biol. Evol. 25, 709-718.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 709-718
-
-
Iida, K.1
Shionyu, M.2
Suso, Y.3
-
70
-
-
33645752060
-
The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA
-
Isshiki, M., Tsumoto, A., and Shimamoto, K. (2006). The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA. Plant Cell 18, 146-158.
-
(2006)
Plant Cell
, vol.18
, pp. 146-158
-
-
Isshiki, M.1
Tsumoto, A.2
Shimamoto, K.3
-
71
-
-
79952360093
-
RNA-seq read alignments with PALMapper
-
11.6.1-11.6.37
-
Jean, G., Kahles, A., Sreedharan, V. T., Bona, F. D., and Rätsch, 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
Bona, F.D.4
Rätsch, G.5
-
72
-
-
64549119707
-
Statistical inferences for isoform expression in RNA-seq
-
Jiang, H., and Wong, W. H. (2009). Statistical inferences for isoform expression in RNA-seq. Bioinformatics 25, 1026.
-
(2009)
Bioinformatics
, vol.25
, pp. 1026
-
-
Jiang, H.1
Wong, W.H.2
-
73
-
-
77957799907
-
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
-
Jiao, Y., and Meyerowitz, E. M. (2010). Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol. Syst. Biol. 6, 419.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 419
-
-
Jiao, Y.1
Meyerowitz, E.M.2
-
74
-
-
0347623371
-
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays
-
Johnson, J. M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P. M., Armour, C. D., Santos, R., Schadt, E. E., Stoughton, R., and Shoemaker, D. D. (2003). Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302, 2141.
-
(2003)
Science
, vol.302
, pp. 2141
-
-
Johnson, J.M.1
Castle, J.2
Garrett-Engele, P.3
Kan, Z.4
Loerch, P.M.5
Armour, C.D.6
Santos, R.7
Schadt, E.E.8
Stoughton, R.9
Shoemaker, D.D.10
-
75
-
-
80053027909
-
Functional consequences of developmentally regulated alternative splicing
-
Kalsotra, A., and Cooper, T. A. (2011). Functional consequences of developmentally regulated alternative splicing. Nat. Rev. Genet. 12, 715-729.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 715-729
-
-
Kalsotra, A.1
Cooper, T.A.2
-
76
-
-
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
-
77
-
-
33750029727
-
Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins
-
Kalyna, M., Lopato, S., Voronin, V., and Barta, A. (2006). Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins. Nucleic Acids Res. 34, 4395-4405.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 4395-4405
-
-
Kalyna, M.1
Lopato, S.2
Voronin, V.3
Barta, A.4
-
78
-
-
0033150256
-
RNA maturation of the rice SPK gene may involve trans-splicing
-
Kawasaki, T., Okumura, S., Kishimoto, N., Shimada, H., Higo, K., and Ichikawa, N. (1999). RNA maturation of the rice SPK gene may involve trans-splicing. Plant J. 18, 625-632.
-
(1999)
Plant J.
, vol.18
, pp. 625-632
-
-
Kawasaki, T.1
Okumura, S.2
Kishimoto, N.3
Shimada, H.4
Higo, K.5
Ichikawa, N.6
-
79
-
-
79960664962
-
IsoformEx: Isoform level gene expression estimation using weighted non-negative least squares from mRNA-seq data
-
doi:10.1186/1471-2105-12-305
-
Kim, H., Bi, Y., Pal, S., Gupta, R., and Davuluri, R. V. (2011). IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-seq data. BMC Bioinformatics 12, 305. doi:10.1186/1471-2105-12-305
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 305
-
-
Kim, H.1
Bi, Y.2
Pal, S.3
Gupta, R.4
Davuluri, R.V.5
-
80
-
-
79958081099
-
Differential expression and alternative splicing of rice sulphate transporter family members regulate sulphur status during plant growth, development and stress conditions
-
Kumar, S., Asif, M. H., Chakrabarty, D., Tripathi, R. D., and Trivedi, P. K. (2011). Differential expression and alternative splicing of rice sulphate transporter family members regulate sulphur status during plant growth, development and stress conditions. Funct. Integr. Genomics 11, 259-273.
-
(2011)
Funct. Integr. Genomics
, vol.11
, pp. 259-273
-
-
Kumar, S.1
Asif, M.H.2
Chakrabarty, D.3
Tripathi, R.D.4
Trivedi, P.K.5
-
81
-
-
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., Toyoda, T., Shinozaki, K., and Seki, M. (2009). Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 106, 2453-2458.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, 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
Toyoda, T.11
Shinozaki, K.12
Seki, M.13
-
82
-
-
39549117801
-
Computational analysis of splicing errors and mutations in human transcripts
-
10.1186/1471-2164-9-13
-
Kurmangaliyev, Y. Z., and Gelfand, M. S. (2008). Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics 9, 13.:10.1186/1471-2164-9-13
-
(2008)
BMC Genomics
, vol.9
, pp. 13
-
-
Kurmangaliyev, Y.Z.1
Gelfand, M.S.2
-
83
-
-
77649098171
-
Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii
-
doi:10.1186/1471-2164-11-114
-
Labadorf, A., Link, A., Rogers, M. F., Thomas, J., Reddy, A. S., and Ben-Hur, A. (2010). Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics 11, 114. doi:10.1186/1471-2164-11-114
-
(2010)
BMC Genomics
, vol.11
, pp. 114
-
-
Labadorf, A.1
Link, A.2
Rogers, M.F.3
Thomas, J.4
Reddy, A.S.5
Ben-Hur, A.6
-
84
-
-
77949521583
-
Exact transcriptome reconstruction from short sequence reads
-
in
-
Lacroix, V., Sammeth, M., Guigo, R., and Bergeron, A. (2008). "Exact transcriptome reconstruction from short sequence reads, " in Proceedings of the 8th International Workshop on Algorithms in Bioinformatics (Karlsruhe: Springer), 63.
-
(2008)
Proceedings of the 8th International Workshop on Algorithms in Bioinformatics (Karlsruhe: Springer)
, pp. 63
-
-
Lacroix, V.1
Sammeth, M.2
Guigo, R.3
Bergeron, A.4
-
85
-
-
0036429269
-
Finding signals that regulate alternative splicing in the post-genomic era
-
Ladd, A. N., and Cooper, T. A. (2002). Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol. 3, reviews0008.
-
(2002)
Genome Biol.
, vol.3
-
-
Ladd, A.N.1
Cooper, T.A.2
-
86
-
-
0036264995
-
UBA1 and UBA2, two proteins that interact with UBP1, a multifunctional effector of pre-mRNA maturation in plants
-
Lambermon, M. H., Fu, Y., Kirk, D. A., Dupasquier, M., Filipowicz, W., and Lorkovic, Z. J. (2002). UBA1 and UBA2, two proteins that interact with UBP1, a multifunctional effector of pre-mRNA maturation in plants. Mol. Cell Biol. 22, 4346-4357.
-
(2002)
Mol. Cell Biol.
, vol.22
, pp. 4346-4357
-
-
Lambermon, M.H.1
Fu, Y.2
Kirk, D.A.3
Dupasquier, M.4
Filipowicz, W.5
Lorkovic, Z.J.6
-
87
-
-
0034599523
-
UBP1, a novel hnRNP-like protein that functions at multiple steps of higher plant nuclear pre-mRNA maturation
-
Lambermon, M. H., Simpson, G. G., Wieczorek, D., Kirk, A., Hemmings-Mieszczak, M., Klahre, U., and Filipowicz, W. (2000). UBP1, a novel hnRNP-like protein that functions at multiple steps of higher plant nuclear pre-mRNA maturation. EMBO J. 19, 1638-1649.
-
(2000)
EMBO J.
, vol.19
, pp. 1638-1649
-
-
Lambermon, M.H.1
Simpson, G.G.2
Wieczorek, D.3
Kirk, A.4
Hemmings-Mieszczak, M.5
Klahre, U.6
Filipowicz, W.7
-
88
-
-
79551494866
-
Accurate quantification of transcriptome from RNA-seq data by effective length normalization
-
Lee, S., Seo, C. H., Lim, B., Yang, J. O., Oh, J., Kim, M., Lee, S., Lee, B., Kang, C., and Lee, S. (2011). Accurate quantification of transcriptome from RNA-seq data by effective length normalization. Nucleic Acids Res. 39, e9.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Lee, S.1
Seo, C.H.2
Lim, B.3
Yang, J.O.4
Oh, J.5
Kim, M.6
Lee, S.7
Lee, B.8
Kang, C.9
Lee, S.10
-
89
-
-
2442541263
-
Determinants of plant u12-dependent intron splicing efficiency
-
Lewandowska, D., Simpson, C. G., Clark, G. P., Jennings, N. S., Barciszewska-Pacak, M., Lin, C. F., Makalowski, W., Brown, J. W., and Jarmolowski, A. (2004). Determinants of plant u12-dependent intron splicing efficiency. Plant Cell 16, 1340-1352.
-
(2004)
Plant Cell
, vol.16
, pp. 1340-1352
-
-
Lewandowska, D.1
Simpson, C.G.2
Clark, G.P.3
Jennings, N.S.4
Barciszewska-Pacak, M.5
Lin, C.F.6
Makalowski, W.7
Brown, J.W.8
Jarmolowski, A.9
-
90
-
-
0037422575
-
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans
-
Lewis, B. P., Green, R. E., and Brenner, S. E. (2003). Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl. Acad. Sci. U.S.A. 100, 189-192.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 189-192
-
-
Lewis, B.P.1
Green, R.E.2
Brenner, S.E.3
-
91
-
-
79961123152
-
RSEM: Accurate transcript quantification from RNA-seq data with or without a reference genome
-
doi:10.1186/1471-2105-12-323
-
Li, B., and Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics 12, 323. doi:10.1186/1471-2105-12-323
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 323
-
-
Li, B.1
Dewey, C.N.2
-
92
-
-
77949507153
-
RNA-seq gene expression estimation with read mapping uncertainty
-
Li, B., Ruotti, V., Stewart, R. M., Thomson, J. A., and Dewey, C. N. (2010). RNA-seq gene expression estimation with read mapping uncertainty. Bioinformatics 26, 493.
-
(2010)
Bioinformatics
, vol.26
, pp. 493
-
-
Li, B.1
Ruotti, V.2
Stewart, R.M.3
Thomson, J.A.4
Dewey, C.N.5
-
93
-
-
79953186446
-
Isolasso: A lasso regression approach to RNA-seq based transcriptome assembly
-
eds V. Bafna and S. Sahinalp (Berlin: Springer), in
-
Li, W., Feng, J., and Jiang, T. (2011). "Isolasso: a lasso regression approach to RNA-seq based transcriptome assembly, " in Research in Computational Molecular Biology eds V. Bafna and S. Sahinalp (Berlin: Springer), 168-188.
-
(2011)
Research in Computational Molecular Biology
, pp. 168-188
-
-
Li, W.1
Feng, J.2
Jiang, T.3
-
94
-
-
17444372788
-
Evidence for the regulation of alternative splicing via complementary DNA sequence repeats
-
Lian, Y., and Garner, H. R. (2005). Evidence for the regulation of alternative splicing via complementary DNA sequence repeats. Bioinformatics 21, 1358-1364.
-
(2005)
Bioinformatics
, vol.21
, pp. 1358-1364
-
-
Lian, Y.1
Garner, H.R.2
-
95
-
-
70349645555
-
Evidence-based gene predictions in plant genomes
-
Liang, C., Mao, L., Ware, D., and Stein, L. (2009). Evidence-based gene predictions in plant genomes. Genome Res. 19, 1912-1923.
-
(2009)
Genome Res.
, vol.19
, pp. 1912-1923
-
-
Liang, C.1
Mao, L.2
Ware, D.3
Stein, L.4
-
96
-
-
72849106592
-
RNA processing and its regulation: Global insights into biological networks
-
Licatalosi, D. D., and Darnell, R. B. (2010). RNA processing and its regulation: global insights into biological networks. Nat. Rev. Genet. 11, 75-87.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 75-87
-
-
Licatalosi, D.D.1
Darnell, R.B.2
-
97
-
-
0033103642
-
A novel family of plant splicing factors with a zn knuckle motif: Examination of RNA binding and splicing activities
-
Lopato, S., Gattoni, R., Fabini, G., Stevenin, J., and Barta, A. (1999). A novel family of plant splicing factors with a zn knuckle motif: examination of RNA binding and splicing activities. Plant Mol. Biol. 39, 761-773.
-
(1999)
Plant Mol. Biol.
, vol.39
, pp. 761-773
-
-
Lopato, S.1
Gattoni, R.2
Fabini, G.3
Stevenin, J.4
Barta, A.5
-
98
-
-
63549135467
-
Role of plant RNA-binding proteins in development, stress response and genome organization
-
Lorkovic, Z. J. (2009). Role of plant RNA-binding proteins in development, stress response and genome organization. Trends Plant Sci. 14, 229-236.
-
(2009)
Trends Plant Sci.
, vol.14
, pp. 229-236
-
-
Lorkovic, Z.J.1
-
99
-
-
0034177911
-
Pre-mRNA splicing in higher plants
-
Lorkovic, Z. J., Wieczorek, D., Kirk, A., Lambermon, M. H., and Filipowicz, W. (2000). Pre-mRNA splicing in higher plants. Trends Plant Sci. 5, 160-167.
-
(2000)
Trends Plant Sci.
, vol.5
, pp. 160-167
-
-
Lorkovic, Z.J.1
Wieczorek, D.2
Kirk, A.3
Lambermon, M.H.4
Filipowicz, W.5
-
100
-
-
77958561137
-
A Brassica exon array for whole-transcript gene expression profiling
-
doi:10.1371/journal.pone.0012812
-
Love, C. G., Graham, N. S., Lochlainn, S. O., Bowen, H. C., May, S. T., White, P. J., Broadley, M. R., Hammond, J. P., and King, G. J. (2010). A Brassica exon array for whole-transcript gene expression profiling. PLoS ONE 5, e12812. doi:10.1371/journal.pone.0012812
-
(2010)
PLoS ONE
, vol.5
-
-
Love, C.G.1
Graham, N.S.2
Lochlainn, S.O.3
Bowen, H.C.4
May, S.T.5
White, P.J.6
Broadley, M.R.7
Hammond, J.P.8
King, G.J.9
-
101
-
-
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., 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
Huang, X.10
Han, B.11
-
102
-
-
78650961149
-
Epigenetics in alternative pre-mRNA splicing
-
Luco, R. F., Allo, M., Schor, I. E., Kornblihtt, A. R., and Misteli, T. (2011). Epigenetics in alternative pre-mRNA splicing. Cell 144, 16-26.
-
(2011)
Cell
, vol.144
, pp. 16-26
-
-
Luco, R.F.1
Allo, M.2
Schor, I.E.3
Kornblihtt, A.R.4
Misteli, T.5
-
103
-
-
75649135574
-
RNA-seq: From technology to biology
-
Marguerat, S., and Bahler, J. (2010). RNA-seq: from technology to biology. Cell. Mol. Life Sci. 67, 569-579.
-
(2010)
Cell. Mol. Life Sci.
, vol.67
, pp. 569-579
-
-
Marguerat, S.1
Bahler, J.2
-
104
-
-
78549246241
-
Rnnotator: An automated de novo transcriptome assembly pipeline from stranded RNA-seq reads
-
doi:10.1186/1471-2164-11-663
-
Martin, J., Bruno, V. M., Fang, Z., Meng, X., Blow, M., Zhang, T., Sherlock, G., Snyder, M., and Wang, Z. (2010). Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-seq reads. BMC Genomics 11, 663. doi:10.1186/1471-2164-11-663
-
(2010)
BMC Genomics
, vol.11
, pp. 663
-
-
Martin, J.1
Bruno, V.M.2
Fang, Z.3
Meng, X.4
Blow, M.5
Zhang, T.6
Sherlock, G.7
Snyder, M.8
Wang, Z.9
-
105
-
-
0030753981
-
Intronic and exonic sequences modulate 5' splice site selection in plant nuclei
-
McCullough, A. J., and Schuler, M. A. (1997). Intronic and exonic sequences modulate 5' splice site selection in plant nuclei. Nucleic Acids Res. 25, 1071-1077.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 1071-1077
-
-
McCullough, A.J.1
Schuler, M.A.2
-
106
-
-
69049116283
-
Stochastic noise in splicing machinery
-
Melamud, E., and Moult, J. (2009). Stochastic noise in splicing machinery. Nucleic Acids Res. 37, 4873-4886.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 4873-4886
-
-
Melamud, E.1
Moult, J.2
-
107
-
-
7044272280
-
Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses
-
Mili, S., and Steitz, J. A. (2004). Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA 10, 1692-1694.
-
(2004)
RNA
, vol.10
, pp. 1692-1694
-
-
Mili, S.1
Steitz, J.A.2
-
108
-
-
10644247621
-
Applications of DNA tiling arrays for whole-genome analysis
-
Mockler, T. C., and Ecker, J. R. (2005). Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 1-15.
-
(2005)
Genomics
, vol.85
, pp. 1-15
-
-
Mockler, T.C.1
Ecker, J.R.2
-
109
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-seq
-
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5, 621-628.
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
110
-
-
70350235050
-
Nucleosomes are preferentially positioned at exons in somatic and sperm cells
-
Nahkuri, S., Taft, R. J., and Mattick, J. S. (2009). Nucleosomes are preferentially positioned at exons in somatic and sperm cells. Cell Cycle 8, 3420-3424.
-
(2009)
Cell Cycle
, vol.8
, pp. 3420-3424
-
-
Nahkuri, S.1
Taft, R.J.2
Mattick, J.S.3
-
111
-
-
33750084381
-
Whole-genome microarray in Arabidopsis facilitates global analysis of retained introns
-
Ner-Gaon, H., and Fluhr, R. (2006). Whole-genome microarray in Arabidopsis facilitates global analysis of retained introns. DNA Res. 13, 111.
-
(2006)
DNA Res.
, vol.13
, pp. 111
-
-
Ner-Gaon, H.1
Fluhr, R.2
-
112
-
-
4944241489
-
Intron retention is a major phenomenon in alternative splicing in Arabidopsis
-
Ner-Gaon, H., Halachmi, R., Savaldi-Goldstein, S., Rubin, E., Ophir, R., and Fluhr, R. (2004). Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J. 39, 877-885.
-
(2004)
Plant J.
, vol.39
, pp. 877-885
-
-
Ner-Gaon, H.1
Halachmi, R.2
Savaldi-Goldstein, S.3
Rubin, E.4
Ophir, R.5
Fluhr, R.6
-
113
-
-
34447123260
-
Comparative cross-species alternative splicing in plants
-
Ner-Gaon, H., Leviatan, N., Rubin, E., and Fluhr, R. (2007). Comparative cross-species alternative splicing in plants. Plant Physiol. 144, 1632.
-
(2007)
Plant Physiol.
, vol.144
, pp. 1632
-
-
Ner-Gaon, H.1
Leviatan, N.2
Rubin, E.3
Fluhr, R.4
-
114
-
-
70349739736
-
The integrated genome browser: Free software for distribution and exploration of genome-scale datasets
-
Nicol, J. W., Helt, G. A., Blanchard, S. G. Jr., Raja, A., and Loraine, A. E. (2009). The integrated genome browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25, 2730-2731.
-
(2009)
Bioinformatics
, vol.25
, pp. 2730-2731
-
-
Nicol, J.W.1
Helt, G.A.2
Blanchard Jr., S.G.3
Raja, A.4
Loraine, A.E.5
-
115
-
-
78049485688
-
Estimation of alternative splicing isoform frequencies from RNA-seq data
-
Nicolae, M., Mangul, S., Mandoiu, I., and Zelikovsky, A. (2010). Estimation of alternative splicing isoform frequencies from RNA-seq data. Algorithm. Bioinformat. 6293, 202-214.
-
(2010)
Algorithm. Bioinformat.
, vol.6293
, pp. 202-214
-
-
Nicolae, M.1
Mangul, S.2
Mandoiu, I.3
Zelikovsky, A.4
-
116
-
-
23844435269
-
Coactivator-associated arginine methyltransferase 1, CARM1, affects pre-mRNA splicing in an isoform-specific manner
-
Ohkura, N., Takahashi, M., Yaguchi, H., Nagamura, Y., and Tsukada, T. (2005). Coactivator-associated arginine methyltransferase 1, CARM1, affects pre-mRNA splicing in an isoform-specific manner. J. Biol. Chem. 280, 28927-28935.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 28927-28935
-
-
Ohkura, N.1
Takahashi, M.2
Yaguchi, H.3
Nagamura, Y.4
Tsukada, T.5
-
117
-
-
33644861283
-
Recognition of unknown conserved alternatively spliced exons
-
doi:10.1371/journal.pcbi.0010015
-
Ohler, U., Shomron, N., and Burge, C. B. (2005). Recognition of unknown conserved alternatively spliced exons. PLoS Comput. Biol. 1, e15. doi:10.1371/journal.pcbi.0010015
-
(2005)
PLoS Comput. Biol.
, vol.1
-
-
Ohler, U.1
Shomron, N.2
Burge, C.B.3
-
118
-
-
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
-
119
-
-
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
-
120
-
-
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
-
121
-
-
70349125488
-
Co-transcriptional splicing of constitutive and alternative exons
-
Pandya-Jones, A., and Black, D. L. (2009). Co-transcriptional splicing of constitutive and alternative exons. RNA 15, 1896-1908.
-
(2009)
RNA
, vol.15
, pp. 1896-1908
-
-
Pandya-Jones, A.1
Black, D.L.2
-
122
-
-
34249987613
-
A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
-
doi:10.1186/1471-2105-8-159
-
Pertea, M., Mount, S. M., and Salzberg, S. L. (2007). A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics 8, 159. doi:10.1186/1471-2105-8-159
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 159
-
-
Pertea, M.1
Mount, S.M.2
Salzberg, S.L.3
-
123
-
-
48249128721
-
FIRMA: A method for detection of alternative splicing from exon array data
-
Purdom, E., Simpson, K. M., Robinson, M. D., Conboy, J. G., Lapuk, A. V., and Speed, T. P. (2008). FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics 24, 1707.
-
(2008)
Bioinformatics
, vol.24
, pp. 1707
-
-
Purdom, E.1
Simpson, K.M.2
Robinson, M.D.3
Conboy, J.G.4
Lapuk, A.V.5
Speed, T.P.6
-
124
-
-
29144512262
-
RASE: Recognition of alternatively spliced exons in C. elegans
-
Ratsch, G., Sonnenburg, S., and Scholkopf, B. (2005). RASE: recognition of alternatively spliced exons in C. elegans. Bioinformatics 21(Suppl. 1), i369-i377.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Ratsch, G.1
Sonnenburg, S.2
Scholkopf, B.3
-
125
-
-
0035212996
-
Nuclear pre-mRNA splicing in plants
-
Reddy, A. S. N. (2001). Nuclear pre-mRNA splicing in plants. CRC Crit. Rev. Plant Sci. 20, 523-571.
-
(2001)
CRC Crit. Rev. Plant Sci.
, vol.20
, pp. 523-571
-
-
Reddy, A.S.N.1
-
126
-
-
34250813107
-
Alternative splicing of pre-messenger RNAs in plants in the genomic era
-
Reddy, A. S. N. (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.N.1
-
127
-
-
84857714524
-
Plant SR proteins: Roles in pre-mRNA splicing, plant development and stress responses
-
Reddy, A. S. N., and Ali, G. S. (2011). Plant SR proteins: roles in pre-mRNA 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.N.1
Ali, G.S.2
-
128
-
-
75949122780
-
Agronomics1: A new resource for Arabidopsis transcriptome profiling
-
Rehrauer, H., Aquino, C., Gruissem, W., Henz, S. R., Hilson, P., Laubinger, S., Naouar, N., Patrignani, A., Rombauts, S., Shu, H., Van de Peer, Y., Vuylsteke, M., Weigel, D., Zeller, G., and Hennig, L. (2010). Agronomics1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol. 152, 487-499.
-
(2010)
Plant Physiol.
, vol.152
, pp. 487-499
-
-
Rehrauer, H.1
Aquino, C.2
Gruissem, W.3
Henz, S.R.4
Hilson, P.5
Laubinger, S.6
Naouar, N.7
Patrignani, A.8
Rombauts, S.9
Shu, H.10
Van de Peer, Y.11
Vuylsteke, M.12
Weigel, D.13
Zeller, G.14
Hennig, L.15
-
129
-
-
77954127002
-
Prediction of alternative isoforms from exon expression levels in RNA-seq experiments
-
Richard, H., Schulz, M. H., Sultan, M., Nürnberger, A., Schrinner, S., Balzereit, D., Dagand, E., Rasche, A., Lehrach, H., Vingron, M., Haas, S. A., and Yaspo, M. L. (2010). Prediction of alternative isoforms from exon expression levels in RNA-seq experiments. Nucleic Acids Res. 38, e112.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Richard, H.1
Schulz, M.H.2
Sultan, M.3
Nürnberger, A.4
Schrinner, S.5
Balzereit, D.6
Dagand, E.7
Rasche, A.8
Lehrach, H.9
Vingron, M.10
Haas, S.A.11
Yaspo, M.L.12
-
130
-
-
80052841057
-
Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: Insights into sub-family classification and extent of alternative splicing
-
doi:10.1371/journal.pone.0024542
-
Richardson, D. N., Rogers, M. F., Labadorf, A., Ben-Hur, A., Guo, H., Paterson, A. H., and Reddy, A. S. N. (2011). Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing. PLoS ONE 6, e24542. doi:10.1371/journal.pone.0024542
-
(2011)
PLoS ONE
, vol.6
-
-
Richardson, D.N.1
Rogers, M.F.2
Labadorf, A.3
Ben-Hur, A.4
Guo, H.5
Paterson, A.H.6
Reddy, A.S.N.7
-
131
-
-
80051941094
-
Identification of novel transcripts in annotated genomes using RNA-seq
-
Roberts, A., Pimentel, H., Trapnell, C., and Pachter, L. (2011). Identification of novel transcripts in annotated genomes using RNA-seq. Bioinformatics. 27, 2325-2329.
-
(2011)
Bioinformatics.
, vol.27
, pp. 2325-2329
-
-
Roberts, A.1
Pimentel, H.2
Trapnell, C.3
Pachter, L.4
-
132
-
-
78049346632
-
De novo assembly and analysis of RNA-seq data
-
Robertson, G., Schein, J., Chiu, R., Corbett, R., Field, M., Jackman, S. D., Mungall, K., Lee, S., Okada, H. M., Qian, J. Q., Griffith, M., Raymond, A., Thiessen, N., Cezard, T., Butterfield, Y. S., Newsome, R., Chan, S. K., She, R., Varhol, R., Kamoh, B., Prabhu, A. L., Tam, A., Zhao, Y., Moore, R. A., Hirst, M., Marra, M. A., Jones, S. J., and Hoodless, P. A. (2010). De novo assembly and analysis of RNA-seq data. Nat. Methods 7, 909-912.
-
(2010)
Nat. Methods
, vol.7
, pp. 909-912
-
-
Robertson, G.1
Schein, J.2
Chiu, R.3
Corbett, R.4
Field, M.5
Jackman, S.D.6
Mungall, K.7
Lee, S.8
Okada, H.M.9
Qian, J.Q.10
Griffith, M.11
Raymond, A.12
Thiessen, N.13
Cezard, T.14
Butterfield, Y.S.15
Newsome, R.16
Chan, S.K.17
She, R.18
Varhol, R.19
Kamoh, B.20
Prabhu, A.L.21
Tam, A.22
Zhao, Y.23
Moore, R.A.24
Hirst, M.25
Marra, M.A.26
Jones, S.J.27
Hoodless, P.A.28
more..
-
133
-
-
78651271733
-
Integrative genomics viewer
-
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., and Mesirov, J. P. (2011). Integrative genomics viewer. Nat. Biotechnol. 29, 24-26.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
Thorvaldsdóttir, H.2
Winckler, W.3
Guttman, M.4
Lander, E.S.5
Getz, G.6
Mesirov, J.P.7
-
134
-
-
84863419877
-
SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data
-
Rogers, M. F., Reddy, A. S. N., and Ben-Hur, A. (2012). SpliceGrapher: detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data. Genome Biol. 13, R4.
-
(2012)
Genome Biol.
, vol.13
-
-
Rogers, M.F.1
Reddy, A.S.N.2
Ben-Hur, A.3
-
135
-
-
79960869305
-
A comparison of analog and next-generation transcriptomic tools for mammalian studies
-
Roy, N. C., Altermann, E., Park, Z. A., and McNabb, W. C. (2011). A comparison of analog and next-generation transcriptomic tools for mammalian studies. Brief. Funct. Genomics 10, 135-150.
-
(2011)
Brief. Funct. Genomics
, vol.10
, pp. 135-150
-
-
Roy, N.C.1
Altermann, E.2
Park, Z.A.3
McNabb, W.C.4
-
136
-
-
51149119342
-
Spliceosomal proteins in plants
-
Ru, Y., Wang, B. B., and Brendel, V. (2008). Spliceosomal proteins in plants. Curr. Top. Microbiol. Immunol. 326, 1-15.
-
(2008)
Curr. Top. Microbiol. Immunol.
, vol.326
, pp. 1-15
-
-
Ru, Y.1
Wang, B.B.2
Brendel, V.3
-
137
-
-
79951768304
-
Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: A emerging model biosystem for plant functional genomics
-
Sablok, G., Gupta, P. K., Baek, J. M., Vazquez, F., and Min, X. J. (2011). Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: a emerging model biosystem for plant functional genomics. Biotechnol. Lett. 33, 629-636.
-
(2011)
Biotechnol. Lett.
, vol.33
, pp. 629-636
-
-
Sablok, G.1
Gupta, P.K.2
Baek, J.M.3
Vazquez, F.4
Min, X.J.5
-
138
-
-
47249104370
-
Bubbles: Alternative splicing events of arbitrary dimension in splicing graphs
-
Sammeth, M., Valiente, G., and Guigo, R. (2008). Bubbles: alternative splicing events of arbitrary dimension in splicing graphs. Lect. Notes Comput. Sci. 4955, 372.
-
(2008)
Lect. Notes Comput. Sci.
, vol.4955
, pp. 372
-
-
Sammeth, M.1
Valiente, G.2
Guigo, R.3
-
139
-
-
78149282260
-
A methyl transferase links the circadian clock to the regulation of alternative splicing
-
Sanchez, S. E., Petrillo, E., Beckwith, E. J., Zhang, X., Rugnone, M. L., Hernando, C. E., Cuevas, J. C., Godoy, M., Herz, A., Depetris-Chauvin, A., Simpson, C. G., Brown, J. W., Cerdan, P. D., Borevitz, J. O., Mas, P., Ceriani, M. F., Kornblihtt, A. R., and Yanovsky, M. J. (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
Petrillo, E.2
Beckwith, E.J.3
Zhang, X.4
Rugnone, M.L.5
Hernando, C.E.6
Cuevas, J.C.7
Godoy, M.8
Herz, A.9
Depetris-Chauvin, A.10
Simpson, C.G.11
Brown, J.W.12
Cerdan, P.D.13
Borevitz, J.O.14
Mas, P.15
Ceriani, M.F.16
Kornblihtt, A.R.17
Yanovsky, M.J.18
-
140
-
-
61849139645
-
Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
-
Sanford, J. R., Wang, X., Mort, M., Vanduyn, N., Cooper, D. N., Mooney, S. D., Edenberg, H. J., and Liu, Y. (2009). Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res. 19, 381-394.
-
(2009)
Genome Res.
, vol.19
, pp. 381-394
-
-
Sanford, J.R.1
Wang, X.2
Mort, M.3
Vanduyn, N.4
Cooper, D.N.5
Mooney, S.D.6
Edenberg, H.J.7
Liu, Y.8
-
141
-
-
43449090677
-
Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes
-
doi:10.1186/1471-2164-9-159
-
Schindler, S., Szafranski, K., Hiller, M., Ali, G. S., Palusa, S. G., Backofen, R., Platzer, M., and Reddy, A. S. (2008). Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes. BMC Genomics 9, 159. doi:10.1186/1471-2164-9-159
-
(2008)
BMC Genomics
, vol.9
, pp. 159
-
-
Schindler, S.1
Szafranski, K.2
Hiller, M.3
Ali, G.S.4
Palusa, S.G.5
Backofen, R.6
Platzer, M.7
Reddy, A.S.8
-
142
-
-
58749102066
-
Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis
-
Schoning, 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
-
-
Schoning, J.C.1
Streitner, C.2
Meyer, I.M.3
Gao, Y.4
Staiger, D.5
-
143
-
-
36849007471
-
Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation
-
Schoning, J. C., Streitner, C., Page, D. R., Hennig, S., Uchida, K., Wolf, E., Furuya, M., and Staiger, D. (2007). Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation. Plant J. 52, 1119-1130.
-
(2007)
Plant J.
, vol.52
, pp. 1119-1130
-
-
Schoning, J.C.1
Streitner, C.2
Page, D.R.3
Hennig, S.4
Uchida, K.5
Wolf, E.6
Furuya, M.7
Staiger, D.8
-
144
-
-
77954752911
-
Intragenic chromatin modifications: A new layer in alternative splicing regulation
-
Schor, I. E., Allo, M., and Kornblihtt, A. R. (2010). Intragenic chromatin modifications: a new layer in alternative splicing regulation. Epigenetics 5, 174-179.
-
(2010)
Epigenetics
, vol.5
, pp. 174-179
-
-
Schor, I.E.1
Allo, M.2
Kornblihtt, A.R.3
-
145
-
-
51149117840
-
Splice site requirements and switches in plants
-
Schuler, M. A. (2008). Splice site requirements and switches in plants. Curr. Top. Microbiol. Immunol. 326, 39-59.
-
(2008)
Curr. Top. Microbiol. Immunol.
, vol.326
, pp. 39-59
-
-
Schuler, M.A.1
-
146
-
-
67849092454
-
SROOGLE: Webserver for integrative, user-friendly visualization of splicing signals
-
Schwartz, S., Hall, E., and Ast, G. (2009a). SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res. 37, W189-W192.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Schwartz, S.1
Hall, E.2
Ast, G.3
-
147
-
-
63549096870
-
Alu exonization events reveal features required for precise recognition of exons by the splicing machinery
-
doi:10.1371/journal.pcbi.1000300
-
Schwartz, S., Gal-Mark, N., Kfir, N., Oren, R., Kim, E., and Ast, G. (2009b). Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput. Biol. 5, e1000300. doi:10.1371/journal.pcbi.1000300
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Schwartz, S.1
Gal-Mark, N.2
Kfir, N.3
Oren, R.4
Kim, E.5
Ast, G.6
-
148
-
-
69949132191
-
Chromatin organization marks exon-intron structure
-
Schwartz, S., Meshorer, E., and Ast, G. (2009c). Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol. 16, 990-995.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 990-995
-
-
Schwartz, S.1
Meshorer, E.2
Ast, G.3
-
149
-
-
60149103676
-
The centrality of RNA
-
Sharp, P. A. (2009). The centrality of RNA. Cell 136, 577-580.
-
(2009)
Cell
, vol.136
, pp. 577-580
-
-
Sharp, P.A.1
-
150
-
-
47949120992
-
Conserved RNA secondary structures promote alternative splicing
-
Shepard, P. J., and Hertel, K. J. (2008). Conserved RNA secondary structures promote alternative splicing. RNA 14, 1463-1469.
-
(2008)
RNA
, vol.14
, pp. 1463-1469
-
-
Shepard, P.J.1
Hertel, K.J.2
-
152
-
-
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
-
153
-
-
0345874787
-
Dual functionality of a plant u-rich intronic sequence element
-
Simpson, C. G., Jennings, S. N., Clark, G. P., Thow, G., and Brown, J. W. (2004). Dual functionality of a plant u-rich intronic sequence element. Plant J. 37, 82-91.
-
(2004)
Plant J.
, vol.37
, pp. 82-91
-
-
Simpson, C.G.1
Jennings, S.N.2
Clark, G.P.3
Thow, G.4
Brown, J.W.5
-
154
-
-
77953263360
-
Regulation of plant gene expression by alternative splicing
-
Simpson, C. G., Manthri, S., Raczynska, K. D., Kalyna, M., Lewandowska, D., Kusenda, B., Maronova, M., Szweykowska-Kulinska, Z., Jarmolowski, A., Barta, A., and Brown, J. W. (2010). Regulation of plant gene expression by alternative splicing. Biochem. Soc. Trans. 38, 667-671.
-
(2010)
Biochem. Soc. Trans.
, vol.38
, pp. 667-671
-
-
Simpson, C.G.1
Manthri, S.2
Raczynska, K.D.3
Kalyna, M.4
Lewandowska, D.5
Kusenda, B.6
Maronova, M.7
Szweykowska-Kulinska, Z.8
Jarmolowski, A.9
Barta, A.10
Brown, J.W.11
-
155
-
-
0036203222
-
Mutational analysis of a plant branchpoint and polypyrimidine tract required for constitutive splicing of a mini-exon
-
Simpson, C. G., Thow, G., Clark, G. P., Jennings, S. N., Watters, J. A., and Brown, J. W. (2002). Mutational analysis of a plant branchpoint and polypyrimidine tract required for constitutive splicing of a mini-exon. RNA 8, 47-56.
-
(2002)
RNA
, vol.8
, pp. 47-56
-
-
Simpson, C.G.1
Thow, G.2
Clark, G.P.3
Jennings, S.N.4
Watters, J.A.5
Brown, J.W.6
-
156
-
-
66449136667
-
ABySS: A parallel assembler for short read sequence data
-
Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. M., and Birol, I. (2009). ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117.
-
(2009)
Genome Res.
, vol.19
, pp. 1117
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.M.5
Birol, I.6
-
157
-
-
77951582118
-
Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens
-
doi:10.1186/1471-2229-10-76
-
Sinha, R., Zimmer, A. D., Bolte, K., Lang, D., Reski, R., Platzer, M., Rensing, S. A., and Backofen, R. (2010). Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens. BMC Plant Biol. 10, 76. doi:10.1186/1471-2229-10-76
-
(2010)
BMC Plant Biol.
, vol.10
, pp. 76
-
-
Sinha, R.1
Zimmer, A.D.2
Bolte, K.3
Lang, D.4
Reski, R.5
Platzer, M.6
Rensing, S.A.7
Backofen, R.8
-
158
-
-
4444291467
-
A non-EST-based method for exon-skipping prediction
-
Sorek, R., Shemesh, R., Cohen, Y., Basechess, O., Ast, G., and Shamir, R. (2004). A non-EST-based method for exon-skipping prediction. Genome Res. 14, 1617-1623.
-
(2004)
Genome Res.
, vol.14
, pp. 1617-1623
-
-
Sorek, R.1
Shemesh, R.2
Cohen, Y.3
Basechess, O.4
Ast, G.5
Shamir, R.6
-
159
-
-
70350013550
-
Biased chromatin signatures around polyadenylation sites and exons
-
Spies, N., Nielsen, C. B., Padgett, R. A., and Burge, C. B. (2009). Biased chromatin signatures around polyadenylation sites and exons. Mol. Cell 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
-
160
-
-
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
-
161
-
-
12344250822
-
Function of alternative splicing
-
Stamm, S., Ben-Ari, S., Rafalska, I., Tang, Y., Zhang, Z., Toiber, D., Thanaraj, T. A., and Soreq, H. (2005). Function of alternative splicing. Gene 344, 1-20.
-
(2005)
Gene
, vol.344
, pp. 1-20
-
-
Stamm, S.1
Ben-Ari, S.2
Rafalska, I.3
Tang, Y.4
Zhang, Z.5
Toiber, D.6
Thanaraj, T.A.7
Soreq, H.8
-
162
-
-
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
-
163
-
-
18644378331
-
The generic genome browser: A building block for a model organism system database
-
Stein, L. D., Mungall, C., Shu, S. Q., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., and Lewis, S. (2002). The generic genome browser: a building block for a model organism system database. Genome Res. 12, 1599-1610.
-
(2002)
Genome Res.
, vol.12
, pp. 1599-1610
-
-
Stein, L.D.1
Mungall, C.2
Shu, S.Q.3
Caudy, M.4
Mangone, M.5
Day, A.6
Nickerson, E.7
Stajich, J.E.8
Harris, T.W.9
Arva, A.10
Lewis, S.11
-
164
-
-
47649124124
-
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
-
Sultan, M., Schulz, M. H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., Schmidt, D., O'Keeffe, S., Haas, S., Vingron, M., Lehrach, H., and Yaspo, M. L. (2008). A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956-959.
-
(2008)
Science
, vol.321
, pp. 956-959
-
-
Sultan, M.1
Schulz, M.H.2
Richard, H.3
Magen, A.4
Klingenhoff, A.5
Scherf, M.6
Seifert, M.7
Borodina, T.8
Soldatov, A.9
Parkhomchuk, D.10
Schmidt, D.11
O'Keeffe, S.12
Haas, S.13
Vingron, M.14
Lehrach, H.15
Yaspo, M.L.16
-
165
-
-
66249128639
-
Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs
-
Szarzynska, B., Sobkowiak, L., Pant, B. D., Balazadeh, S., Scheible, W. R., Mueller-Roeber, B., Jarmolowski, A., and Szweykowska-Kulinska, Z. (2009). Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs. Nucleic Acids Res. 37, 3083-3093.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 3083-3093
-
-
Szarzynska, B.1
Sobkowiak, L.2
Pant, B.D.3
Balazadeh, S.4
Scheible, W.R.5
Mueller-Roeber, B.6
Jarmolowski, A.7
Szweykowska-Kulinska, Z.8
-
166
-
-
33847697379
-
Retained introns increase putative microRNA targets within 3' UTRs of human mRNA
-
Tan, S., Guo, J., Huang, Q., Chen, X., Li-Ling, J., Li, Q., and Ma, F. (2007). Retained introns increase putative microRNA targets within 3' UTRs of human mRNA. FEBS Lett. 581, 1081-1086.
-
(2007)
FEBS Lett.
, vol.581
, pp. 1081-1086
-
-
Tan, S.1
Guo, J.2
Huang, Q.3
Chen, X.4
Li-Ling, J.5
Li, Q.6
Ma, F.7
-
167
-
-
67349146589
-
mRNA-seq whole-transcriptome analysis of a single cell
-
Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B. B., Siddiqui, A., Lao, K., and Surani, M. A. (2009). mRNA-seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377-382.
-
(2009)
Nat. Methods
, vol.6
, pp. 377-382
-
-
Tang, F.1
Barbacioru, C.2
Wang, Y.3
Nordman, E.4
Lee, C.5
Xu, N.6
Wang, X.7
Bodeau, J.8
Tuch, B.B.9
Siddiqui, A.10
Lao, K.11
Surani, M.A.12
-
168
-
-
0036351379
-
Ribonomics: Identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays
-
Tenenbaum, S. A., Lager, P. J., Carson, C. C., and Keene, J. D. (2002). Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods 26, 191-198.
-
(2002)
Methods
, vol.26
, pp. 191-198
-
-
Tenenbaum, S.A.1
Lager, P.J.2
Carson, C.C.3
Keene, J.D.4
-
169
-
-
69949124307
-
Nucleosome positioning as a determinant of exon recognition
-
Tilgner, H., Nikolaou, C., Althammer, S., Sammeth, M., Beato, M., Valcarcel, J., and Guigo, R. (2009). Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol. 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
-
170
-
-
0030878280
-
A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites
-
Tolstrup, N., Rouze, P., and Brunak, S. (1997). A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res. 25, 3159-3163.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3159-3163
-
-
Tolstrup, N.1
Rouze, P.2
Brunak, S.3
-
171
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-seq
-
Trapnell, C., Pachter, L., and Salzberg, S. L. (2009). TopHat: discovering splice junctions with RNA-seq. Bioinformatics. 25, 1105-1111.
-
(2009)
Bioinformatics.
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
172
-
-
66149192669
-
How to map billions of short reads onto genomes
-
Trapnell, C., and Salzberg, S. L. (2009). How to map billions of short reads onto genomes. Nat. Biotechnol. 27, 455-457.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 455-457
-
-
Trapnell, C.1
Salzberg, S.L.2
-
173
-
-
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. Biotechnol. 28, 511-515.
-
(2010)
Nat. Biotechnol.
, 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
-
174
-
-
79251644774
-
Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease
-
doi:10.1371/journal.pone.0016266
-
Twine, N. A., Janitz, K., Wilkins, M. R., and Janitz, M. (2011). Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease. PLoS ONE 6, e16266. doi:10.1371/journal.pone.0016266
-
(2011)
PLoS ONE
, vol.6
-
-
Twine, N.A.1
Janitz, K.2
Wilkins, M.R.3
Janitz, M.4
-
175
-
-
67149138094
-
SWI/SNF associates with nascent pre-mRNPs and regulates alternative pre-mRNA processing
-
doi:10.1371/journal.pgen.1000470
-
Tyagi, A., Ryme, J., Brodin, D., Ostlund Farrants, A. K., and Visa, N. (2009). SWI/SNF associates with nascent pre-mRNPs and regulates alternative pre-mRNA processing. PLoS Genet. 5, e1000470. doi:10.1371/journal.pgen.1000470
-
(2009)
PLoS Genet.
, vol.5
-
-
Tyagi, A.1
Ryme, J.2
Brodin, D.3
Ostlund Farrants, A.K.4
Visa, N.5
-
176
-
-
27944508215
-
CLIP: A method for identifying protein-RNA interaction sites in living cells
-
Ule, J., Jensen, K., Mele, A., and Darnell, R. B. (2005). CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 37, 376-386.
-
(2005)
Methods
, vol.37
, pp. 376-386
-
-
Ule, J.1
Jensen, K.2
Mele, A.3
Darnell, R.B.4
-
177
-
-
0242497663
-
CLIP identifies Nova-regulated RNA networks in the brain
-
Ule, J., Jensen, K. B., Ruggiu, M., Mele, A., Ule, A., and Darnell, R. B. (2003). CLIP identifies Nova-regulated RNA networks in the brain. Science 302, 1212-1215.
-
(2003)
Science
, vol.302
, pp. 1212-1215
-
-
Ule, J.1
Jensen, K.B.2
Ruggiu, M.3
Mele, A.4
Ule, A.5
Darnell, R.B.6
-
178
-
-
33749056769
-
An RNA map predicting nova-dependent splicing regulation
-
Ule, J., Stefani, G., Mele, A., Ruggiu, M., Wang, X., Taneri, B., Gaasterland, T., Blencowe, B. J., and Darnell, R. B. (2006). An RNA map predicting nova-dependent splicing regulation. Nature 444, 580-586.
-
(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
-
179
-
-
78449290661
-
The spliceosomal proteome: At the heart of the largest cellular ribonucleoprotein machine
-
Valadkhan, S., and Jaladat, Y. (2010). The spliceosomal proteome: at the heart of the largest cellular ribonucleoprotein machine. Proteomics. 10, 4128-4141.
-
(2010)
Proteomics.
, vol.10
, pp. 4128-4141
-
-
Valadkhan, S.1
Jaladat, Y.2
-
180
-
-
60149086351
-
Origin, biogenesis, and activity of plant microRNAs
-
Voinnet, O. (2009). Origin, biogenesis, and activity of plant microRNAs. Cell 136, 669-687.
-
(2009)
Cell
, vol.136
, pp. 669-687
-
-
Voinnet, O.1
-
181
-
-
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
-
182
-
-
37849045636
-
Riboswitch control of gene expression in plants by splicing and alternative 3' 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 3' 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
-
183
-
-
60349104299
-
The spliceosome: Design principles of a dynamic rnp machine
-
Wahl, M. C., Will, C. L., and Luhrmann, R. (2009). The spliceosome: design principles of a dynamic rnp machine. Cell 136, 701-718.
-
(2009)
Cell
, vol.136
, pp. 701-718
-
-
Wahl, M.C.1
Will, C.L.2
Luhrmann, R.3
-
184
-
-
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. U.S.A. 103, 7175-7180.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 7175-7180
-
-
Wang, B.B.1
Brendel, V.2
-
185
-
-
41549147666
-
Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes
-
doi:10.1186/1471-2229-8-17
-
Wang, B. B., O'Toole, M., Brendel, V., and Young, N. D. (2008a). Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes. BMC Plant Biol. 8, 17. doi:10.1186/1471-2229-8-17
-
(2008)
BMC Plant Biol.
, vol.8
, pp. 17
-
-
Wang, B.B.1
O'Toole, M.2
Brendel, V.3
Young, N.D.4
-
186
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., and Burge, C. B. (2008b). Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476.
-
(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
-
187
-
-
78649345104
-
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
-
Wang, K., Singh, D., Zeng, Z., Coleman, S. J., Huang, Y., Savich, G. L., He, X., Mieczkowski, P., Grimm, S. A., Perou, C. M., MacLeod, J. N., Chiang, D. Y., Prins, J. F., and Liu, J. (2010). MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 38, e178.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Wang, K.1
Singh, D.2
Zeng, Z.3
Coleman, S.J.4
Huang, Y.5
Savich, G.L.6
He, X.7
Mieczkowski, P.8
Grimm, S.A.9
Perou, C.M.10
McLeod, J.N.11
Chiang, D.Y.12
Prins, J.F.13
Liu, J.14
-
188
-
-
42449098125
-
Splicing regulation: From a parts list of regulatory elements to an integrated splicing code
-
Wang, Z., and Burge, C. B. (2008). Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14, 802-813.
-
(2008)
RNA
, vol.14
, pp. 802-813
-
-
Wang, Z.1
Burge, C.B.2
-
189
-
-
57749195712
-
RNA-seq: A revolutionary tool for transcriptomics
-
Wang, Z., Gerstein, M., and Snyder, M. (2009a). RNA-seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
190
-
-
60549117342
-
Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing
-
doi:10.1186/1471-2164-10-S1-S4
-
Wang, X., Wang, K., Radovich, M., Wang, Y., Wang, G., Feng, W., Sanford, J. R., and Liu, Y. (2009b). Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing. BMC Genomics 10(Suppl. 1), S4. doi:10.1186/1471-2164-10-S1-S4
-
(2009)
BMC Genomics
, vol.10
, Issue.SUPPL. 1
-
-
Wang, X.1
Wang, K.2
Radovich, M.3
Wang, Y.4
Wang, G.5
Feng, W.6
Sanford, J.R.7
Liu, Y.8
-
191
-
-
67649840910
-
CLIP: Construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo
-
Wang, Z., Tollervey, J., Briese, M., Turner, D., and Ule, J. (2009c). CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. Methods 48, 287-293.
-
(2009)
Methods
, vol.48
, pp. 287-293
-
-
Wang, Z.1
Tollervey, J.2
Briese, M.3
Turner, D.4
Ule, J.5
-
192
-
-
77950552549
-
The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events
-
Warzecha, C. C., Shen, S., Xing, Y., and Carstens, R. P. (2009). The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events. RNA Biol. 6, 546.
-
(2009)
RNA Biol.
, vol.6
, pp. 546
-
-
Warzecha, C.C.1
Shen, S.2
Xing, Y.3
Carstens, R.P.4
-
193
-
-
80054931745
-
SpliceTrap: A method to quantify alternative splicing under single cellular conditions
-
Wu, J., Akerman, M., Sun, S., McCombie, W. R., Krainer, A. R., and Zhang, M. Q. (2011). SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics. 27, 3010-3016.
-
(2011)
Bioinformatics.
, vol.27
, pp. 3010-3016
-
-
Wu, J.1
Akerman, M.2
Sun, S.3
McCombie, W.R.4
Krainer, A.R.5
Zhang, M.Q.6
-
194
-
-
33845660883
-
Identification of alternative 5'/3'splice sites based on the mechanism of splice site competition
-
Xia, H., Bi, J., and Li, Y. (2006). Identification of alternative 5'/3'splice sites based on the mechanism of splice site competition. Nucleic Acids Res. 34, 6305-6313.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 6305-6313
-
-
Xia, H.1
Bi, J.2
Li, Y.3
-
195
-
-
79955914959
-
NSMAP: A method for spliced isoforms identification and quantification from RNA-seq
-
doi:10.1186/1471-2105-12-162
-
Xia, Z., Wen, J., Chang, C., and Zhou, X. (2011). NSMAP: a method for spliced isoforms identification and quantification from RNA-seq. BMC Bioinformatics 12, 162. doi:10.1186/1471-2105-12-162
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 162
-
-
Xia, Z.1
Wen, J.2
Chang, C.3
Zhou, X.4
-
196
-
-
84934434637
-
Reconstruction of full-length isoforms from splice graphs
-
Xing, Y., and Lee, C. (2008). Reconstruction of full-length isoforms from splice graphs. Methods Mol. Biol. 452, 199.
-
(2008)
Methods Mol. Biol.
, vol.452
, pp. 199
-
-
Xing, Y.1
Lee, C.2
-
197
-
-
1542316923
-
The multiassembly problem: Reconstructing multiple transcript isoforms from EST fragment mixtures
-
Xing, Y., Resch, A., and Lee, C. (2004). The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Res. 14, 426.
-
(2004)
Genome Res.
, vol.14
, pp. 426
-
-
Xing, Y.1
Resch, A.2
Lee, C.3
-
198
-
-
48149096726
-
MADS: A new and improved method for analysis of differential alternative splicing by exon-tiling microarrays
-
Xing, Y., Stoilov, P., Kapur, K., Han, A., Jiang, H., Shen, S., Black, D. L., and Wong, W. H. (2008). MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA 14, 1470.
-
(2008)
RNA
, vol.14
, pp. 1470
-
-
Xing, Y.1
Stoilov, P.2
Kapur, K.3
Han, A.4
Jiang, H.5
Shen, S.6
Black, D.L.7
Wong, W.H.8
-
199
-
-
14544277546
-
Identification and analysis of alternative splicing events conserved in human and mouse
-
Yeo, G. W., Van Nostrand, E., Holste, D., Poggio, T., and Burge, C. B. (2005). Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl. Acad. Sci. U.S.A. 102, 2850-2855.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 2850-2855
-
-
Yeo, G.W.1
Van Nostrand, E.2
Holste, D.3
Poggio, T.4
Burge, C.B.5
-
200
-
-
0037175010
-
Identification of acid element for tissue-specific alternative splicing of chloroplast ascorbate peroxidase pre-mRNA in higher plants
-
Yoshimura, K., Yabuta, Y., Ishikawa, T., and Shigeoka, S. (2002). Identification of acid element for tissue-specific alternative splicing of chloroplast ascorbate peroxidase pre-mRNA in higher plants. J. Biol. Chem. 277, 40623-40632.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 40623-40632
-
-
Yoshimura, K.1
Yabuta, Y.2
Ishikawa, T.3
Shigeoka, S.4
-
201
-
-
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
-
202
-
-
77951871117
-
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
-
Zhang, G., Guo, G., Hu, X., Zhang, Y., Li, Q., Li, R., Zhuang, R., Lu, Z., He, Z., Fang, X., Chen, L., Tian, W., Tao, Y., Kristiansen, K., Zhang, X., Li, S., Yang, H., Wang, J., and Wang, J. (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
Guo, G.2
Hu, X.3
Zhang, Y.4
Li, Q.5
Li, R.6
Zhuang, R.7
Lu, Z.8
He, Z.9
Fang, X.10
Chen, L.11
Tian, W.12
Tao, Y.13
Kristiansen, K.14
Zhang, X.15
Li, S.16
Yang, H.17
Wang, J.18
Wang, J.19
|