-
2
-
-
33747823564
-
MEME: Discovering and analyzing DNA and protein sequence motifs
-
Bailey, T.L., Williams, N., Misleh, C, and Li, W.W. 2006. MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34: W369-W373.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Bailey, T.L.1
Williams, N.2
Misleh, C.3
Li, W.W.4
-
3
-
-
40149099212
-
-
Barberan-Soler, S. and Zahler, A.M. 2008. Alternative splicing regulation during C. elegans development: Splicing factors as regulated targets. PLoS Genet. 4: e1000001. doi: 10.1371/journal.pgen.1000001.
-
Barberan-Soler, S. and Zahler, A.M. 2008. Alternative splicing regulation during C. elegans development: Splicing factors as regulated targets. PLoS Genet. 4: e1000001. doi: 10.1371/journal.pgen.1000001.
-
-
-
-
4
-
-
2542542256
-
Ultraconserved elements in the human genome
-
Bejerano, G., Pheasant, M., Makunin, L, Stephen, S., Kent, W.J., Mattick, J.S., and Haussler, D. 2004. Ultraconserved elements in the human genome. Science 304: 1321-1325.
-
(2004)
Science
, vol.304
, pp. 1321-1325
-
-
Bejerano, G.1
Pheasant, M.2
Makunin, L.3
Stephen, S.4
Kent, W.J.5
Mattick, J.S.6
Haussler, D.7
-
5
-
-
0034089698
-
Children with ocular motor apraxia type Cogan carry deletions in the gene (NPHP1) for juvenile nephronophthisis
-
Betz, R., Rensing, C, Otto, E., Mincheva, A., Zehnder, D., Lichter, P., and Hildebrandt, F. 2000. Children with ocular motor apraxia type Cogan carry deletions in the gene (NPHP1) for juvenile nephronophthisis. J. Pediatr. 136: 828-831.
-
(2000)
J. Pediatr
, vol.136
, pp. 828-831
-
-
Betz, R.1
Rensing, C.2
Otto, E.3
Mincheva, A.4
Zehnder, D.5
Lichter, P.6
Hildebrandt, F.7
-
6
-
-
18044379515
-
Microarray identification of FMRP-associated brain mENAs 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., et al. 2001. Microarray identification of FMRP-associated brain mENAs 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
-
7
-
-
0031929940
-
A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm
-
Caceres, J.E, Screaton, G.R., and Krainer, A.R. 1998. A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. Genes & Dev. 12: 55-66.
-
(1998)
Genes & Dev
, vol.12
, pp. 55-66
-
-
Caceres, J.E.1
Screaton, G.R.2
Krainer, A.R.3
-
8
-
-
0028232359
-
A novel bipartite splicing enhancer modulates the differential processing of the human fibronectin EDA exon
-
Caputi, M., Casari, G., Guenzi, S., Tagliabue, R., Sidoli, A., Melo, C.A., and Baralle, EE. 1994. A novel bipartite splicing enhancer modulates the differential processing of the human fibronectin EDA exon. Nucleic Acids Res. 22: 1018-1022.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 1018-1022
-
-
Caputi, M.1
Casari, G.2
Guenzi, S.3
Tagliabue, R.4
Sidoli, A.5
Melo, C.A.6
Baralle, E.E.7
-
9
-
-
0036544654
-
Disruption of an SFRSl-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMNl
-
Cartegni, L. and Krainer, A.R. 2002. Disruption of an SFRSl-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMNl. Nat. Genet. 30: 377-384.
-
(2002)
Nat. Genet
, vol.30
, pp. 377-384
-
-
Cartegni, L.1
Krainer, A.R.2
-
10
-
-
0033017499
-
The splicing factors 9G8 and SRp20 transactivate splicing through different and specific enhancers
-
Cavaloc, Y., Bourgeois, C.R, Kister, L., and Stevenin, J. 1999. The splicing factors 9G8 and SRp20 transactivate splicing through different and specific enhancers. RNA 5: 468-483.
-
(1999)
RNA
, vol.5
, pp. 468-483
-
-
Cavaloc, Y.1
Bourgeois, C.R.2
Kister, L.3
Stevenin, J.4
-
11
-
-
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
-
12
-
-
19344367734
-
Single nucleotide polymorphism-based validation of exonic splicing enhancers
-
doi: 10.1371/journal.pbio.0020268
-
Fairbrother, W.G., Holste, D., Burge, C.B., and Sharp, RA. 2004. Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol. 2: e268. doi: 10.1371/)journal.pbio.0020268.
-
(2004)
PLoS Biol
, vol.2
-
-
Fairbrother, W.G.1
Holste, D.2
Burge, C.B.3
Sharp, R.A.4
-
13
-
-
0030034795
-
A hidden Markov model approach to variation among sites in rate of evolution
-
Felsenstein, J. and Churchill, G.A. 1996. A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13: 93-104.
-
(1996)
Mol. Biol. Evol
, vol.13
, pp. 93-104
-
-
Felsenstein, J.1
Churchill, G.A.2
-
14
-
-
53549103032
-
Ab initio identification of functionally interacting pairs of ris-regulatory elements
-
Friedman, B.A., Stadler, M.B., Shomron, N., Ding, Y., and Burge, C.B. 2008. Ab initio identification of functionally interacting pairs of ris-regulatory elements. Genome Res. 18: 1643-1651.
-
(2008)
Genome Res
, vol.18
, pp. 1643-1651
-
-
Friedman, B.A.1
Stadler, M.B.2
Shomron, N.3
Ding, Y.4
Burge, C.B.5
-
15
-
-
0027424442
-
Specific commitment of different pre-mRNAs to splicing by single SR proteins
-
Fu, X.D. 1993. Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature 365: 82-85.
-
(1993)
Nature
, vol.365
, pp. 82-85
-
-
Fu, X.D.1
-
16
-
-
33847693938
-
Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocvtoplasmic-shuttling mammalian splicing factors
-
doi: 10.1186/gb-2006-7-11-r113
-
Gama-Carvalho, M., Barbosa-Morais, N.L., Brodsky, A.S., Silver, P.A., and Carmo-Fonseca, M. 2006. Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocvtoplasmic-shuttling mammalian splicing factors. Genome Biol. 7: R113. doi: 10.1186/gb-2006-7-11-r113.
-
(2006)
Genome Biol
, vol.7
-
-
Gama-Carvalho, M.1
Barbosa-Morais, N.L.2
Brodsky, A.S.3
Silver, P.A.4
Carmo-Fonseca, M.5
-
17
-
-
0025827463
-
Primary structure of the human splicing factor ASF reveals similarities with Drosophila regulators
-
Ge, H., Zuo, R, and Manley, J.L. 1991. Primary structure of the human splicing factor ASF reveals similarities with Drosophila regulators. Cell 66: 373-382.
-
(1991)
Cell
, vol.66
, pp. 373-382
-
-
Ge, H.1
Zuo, R.2
Manley, J.L.3
-
18
-
-
19344365947
-
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
-
doi: 10.1371/journal.pbio. 0020079
-
Gerber, A.P., Herschlag, D., and Brown, P.O. 2004. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol. 2: E79. doi: 10.1371/journal.pbio. 0020079.
-
(2004)
PLoS Biol
, vol.2
-
-
Gerber, A.P.1
Herschlag, D.2
Brown, P.O.3
-
19
-
-
29144447982
-
Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene
-
Ghigna, C, Giordano, S., Shen, H., Benvenuto, E, Castiglioni, E, Comoglio, P.M., Green, M.R., Riva, S., and Biamonti, G. 2005. Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. Mol. Cell 20: 881-890.
-
(2005)
Mol. Cell
, vol.20
, pp. 881-890
-
-
Ghigna, C.1
Giordano, S.2
Shen, H.3
Benvenuto, E.4
Castiglioni, E.5
Comoglio, P.M.6
Green, M.R.7
Riva, S.8
Biamonti, G.9
-
20
-
-
0032038213
-
Arginine/serine-rich domains of SR proteins can function as activators of pre-mRNA splicing
-
Graveley, B.R. and Maniatis, T. 1998. Arginine/serine-rich domains of SR proteins can function as activators of pre-mRNA splicing. Mol. Cell 1: 765-771.
-
(1998)
Mol. Cell
, vol.1
, pp. 765-771
-
-
Graveley, B.R.1
Maniatis, T.2
-
21
-
-
0034743627
-
The role of U2AF35 and U2AF65 in enhancer-dependent splicing
-
Graveley, B.R., Hertel, K.J., and Maniatis, T. 2001. The role of U2AF35 and U2AF65 in enhancer-dependent splicing. RNA 7: 806-818.
-
(2001)
RNA
, vol.7
, pp. 806-818
-
-
Graveley, B.R.1
Hertel, K.J.2
Maniatis, T.3
-
22
-
-
0037252684
-
Rfam: An RNA family database
-
Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A., and Eddy, S.R. 2003. Rfam: An RNA family database. Nucleic Acids Res. 31: 439-441.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
23
-
-
0344074646
-
Regulated tissue-specific expression of antagonistic pre-mRNA splicing factors
-
Hanamura, A., Caceres, J.F, Mayeda, A., Franza Jr., B.R., and Krainer, A.R. 1998. Regulated tissue-specific expression of antagonistic pre-mRNA splicing factors. RNA 4: 430-444.
-
(1998)
RNA
, vol.4
, pp. 430-444
-
-
Hanamura, A.1
Caceres, J.F.2
Mayeda, A.3
Franza Jr., B.R.4
Krainer, A.R.5
-
24
-
-
0037313537
-
Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery
-
Hieronymus, H. and Silver, PA. 2003. Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat. Genet. 33: 155-161.
-
(2003)
Nat. Genet
, vol.33
, pp. 155-161
-
-
Hieronymus, H.1
Silver, P.A.2
-
25
-
-
0344319833
-
Identifying biological themes within lists of genes with EASE
-
doi: 10.1186/gb-2003-4-10-r70
-
Hosack, D.A., Dennis jr., G., Sherman, B.T., Lane, H.C., and Lempicki, R.A. 2003. Identifying biological themes within lists of genes with EASE. Genome Biol. 4: R70. doi: 10.1186/gb-2003-4-10-r70.
-
(2003)
Genome Biol
, vol.4
-
-
Hosack, D.A.1
Dennis jr, G.2
Sherman, B.T.3
Lane, H.C.4
Lempicki, R.A.5
-
26
-
-
0035025061
-
Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA
-
Huang, Y. and Steitz, J.A. 2001. Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA. Mol. Cell 7: 899-905.
-
(2001)
Mol. Cell
, vol.7
, pp. 899-905
-
-
Huang, Y.1
Steitz, J.A.2
-
27
-
-
33847630730
-
The gene encoding the splicing factor SF2/ASF is a protooncogene
-
Karni, R., de Stanchina, E., Lowe, S.W., Sinha, R., Mu, D., and Krainer, A.R. 2007. The gene encoding the splicing factor SF2/ASF is a protooncogene. Nat. Struct. Mol. Biol. 14: 185-193.
-
(2007)
Nat. Struct. Mol. Biol
, vol.14
, pp. 185-193
-
-
Karni, R.1
de Stanchina, E.2
Lowe, S.W.3
Sinha, R.4
Mu, D.5
Krainer, A.R.6
-
28
-
-
38549131376
-
The UCSC Genome Browser Database: 2008 update
-
Karolchik, D., Kuhn, R.M., Baertsch, R., Barber, G.P., Clawson, H., Diekhans, M., Giardine, B., Harte, R.A., Hinrichs, A.S., Hsu, E, et al. 2008. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 36: D773-D779.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Karolchik, D.1
Kuhn, R.M.2
Baertsch, R.3
Barber, G.P.4
Clawson, H.5
Diekhans, M.6
Giardine, B.7
Harte, R.A.8
Hinrichs, A.S.9
Hsu, E.10
-
29
-
-
0041665176
-
A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy
-
Kashima, T. and Manley, J.L. 2003. A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy. Nat Genet. 34: 460-463.
-
(2003)
Nat Genet
, vol.34
, pp. 460-463
-
-
Kashima, T.1
Manley, J.L.2
-
30
-
-
34250735674
-
RNA regulons: Coordination of post-transcriptional events
-
Keene, J.D. 2007. RNA regulons: Coordination of post-transcriptional events. Nat. Rev. Genet. 8: 533-543.
-
(2007)
Nat. Rev. Genet
, vol.8
, pp. 533-543
-
-
Keene, J.D.1
-
31
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent, W.J. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12: 656-664.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
32
-
-
0028289188
-
Protein-protein interactions and 5'-splice-site recognition in mammalian mRNA precursors
-
Kohtz, J.D., Jamison, S.E, Will, C.L., Zuo, P., Luhrmann, R., Garcia-Blanco, M.A., and Manley, J.L. 1994. Protein-protein interactions and 5'-splice-site recognition in mammalian mRNA precursors. Nature 368:119-124.
-
(1994)
Nature
, vol.368
, pp. 119-124
-
-
Kohtz, J.D.1
Jamison, S.E.2
Will, C.L.3
Zuo, P.4
Luhrmann, R.5
Garcia-Blanco, M.A.6
Manley, J.L.7
-
33
-
-
0025743575
-
Functional expression of cloned human splicing factor SF2: Homology to RNA-binding proteins, U1 70K, and Drosophila splicing regulators
-
Krainer, A.R., Mayeda, A., Kozak, D., and Binns, G. 1991. Functional expression of cloned human splicing factor SF2: Homology to RNA-binding proteins, U1 70K, and Drosophila splicing regulators. Cell 66: 383-394.
-
(1991)
Cell
, vol.66
, pp. 383-394
-
-
Krainer, A.R.1
Mayeda, A.2
Kozak, D.3
Binns, G.4
-
34
-
-
34247330971
-
Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
-
Lareau, L.F., Inada, M., Green, R.E., Wengrod, J.C., and Brenner, S.E. 2007. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446: 926-929.
-
(2007)
Nature
, vol.446
, pp. 926-929
-
-
Lareau, L.F.1
Inada, M.2
Green, R.E.3
Wengrod, J.C.4
Brenner, S.E.5
-
35
-
-
0036500149
-
Stability of a PKC1-1-related mRNA is controlled by the splicing factor ASF/SF2: A novel function for SR proteins
-
Lemaire, R., Prasad, J., Kashima, T, Gustafson, J., Manley, J.L., and Lafyatis, R. 2002. Stability of a PKC1-1-related mRNA is controlled by the splicing factor ASF/SF2: A novel function for SR proteins. Genes & Dev. 16: 594-607.
-
(2002)
Genes & Dev
, vol.16
, pp. 594-607
-
-
Lemaire, R.1
Prasad, J.2
Kashima, T.3
Gustafson, J.4
Manley, J.L.5
Lafyatis, R.6
-
36
-
-
23744455164
-
Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability
-
Li, X. and Manley, J.L. 2005. Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 122: 365-378.
-
(2005)
Cell
, vol.122
, pp. 365-378
-
-
Li, X.1
Manley, J.L.2
-
37
-
-
42449159377
-
SR proteins and related factors in alternative splicing
-
Lin, S. and Fu, X.D. 2007. SR proteins and related factors in alternative splicing. Adv. Exp. Med. Biol. 623:107-122.
-
(2007)
Adv. Exp. Med. Biol
, vol.623
, pp. 107-122
-
-
Lin, S.1
Fu, X.D.2
-
38
-
-
0032128255
-
Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins
-
Liu, H.X., Zhang, M., and Krainer, A.R. 1998. Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes & Dev. 12: 1998-2012.
-
(1998)
Genes & Dev
, vol.12
, pp. 1998-2012
-
-
Liu, H.X.1
Zhang, M.2
Krainer, A.R.3
-
39
-
-
0035158730
-
A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes
-
Liu, H.X., Cartegni, L., Zhang, M.Q., and Krainer, A.R. 2001. A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nat Genet. 27: 55-58.
-
(2001)
Nat Genet
, vol.27
, pp. 55-58
-
-
Liu, H.X.1
Cartegni, L.2
Zhang, M.Q.3
Krainer, A.R.4
-
40
-
-
0034599949
-
Functional characterization of SR and SR-related genes in Caenorhabditis elegans
-
Longman, D., Johnstone, I.E., and Caceres, J.F. 2000. Functional characterization of SR and SR-related genes in Caenorhabditis elegans. EMBO J. 19: 1625-1637.
-
(2000)
EMBO J
, vol.19
, pp. 1625-1637
-
-
Longman, D.1
Johnstone, I.E.2
Caceres, J.F.3
-
41
-
-
0036911605
-
Distribution and characterization of regulatory elements in the human genome
-
Majewski, J. and Ott, J. 2002. Distribution and characterization of regulatory elements in the human genome. Genome Res. 12: 1827-1836.
-
(2002)
Genome Res
, vol.12
, pp. 1827-1836
-
-
Majewski, J.1
Ott, J.2
-
42
-
-
0037062982
-
Alternative pre-mRNA splicing and proteome expansion In metazoans
-
Maniatis, T. and Tasic, B. 2002. Alternative pre-mRNA splicing and proteome expansion In metazoans. Nature 418: 236-243.
-
(2002)
Nature
, vol.418
, pp. 236-243
-
-
Maniatis, T.1
Tasic, B.2
-
43
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies, M., Egholm, M., Aitman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Aitman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.J.9
Chen, Z.10
-
44
-
-
7044272280
-
Evidence for reassociatlon of RNA-binding proteins after cell lysis: Implications for the interpretation of immunopreclpitation analyses
-
Mill, S. and Steitz, J.A. 2004. Evidence for reassociatlon of RNA-binding proteins after cell lysis: Implications for the interpretation of immunopreclpitation analyses. RNA 10: 1692-1694.
-
(2004)
RNA
, vol.10
, pp. 1692-1694
-
-
Mill, S.1
Steitz, J.A.2
-
45
-
-
0036171787
-
-
Moseley, C.T., Mullis, P.E., Prince, M.A., and Phillips 111, j.A. 2002. An exon splice enhancer mutation causes autosomal dominant GH deficiency. J. Clin. Endocrinol. Metab. 87: 847-852.
-
Moseley, C.T., Mullis, P.E., Prince, M.A., and Phillips 111, j.A. 2002. An exon splice enhancer mutation causes autosomal dominant GH deficiency. J. Clin. Endocrinol. Metab. 87: 847-852.
-
-
-
-
46
-
-
33947305594
-
Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay
-
Ni, J.Z., Grate, L., Donohue, J.P., Preston, C, Nobida, N., O'Brien, G., Shiue, L., Clark, T.A., Blume, J.E., and Ares Jr., M. 2007. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes & Dev. 21: 708-718.
-
(2007)
Genes & Dev
, vol.21
, pp. 708-718
-
-
Ni, J.Z.1
Grate, L.2
Donohue, J.P.3
Preston, C.4
Nobida, N.5
O'Brien, G.6
Shiue, L.7
Clark, T.A.8
Blume, J.E.9
Ares Jr., M.10
-
47
-
-
36849015934
-
A regulator of Dscam mutually exclusive splicing fidelity
-
Olson, S., Blanchette, M., Park, J., Sawa, Y., Yeo, G.W., Yeakley, J.M., Rio, D.C., and Graveley, B.R. 2007. A regulator of Dscam mutually exclusive splicing fidelity. Nat Struct. Mol. Biol 14: 1134-1140.
-
(2007)
Nat Struct. Mol. Biol
, vol.14
, pp. 1134-1140
-
-
Olson, S.1
Blanchette, M.2
Park, J.3
Sawa, Y.4
Yeo, G.W.5
Yeakley, J.M.6
Rio, D.C.7
Graveley, B.R.8
-
48
-
-
0038712558
-
Missense, nonsense, and neutral mutations define juxtaposed regulatory elements of splicing in cystic fibrosis transmembrane regulator exon 9
-
Pagani, K, Buratti, E., Stuani, C., and Baralle, EE. 2003. Missense, nonsense, and neutral mutations define juxtaposed regulatory elements of splicing in cystic fibrosis transmembrane regulator exon 9. J. Biol. Chem. 278: 26580-26588.
-
(2003)
J. Biol. Chem
, vol.278
, pp. 26580-26588
-
-
Pagani, K.1
Buratti, E.2
Stuani, C.3
Baralle, E.E.4
-
49
-
-
30744469841
-
Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
-
Parmley, J.L., Chamary, J.V., and Hurst, L.D. 2006. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol. Biol. Evol. 23: 301-309.
-
(2006)
Mol. Biol. Evol
, vol.23
, pp. 301-309
-
-
Parmley, J.L.1
Chamary, J.V.2
Hurst, L.D.3
-
50
-
-
0029144216
-
A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer
-
Ramchatesingh, J., Zahler, A.M., Neugebauer, K.M., Roth, M.B., and Cooper, T.A. 1995. A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer. Mol. Cell. Biol. 15: 4898-4907.
-
(1995)
Mol. Cell. Biol
, vol.15
, pp. 4898-4907
-
-
Ramchatesingh, J.1
Zahler, A.M.2
Neugebauer, K.M.3
Roth, M.B.4
Cooper, T.A.5
-
51
-
-
46149112362
-
Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay
-
Saltzman, A.L., Kim, Y.K., Pan, Q., Fagnani, M.M., Maquat, L.E., and Blencowe, B.J. 2008. Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol. Cell. Biol. 28: 4320-4330.
-
(2008)
Mol. Cell. Biol
, vol.28
, pp. 4320-4330
-
-
Saltzman, A.L.1
Kim, Y.K.2
Pan, Q.3
Fagnani, M.M.4
Maquat, L.E.5
Blencowe, B.J.6
-
52
-
-
33751247876
-
Post-transcription meets post-genomic: The saga of RNA binding proteins in a new era
-
Sanchez-Diaz, P. and Penalva, L.O. 2006. Post-transcription meets post-genomic: The saga of RNA binding proteins in a new era. RNA Biol. 3: 101-109.
-
(2006)
RNA Biol
, vol.3
, pp. 101-109
-
-
Sanchez-Diaz, P.1
Penalva, L.O.2
-
53
-
-
1842632326
-
A novel role for shuttling SR proteins in mRNA translation
-
Sanford, J.R., Gray, N.K., Beckmann, K., and Caceres, J.F. 2004. A novel role for shuttling SR proteins in mRNA translation. Genes & Dev. 18: 755-768.
-
(2004)
Genes & Dev
, vol.18
, pp. 755-768
-
-
Sanford, J.R.1
Gray, N.K.2
Beckmann, K.3
Caceres, J.F.4
-
54
-
-
27244441805
-
Reversible phosphorylation differentially affects nuclear and cytoplasmic functions of splicing factor 2/altemative splicing factor
-
Sanford, J.R., Ellis, J.D., Cazalla, D., and Caceres, J.F. 2005. Reversible phosphorylation differentially affects nuclear and cytoplasmic functions of splicing factor 2/altemative splicing factor. Proc. Natl. Acad. Sci. 102: 15042-15047.
-
(2005)
Proc. Natl. Acad. Sci
, vol.102
, pp. 15042-15047
-
-
Sanford, J.R.1
Ellis, J.D.2
Cazalla, D.3
Caceres, J.F.4
-
55
-
-
54849438715
-
Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASE
-
doi: 10.1371/journal.pone.0003369
-
Sanford, J.R., Coutinho, P., Hackett, J.A., Wang, X., Ranahan, W., and Caceres, J.F. 2008. Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASE. PLoS One 3: e3369. doi: 10.1371/journal.pone.0003369.
-
(2008)
PLoS One
, vol.3
-
-
Sanford, J.R.1
Coutinho, P.2
Hackett, J.A.3
Wang, X.4
Ranahan, W.5
Caceres, J.F.6
-
56
-
-
8644268780
-
A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly
-
Shen, H. and Green, M.R. 2004. A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly. Mol. Cell 16: 363-373.
-
(2004)
Mol. Cell
, vol.16
, pp. 363-373
-
-
Shen, H.1
Green, M.R.2
-
57
-
-
23744458086
-
Evolutionarlly conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A.S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., et al. 2005. Evolutionarlly conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15: 1034-1050.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
-
58
-
-
27544491192
-
ROCR: Visualizing classifier performance in R
-
Sing, T., Sander, O., Beerenwinkel, N., and Lengauer, T. 2005. ROCR: Visualizing classifier performance in R. Bioinformatics 21: 3940-3941.
-
(2005)
Bioinformatics
, vol.21
, pp. 3940-3941
-
-
Sing, T.1
Sander, O.2
Beerenwinkel, N.3
Lengauer, T.4
-
59
-
-
33747891736
-
An increased specificity score matrix for the prediction of SFRS1-specific exonic splicing enhancers
-
Smith, P.J., Zhang, C, Wang, J., Chew, S.L., Zhang, M.Q., and Kramer, A.R. 2006. An increased specificity score matrix for the prediction of SFRS1-specific exonic splicing enhancers. Hum. Mol. Genet. 15: 2490-2508.
-
(2006)
Hum. Mol. Genet
, vol.15
, pp. 2490-2508
-
-
Smith, P.J.1
Zhang, C.2
Wang, J.3
Chew, S.L.4
Zhang, M.Q.5
Kramer, A.R.6
-
60
-
-
0037903275
-
Human Gene Mutation Database (HGMD): 2003 update
-
Stenson, P.D., Ball, E.V., Mort, M., Phillips, A.D., Shiel, J.A., Thomas, N.S., Abeyslnghe, S., Krawczak, M., and Cooper, D.N, 2003. Human Gene Mutation Database (HGMD): 2003 update. Hum. Mutat. 21: 577-581.
-
(2003)
Hum. Mutat
, vol.21
, pp. 577-581
-
-
Stenson, P.D.1
Ball, E.V.2
Mort, M.3
Phillips, A.D.4
Shiel, J.A.5
Thomas, N.S.6
Abeyslnghe, S.7
Krawczak, M.8
Cooper, D.N.9
-
61
-
-
0029064220
-
The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities
-
Tacke, R. and Manley, J.L. 1995. The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J. 14: 3540-3551.
-
(1995)
EMBO J
, vol.14
, pp. 3540-3551
-
-
Tacke, R.1
Manley, J.L.2
-
62
-
-
0036351379
-
Ribonomlcs: 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. Ribonomlcs: 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
-
63
-
-
0039108539
-
Splicing defects in the ataxia-telangiectasia gene, ATM: Underlying mutations and consequences
-
Teraoka, S.N., Telatar, M., Becker-Catania, S., Liang, T., Onengut, S., Tolun, A., Chessa, L., Sanal, O., Bernatowska, E., Gatti, R.A., et al. 1999. Splicing defects in the ataxia-telangiectasia gene, ATM: Underlying mutations and consequences. Am. J. Hum. Genet. 64: 1617-1631.
-
(1999)
Am. J. Hum. Genet
, vol.64
, pp. 1617-1631
-
-
Teraoka, S.N.1
Telatar, M.2
Becker-Catania, S.3
Liang, T.4
Onengut, S.5
Tolun, A.6
Chessa, L.7
Sanal, O.8
Bernatowska, E.9
Gatti, R.A.10
-
64
-
-
0025194307
-
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
-
Tuerk, C. and Gold, L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
-
(1990)
Science
, vol.249
, pp. 505-510
-
-
Tuerk, C.1
Gold, L.2
-
65
-
-
32344440041
-
RNA binding proteins and the regulation of neuronal synaptic plasticity
-
Ule, J. and Darnell, R.B. 2006. RNA binding proteins and the regulation of neuronal synaptic plasticity. Curr. Opin. Neurobiol. 16: 102-110.
-
(2006)
Curr. Opin. Neurobiol
, vol.16
, pp. 102-110
-
-
Ule, J.1
Darnell, R.B.2
-
66
-
-
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
-
67
-
-
27944508215
-
CLIP: A method for identifying protein-RNA interaction sites in living cells
-
Ule, J., Jensen, K., Mele, A., and Darnell, R.B. 2005a. 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
-
68
-
-
23044431574
-
Nova regulates brain-specific splicing to shape the synapse
-
Ule, J., Ule, A., Spencer, J., Williams, A., Hu, J.S., Cline, M., Wang, H., Clark, T, Eraser, C, Ruggiu, M., et al. 2005b. Nova regulates brain-specific splicing to shape the synapse. Nat. Genet. 37: 844-852.
-
(2005)
Nat. Genet
, vol.37
, pp. 844-852
-
-
Ule, J.1
Ule, A.2
Spencer, J.3
Williams, A.4
Hu, J.S.5
Cline, M.6
Wang, H.7
Clark, T.8
Eraser, C.9
Ruggiu, M.10
-
69
-
-
33749056769
-
An RNA map predicting Nova-dependent splicing regulation
-
Ule, J., Stefani, G., Mele, A., Ruggiu, M., Wang, X., Tanerl, 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
Tanerl, B.6
Gaasterland, T.7
Blencowe, B.J.8
Darnell, R.B.9
-
70
-
-
34548758543
-
Splicing in disease: Disruption of the splicing code and the decoding machinery
-
Wang, G.S. and Cooper, T.A. 2007. Splicing in disease: Disruption of the splicing code and the decoding machinery. Nat. Rev. Genet. 8: 749-761.
-
(2007)
Nat. Rev. Genet
, vol.8
, pp. 749-761
-
-
Wang, G.S.1
Cooper, T.A.2
-
71
-
-
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
-
72
-
-
0029859659
-
Targeted disruption of an essential vertebrate gene: ASF/SF2 is required for cell viability
-
Wang, J., Takagaki, Y., and Manley, J.L. 1996. Targeted disruption of an essential vertebrate gene: ASF/SF2 is required for cell viability. Genes & Dev. 10: 2588-2599.
-
(1996)
Genes & Dev
, vol.10
, pp. 2588-2599
-
-
Wang, J.1
Takagaki, Y.2
Manley, J.L.3
-
73
-
-
33745501015
-
General and specific functions of exonic splicing silencers in splicing control
-
Wang, Z., Xiao, X., Van Nostrand, E., and Burge, C.B. 2006. General and specific functions of exonic splicing silencers in splicing control. Mol. Cell 23: 61-70.
-
(2006)
Mol. Cell
, vol.23
, pp. 61-70
-
-
Wang, Z.1
Xiao, X.2
Van Nostrand, E.3
Burge, C.B.4
-
74
-
-
37749047490
-
Sequence census methods for functional genomics
-
Wold, B. and Myers, R.M. 2008. Sequence census methods for functional genomics. Nat. Methods 5: 19-21.
-
(2008)
Nat. Methods
, vol.5
, pp. 19-21
-
-
Wold, B.1
Myers, R.M.2
-
75
-
-
36749057933
-
Coevolutionary networks of splicing cis-regulatory elements
-
Xiao, X., Wang, Z., Jang, M., and Burge, C.B. 2007. Coevolutionary networks of splicing cis-regulatory elements. Proc. Natl. Acad. Sci. 104: 18583-18588.
-
(2007)
Proc. Natl. Acad. Sci
, vol.104
, pp. 18583-18588
-
-
Xiao, X.1
Wang, Z.2
Jang, M.3
Burge, C.B.4
-
76
-
-
19944427655
-
ASF/SF2-regulated CaMKIIdelta alternative splicing temporally reprograms excitation-contraction coupling in cardiac muscle
-
Xu, X., Yang, D., Ding, J.H., Wang, W., Chu, P.H., Dalton, N.D., Wang, H.Y., Bermingham Jr., J.R., Ye, Z., Liu, F, et al. 2005. ASF/SF2-regulated CaMKIIdelta alternative splicing temporally reprograms excitation-contraction coupling in cardiac muscle. Cell 120: 59-72.
-
(2005)
Cell
, vol.120
, pp. 59-72
-
-
Xu, X.1
Yang, D.2
Ding, J.H.3
Wang, W.4
Chu, P.H.5
Dalton, N.D.6
Wang, H.Y.7
Bermingham Jr., J.R.8
Ye, Z.9
Liu, F.10
-
77
-
-
2642525438
-
Computational definition of sequence motifs governing constitutive exon splicing
-
Zhang, X.H. and Chasin, L.A. 2004. Computational definition of sequence motifs governing constitutive exon splicing. Genes & Dev. 18: 1241-1250.
-
(2004)
Genes & Dev
, vol.18
, pp. 1241-1250
-
-
Zhang, X.H.1
Chasin, L.A.2
-
78
-
-
8844219677
-
Involvement of SR proteins in mRNA surveillance
-
Zhang, Z. and Krainer, A.R. 2004. Involvement of SR proteins in mRNA surveillance. Mol. Cell 16: 597-607.
-
(2004)
Mol. Cell
, vol.16
, pp. 597-607
-
-
Zhang, Z.1
Krainer, A.R.2
-
79
-
-
22344439658
-
Dichotomous splicing signals in exon flanks
-
Zhang, X.H., Leslie, C.S., and Chasin, L.A. 2005. Dichotomous splicing signals in exon flanks. Genome Res. 15: 768-779.
-
(2005)
Genome Res
, vol.15
, pp. 768-779
-
-
Zhang, X.H.1
Leslie, C.S.2
Chasin, L.A.3
|