-
1
-
-
59049103023
-
The immunoglobulin superfamily of neuronal cell adhesion molecules: Lessons from animal models and correlation with human disease
-
Katidou, M.; Vidaki, M.; Strigini, M.; Karagogeos, D. The immunoglobulin superfamily of neuronal cell adhesion molecules: lessons from animal models and correlation with human disease Biotechnol. J. 2008, 3 (12) 1564-80
-
(2008)
Biotechnol. J.
, vol.3
, Issue.12
, pp. 1564-1580
-
-
Katidou, M.1
Vidaki, M.2
Strigini, M.3
Karagogeos, D.4
-
2
-
-
58149193242
-
AS-ALPS: A database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse
-
Shionyu, M.; Yamaguchi, A.; Shinoda, K.; Takahashi, K.; Go, M. AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse Nucleic Acids Res. 2009, 37 (Database issue) D305-9
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 305-309
-
-
Shionyu, M.1
Yamaguchi, A.2
Shinoda, K.3
Takahashi, K.4
Go, M.5
-
3
-
-
65449187606
-
SpliceAid: A database of experimental RNA target motifs bound by splicing proteins in humans
-
Piva, F.; Giulietti, M.; Nocchi, L.; Principato, G. SpliceAid: a database of experimental RNA target motifs bound by splicing proteins in humans Bioinformatics 2009, 25 (9) 1211-3
-
(2009)
Bioinformatics
, vol.25
, Issue.9
, pp. 1211-1213
-
-
Piva, F.1
Giulietti, M.2
Nocchi, L.3
Principato, G.4
-
4
-
-
78651298898
-
ASPicDB: A database of annotated transcript and protein variants generated by alternative splicing
-
Martelli, P. L.; D'Antonio, M.; Bonizzoni, P.; Castrignano, T.; D'Erchia, A. M.; D'Onorio De Meo, P.; Fariselli, P.; Finelli, M.; Licciulli, F.; Mangiulli, M.; Mignone, F.; Pavesi, G.; Picardi, E.; Rizzi, R.; Rossi, I.; Valletti, A.; Zauli, A.; Zambelli, F.; Casadio, R.; Pesole, G. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing Nucleic Acids Res. 2011, 39 (Database issue) D80-5
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 80-85
-
-
Martelli, P.L.1
D'Antonio, M.2
Bonizzoni, P.3
Castrignano, T.4
D'Erchia, A.M.5
D'Onorio De Meo, P.6
Fariselli, P.7
Finelli, M.8
Licciulli, F.9
Mangiulli, M.10
Mignone, F.11
Pavesi, G.12
Picardi, E.13
Rizzi, R.14
Rossi, I.15
Valletti, A.16
Zauli, A.17
Zambelli, F.18
Casadio, R.19
Pesole, G.20
more..
-
5
-
-
84876562648
-
HEXEvent: A database of Human EXon splicing Events
-
Busch, A.; Hertel, K. J. HEXEvent: a database of Human EXon splicing Events Nucleic Acids Res. 2013, 41 (Database issue) D118-24
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 118-124
-
-
Busch, A.1
Hertel, K.J.2
-
6
-
-
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.; Pachter, L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat. Biotechnol. 2010, 28 (5) 511-5
-
(2010)
Nat. Biotechnol.
, vol.28
, Issue.5
, 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
-
7
-
-
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.; Regev, A. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs Nat. Biotechnol. 2010, 28 (5) 503-10
-
(2010)
Nat. Biotechnol.
, vol.28
, Issue.5
, 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
-
8
-
-
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.; Mockler, T. C. Genome-wide mapping of alternative splicing in Arabidopsis thaliana Genome Res. 2010, 20 (1) 45-58
-
(2010)
Genome Res.
, vol.20
, Issue.1
, 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
-
9
-
-
84863419877
-
SpliceGrapher: Detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data
-
Rogers, M. F.; Thomas, J.; Reddy, A. S.; Ben-Hur, A. SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data Genome Biol. 2012, 13 (1) R4
-
(2012)
Genome Biol.
, vol.13
, Issue.1
, pp. 4
-
-
Rogers, M.F.1
Thomas, J.2
Reddy, A.S.3
Ben-Hur, A.4
-
10
-
-
0030858386
-
Characterization of guanylate kinase-associated protein, a postsynaptic density protein at excitatory synapses that interacts directly with postsynaptic density-95/synapse-associated protein 90
-
Naisbitt, S.; Kim, E.; Weinberg, R. J.; Rao, A.; Yang, F. C.; Craig, A. M.; Sheng, M. Characterization of guanylate kinase-associated protein, a postsynaptic density protein at excitatory synapses that interacts directly with postsynaptic density-95/synapse-associated protein 90 J. Neurosci. 1997, 17 (15) 5687-96
-
(1997)
J. Neurosci.
, vol.17
, Issue.15
, pp. 5687-5696
-
-
Naisbitt, S.1
Kim, E.2
Weinberg, R.J.3
Rao, A.4
Yang, F.C.5
Craig, A.M.6
Sheng, M.7
-
11
-
-
19444364405
-
Dynamics of transcription and mRNA export
-
Darzacq, X.; Singer, R. H.; Shav-Tal, Y. Dynamics of transcription and mRNA export Curr. Opin. Cell Biol. 2005, 17 (3) 332-9
-
(2005)
Curr. Opin. Cell Biol.
, vol.17
, Issue.3
, pp. 332-339
-
-
Darzacq, X.1
Singer, R.H.2
Shav-Tal, Y.3
-
12
-
-
84879772009
-
Alternative splicing of human insulin receptor gene (INSR) in type i and type II skeletal muscle fibers of patients with myotonic dystrophy type 1 and type 2
-
Santoro, M.; Masciullo, M.; Bonvissuto, D.; Bianchi, M. L.; Michetti, F.; Silvestri, G. Alternative splicing of human insulin receptor gene (INSR) in type I and type II skeletal muscle fibers of patients with myotonic dystrophy type 1 and type 2 Mol. Cell. Biochem. 2013, 380, 259-265
-
(2013)
Mol. Cell. Biochem.
, vol.380
, pp. 259-265
-
-
Santoro, M.1
Masciullo, M.2
Bonvissuto, D.3
Bianchi, M.L.4
Michetti, F.5
Silvestri, G.6
-
13
-
-
84862594116
-
Transcriptomics: MRNA and alternative splicing
-
Sanchez-Pla, A.; Reverter, F.; Ruiz de Villa, M. C.; Comabella, M. Transcriptomics: mRNA and alternative splicing J. Neuroimmunol. 2012, 248 (1-2) 23-31
-
(2012)
J. Neuroimmunol.
, vol.248
, Issue.12
, pp. 23-31
-
-
Sanchez-Pla, A.1
Reverter, F.2
Ruiz De Villa, M.C.3
Comabella, M.4
-
14
-
-
84865676796
-
Detection and quantification of alternative splicing variants using RNA-seq
-
Bryant, D. W., Jr.; Priest, H. D.; Mockler, T. C. Detection and quantification of alternative splicing variants using RNA-seq Methods Mol. Biol. 2012, 883, 97-110
-
(2012)
Methods Mol. Biol.
, vol.883
, pp. 97-110
-
-
Bryant Jr., D.W.1
Priest, H.D.2
Mockler, T.C.3
-
15
-
-
60849121125
-
The database dbEST correctly predicts gene expression in colon cancer patients
-
Radeva, M.; Hofmann, T.; Altenberg, B.; Mothes, H.; Richter, K. K.; Pool-Zobel, B.; Greulich, K. O. The database dbEST correctly predicts gene expression in colon cancer patients Curr. Pharm. Biotechnol. 2008, 9 (6) 510-5
-
(2008)
Curr. Pharm. Biotechnol.
, vol.9
, Issue.6
, pp. 510-515
-
-
Radeva, M.1
Hofmann, T.2
Altenberg, B.3
Mothes, H.4
Richter, K.K.5
Pool-Zobel, B.6
Greulich, K.O.7
-
16
-
-
79955785746
-
Gene-centric view on the human proteome project: The example of the Russian roadmap for chromosome 18
-
Archakov, A.; Aseev, A.; Bykov, V.; Grigoriev, A.; Govorun, V.; Ivanov, V.; Khlunov, A.; Lisitsa, A.; Mazurenko, S.; Makarov, A. A.; Ponomarenko, E.; Sagdeev, R.; Skryabin, K. Gene-centric view on the human proteome project: the example of the Russian roadmap for chromosome 18 Proteomics 2011, 11 (10) 1853-6
-
(2011)
Proteomics
, vol.11
, Issue.10
, pp. 1853-1856
-
-
Archakov, A.1
Aseev, A.2
Bykov, V.3
Grigoriev, A.4
Govorun, V.5
Ivanov, V.6
Khlunov, A.7
Lisitsa, A.8
Mazurenko, S.9
Makarov, A.A.10
Ponomarenko, E.11
Sagdeev, R.12
Skryabin, K.13
-
17
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D.; Pertea, G.; Trapnell, C.; Pimentel, H.; Kelley, R.; Salzberg, S. L. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biol. 2013, 14 (4) R36
-
(2013)
Genome Biol.
, vol.14
, Issue.4
, pp. 36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
18
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B.; Trapnell, C.; Pop, M.; Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 2009, 10 (3) R25
-
(2009)
Genome Biol.
, vol.10
, Issue.3
, pp. 25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
19
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell, C.; Roberts, A.; Goff, L.; Pertea, G.; Kim, D.; Kelley, D. R.; Pimentel, H.; Salzberg, S. L.; Rinn, J. L.; Pachter, L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nat. Protoc. 2012, 7 (3) 562-78
-
(2012)
Nat. Protoc.
, vol.7
, Issue.3
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
Pimentel, H.7
Salzberg, S.L.8
Rinn, J.L.9
Pachter, L.10
-
20
-
-
77954210153
-
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
-
Webb-Robertson, B. J.; Cannon, W. R.; Oehmen, C. S.; Shah, A. R.; Gurumoorthi, V.; Lipton, M. S.; Waters, K. M. A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics Bioinformatics 2010, 26 (13) 1677-83
-
(2010)
Bioinformatics
, vol.26
, Issue.13
, pp. 1677-1683
-
-
Webb-Robertson, B.J.1
Cannon, W.R.2
Oehmen, C.S.3
Shah, A.R.4
Gurumoorthi, V.5
Lipton, M.S.6
Waters, K.M.7
-
21
-
-
75549087533
-
PROSITE, a protein domain database for functional characterization and annotation
-
Sigrist, C. J.; Cerutti, L.; de Castro, E.; Langendijk-Genevaux, P. S.; Bulliard, V.; Bairoch, A.; Hulo, N. PROSITE, a protein domain database for functional characterization and annotation Nucleic Acids Res. 2010, 38 (Database issue) D161-6
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 161-166
-
-
Sigrist, C.J.1
Cerutti, L.2
De Castro, E.3
Langendijk-Genevaux, P.S.4
Bulliard, V.5
Bairoch, A.6
Hulo, N.7
-
22
-
-
0013394889
-
Mechanisms of alternative pre-messenger RNA splicing
-
Black, D. L. Mechanisms of alternative pre-messenger RNA splicing Annu. Rev. Biochem. 2003, 72, 291-336
-
(2003)
Annu. Rev. Biochem.
, vol.72
, pp. 291-336
-
-
Black, D.L.1
-
23
-
-
79957865299
-
Pre-mRNA splicing: Where and when in the nucleus
-
Han, J.; Xiong, J.; Wang, D.; Fu, X. D. Pre-mRNA splicing: where and when in the nucleus Trends Cell Biol. 2011, 21 (6) 336-43
-
(2011)
Trends Cell Biol.
, vol.21
, Issue.6
, pp. 336-343
-
-
Han, J.1
Xiong, J.2
Wang, D.3
Fu, X.D.4
-
24
-
-
33748351186
-
Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells
-
Listerman, I.; Sapra, A. K.; Neugebauer, K. M. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells Nat. Struct. Mol. Biol. 2006, 13 (9) 815-22
-
(2006)
Nat. Struct. Mol. Biol.
, vol.13
, Issue.9
, pp. 815-822
-
-
Listerman, I.1
Sapra, A.K.2
Neugebauer, K.M.3
-
25
-
-
84861848461
-
Co-transcriptional regulation of alternative pre-mRNA splicing
-
Shukla, S.; Oberdoerffer, S. Co-transcriptional regulation of alternative pre-mRNA splicing Biochim. Biophys. Acta 2012, 1819 (7) 673-83
-
(2012)
Biochim. Biophys. Acta
, vol.1819
, Issue.7
, pp. 673-683
-
-
Shukla, S.1
Oberdoerffer, S.2
-
26
-
-
84868381117
-
Comparative ranking of human chromosomes based on post-genomic data
-
Ponomarenko, E.; Poverennaya, E.; Pyatnitskiy, M.; Lisitsa, A.; Moshkovskii, S.; Ilgisonis, E.; Chernobrovkin, A.; Archakov, A. Comparative ranking of human chromosomes based on post-genomic data OMICS 2012, 16 (11) 604-11
-
(2012)
OMICS
, vol.16
, Issue.11
, pp. 604-611
-
-
Ponomarenko, E.1
Poverennaya, E.2
Pyatnitskiy, M.3
Lisitsa, A.4
Moshkovskii, S.5
Ilgisonis, E.6
Chernobrovkin, A.7
Archakov, A.8
-
27
-
-
84875444381
-
Alternative splicing: A pivotal step between eukaryotic transcription and translation. Nature reviews
-
Kornblihtt, A. R.; Schor, I. E.; Allo, M.; Dujardin, G.; Petrillo, E.; Munoz, M. J. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nature reviews Mol. Cell Biol. 2013, 14 (3) 153-65
-
(2013)
Mol. Cell Biol.
, vol.14
, Issue.3
, pp. 153-165
-
-
Kornblihtt, A.R.1
Schor, I.E.2
Allo, M.3
Dujardin, G.4
Petrillo, E.5
Munoz, M.J.6
-
28
-
-
0015611135
-
Studies by DNA-RNA hybridization of transcriptional diversity in human brain
-
Grouse, L.; Omenn, G. A.; McCarthy, B. J. Studies by DNA-RNA hybridization of transcriptional diversity in human brain J. Neurochem. 1973, 20 (4) 1063-73
-
(1973)
J. Neurochem.
, vol.20
, Issue.4
, pp. 1063-1073
-
-
Grouse, L.1
Omenn, G.A.2
McCarthy, B.J.3
-
29
-
-
65649112466
-
Functional and evolutionary insights into human brain development through global transcriptome analysis
-
Johnson, M. B.; Kawasawa, Y. I.; Mason, C. E.; Krsnik, Z.; Coppola, G.; Bogdanovic, D.; Geschwind, D. H.; Mane, S. M.; State, M. W.; Sestan, N. Functional and evolutionary insights into human brain development through global transcriptome analysis Neuron 2009, 62 (4) 494-509
-
(2009)
Neuron
, vol.62
, Issue.4
, pp. 494-509
-
-
Johnson, M.B.1
Kawasawa, Y.I.2
Mason, C.E.3
Krsnik, Z.4
Coppola, G.5
Bogdanovic, D.6
Geschwind, D.H.7
Mane, S.M.8
State, M.W.9
Sestan, N.10
-
30
-
-
10944229314
-
Variation in alternative splicing across human tissues
-
Yeo, G.; Holste, D.; Kreiman, G.; Burge, C. B. Variation in alternative splicing across human tissues Genome Biol. 2004, 5 (10) R74
-
(2004)
Genome Biol.
, vol.5
, Issue.10
, pp. 74
-
-
Yeo, G.1
Holste, D.2
Kreiman, G.3
Burge, C.B.4
-
31
-
-
2342428552
-
ETR-3 and CELF4 protein domains required for RNA binding and splicing activity in vivo
-
Singh, G.; Charlet, B. N.; Han, J.; Cooper, T. A. ETR-3 and CELF4 protein domains required for RNA binding and splicing activity in vivo Nucleic Acids Res. 2004, 32 (3) 1232-41
-
(2004)
Nucleic Acids Res.
, vol.32
, Issue.3
, pp. 1232-1241
-
-
Singh, G.1
Charlet, B.N.2
Han, J.3
Cooper, T.A.4
-
32
-
-
84870701359
-
CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function
-
Wagnon, J. L.; Briese, M.; Sun, W.; Mahaffey, C. L.; Curk, T.; Rot, G.; Ule, J.; Frankel, W. N. CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function PLoS Genet. 2012, 8 (11) e1003067
-
(2012)
PLoS Genet.
, vol.8
, Issue.11
, pp. 1003067
-
-
Wagnon, J.L.1
Briese, M.2
Sun, W.3
Mahaffey, C.L.4
Curk, T.5
Rot, G.6
Ule, J.7
Frankel, W.N.8
-
33
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A.; Williams, B. A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat. Methods 2008, 5 (7) 621-8
-
(2008)
Nat. Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
34
-
-
77954197428
-
Supersplat - Spliced RNA-seq alignment
-
Bryant, D. W., Jr.; Shen, R.; Priest, H. D.; Wong, W. K.; Mockler, T. C. Supersplat - spliced RNA-seq alignment Bioinformatics 2010, 26 (12) 1500-5
-
(2010)
Bioinformatics
, vol.26
, Issue.12
, pp. 1500-1505
-
-
Bryant Jr., D.W.1
Shen, R.2
Priest, H.D.3
Wong, W.K.4
Mockler, T.C.5
-
35
-
-
84865111219
-
AS-EAST: A functional annotation tool for putative proteins encoded by alternatively spliced transcripts
-
Shionyu, M.; Takahashi, K.; Go, M. AS-EAST: a functional annotation tool for putative proteins encoded by alternatively spliced transcripts Bioinformatics 2012, 28 (15) 2076-7
-
(2012)
Bioinformatics
, vol.28
, Issue.15
, pp. 2076-2077
-
-
Shionyu, M.1
Takahashi, K.2
Go, M.3
-
36
-
-
36549003965
-
InterPro and InterProScan: Tools for protein sequence classification and comparison
-
Mulder, N.; Apweiler, R. InterPro and InterProScan: tools for protein sequence classification and comparison Methods Mol. Biol. 2007, 396, 59-70
-
(2007)
Methods Mol. Biol.
, vol.396
, pp. 59-70
-
-
Mulder, N.1
Apweiler, R.2
-
37
-
-
84880331416
-
Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing
-
Sun, W.; You, X.; Gogol-Doring, A.; He, H.; Kise, Y.; Sohn, M.; Chen, T.; Klebes, A.; Schmucker, D.; Chen, W. Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing EMBO J. 2013, 32 (14) 2029-38
-
(2013)
EMBO J.
, vol.32
, Issue.14
, pp. 2029-2038
-
-
Sun, W.1
You, X.2
Gogol-Doring, A.3
He, H.4
Kise, Y.5
Sohn, M.6
Chen, T.7
Klebes, A.8
Schmucker, D.9
Chen, W.10
-
38
-
-
84871435525
-
Function of alternative splicing
-
Kelemen, O.; Convertini, P.; Zhang, Z.; Wen, Y.; Shen, M.; Falaleeva, M.; Stamm, S. Function of alternative splicing Gene 2013, 514 (1) 1-30
-
(2013)
Gene
, vol.514
, Issue.1
, pp. 1-30
-
-
Kelemen, O.1
Convertini, P.2
Zhang, Z.3
Wen, Y.4
Shen, M.5
Falaleeva, M.6
Stamm, S.7
-
39
-
-
79959567198
-
Alternative splicing of RAGE: Roles in biology and disease
-
Kalea, A. Z.; Schmidt, A. M.; Hudson, B. I. Alternative splicing of RAGE: roles in biology and disease Front. Biosci. 2011, 16, 2756-70
-
(2011)
Front. Biosci.
, vol.16
, pp. 2756-2770
-
-
Kalea, A.Z.1
Schmidt, A.M.2
Hudson, B.I.3
-
40
-
-
84878783597
-
TGM2 and implications for human disease: Role of alternative splicing
-
Lai, T. S.; Greenberg, C. S. TGM2 and implications for human disease: role of alternative splicing Front. Biosci. 2013, 18, 504-19
-
(2013)
Front. Biosci.
, vol.18
, pp. 504-519
-
-
Lai, T.S.1
Greenberg, C.S.2
-
41
-
-
79954583408
-
Cyclic AMP-dependent protein kinase regulates the alternative splicing of tau exon 10: A mechanism involved in tau pathology of Alzheimer disease
-
Shi, J.; Qian, W.; Yin, X.; Iqbal, K.; Grundke-Iqbal, I.; Gu, X.; Ding, F.; Gong, C. X.; Liu, F. Cyclic AMP-dependent protein kinase regulates the alternative splicing of tau exon 10: a mechanism involved in tau pathology of Alzheimer disease J. Biol. Chem. 2011, 286 (16) 14639-48
-
(2011)
J. Biol. Chem.
, vol.286
, Issue.16
, pp. 14639-14648
-
-
Shi, J.1
Qian, W.2
Yin, X.3
Iqbal, K.4
Grundke-Iqbal, I.5
Gu, X.6
Ding, F.7
Gong, C.X.8
Liu, F.9
-
42
-
-
43149094164
-
Pfam 10 years on: 10,000 families and still growing
-
Sammut, S. J.; Finn, R. D.; Bateman, A. Pfam 10 years on: 10,000 families and still growing Briefings Bioinf. 2008, 9 (3) 210-9
-
(2008)
Briefings Bioinf.
, vol.9
, Issue.3
, pp. 210-219
-
-
Sammut, S.J.1
Finn, R.D.2
Bateman, A.3
-
43
-
-
13444305296
-
The ProDom database of protein domain families: More emphasis on 3D
-
Bru, C.; Courcelle, E.; Carrere, S.; Beausse, Y.; Dalmar, S.; Kahn, D. The ProDom database of protein domain families: more emphasis on 3D Nucleic Acids Res. 2005, 33 (Database issue) D212-5
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 212-215
-
-
Bru, C.1
Courcelle, E.2
Carrere, S.3
Beausse, Y.4
Dalmar, S.5
Kahn, D.6
-
44
-
-
84876134492
-
TIGRFAMs and Genome Properties in 2013
-
Haft, D. H.; Selengut, J. D.; Richter, R. A.; Harkins, D.; Basu, M. K.; Beck, E. TIGRFAMs and Genome Properties in 2013 Nucleic Acids Res. 2013, 41 (Database issue) D387-95
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 387-395
-
-
Haft, D.H.1
Selengut, J.D.2
Richter, R.A.3
Harkins, D.4
Basu, M.K.5
Beck, E.6
-
45
-
-
80051503006
-
Congenital cataracts, facial dysmorphism, and neuropathy syndrome
-
Tzifi, F.; Pons, R.; Athanassaki, C.; Poulou, M.; Kanavakis, E. Congenital cataracts, facial dysmorphism, and neuropathy syndrome J. Pediatr. Neurol. 2011, 45 (3) 206-8
-
(2011)
J. Pediatr. Neurol.
, vol.45
, Issue.3
, pp. 206-208
-
-
Tzifi, F.1
Pons, R.2
Athanassaki, C.3
Poulou, M.4
Kanavakis, E.5
-
46
-
-
83855160781
-
StackTIS: A stacked generalization approach for effective prediction of translation initiation sites
-
Tzanis, G.; Berberidis, C.; Vlahavas, I. StackTIS: a stacked generalization approach for effective prediction of translation initiation sites Comput. Biol. Med. 2012, 42 (1) 61-9
-
(2012)
Comput. Biol. Med.
, vol.42
, Issue.1
, pp. 61-69
-
-
Tzanis, G.1
Berberidis, C.2
Vlahavas, I.3
-
47
-
-
56449107195
-
MetWAMer: Eukaryotic translation initiation site prediction
-
Sparks, M. E.; Brendel, V. MetWAMer: eukaryotic translation initiation site prediction BMC Bioinf. 2008, 9, 381
-
(2008)
BMC Bioinf.
, vol.9
, pp. 381
-
-
Sparks, M.E.1
Brendel, V.2
-
48
-
-
84865561269
-
Gene and translation initiation site prediction in metagenomic sequences
-
Hyatt, D.; LoCascio, P. F.; Hauser, L. J.; Uberbacher, E. C. Gene and translation initiation site prediction in metagenomic sequences Bioinformatics 2012, 28 (17) 2223-30
-
(2012)
Bioinformatics
, vol.28
, Issue.17
, pp. 2223-2230
-
-
Hyatt, D.1
Locascio, P.F.2
Hauser, L.J.3
Uberbacher, E.C.4
-
49
-
-
14644415892
-
The hepatitis C virus alternate reading frame (ARF) and its family of novel products: The alternate reading frame protein/F-protein, the double-frameshift protein, and others
-
Branch, A. D.; Stump, D. D.; Gutierrez, J. A.; Eng, F.; Walewski, J. L. The hepatitis C virus alternate reading frame (ARF) and its family of novel products: the alternate reading frame protein/F-protein, the double-frameshift protein, and others Semin. Liver Dis. 2005, 25 (1) 105-17
-
(2005)
Semin. Liver Dis.
, vol.25
, Issue.1
, pp. 105-117
-
-
Branch, A.D.1
Stump, D.D.2
Gutierrez, J.A.3
Eng, F.4
Walewski, J.L.5
-
50
-
-
33746858906
-
Influenza A virus PB1-F2 protein contributes to viral pathogenesis in mice
-
Zamarin, D.; Ortigoza, M. B.; Palese, P. Influenza A virus PB1-F2 protein contributes to viral pathogenesis in mice J. Virol. 2006, 80 (16) 7976-83
-
(2006)
J. Virol.
, vol.80
, Issue.16
, pp. 7976-7983
-
-
Zamarin, D.1
Ortigoza, M.B.2
Palese, P.3
-
51
-
-
0035898609
-
Two overlapping reading frames in a single exon encode interacting proteins - A novel way of gene usage
-
Klemke, M.; Kehlenbach, R. H.; Huttner, W. B. Two overlapping reading frames in a single exon encode interacting proteins - a novel way of gene usage EMBO J. 2001, 20 (14) 3849-60
-
(2001)
EMBO J.
, vol.20
, Issue.14
, pp. 3849-3860
-
-
Klemke, M.1
Kehlenbach, R.H.2
Huttner, W.B.3
-
52
-
-
84881529829
-
Direct detection of alternative open reading frames translation products in human significantly expands the proteome
-
Vanderperre, B.; Lucier, J. F.; Bissonnette, C.; Motard, J.; Tremblay, G.; Vanderperre, S.; Wisztorski, M.; Salzet, M.; Boisvert, F. M.; Roucou, X. Direct detection of alternative open reading frames translation products in human significantly expands the proteome PloS One 2013, 8 (8) e70698
-
(2013)
PloS One
, vol.8
, Issue.8
, pp. 70698
-
-
Vanderperre, B.1
Lucier, J.F.2
Bissonnette, C.3
Motard, J.4
Tremblay, G.5
Vanderperre, S.6
Wisztorski, M.7
Salzet, M.8
Boisvert, F.M.9
Roucou, X.10
-
53
-
-
84862250906
-
HAltORF: A database of predicted out-of-frame alternative open reading frames in human
-
Vanderperre, B.; Lucier, J. F.; Roucou, X. HAltORF: a database of predicted out-of-frame alternative open reading frames in human Database 2012, 2012, bas025
-
(2012)
Database
, vol.2012
, pp. 025
-
-
Vanderperre, B.1
Lucier, J.F.2
Roucou, X.3
-
54
-
-
77649258954
-
Threading the needle: Getting selenocysteine into proteins
-
Donovan, J.; Copeland, P. R. Threading the needle: getting selenocysteine into proteins Antioxid. Redox Signaling 2010, 12 (7) 881-92
-
(2010)
Antioxid. Redox Signaling
, vol.12
, Issue.7
, pp. 881-892
-
-
Donovan, J.1
Copeland, P.R.2
-
55
-
-
84883482725
-
SECISearch3 and Seblastian: New tools for prediction of SECIS elements and selenoproteins
-
Mariotti, M.; Lobanov, A. V.; Guigo, R.; Gladyshev, V. N. SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins Nucleic Acids Res. 2013, 41 (15) e149
-
(2013)
Nucleic Acids Res.
, vol.41
, Issue.15
, pp. 149
-
-
Mariotti, M.1
Lobanov, A.V.2
Guigo, R.3
Gladyshev, V.N.4
-
56
-
-
0035834489
-
Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles
-
Gautheret, D.; Lambert, A. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles J. Mol. Biol. 2001, 313 (5) 1003-11
-
(2001)
J. Mol. Biol.
, vol.313
, Issue.5
, pp. 1003-1011
-
-
Gautheret, D.1
Lambert, A.2
-
57
-
-
61349135517
-
Neto1 is a novel CUB-domain NMDA receptor-interacting protein required for synaptic plasticity and learning
-
Ng, D.; Pitcher, G. M.; Szilard, R. K.; Sertie, A.; Kanisek, M.; Clapcote, S. J.; Lipina, T.; Kalia, L. V.; Joo, D.; McKerlie, C.; Cortez, M.; Roder, J. C.; Salter, M. W.; McInnes, R. R. Neto1 is a novel CUB-domain NMDA receptor-interacting protein required for synaptic plasticity and learning PLoS Biol. 2009, 7 (2) e41
-
(2009)
PLoS Biol.
, vol.7
, Issue.2
, pp. 41
-
-
Ng, D.1
Pitcher, G.M.2
Szilard, R.K.3
Sertie, A.4
Kanisek, M.5
Clapcote, S.J.6
Lipina, T.7
Kalia, L.V.8
Joo, D.9
McKerlie, C.10
Cortez, M.11
Roder, J.C.12
Salter, M.W.13
McInnes, R.R.14
-
58
-
-
0033613942
-
OC-2, a novel mammalian member of the ONECUT class of homeodomain transcription factors whose function in liver partially overlaps with that of hepatocyte nuclear factor-6
-
Jacquemin, P.; Lannoy, V. J.; Rousseau, G. G.; Lemaigre, F. P. OC-2, a novel mammalian member of the ONECUT class of homeodomain transcription factors whose function in liver partially overlaps with that of hepatocyte nuclear factor-6 J. Biol. Chem. 1999, 274 (5) 2665-71
-
(1999)
J. Biol. Chem.
, vol.274
, Issue.5
, pp. 2665-2671
-
-
Jacquemin, P.1
Lannoy, V.J.2
Rousseau, G.G.3
Lemaigre, F.P.4
-
59
-
-
79959484787
-
Localization of cerebellin-2 in late embryonic chicken brain: Implications for a role in synapse formation and for brain evolution
-
Reiner, A.; Yang, M.; Cagle, M. C.; Honig, M. G. Localization of cerebellin-2 in late embryonic chicken brain: implications for a role in synapse formation and for brain evolution J. Comp. Neurol. 2011, 519 (11) 2225-51
-
(2011)
J. Comp. Neurol.
, vol.519
, Issue.11
, pp. 2225-2251
-
-
Reiner, A.1
Yang, M.2
Cagle, M.C.3
Honig, M.G.4
-
60
-
-
57849150788
-
Alternative splicing and disease
-
Tazi, J.; Bakkour, N.; Stamm, S. Alternative splicing and disease Biochim. Biophys. Acta 2009, 1792 (1) 14-26
-
(2009)
Biochim. Biophys. Acta
, vol.1792
, Issue.1
, pp. 14-26
-
-
Tazi, J.1
Bakkour, N.2
Stamm, S.3
-
61
-
-
84867852880
-
Alternative transcription and alternative splicing in cancer
-
Pal, S.; Gupta, R.; Davuluri, R. V. Alternative transcription and alternative splicing in cancer Pharmacol. Ther. 2012, 136 (3) 283-94
-
(2012)
Pharmacol. Ther.
, vol.136
, Issue.3
, pp. 283-294
-
-
Pal, S.1
Gupta, R.2
Davuluri, R.V.3
-
62
-
-
77954131742
-
Alternative splice variants, a new class of protein cancer biomarker candidates: Findings in pancreatic cancer and breast cancer with systems biology implications
-
Omenn, G. S.; Yocum, A. K.; Menon, R. Alternative splice variants, a new class of protein cancer biomarker candidates: findings in pancreatic cancer and breast cancer with systems biology implications Dis. Markers 2010, 28 (4) 241-51
-
(2010)
Dis. Markers
, vol.28
, Issue.4
, pp. 241-251
-
-
Omenn, G.S.1
Yocum, A.K.2
Menon, R.3
-
63
-
-
0029083790
-
Alternate splicing produces a novel cyclin D1 transcript
-
Betticher, D. C.; Thatcher, N.; Altermatt, H. J.; Hoban, P.; Ryder, W. D.; Heighway, J. Alternate splicing produces a novel cyclin D1 transcript Oncogene 1995, 11 (5) 1005-11
-
(1995)
Oncogene
, vol.11
, Issue.5
, pp. 1005-1011
-
-
Betticher, D.C.1
Thatcher, N.2
Altermatt, H.J.3
Hoban, P.4
Ryder, W.D.5
Heighway, J.6
-
64
-
-
0242526150
-
An alternatively spliced cyclin D1 isoform, cyclin D1b, is a nuclear oncogene
-
Lu, F.; Gladden, A. B.; Diehl, J. A. An alternatively spliced cyclin D1 isoform, cyclin D1b, is a nuclear oncogene Cancer Res. 2003, 63 (21) 7056-61
-
(2003)
Cancer Res.
, vol.63
, Issue.21
, pp. 7056-7061
-
-
Lu, F.1
Gladden, A.B.2
Diehl, J.A.3
-
65
-
-
80053377363
-
Alternative splicings on p53, BRCA1 and PTEN genes involved in breast cancer
-
Okumura, N.; Yoshida, H.; Kitagishi, Y.; Nishimura, Y.; Matsuda, S. Alternative splicings on p53, BRCA1 and PTEN genes involved in breast cancer Biochem. Biophys. Res. Commun. 2011, 413 (3) 395-9
-
(2011)
Biochem. Biophys. Res. Commun.
, vol.413
, Issue.3
, pp. 395-399
-
-
Okumura, N.1
Yoshida, H.2
Kitagishi, Y.3
Nishimura, Y.4
Matsuda, S.5
-
66
-
-
79960918747
-
RNA structure and the mechanisms of alternative splicing
-
McManus, C. J.; Graveley, B. R. RNA structure and the mechanisms of alternative splicing Curr. Opin. Genet. Dev. 2011, 21 (4) 373-9
-
(2011)
Curr. Opin. Genet. Dev.
, vol.21
, Issue.4
, pp. 373-379
-
-
McManus, C.J.1
Graveley, B.R.2
-
67
-
-
70350569286
-
Mechanisms of alternative splicing regulation: Insights from molecular and genomics approaches
-
Chen, M.; Manley, J. L. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches Nat. Rev. Mol. Cell Biol. 2009, 10 (11) 741-54
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, Issue.11
, pp. 741-754
-
-
Chen, M.1
Manley, J.L.2
-
68
-
-
77149175671
-
Regulation of alternative splicing by histone modifications
-
Luco, R. F.; Pan, Q.; Tominaga, K.; Blencowe, B. J.; Pereira-Smith, O. M.; Misteli, T. Regulation of alternative splicing by histone modifications Science 2010, 327 (5968) 996-1000
-
(2010)
Science
, vol.327
, Issue.5968
, pp. 996-1000
-
-
Luco, R.F.1
Pan, Q.2
Tominaga, K.3
Blencowe, B.J.4
Pereira-Smith, O.M.5
Misteli, T.6
-
69
-
-
84862650101
-
A conserved role for intragenic DNA methylation in alternative pre-mRNA splicing
-
Oberdoerffer, S. A conserved role for intragenic DNA methylation in alternative pre-mRNA splicing Transcription 2012, 3 (3) 106-9
-
(2012)
Transcription
, vol.3
, Issue.3
, pp. 106-109
-
-
Oberdoerffer, S.1
-
70
-
-
80455176999
-
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
-
Shukla, S.; Kavak, E.; Gregory, M.; Imashimizu, M.; Shutinoski, B.; Kashlev, M.; Oberdoerffer, P.; Sandberg, R.; Oberdoerffer, S. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing Nature 2011, 479 (7371) 74-9
-
(2011)
Nature
, vol.479
, Issue.7371
, pp. 74-79
-
-
Shukla, S.1
Kavak, E.2
Gregory, M.3
Imashimizu, M.4
Shutinoski, B.5
Kashlev, M.6
Oberdoerffer, P.7
Sandberg, R.8
Oberdoerffer, S.9
-
71
-
-
84887214395
-
Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition
-
Maunakea, A. K.; Chepelev, I.; Cui, K.; Zhao, K. Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition Cell Res. 2013, 23 (11) 1256-69
-
(2013)
Cell Res.
, vol.23
, Issue.11
, pp. 1256-1269
-
-
Maunakea, A.K.1
Chepelev, I.2
Cui, K.3
Zhao, K.4
-
72
-
-
84876022525
-
Genetic variations and alternative splicing: The Glioma associated oncogene 1, GLI1
-
Zaphiropoulos, P. G. Genetic variations and alternative splicing: the Glioma associated oncogene 1, GLI1 Front. Genet. 2012, 3, 119
-
(2012)
Front. Genet.
, vol.3
, pp. 119
-
-
Zaphiropoulos, P.G.1
-
73
-
-
84875490185
-
Cancer genome landscapes
-
Vogelstein, B.; Papadopoulos, N.; Velculescu, V. E.; Zhou, S.; Diaz, L. A., Jr.; Kinzler, K. W. Cancer genome landscapes Science 2013, 339 (6127) 1546-58
-
(2013)
Science
, vol.339
, Issue.6127
, pp. 1546-1558
-
-
Vogelstein, B.1
Papadopoulos, N.2
Velculescu, V.E.3
Zhou, S.4
Diaz Jr., L.A.5
Kinzler, K.W.6
-
74
-
-
84867145980
-
On the presence and role of human gene-body DNA methylation
-
Jjingo, D.; Conley, A. B.; Yi, S. V.; Lunyak, V. V.; Jordan, I. K. On the presence and role of human gene-body DNA methylation Oncotarget 2012, 3 (4) 462-74
-
(2012)
Oncotarget
, vol.3
, Issue.4
, pp. 462-474
-
-
Jjingo, D.1
Conley, A.B.2
Yi, S.V.3
Lunyak, V.V.4
Jordan, I.K.5
-
75
-
-
84856474843
-
Intragenic DNA methylation: Implications of this epigenetic mechanism for cancer research
-
Shenker, N.; Flanagan, J. M. Intragenic DNA methylation: implications of this epigenetic mechanism for cancer research Br. J. Cancer 2012, 106 (2) 248-53
-
(2012)
Br. J. Cancer
, vol.106
, Issue.2
, pp. 248-253
-
-
Shenker, N.1
Flanagan, J.M.2
-
76
-
-
77951718967
-
Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers
-
Menon, R.; Omenn, G. S. Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers Cancer Res. 2010, 70 (9) 3440-9
-
(2010)
Cancer Res.
, vol.70
, Issue.9
, pp. 3440-3449
-
-
Menon, R.1
Omenn, G.S.2
-
77
-
-
82755181925
-
Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers
-
Menon, R.; Roy, A.; Mukherjee, S.; Belkin, S.; Zhang, Y.; Omenn, G. S. Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers J. Proteome Res. 2011, 10 (12) 5503-11
-
(2011)
J. Proteome Res.
, vol.10
, Issue.12
, pp. 5503-5511
-
-
Menon, R.1
Roy, A.2
Mukherjee, S.3
Belkin, S.4
Zhang, Y.5
Omenn, G.S.6
|