Access the full text.
Sign up today, get DeepDyve free for 14 days.
Loading next page...
/lp/unpaywall/alternative-splicing-new-insights-from-global-analyses-SfZaUMIts9
References (88)
-
B. Graveley (2005)
Mutually Exclusive Splicing of the Insect Dscam Pre-mRNA Directed by Competing Intronic RNA Secondary StructuresCell, 123
-
J. Yeakley, Jian-Bing Fan, Dennis Doucet, Lin Luo, Eliza Wickham, Z. Ye, M. Chee, Xiang-Dong Fu (2002)
Profiling alternative splicing on fiber-optic arraysNature Biotechnology, 20
-
Alissa Resch, Yi Xing, B. Modrek, M. Gorlick, R. Riley, Christopher Lee (2004)
Assessing the impact of alternative splicing on domain interactions in the human proteome.Journal of proteome research, 3 1
-
N. Gromak, Alexis Rideau, J. Southby, A. Scadden, C. Gooding, S. Hüttelmaier, R. Singer, Christopher Smith (2003)
The PTB interacting protein raver1 regulates α‐tropomyosin alternative splicingThe EMBO Journal, 22
-
Chaolin Zhang, Hai-Ri Li, Jian-Bing Fan, J. Wang-Rodriguez, T. Downs, Xiang-Dong Fu, Michael Zhang (2006)
Profiling alternatively spliced mRNA isoforms for prostate cancer classificationBMC Bioinformatics, 7
-
F. Watson, Roland Püttmann-Holgado, F. Thomas, David Lamar, Michael Hughes, M. Kondo, V. Rebel, D. Schmucker (2005)
Extensive Diversity of Ig-Superfamily Proteins in the Immune System of InsectsScience, 309
-
R. Kanadia, K. Johnstone, A. Mankodi, C. Lungu, C. Thornton, D. Esson, A. Timmers, W. Hauswirth, M. Swanson (2003)
A Muscleblind Knockout Model for Myotonic DystrophyScience, 302
-
Heebal Kim, R. Klein, J. Majewski, J. Ott (2004)
Estimating rates of alternative splicing in mammals and invertebratesNature Genetics, 36
-
Keith Le, K. Mitsouras, Meenakshi Roy, Qi Wang, Qiang Xu, S. Nelson, Christopher Lee (2004)
Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data.Nucleic acids research, 32 22
-
Shai (2006)
Inferring global levels of alternative splicing isoforms using a generative model of microarray dataBioinformatics, 22
-
A. Matlin, F. Clark, Christopher Smith (2005)
Understanding alternative splicing: towards a cellular codeNature Reviews Molecular Cell Biology, 6
-
Simon Minovitsky, S. Gee, S. Schokrpur, I. Dubchak, J. Conboy (2005)
The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exonsNucleic Acids Research, 33
-
B. Modrek, Christopher Lee (2003)
Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or lossNature Genetics, 34
-
J. Ule, K. Jensen, M. Ruggiu, Aldo Mele, A. Ule, R. Darnell (2003)
CLIP Identifies Nova-Regulated RNA Networks in the BrainScience, 302
-
A. Watahiki, K. Waki, N. Hayatsu, T. Shiraki, S. Kondo, Mari Nakamura, D. Sasaki, T. Arakawa, J. Kawai, M. Harbers, Y. Hayashizaki, Piero Carninci (2004)
Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomasNature Methods, 1
-
Tzu-Ming Chern, E. Nimwegen, C. Kai, J. Kawai, Piero Carninci, Y. Hayashizaki, M. Zavolan (2006)
A Simple Physical Model Predicts Small Exon Length VariationsPLoS Genetics, 2
-
M. Blanchette, R. Green, S. Brenner, D. Rio (2005)
Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila.Genes & development, 19 11
-
F. Pagani, F. Baralle (2004)
Genomic variants in exons and introns: identifying the splicing spoilersNature Reviews Genetics, 5
-
Q. Pan, M. Bakowski, Q. Morris, Wen Zhang, B. Frey, T. Hughes, B. Blencowe (2005)
Alternative splicing of conserved exons is frequently species-specific in human and mouse.Trends in genetics : TIG, 21 2
-
A. Kornblihtt (2005)
Promoter usage and alternative splicing.Current opinion in cell biology, 17 3
-
Wen Zhang, Q. Morris, Richard Chang, O. Shai, M. Bakowski, N. Mitsakakis, N. Mohammad, M. Robinson, R. Zirngibl, E. Somogyi, N. Laurin, E. Eftekharpour, E. Sat, J. Grigull, Q. Pan, W. Peng, N. Krogan, J. Greenblatt, M. Fehlings, D. Kooy, J. Aubin, B. Bruneau, J. Rossant, B. Blencowe, B. Frey, T. Hughes (2004)
The functional landscape of mouse gene expressionJournal of Biology, 3
-
Soergel (2005)
Regulation of gene expression by coupling of alternative splicing and NMD -
D. Schmucker, J. Clemens, Huidy Shu, C. Worby, Jian Xiao, M. Muda, J. Dixon, S. Zipursky (2000)
Drosophila Dscam Is an Axon Guidance Receptor Exhibiting Extraordinary Molecular DiversityCell, 101
-
C. Sugnet, Karpagam Srinivasan, Tyson Clark, Georgeann O'Brien, M. Cline, Hui Wang, Alan Williams, D. Kulp, J. Blume, D. Haussler, M. Ares (2005)
Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing MicroarraysPLoS Computational Biology, 2
-
S. Teraoka, M. Telatar, Sara Becker-Catania, T. Liang, S. Onengut, A. Tolun, L. Chessa, O. Sanal, E. Bernatowska, R. Gatti, P. Concannon (1999)
Splicing defects in the ataxia-telangiectasia gene, ATM: underlying mutations and consequences.American journal of human genetics, 64 6
-
Dana Philipps, J. Park, B. Graveley (2004)
A computational and experimental approach toward a priori identification of alternatively spliced exons.RNA, 10 12
-
D. Brett, H. Pospisil, J. Valcárcel, J. Reich, P. Bork (2002)
Alternative splicing and genome complexityNature Genetics, 30
-
J. Keene, P. Lager (2005)
Post-transcriptional operons and regulons co-ordinating gene expressionChromosome Research, 13
-
B. Chen, M. Kondo, A. Garnier, F. Watson, Roland Püettmann-Holgado, David Lamar, D. Schmucker (2006)
The Molecular Diversity of Dscam Is Functionally Required for Neuronal Wiring Specificity in DrosophilaCell, 125
-
A. Kidd, J. Siegfried, K. Kimble, K. Siegfried, M. Chesney, Kimble
Sex and the Single Splice -
Xiang Zhang, L. Chasin (2004)
Computational definition of sequence motifs governing constitutive exon splicing.Genes & development, 18 11
-
E. Ars, E. Serra, Judit García, H. Kruyer, A. Gaona, C. Lázaro, X. Estivill (2000)
Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1.Human molecular genetics, 9 2
-
B. Lewis, R. Green, S. Brenner (2002)
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humansProceedings of the National Academy of Sciences of the United States of America, 100
-
M. Dye, N. Gromak, N. Proudfoot (2006)
Exon tethering in transcription by RNA polymerase II.Molecular cell, 21 6
-
Gene Yeo, D. Holste, Gabriel Kreiman, C. Burge (2004)
Variation in alternative splicing across human tissuesGenome Biology, 5
-
P. Senapathy, M. Shapiro, N. Harris (1990)
Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome project.Methods in enzymology, 183
-
J. Ule, R. Darnell (2006)
RNA binding proteins and the regulation of neuronal synaptic plasticityCurrent Opinion in Neurobiology, 16
-
L. Cartegni, S. Chew, A. Krainer (2002)
Listening to silence and understanding nonsense: exonic mutations that affect splicingNature Reviews Genetics, 3
-
Q. Pan, O. Shai, C. Misquitta, Wen Zhang, Arneet Saltzman, N. Mohammad, T. Babak, Henry Siu, T. Hughes, Q. Morris, B. Frey, B. Blencowe (2004)
Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform.Molecular cell, 16 6
-
Takayuki Horiuchi, T. Aigaki (2006)
Alternative trans‐splicing: a novel mode of pre‐mRNA processingBiology of the Cell, 98
-
Wang (2004)
Systematic identification and analysis of exonic splicing silencersCell, 119
-
O. Shai, Q. Morris, B. Blencowe, B. Frey (2006)
Data and text mining Inferring global levels of alternative splicing isoforms using a generative model of microarray data -
Q. Pan, Arneet Saltzman, Yoon Kim, C. Misquitta, O. Shai, L. Maquat, B. Frey, B. Blencowe (2006)
Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression.Genes & development, 20 2
-
Gene Yeo, Eric Nostrand, D. Holste, T. Poggio, C. Burge (2005)
Identification and analysis of alternative splicing events conserved in human and mouse.Proceedings of the National Academy of Sciences of the United States of America, 102 8
-
M. Hiller, K. Huse, K. Szafranski, N. Jahn, J. Hampe, S. Schreiber, R. Backofen, M. Platzer (2004)
Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticityNature Genetics, 36
-
Hanzhen Sun, L. Chasin (2000)
Multiple Splicing Defects in an Intronic False ExonMolecular and Cellular Biology, 20
-
Yi Xing, Christopher Lee (2005)
Protein Modularity of Alternatively Spliced Exons Is Associated with Tissue-Specific Regulation of Alternative SplicingPLoS Genetics, 1
-
L. Maquat (2002)
Nonsense-mediated mRNA decayCurrent Biology, 12
-
Daehyun Baek, P. Green (2005)
Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing.Proceedings of the National Academy of Sciences of the United States of America, 102 36
-
Lani Wu, T. Hughes, A. Davierwala, M. Robinson, R. Stoughton, S. Altschuler (2002)
Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clustersNature Genetics, 31
-
R. Miki, K. Kadota, H. Bono, Y. Mizuno, Y. Tomaru, Piero Carninci, M. Itoh, K. Shibata, J. Kawai, H. Konno, S. Watanabe, K. Sato, Y. Tokusumi, N. Kikuchi, Y. Ishii, Y. Hamaguchi, I. Nishizuka, H. Goto, H. Nitanda, S. Satomi, A. Yoshiki, M. Kusakabe, J. Derisi, M. Eisen, V. Iyer, P. Brown, M. Muramatsu, H. Shimada, Y. Okazaki, Y. Hayashizaki (2001)
Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arraysProceedings of the National Academy of Sciences of the United States of America, 98
-
A. Hughes, R. Friedman (2005)
Gene Duplication and the Properties of Biological NetworksJournal of Molecular Evolution, 61
-
B. Modrek, Alissa Resch, C. Grasso, Christopher Lee (2001)
Genome-wide detection of alternative splicing in expressed sequences of human genesNucleic acids research, 29 13
-
Carrie Davis, Leslie Grate, Marc Spingola, Manuel Ares (2000)
Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast.Nucleic acids research, 28 8
-
J. Ule, A. Ule, J. Spencer, Alan Williams, Jing-Shan Hu, M. Cline, Hui Wang, Tyson Clark, C. Fraser, M. Ruggiu, B. Zeeberg, D. Kane, J. Weinstein, J. Blume, R. Darnell (2005)
Nova regulates brain-specific splicing to shape the synapseNature Genetics, 37
-
Galit Lev-Maor, R. Sorek, N. Shomron, G. Ast (2003)
The Birth of an Alternatively Spliced Exon: 3' Splice-Site Selection in Alu ExonsScience, 300
-
Xing (2005)
Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequencesProc. Natl. Acad. Sci. USA, 102
-
Jason Johnson, J. Castle, P. Garrett-engele, Zhengyan Kan, P. Loerch, C. Armour, R. Santos, E. Schadt, R. Stoughton, D. Shoemaker (2003)
Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction MicroarraysScience, 302
-
T. Thanaraj, S. Stamm, F. Clark, J. Riethoven, V. Texier, J. Muilu (2004)
ASD: the Alternative Splicing DatabaseNucleic acids research, 32 Database issue
-
Lorrie Boucher, C. Ouzounis, Anton Enright, B. Blencowe (2001)
A genome-wide survey of RS domain proteins.RNA, 7 12
-
Yi Xing, Christopher Lee (2005)
Evidence of functional selection pressure for alternative splicingevents that accelerate evolution of protein subsequencesGenome Biology, 6
-
A. Kornblihtt (2006)
Chromatin, transcript elongation and alternative splicingNature Structural &Molecular Biology, 13
-
Christina Zheng, Young‐Soo Kwon, Hai-Ri Li, Kui-Dong Zhang, Gabriela Coutinho-Mansfield, Canzhu Yang, T. Nair, M. Gribskov, Xiang-Dong Fu (2005)
MAASE: an alternative splicing database designed for supporting splicing microarray applications.RNA, 11 12
-
D. Black (2003)
Mechanisms of alternative pre-messenger RNA splicing.Annual review of biochemistry, 72
-
M. Zavolan, S. Kondo, C. Schonbach, J. Adachi, D. Hume, Y. Hayashizaki, T. Gaasterland (2003)
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome.Genome research, 13 6B
-
Zefeng Wang, Xinshu Xiao, Eric Nostrand, C. Burge (2006)
General and specific functions of exonic splicing silencers in splicing control.Molecular cell, 23 1
-
R. Sorek, R. Shamir, G. Ast (2004)
How prevalent is functional alternative splicing in the human genome?Trends in genetics : TIG, 20 2
-
Rebeca Martínez-Contreras, Jean-François Fisette, F. Nasim, R. Madden, Mélanie Cordeau, B. Chabot (2006)
Intronic Binding Sites for hnRNP A/B and hnRNP F/H Proteins Stimulate Pre-mRNA SplicingPLoS Biology, 4
-
M. Brudno, M. Gelfand, S. Spengler, M. Zorn, I-Min Dubchak, J. Conboy (2001)
Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing.Nucleic acids research, 29 11
-
D. Bentley (2005)
Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors.Current opinion in cell biology, 17 3
-
N. Kopelman, D. Lancet, I. Yanai (2005)
Alternative splicing and gene duplication are inversely correlated evolutionary mechanismsNature Genetics, 37
-
El Ibrahim, T. Schaal, K. Hertel, R. Reed, T. Maniatis (2005)
Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers.Proceedings of the National Academy of Sciences of the United States of America, 102 14
-
B. Modrek, Christopher Lee (2002)
A genomic view of alternative splicingNature Genetics, 30
-
V. Štolc, Zareen Gauhar, Christopher Mason, G. Halász, M. Batenburg, Scott Rifkin, S. Hua, Tine Herreman, W. Tongprasit, P. Barbano, H. Bussemaker, K. White (2004)
A Gene Expression Map for the Euchromatic Genome of Drosophila melanogasterScience, 306
-
International Consortium (2001)
Initial sequencing and analysis of the human genomeNature, 409
-
P. Förch, J. Valcárcel (2003)
Splicing regulation in Drosophila sex determination.Progress in molecular and subcellular biology, 31
-
Peng Wang, Bo Yan, Jun-tao Guo, C. Hicks, Ying Xu (2005)
Structural genomics analysis of alternative splicing and application to isoform structure modeling.Proceedings of the National Academy of Sciences of the United States of America, 102 52
-
N. Gromak, Alexis Rideau, J. Southby, A. Scadden, C. Gooding, S. Hüttelmaier, R. Singer, Christopher Smith (2003)
The PTB interacting protein raver1 regulates alpha-tropomyosin alternative splicing.The EMBO journal, 22 23
-
Zhixi Su, Jianmin Wang, Jun Yu, Xiaoqiu Huang, X. Gu (2005)
Evolution of alternative splicing after gene duplication.Genome research, 16 2
-
U. Ohler, N. Shomron, C. Burge (2005)
Recognition of Unknown Conserved Alternatively Spliced ExonsPLoS Computational Biology, 1
-
D. Lipscombe (2005)
Neuronal proteins custom designed by alternative splicingCurrent Opinion in Neurobiology, 15
-
U. Beffert, E. Weeber, Andre Durudas, Shenfeng Qiu, Irene Masiulis, J. Sweatt, Wei Li, G. Adelmann, M. Frotscher, R. Hammer, J. Herz, J. Herz (2005)
Modulation of Synaptic Plasticity and Memory by Reelin Involves Differential Splicing of the Lipoprotein Receptor Apoer2Neuron, 47
-
Christopher Lee, Levan Atanelov, B. Modrek, Yi Xing (2003)
ASAP: the Alternative Splicing Annotation ProjectNucleic acids research, 31 1
-
Richard Seifert, K. Nauhaus, T. Treude, Volker Thiel, M. Blumenberg, K. Knittel, A. Gieseke, K. Peterknecht, Thomas Pape, A. Boetius, Rudolf Amann, Bo Jørgensen, Friedrich Widdel, Jörn Peckmann, Nikolai Pimenov
Predictive Identification of Exonic Splicing Enhancers in Human Genes -
Hai-Ri Li, J. Wang-Rodriguez, T. Nair, J. Yeakley, Young‐Soo Kwon, M. Bibikova, Christina Zheng, Lixin Zhou, Kui-Dong Zhang, T. Downs, Xiang-Dong Fu, Jian-Bing Fan (2006)
Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens.Cancer research, 66 8
-
R. Lührmann (2005)
Faculty Opinions recommendation of Systematic identification and analysis of exonic splicing silencers. -
Hui Wang, E. Hubbell, Jing-Shan Hu, Gangwu Mei, M. Cline, Gang Lu, Tyson Clark, Michael Siani-Rose, M. Ares, D. Kulp, D. Haussler (2003)
Gene structure-based splice variant deconvolution using a microarry platformBioinformatics, 19 Suppl 1
-
Alissa Resch, Yi Xing, A. Alekseyenko, B. Modrek, Christopher Lee (2004)
Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation.Nucleic acids research, 32 4
- Publisher
- Unpaywall
- ISSN
- 0092-8674
- DOI
- 10.1016/j.cell.2006.06.023
- Publisher site
- See Article on Publisher Site
Abstract
Journal
Cell – Unpaywall
Published: Jul 1, 2006