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Analysis of alternative splicing with microarrays: successes and challenges
Christopher Lee, Meenakshi Roy
Genome Biol. 2004; 5(7): 231. Published online 2004 June 21. doi: 10.1186/gb-2004-5-7-231
PMCID:
PMC463277
Abstract Full Text PDF–67K
 Is Cited by the Following 20 Articles in this Archive:
Ontogenomic study of the relationship between number of gene splice variants and GO categorization
Ari B. Kahn, Barry R. Zeeberg, Michael C. Ryan, D. Curtis Jamison, David M. Rockoff, Yves Pommier, John N. Weinstein
Bioinformatics. 2010 August 15; 26(16): 1945–1949. Published online 2010 July 8. doi: 10.1093/bioinformatics/btq335
PMCID:
PMC2916722
Abstract Full Text PDF–485K
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
Hugues Richard, Marcel H. Schulz, Marc Sultan, Asja Nürnberger, Sabine Schrinner, Daniela Balzereit, Emilie Dagand, Axel Rasche, Hans Lehrach, Martin Vingron, Stefan A. Haas, Marie-Laure Yaspo
Nucleic Acids Res. 2010 June; 38(10): e112. Published online 2010 February 11. doi: 10.1093/nar/gkq041
PMCID:
PMC2879520
Abstract Full Text PDF–7.3M Supplementary Material
Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation
Kevin CH Ha, Jasmin Coulombe-Huntington, Jacek Majewski
BMC Genomics. 2009; 10: 519. Published online 2009 November 12. doi: 10.1186/1471-2164-10-519
PMCID:
PMC2780461
Abstract Full Text PDF–1.3M Supplementary Material
Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3
Nikolai P Kandul, Mohamed AF Noor
BMC Genet. 2009; 10: 67. Published online 2009 October 19. doi: 10.1186/1471-2156-10-67
PMCID:
PMC2767349
Abstract Full Text PDF–1.4M Supplementary Material
Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays
Amandine Bemmo, David Benovoy, Tony Kwan, Daniel J Gaffney, Roderick V Jensen, Jacek Majewski
BMC Genomics. 2008; 9: 529. Published online 2008 November 7. doi: 10.1186/1471-2164-9-529
Correction in:
BMC Genomics. 2009; 10: 121.
PMCID:
PMC2585104
Abstract Full Text PDF–1.6M Supplementary Material Correction
Heritability of alternative splicing in the human genome
Tony Kwan, David Benovoy, Christel Dias, Scott Gurd, David Serre, Harry Zuzan, Tyson A. Clark, Anthony Schweitzer, Michelle K. Staples, Hui Wang, John E. Blume, Thomas J. Hudson, Rob Sladek, Jacek Majewski
Genome Res. 2007 August; 17(8): 1210–1218. doi: 10.1101/gr.6281007
PMCID:
PMC1933514
Abstract Full Text PDF–562K
Functional coordination of alternative splicing in the mammalian central nervous system
Matthew Fagnani, Yoseph Barash, Joanna Y Ip, Christine Misquitta, Qun Pan, Arneet L Saltzman, Ofer Shai, Leo Lee, Aviad Rozenhek, Naveed Mohammad, Sandrine Willaime-Morawek, Tomas Babak, Wen Zhang, Timothy R Hughes, Derek van der Kooy, Brendan J Frey, Benjamin J Blencowe
Genome Biol. 2007; 8(6): R108. Published online 2007 June 12. doi: 10.1186/gb-2007-8-6-r108
PMCID:
PMC2394768
Abstract Full Text PDF–1.7M Supplementary Material
Exon arrays provide accurate assessments of gene expression
Karen Kapur, Yi Xing, Zhengqing Ouyang, Wing Hung Wong
Genome Biol. 2007; 8(5): R82. Published online 2007 May 15. doi: 10.1186/gb-2007-8-5-r82
PMCID:
PMC1929160
Abstract Full Text PDF–3.9M
Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays
Ann Hess, Hari Iyer
BMC Genomics. 2007; 8: 96. Published online 2007 April 9. doi: 10.1186/1471-2164-8-96
PMCID:
PMC1854896
Abstract Full Text PDF–614K
Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data
Davide Rambaldi, Barbara Felice, Viviane Praz, Philip Bucher, Davide Cittaro, Alessandro Guffanti
BMC Bioinformatics. 2007; 8(Suppl 1): S17. Published online 2007 March 8. doi: 10.1186/1471-2105-8-S1-S17
PMCID:
PMC1885846
Abstract Full Text PDF–435K
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis
Ari B Kahn, Michael C Ryan, Hongfang Liu, Barry R Zeeberg, D Curtis Jamison, John N Weinstein
BMC Bioinformatics. 2007; 8: 75. Published online 2007 March 5. doi: 10.1186/1471-2105-8-75
PMCID:
PMC1839109
Abstract Full Text PDF–717K Supplementary Material
Probe Selection and Expression Index Computation of Affymetrix Exon Arrays
Yi Xing, Karen Kapur, Wing Hung Wong
PLoS ONE. 2006; 1(1): e88. Published online 2006 December 20. doi: 10.1371/journal.pone.0000088
PMCID:
PMC1762343
Abstract Full Text PDF–434K Supplementary Material
Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis
Andrew J Holloway, Alicia Oshlack, Dileepa S Diyagama, David DL Bowtell, Gordon K Smyth
BMC Bioinformatics. 2006; 7: 511. Published online 2006 November 22. doi: 10.1186/1471-2105-7-511
PMCID:
PMC1664592
Abstract Full Text PDF–850K
An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs
Yi Xing, Tianwei Yu, Ying Nian Wu, Meenakshi Roy, Joseph Kim, Christopher Lee
Nucleic Acids Res. 2006; 34(10): 3150–3160. Published online 2006 June 6. doi: 10.1093/nar/gkl396
PMCID:
PMC1475746
Abstract Full Text PDF–685K
Identification of RNA-binding proteins that regulate FGFR2 splicing through the use of sensitive and specific dual color fluorescence minigene assays
Emily A. Newman, Stephanie J. Muh, Ruben H. Hovhannisyan, Claude C. Warzecha, Richard B. Jones, Wallace L. Mckeehan, Russ P. Carstens
RNA. 2006 June; 12(6): 1129–1141. doi: 10.1261/rna.34906
PMCID:
PMC1464843
Abstract Full Text PDF–779K
ASEtrap: A biological method for speeding up the exploration of spliceomes
Gilbert Thill, Vanina Castelli, Sophie Pallud, Marcel Salanoubat, Patrick Wincker, Pierre de la Grange, Didier Auboeuf, Vincent Schächter, Jean Weissenbach
Genome Res. 2006 June; 16(6): 776–786. doi: 10.1101/gr.5063306
PMCID:
PMC1479860
Abstract Full Text PDF–437K
Profiling alternatively spliced mRNA isoforms for prostate cancer classification
Chaolin Zhang, Hai-Ri Li, Jian-Bing Fan, Jessica Wang-Rodriguez, Tracy Downs, Xiang-Dong Fu, Michael Q Zhang
BMC Bioinformatics. 2006; 7: 202. Published online 2006 April 11. doi: 10.1186/1471-2105-7-202
PMCID:
PMC1458362
Abstract Full Text PDF–520K Supplementary Material
Microarray analysis reveals differential gene expression in hybrid sunflower species
ZHAO LAI, BRIANA L. GROSS, YIZOU, JUSTEN ANDREWS, LOREN H. RIESEBERG
Mol Ecol. Author manuscript; available in PMC 2008 September 16.
Published in final edited form as: Mol Ecol. 2006 April; 15(5): 1213–1227. doi: 10.1111/j.1365-294X.2006.02775.x
PMCID:
PMC2536761
Abstract Full Text PDF–1.1M Supplementary Material
Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila
Marco Blanchette, Richard E. Green, Steven E. Brenner, Donald C. Rio
Genes Dev. 2005 June 1; 19(11): 1306–1314. doi: 10.1101/gad.1314205
PMCID:
PMC1142554
Abstract Full Text PDF–433K
Genome-wide assembly and analysis of alternative transcripts in mouse
Alexei A. Sharov, Dawood B. Dudekula, Minoru S.H. Ko
Genome Res. 2005 May; 15(5): 748–754. doi: 10.1101/gr.3269805
PMCID:
PMC1088304
Abstract Full Text PDF–377K
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