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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
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 Is Cited by the Following 40 Articles in this Archive:
Identification of Novel Androgen-Regulated Pathways and mRNA Isoforms through Genome-Wide Exon-Specific Profiling of the LNCaP Transcriptome
Prabhakar Rajan, Caroline Dalgliesh, Phillippa J. Carling, Thomas Buist, Chaolin Zhang, Sushma N. Grellscheid, Kelly Armstrong, Jacqueline Stockley, Cedric Simillion, Luke Gaughan, Gabriela Kalna, Michael Q. Zhang, Craig N. Robson, Hing Y. Leung, David J. Elliott
PLoS One. 2011; 6(12): e29088. Published online 2011 December 14. doi: 10.1371/journal.pone.0029088
PMCID:
PMC3237596
Abstract Full Text PDF–873K Supplementary Material
Cell-Type Independent MYC Target Genes Reveal a Primordial Signature Involved in Biomass Accumulation
Hongkai Ji, George Wu, Xiangcan Zhan, Alexandra Nolan, Cheryl Koh, Angelo De Marzo, Hoang Mai Doan, Jinshui Fan, Christopher Cheadle, Mohammad Fallahi, John L. Cleveland, Chi V. Dang, Karen I. Zeller
PLoS One. 2011; 6(10): e26057. Published online 2011 October 19. doi: 10.1371/journal.pone.0026057
PMCID:
PMC3198433
Abstract Full Text PDF–1.2M Supplementary Material
Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants
Ping Chen, Tatiana Lepikhova, Yizhou Hu, Outi Monni, Sampsa Hautaniemi
Nucleic Acids Res. 2011 October; 39(18): e123. Published online 2011 July 9. doi: 10.1093/nar/gkr513
PMCID:
PMC3185423
Abstract Full Text PDF–2.6M Supplementary Material
Computational Detection of Alternative Exon Usage
Ted G. Laderas, Nicole A. R. Walter, Michael Mooney, Kristina Vartanian, Priscila Darakjian, Kari Buck, Christina A. Harrington, John Belknap, Robert Hitzemann, Shannon K. McWeeney
Front Neurosci. 2011; 5: 69. Published online 2011 May 13. doi: 10.3389/fnins.2011.00069
PMCID:
PMC3097375
Abstract Full Text PDF–1.7M Supplementary Material
A New FACS Approach Isolates hESC Derived Endoderm Using Transcription Factors
Yuqiong Pan, Zhengqing Ouyang, Wing Hung Wong, Julie C. Baker
PLoS One. 2011; 6(3): e17536. Published online 2011 March 9. doi: 10.1371/journal.pone.0017536
PMCID:
PMC3052315
Abstract Full Text PDF–1.9M Supplementary Material
Human transcriptome array for high-throughput clinical studies
Weihong Xu, Junhee Seok, Michael N. Mindrinos, Anthony C. Schweitzer, Hui Jiang, Julie Wilhelmy, Tyson A. Clark, Karen Kapur, Yi Xing, Malek Faham, John D. Storey, Lyle L. Moldawer, Ronald V. Maier, Ronald G. Tompkins, Wing Hung Wong, Ronald W. Davis, Wenzhong Xiao, the Inflammation and Host Response to Injury Large-Scale Collaborative Research Program, Mehmet Toner, H. Shaw Warren, David A. Schoenfeld, Laurence Rahme, Grace P. McDonald-Smith, Douglas Hayden, Philip Mason, Shawn Fagan, Yong-Ming Yu, J. Perren Cobb, Daniel G. Remick, John A. Mannick, James A. Lederer, Richard L. Gamelli, Geoffrey M. Silver, Michael A. West, Michael B. Shapiro, Richard Smith, David G. Camp, II, Weijun Qian, Rob Tibshirani, Stephen Lowry, Steven Calvano, Irshad Chaudry, Mitchell Cohen, Ernest E. Moore, Jeffrey Johnson, Henry V. Baker, Philip A. Efron, Ulysses G. J. Balis, Timothy R. Billiar, Juan B. Ochoa, Jason L. Sperry, Carol L. Miller-Graziano, Asit K. De, Paul E. Bankey, David N. Herndon, Celeste C. Finnerty, Marc G. Jeschke, Joseph P. Minei, Brett D. Arnoldo, John L. Hunt, Jureta Horton, J. Perren Cobb, Bernard Brownstein, Bradley Freeman, Avery B. Nathens, Joseph Cuschieri, Nicole Gibran, Matthew Klein, Grant O'Keefe
Proc Natl Acad Sci U S A. 2011 March 1; 108(9): 3707–3712. Published online 2011 February 11. doi: 10.1073/pnas.1019753108
PMCID:
PMC3048146
Abstract Full Text PDF–523K Supplementary Material
Exon Array Analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer
Wolfram Langer, Florian Sohler, Gabriele Leder, Georg Beckmann, Henrik Seidel, Jörn Gröne, Michael Hummel, Anette Sommer
BMC Genomics. 2010; 11: 676. Published online 2010 November 30. doi: 10.1186/1471-2164-11-676
PMCID:
PMC3053589
Abstract Full Text PDF–1.0M Supplementary Material
Detection of Clinically Relevant Exonic Copy-Number Changes by Array CGH
Philip M. Boone, Carlos A. Bacino, Chad A. Shaw, Patricia A. Eng, Patricia M. Hixson, Amber N. Pursley, Sung-Hae L. Kang, Yaping Yang, Joanna Wiszniewska, Beata A. Nowakowska, Daniela del Gaudio, Zhilian Xia, Gayle Simpson-Patel, LaDonna L. Immken, James B. Gibson, Anne C.-H. Tsai, Jennifer A. Bowers, Tyler E. Reimschisel, Christian P. Schaaf, Lorraine Potocki, Fernando Scaglia, Tomasz Gambin, Maciej Sykulski, Magdalena Bartnik, Katarzyna Derwinska, Barbara Wisniowiecka-Kowalnik, Seema R. Lalani, Frank J. Probst, Weimin Bi, Arthur L. Beaudet, Ankita Patel, James R. Lupski, Sau Wai Cheung, Pawel Stankiewicz
Hum Mutat. Author manuscript; available in PMC 2011 August 19.
Published in final edited form as: Hum Mutat. 2010 December; 31(12): 1326–1342. Published online 2010 November 2. doi: 10.1002/humu.21360
PMCID:
PMC3158569
Abstract Full Text PDF–2.9M Supplementary Material
A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
Song Liu, Lan Lin, Peng Jiang, Dan Wang, Yi Xing
Nucleic Acids Res. 2011 January; 39(2): 578–588. Published online 2010 September 22. doi: 10.1093/nar/gkq817
PMCID:
PMC3025565
Abstract Full Text PDF–537K Supplementary Material
A Brassica Exon Array for Whole-Transcript Gene Expression Profiling
Christopher G. Love, Neil S. Graham, Seosamh Ó Lochlainn, Helen C. Bowen, Sean T. May, Philip J. White, Martin R. Broadley, John P. Hammond, Graham J. King
PLoS One. 2010; 5(9): e12812. Published online 2010 September 16. doi: 10.1371/journal.pone.0012812
PMCID:
PMC2940909
Abstract Full Text PDF–898K Supplementary Material
Exon-Level Transcriptome Profiling in Murine Breast Cancer Reveals Splicing Changes Specific to Tumors with Different Metastatic Abilities
Amandine Bemmo, Christel Dias, April A. N. Rose, Caterina Russo, Peter Siegel, Jacek Majewski
PLoS One. 2010; 5(8): e11981. Published online 2010 August 6. doi: 10.1371/journal.pone.0011981
PMCID:
PMC2917353
Abstract Full Text PDF–374K Supplementary Material
Evolution of alternative splicing in primate brain transcriptomes
Lan Lin, Shihao Shen, Peng Jiang, Seiko Sato, Beverly L. Davidson, Yi Xing
Hum Mol Genet. 2010 August 1; 19(15): 2958–2973. Published online 2010 May 11. doi: 10.1093/hmg/ddq201
PMCID:
PMC2901138
Abstract Full Text PDF–438K Supplementary Material
Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis
Eunice Y. Lee, Hongkai Ji, Zhengqing Ouyang, Baiyu Zhou, Wenxiu Ma, Steven A. Vokes, Andrew P. McMahon, Wing H. Wong, Matthew P. Scott
Proc Natl Acad Sci U S A. 2010 May 25; 107(21): 9736–9741. Published online 2010 May 11. doi: 10.1073/pnas.1004602107
PMCID:
PMC2906878
Abstract Full Text PDF–753K Supplementary Material
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
James R Bradford, Yvonne Hey, Tim Yates, Yaoyong Li, Stuart D Pepper, Crispin J Miller
BMC Genomics. 2010; 11: 282. Published online 2010 May 5. doi: 10.1186/1471-2164-11-282
PMCID:
PMC2877694
Abstract Full Text PDF–1019K Supplementary Material
The Comparison of Different Pre- and Post-Analysis Filters for Determination of Exon-Level Alternative Splicing Events Using Affymetrix Arrays
Toni Whistler, Cheng-Feng Chiang, Jin-Mann Lin, William Lonergan, William C. Reeves
J Biomol Tech. 2010 April; 21(1): 44–53.
PMCID:
PMC2841991
Abstract Full Text PDF–700K Supplementary Material
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
A Review of Statistical Methods for Preprocessing Oligonucleotide Microarrays
Zhijin Wu
Stat Methods Med Res. Author manuscript; available in PMC 2011 August 9.
Published in final edited form as: Stat Methods Med Res. 2009 December; 18(6): 533–541. doi: 10.1177/0962280209351924
PMCID:
PMC3152825
Abstract Full Text PDF–339K
Genome-Wide Analysis of Immune Activation in Human T and B Cells Reveals Distinct Classes of Alternatively Spliced Genes
Yevgeniy A. Grigoryev, Sunil M. Kurian, Aleksey A. Nakorchevskiy, John P. Burke, Daniel Campbell, Steve R. Head, Jun Deng, Aaron B. Kantor, John R. Yates, III, Daniel R. Salomon
PLoS One. 2009; 4(11): e7906. Published online 2009 November 19. doi: 10.1371/journal.pone.0007906
PMCID:
PMC2775942
Abstract Full Text PDF–943K Supplementary Material
MADS+: discovery of differential splicing events from Affymetrix exon junction array data
Shihao Shen, Claude C. Warzecha, Russ P. Carstens, Yi Xing
Bioinformatics. 2010 January 15; 26(2): 268–269. Published online 2009 November 17. doi: 10.1093/bioinformatics/btp643
PMCID:
PMC2804303
Abstract Full Text PDF–163K
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
Exon expression in lymphoblastoid cell lines from subjects with schizophrenia before and after glucose deprivation
Maureen V Martin, Brandi Rollins, P Adolfo Sequeira, Andrea Mesén, William Byerley, Richard Stein, Emily A Moon, Huda Akil, Edward G Jones, Stanley J Watson, Jack Barchas, Lynn E DeLisi, Richard M Myers, Alan Schatzberg, William E Bunney, Marquis P Vawter
BMC Med Genomics. 2009; 2: 62. Published online 2009 September 22. doi: 10.1186/1755-8794-2-62
PMCID:
PMC2760574
Abstract Full Text PDF–1.5M Supplementary Material
TileProbe: modeling tiling array probe effects using publicly available data
Jennifer Toolan Judy, Hongkai Ji
Bioinformatics. 2009 September 15; 25(18): 2369–2375. Published online 2009 July 9. doi: 10.1093/bioinformatics/btp425
PMCID:
PMC2735670
Abstract Full Text PDF–490K
Using high-density exon arrays to profile gene expression in closely related species
Lan Lin, Song Liu, Heather Brockway, Junhee Seok, Peng Jiang, Wing Hung Wong, Yi Xing
Nucleic Acids Res. 2009 July; 37(12): e90. Published online 2009 July. doi: 10.1093/nar/gkp420
PMCID:
PMC2709591
Abstract Full Text PDF–877K Supplementary Material
A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level
Sika Zheng, Liang Chen
Nucleic Acids Res. 2009 June; 37(10): e75. Published online 2009 June. doi: 10.1093/nar/gkp282
PMCID:
PMC2691848
Abstract Full Text PDF–1.6M Supplementary Material
Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes
Lan Lin, Peng Jiang, Shihao Shen, Seiko Sato, Beverly L. Davidson, Yi Xing
Hum Mol Genet. 2009 June 15; 18(12): 2204–2214. Published online 2009 March 26. doi: 10.1093/hmg/ddp152
PMCID:
PMC2685757
Abstract Full Text PDF–229K Supplementary Material
Prediction of breast cancer metastasis by genomic profiling: where do we stand?
Ulrich Pfeffer, Francesco Romeo, Douglas M. Noonan, Adriana Albini
Clin Exp Metastasis. 2009 August; 26(6): 547–558. Published online 2009 March 24. doi: 10.1007/s10585-009-9254-y
PMCID:
PMC2717389
Abstract Full Text PDF–595K
REMAS: a new regression model to identify alternative splicing events from exon array data
Hao Zheng, Xingyi Hang, Ji Zhu, Minping Qian, Wubin Qu, Chenggang Zhang, Minghua Deng
BMC Bioinformatics. 2009; 10(Suppl 1): S18. Published online 2009 January 30. doi: 10.1186/1471-2105-10-S1-S18
PMCID:
PMC2648792
Abstract Full Text PDF–526K
Use of Cell Lines in the Investigation of Pharmacogenetic Loci
Wei Zhang, M. Eileen Dolan
Curr Pharm Des. Author manuscript; available in PMC 2009 November 25.
Published in final edited form as: Curr Pharm Des. 2009; 15(32): 3782–3795.
PMCID:
PMC2782819
Abstract Full Text PDF–398K
Inference on Low-Rank Data Matrices with Applications to Microarray Data
Xingdong Feng, Xuming He
Ann Appl Stat. Author manuscript; available in PMC 2010 May 26.
Published in final edited form as: Ann Appl Stat. 2009; 3(4): 1634–1654. doi: 10.1214/09-AOAS262SUPP
PMCID:
PMC2876352
Abstract Full Text PDF–1.2M 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
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