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Thomas Royce, J. Rozowsky, Paul Bertone, M. Samanta, V. Štolc, S. Weissman, M. Snyder, M. Gerstein (2005)
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.Trends in genetics : TIG, 21 8
Christopher Lee, Meenakshi Roy (2004)
Analysis of alternative splicing with microarrays: successes and challengesGenome Biology, 5
M. Boguski, C. Tolstoshev, D. Bassett (1994)
Gene discovery in dbEST.Science, 265 5181
S. Altschul, W. Gish, W. Miller, E. Myers, D. Lipman (1990)
Basic local alignment search tool.Journal of molecular biology, 215 3
R. Lister, Ronan O’Malley, Julian Tonti-Filippini, B. Gregory, C. Berry, A. Millar, J. Ecker (2008)
Highly Integrated Single-Base Resolution Maps of the Epigenome in ArabidopsisCell, 133
M. Okoniewski, Crispin Miller (2006)
Hybridization interactions between probesets in short oligo microarrays lead to spurious correlationsBMC Bioinformatics, 7
T. Casneuf, Y. Peer, W. Huber (2007)
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlationBMC Bioinformatics, 8
B. Wilhelm, S. Marguerat, S. Watt, Falk Schubert, V. Wood, I. Goodhead, C. Penkett, J. Rogers, J. Bähler (2008)
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolutionNature, 453
G. Galau, W. Klein, R. Britten, E. Davidson (1977)
Significance of rare mRNA sequences in liverArchives of Biochemistry and Biophysics, 179
M. Harbers, Piero Carninci (2005)
Tag-based approaches for transcriptome research and genome annotationNature Methods, 2
P. Kapranov, Jill Cheng, S. Dike, D. Nix, R. Duttagupta, A. Willingham, P. Stadler, Jana Hertel, J. Hackermüller, I. Hofacker, I. Bell, E. Cheung, J. Drenkow, E. Dumais, Sandeep Patel, G. Helt, M. Ganesh, Srinka Ghosh, A. Piccolboni, V. Sementchenko, H. Tammana, T. Gingeras (2007)
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive TranscriptionScience, 316
Ji Huang, Hongsheng Zhang, Dong Wang, Ya-Jun Cao, Jin-shui Yang (2002)
[Serial analysis of gene expression].Yi chuan = Hereditas, 24 2
S. Brenner, Maria Johnson, J. Bridgham, G. Golda, D. Lloyd, David Johnson, Shujun Luo, S. Mccurdy, M. Foy, Mark Ewan, Rithy Roth, Dave George, S. Eletr, G. Albrecht, Eric Vermaas, Steven Williams, Keith Moon, T. Burcham, Michael Pallas, R. Dubridge, James Kirchner, K. Fearon, J. Mao, K. Corcoran (2000)
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arraysNature Biotechnology, 18
A. Eklund, L. Turner, Pengchin Chen, R. Jensen, G. DeFeo, A. Kopf‐Sill, Z. Szallasi (2006)
Replacing cRNA targets with cDNA reduces microarray cross-hybridizationNature Biotechnology, 24
K. Kapur, Yi Xing, Z. Ouyang, W. Wong (2007)
Exon arrays provide accurate assessments of gene expressionGenome Biology, 8
James Martin, J. Miano, C. Hustad, N. Copeland, N. Jenkins, E. Olson (1994)
A Mef2 gene that generates a muscle-specific isoform via alternative mRNA splicingMolecular and Cellular Biology, 14
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
E. Neto, R. Correa, S. Verjovski-Almeida, M. Briones, M. Nagai, Wilson Silva, M. Zago, S. Bordin, F. Costa, G. Goldman, A. Carvalho, A. Matsukuma, Gilson Baia, David Simpson, A. Brunstein, Paulo Oliveira, P. Bucher, C. Jongeneel, M. O'hare, F. Soares, R. Brentani, Luis Reis, Sandro Souza, A. Simpson (2000)
Shotgun sequencing of the human transcriptome with ORF expressed sequence tags.Proceedings of the National Academy of Sciences of the United States of America, 97 7
D. Gerhard, L. Wagner, E. Feingold, C. Shenmen, L. Grouse, G. Schuler, S. Klein, S. Old, R. Rasooly, P. Good, M. Guyer, Allison Peck, J. Derge, D. Lipman, F. Collins, W. Jang, S. Sherry, M. Feolo, L. Misquitta, Eduardo Lee, K. Rotmistrovsky, S. Greenhut, C. Schaefer, K. Buetow, T. Bonner, D. Haussler, Jim Kent, Mark Kiekhaus, T. Furey, M. Brent, C. Prange, Kirsten Schreiber, N. Shapiro, N. Bhat, R. Hopkins, Florence Hsie, Tom Driscoll, M. Soares, T. Casavant, T. Scheetz, M. Brown-stein, T. Usdin, Shiraki Toshiyuki, Piero Carninci, Y. Piao, D. Dudekula, M. Ko, K. Kawakami, Yutaka Suzuki, S. Sugano, C. Gruber, M. Smith, B. Simmons, T. Moore, R. Waterman, Stephen Johnson, Y. Ruan, Chia-Lin Wei, S. Mathavan, P. Gunaratne, Jiaqian Wu, A. Garcia, Stephen Hulyk, Edwin Fuh, Ye Yuan, Anna Sneed, Carla Kowis, A. Hodgson, D. Muzny, J. McPherson, R. Gibbs, J. Fahey, Erin Helton, Mark Ketteman, A. Madan, Stephanie Rodrigues, Amy Sanchez, Michelle Whiting, A. Madari, Alice Young, Keith Wetherby, S. Granite, Peggy Kwong, Charles Brinkley, R. Pearson, G. Bouffard, Robert Blakesly, E. Green, M. Dickson, Alex Rodriguez, J. Grimwood, J. Schmutz, R. Myers, Y. Butterfield, M. Griffith, O. Griffith, M. Krzywinski, Nancy Liao, Ryan Morin, Diana Palmquist, A. Petrescu, U. Skalska, D. Smailus, J. Stott, A. Schnerch, J. Schein, Steven Jones, R. Holt, Ágnes Baross, M. Marra, S. Clifton, K. Makowski, Stephanie Bosak, J. Malek (2004)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).Genome research, 14 10B
U. Nagalakshmi, Zhong Wang, Karl Waern, C. Shou, D. Raha, M. Gerstein, Michael Snyder (2008)
The Transcriptional Landscape of the Yeast Genome Defined by RNA SequencingScience, 320
P. Kapranov, A. Willingham, T. Gingeras (2007)
Genome-wide transcription and the implications for genomic organizationNature Reviews Genetics, 8
U Nagalakshmi (2008)
Science
Paul Bertone, V. Štolc, Thomas Royce, J. Rozowsky, A. Urban, Xiaowei Zhu, J. Rinn, W. Tongprasit, M. Samanta, S. Weissman, M. Gerstein, M. Snyder (2004)
Global Identification of Human Transcribed Sequences with Genome Tiling ArraysScience, 306
Jill Cheng, P. Kapranov, J. Drenkow, S. Dike, Shane Brubaker, Sandeep Patel, J. Long, D. Stern, H. Tammana, G. Helt, V. Sementchenko, A. Piccolboni, S. Bekiranov, D. Bailey, M. Ganesh, Srinka Ghosh, I. Bell, D. Gerhard, T. Gingeras (2005)
Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide ResolutionScience, 308
The mouse transcriptome in three tissue types has been analyzed using Illumina next-generation sequencing technology. This quantitative RNA-Seq methodology has been used for expression analysis and splice isoform discovery and to confirm or extend reference gene models. Also in this issue, another paper reports application of the ABI SOLiD technology to sequence the transcriptome in mouse embryonic stem cells.
Nature Methods – Springer Journals
Published: May 30, 2008
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