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Research: Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis
- Huan Wang,
- Pil Joong Chung,
- Jun Liu,
- In-Cheol Jang,
- Michelle J. Kean,
- Jun Xu,
- and Nam-Hai Chua
Genome Res. March 2014 24: 444-453; Published in Advance January 8, 2014, doi:10.1101/gr.165555.113
...Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis Huan Wang 1 , 4 , Pil Joong Chung 1 , 2 , 4 , Jun Liu 1 , In-Cheol Jang 1 , 3 , Michelle J. Kean 1 , Jun Xu...
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Research: CBX3 regulates efficient RNA processing genome-wide
- Andrea Smallwood,
- Gary C. Hon,
- Fulai Jin,
- Ryan E. Henry,
- Joaquín M. Espinosa,
- and Bing Ren
Genome Res. August 2012 22: 1426-1436; Published in Advance June 8, 2012, doi:10.1101/gr.124818.111
...CBX3 regulates efficient RNA processing genome-wide Andrea Smallwood 1 , Gary C. Hon 1 , Fulai Jin 1 , Ryan E. Henry 2 , Joaquín M. Espinosa 2 and Bing Ren 1 , 3 , 4 1 Ludwig Institute for Cancer Research, La...
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Letter: Genome-wide mapping of alternative splicing in Arabidopsis thaliana
- Sergei A. Filichkin,
- Henry D. Priest,
- Scott A. Givan,
- Rongkun Shen,
- Douglas W. Bryant,
- Samuel E. Fox,
- Weng-Keen Wong,
- and Todd C. Mockler
Genome Res. January 2010 20: 45-58; Published in Advance October 26, 2009, doi:10.1101/gr.093302.109
...(RUST) (Lewis et al. 2003; Lareau et al. 2007). Genome-wide studies of alternative pre-mRNA splicing in a variety of organisms have relied on Sanger sequencing of expressed sequence tags (ESTs) and cDNAs, high-density DNA microarrays (for review, see Mockler et al. 2005) and most recently ultrahigh...
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LETTER: Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray
- Housheng He,
- Jie Wang,
- Tao Liu,
- X. Shirley Liu,
- Tiantian Li,
- Yunfei Wang,
- Zuwei Qian,
- Haixia Zheng,
- Xiaopeng Zhu,
- Tao Wu,
- Baochen Shi,
- Wei Deng,
- Wei Zhou,
- Geir Skogerbø,
- and Runsheng Chen
Genome Res. October 2007 17: 1471-1477; Published in Advance September 4, 2007, doi:10.1101/gr.6611807
....M. ( 2000 ) Conservation, regulation, synteny, and introns in a large-scale C. briggsae–C. elegans genomic alignment . Genome Res. 10 : 1115 – 1125 . ↵ Li, L. , Wang, X. , Stolc, V. , Li, X. , Zhang, D. , Su, N. , Tongprasit, W. , Li, S. , Cheng, Z. , Wang, J. , et al. ( 2006 ) Genome-wide transcription...
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Method: Differential genome-wide profiling of tandem 3′ UTRs among human breast cancer and normal cells by high-throughput sequencing
- Yonggui Fu,
- Yu Sun,
- Yuxin Li,
- Jie Li,
- Xingqiang Rao,
- Chong Chen,
- and Anlong Xu
Genome Res. May 2011 21: 741-747; Published in Advance April 7, 2011, doi:10.1101/gr.115295.110
...Differential genome-wide profiling of tandem 3′ UTRs among human breast cancer and normal cells by high-throughput sequencing Yonggui Fu 1 , Yu Sun 1 , Yuxin Li 1 , Jie Li , Xingqiang Rao , Chong Chen and Anlong Xu 2...
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RESOURCE: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- Vardhman K. Rakyan,
- Thomas A. Down,
- Natalie P. Thorne,
- Paul Flicek,
- Eugene Kulesha,
- Stefan Gräf,
- Eleni M. Tomazou,
- Liselotte Bäckdahl,
- Nathan Johnson,
- Marlis Herberth,
- Kevin L. Howe,
- David K. Jackson,
- Marcos M. Miretti,
- Heike Fiegler,
- John C. Marioni,
- Ewan Birney,
- Tim J.P. Hubbard,
- Nigel P. Carter,
- Simon Tavaré,
- and Stephan Beck
Genome Res. September 2008 18: 1518-1529; Published in Advance June 24, 2008, doi:10.1101/gr.077479.108
...An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) Vardhman K. Rakyan 1 , 9 , 10 , Thomas A. Down 2 , 9 , Natalie P. Thorne 3 , 9 , Paul Flicek 4 , 9...
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PERSPECTIVE: Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
- W. Brad Barbazuk,
- Yan Fu,
- and Karen M. McGinnis
Genome Res. September 2008 18: 1381-1392; Published in Advance July 30, 2008, doi:10.1101/gr.053678.106
...et al. 2004 ). Combining microarrays with protein–RNA cross-linking and immunoprecipitation (CLIP) provides the opportunity to discover those mRNAs associated with specific SR proteins or other trans -acting protein factors involved in splice-site recognition. Genome-wide RNA-binding analysis of Nova...
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LETTER: Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum
- Tobias Mourier,
- Celine Carret,
- Sue Kyes,
- Zoe Christodoulou,
- Paul P. Gardner,
- Daniel C. Jeffares,
- Robert Pinches,
- Bart Barrell,
- Matt Berriman,
- Sam Griffiths-Jones,
- Alasdair Ivens,
- Chris Newbold,
- and Arnab Pain
Genome Res. February 2008 18: 281-292; Published in Advance December 20, 2007, doi:10.1101/gr.6836108
...Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum Tobias Mourier 1 , 2 , 7 , Celine Carret 3 , 7 , Sue Kyes 4 , 7 , Zoe Christodoulou 4 , Paul P. Gardner 5 , Daniel C. Jeffares 3...
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LETTER: Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
- Daniel L. Halligan and
- Peter D. Keightley
Genome Res. July 2006 16: 875-884; Published in Advance June 2, 2006, doi:10.1101/gr.5022906
...Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison Daniel L. Halligan 1 and Peter D. Keightley Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom...
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LETTER: Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
- Leah O. Barrera,
- Zirong Li,
- Andrew D. Smith,
- Karen C. Arden,
- Webster K. Cavenee,
- Michael Q. Zhang,
- Roland D. Green,
- and Bing Ren
Genome Res. January 2008 18: 46-59; Published in Advance November 27, 2007, doi:10.1101/gr.6654808
...Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs Leah O. Barrera 1 , 2 , 7 , Zirong Li 1 , 7 , Andrew D. Smith 3 , Karen C. Arden 1 , 4 , Webster K. Cavenee 1 , 4 , Michael Q...

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