Searching journal content for articles similar to Ruan et al. 17 (6): 828.

Displaying results 1-9 of 9

For checked items

view abstracts
download to citation manager

Select this article
Research: Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
- Axel M. Hillmer,
- Fei Yao,
- Koichiro Inaki,
- Wah Heng Lee,
- Pramila N. Ariyaratne,
- Audrey S.M. Teo,
- Xing Yi Woo,
- Zhenshui Zhang,
- Hao Zhao,
- Leena Ukil,
- Jieqi P. Chen,
- Feng Zhu,
- Jimmy B.Y. So,
- Manuel Salto-Tellez,
- Wan Ting Poh,
- Kelson F.B. Zawack,
- Niranjan Nagarajan,
- Song Gao,
- Guoliang Li,
- Vikrant Kumar,
- Hui Ping J. Lim,
- Yee Yen Sia,
- Chee Seng Chan,
- See Ting Leong,
- Say Chuan Neo,
- Poh Sum D. Choi,
- Hervé Thoreau,
- Patrick B.O. Tan,
- Atif Shahab,
- Xiaoan Ruan,
- Jonas Bergh,
- Per Hall,
- Valère Cacheux-Rataboul,
- Chia-Lin Wei,
- Khay Guan Yeoh,
- Wing-Kin Sung,
- Guillaume Bourque,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. May 2011 21: 665-675; Published in Advance April 5, 2011, doi:10.1101/gr.113555.110
..., and complex rearrangements are over-represented among somatic rearrangements in cancer genomes. We demonstrate that the quantitative and connective nature of DNA–PET data is precise in delineating the genealogy of complex rearrangement events, we observe signatures that are compatible with breakage-fusion...
OPEN ACCESS ARTICLE
Select this article
Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
- Melissa J. Fullwood,
- Chia-Lin Wei,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
...platforms ( Fig. 1 ). An even more straightforward RNA-PET strategy would be to simply perform shotgun paired-end sequencing of cDNA templates that have been fragmented to a few hundred base pairs. In theory, this shotgun RNA-PET approach should be able to identify the junction points of potential fusion...
OPEN ACCESS ARTICLE
Select this article
Research: Transcriptional consequences of genomic structural aberrations in breast cancer
- Koichiro Inaki,
- Axel M. Hillmer,
- Leena Ukil,
- Fei Yao,
- Xing Yi Woo,
- Leah A. Vardy,
- Kelson Folkvard Braaten Zawack,
- Charlie Wah Heng Lee,
- Pramila Nuwantha Ariyaratne,
- Yang Sun Chan,
- Kartiki Vasant Desai,
- Jonas Bergh,
- Per Hall,
- Thomas Choudary Putti,
- Wai Loon Ong,
- Atif Shahab,
- Valere Cacheux-Rataboul,
- Radha Krishna Murthy Karuturi,
- Wing-Kin Sung,
- Xiaoan Ruan,
- Guillaume Bourque,
- Yijun Ruan,
- and Edison T. Liu
Genome Res. May 2011 21: 676-687; Published in Advance April 5, 2011, doi:10.1101/gr.113225.110
...no evidence for a transcript in current databases (see Supplemental Glossary). Genome Research 677 www..org Fusion genes in breast cancer had previously pioneered pair-end-tag sequencing of full-length cDNA from the MCF-7 transcriptome (Ruan et al. 2007). This RNA paired-end-tag (RNA-PET) approach captures...
OPEN ACCESS ARTICLE
Select this article
Method: Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
- Markus Brosch,
- Gary I. Saunders,
- Adam Frankish,
- Mark O. Collins,
- Lu Yu,
- James Wright,
- Ruth Verstraten,
- David J. Adams,
- Jennifer Harrow,
- Jyoti S. Choudhary,
- and Tim Hubbard
Genome Res. May 2011 21: 756-767; Published in Advance April 1, 2011, doi:10.1101/gr.114272.110
...is a fusion protein that spans the Ins2 and Igf2 loci to produce a transcript encoding the insulin II and the insulin-like growth factor 2–derived peptides. We also report nine processed pseudogenes that have unique peptide hits, demonstrating, for the first time, that they are not just transcribed...
OPEN ACCESS ARTICLE
Select this article
LETTER: A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
- Oliver A. Hampton,
- Petra Den Hollander,
- Christopher A. Miller,
- David A. Delgado,
- Jian Li,
- Cristian Coarfa,
- Ronald A. Harris,
- Stephen Richards,
- Steven E. Scherer,
- Donna M. Muzny,
- Richard A. Gibbs,
- Adrian V. Lee,
- and Aleksandar Milosavljevic
Genome Res. February 2009 19: 167-177; Published in Advance December 3, 2008, doi:10.1101/gr.080259.108
...if other sources reported the same fusion transcripts in MCF-7, other cell lines or primary tumors, we queried 70 MCF-7 and HCT116 (colon cancer) paired-end ditag fusion transcript sets reported by Ruan et al. (2007) and 237 fusion transcripts from the Cancer Genome Anatomy Project Recurrent Chromosome...
OPEN ACCESS ARTICLE
Select this article
Methods: Scanning the human genome at kilobase resolution
- Jun Chen,
- Yeong C. Kim,
- Yong-Chul Jung,
- Zhenyu Xuan,
- Geoff Dworkin,
- Yanming Zhang,
- Michael Q. Zhang,
- and San Ming Wang
Genome Res. May 2008 18: 751-762; Published in Advance February 21, 2008, doi:10.1101/gr.068304.107
...of different chromosome origin were ligated together and cloning into a single vector that contributes to an artificial “translocation” ditag. Similar results were also observed in mRNA ditags used in fusion transcript detection, in which a substantial number of ditags representing “fusion transcripts” could...
Select this article
COMMENTARY: ENCODE: More genomic empowerment
- George M. Weinstock
Genome Res. June 2007 17: 667-668; doi:10.1101/gr.6534207
..., C.Y. , Liu, J. , Ariyaratne, P. , et al. ( 2007 ) Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs) Genome Res. doi: 10.1101/gr.6018607 , (this issue) . ↵ Thurman, R.E. , Day, N. , Noble, W...
OPEN ACCESS ARTICLE
Select this article
Research: Understanding transcriptional regulation by integrative analysis of transcription factor binding data
- Chao Cheng,
- Roger Alexander,
- Renqiang Min,
- Jing Leng,
- Kevin Y. Yip,
- Joel Rozowsky,
- Koon-Kiu Yan,
- Xianjun Dong,
- Sarah Djebali,
- Yijun Ruan,
- Carrie A. Davis,
- Piero Carninci,
- Timo Lassman,
- Thomas R. Gingeras,
- Roderic Guigó,
- Ewan Birney,
- Zhiping Weng,
- Michael Snyder,
- and Mark Gerstein
Genome Res. September 2012 22: 1658-1667; doi:10.1101/gr.136838.111
...generated >400 TF-binding profiles for more than 120 human TFs or transcription related proteins, including both general and sequence-specific TFs (Gerstein et al. 2012). The completeness of the ENCODE data enable us to study the transcriptional regulation of TFs more accurately and comprehensively...
OPEN ACCESS ARTICLE
Select this article
Research: Sequence features that drive human promoter function and tissue specificity
- Jane M. Landolin,
- David S. Johnson,
- Nathan D. Trinklein,
- Shelly F. Aldred,
- Catherine Medina,
- Hennady Shulha,
- Zhiping Weng,
- and Richard M. Myers
Genome Res. July 2010 20: 890-898; Published in Advance May 25, 2010, doi:10.1101/gr.100370.109
.... Nature 444: 499– 502. Sequence features in human promoters Genome Research 897 www..org Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, et al. 2007. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Ruan et al. 17 (6): 828.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: