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A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE
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“However, even with limited sequence length, approaches have been developed to successfully assay the repetitive fraction of a genome with short reads (for example, [18]).”
From The case for not masking away repetitive DNA (2018) · cites this paper as [18]
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A gene atlas of the mouse and human protein-encoding transcriptomes
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400782101 · Cited by 3,475
Genome-wide analysis of mammalian promoter architecture and evolution
Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C. A. M., Taylor, M. S., Engström, P. G., Frith, M. C., et al. (2006) · Nature Genetics · doi:10.1038/ng1789 · Cited by 1,350
Self-citation
Research works printed but not linked: 22
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Cited by
Sorted by citations
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179
RNA-Seq gene expression estimation with read mapping uncertainty
Li, B., Ruotti, V., Stewart, R. M., Thomson, J. A., & Dewey, C. N. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp692 · Cited by 1,198
Genome-wide mapping of autonomous promoter activity in human cells
van Arensbergen, J., FitzPatrick, V. D., de Haas, M., Pagie, L., Sluimer, J., Bussemaker, H. J., & van Steensel, B. (2017) · Nature Biotechnology · doi:10.1038/nbt.3754 · Cited by 140
The case for not masking away repetitive DNA
Slotkin, R. K. (2018) · Mobile DNA · doi:10.1186/s13100-018-0120-9 · Cited by 61
Metadata
- Authors
- Faulkner, G. J., Forrest, A. R. R., Chalk, A. M., Schroder, K., Hayashizaki, Y., Carninci, P., Hume, D. A., & Grimmond, S. M.
- Venue
- Genomics
- Publisher
- Elsevier BV
- Published
- 2008-03
- Volume
- 91
- Issue
- 3
- Pages
- 281-288
- ISSN
- 0888-7543
- Cited by
- 82
- References
- 2
- Language
- en
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- Faulkner, G. J., Forrest, A. R. R., Chalk, A. M., Schroder, K., Hayashizaki, Y., Carninci, P., Hume, D. A., & Grimmond, S. M. (2008). A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics. https://doi.org/10.1016/j.ygeno.2007.11.003
