The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Open accessAbstract
Numerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization or trans-splicing are often neglected. We introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, our approach accommodates multi-junction structures. Our method compares favorably with competing tools for conventionally spliced mRNAs and, with a gain of up to 40% of recall, systematically outperforms them on reads with multiple splits, trans-splicing and circular products. The algorithm is integrated into our mapping tool (http://www.bioinf.uni-leipzig.de/Software/segemehl/).
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Cites
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Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
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TopHat: discovering splice junctions with RNA-Seq
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<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Circular RNAs are a large class of animal RNAs with regulatory potency
Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., et al. (2013) · Nature · doi:10.1038/nature11928 · Cited by 7,990
Natural RNA circles function as efficient microRNA sponges
Hansen, T. B., Jensen, T. I., Clausen, B. H., Bramsen, J. B., Finsen, B., Damgaard, C. K., & Kjems, J. (2013) · Nature · doi:10.1038/nature11993 · Cited by 7,985
Landscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187
Circular RNAs are abundant, conserved, and associated with ALU repeats
Jeck, W. R., Sorrentino, J. A., Wang, K., Slevin, M. K., Burd, C. E., Liu, J., Marzluff, W. F., & Sharpless, N. E. (2013) · RNA · doi:10.1261/rna.035667.112 · Cited by 4,388
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Cited by
GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
Tsai, S. Q., Zheng, Z., Nguyen, N. T., Liebers, M., Topkar, V. V., Thapar, V., Wyvekens, N., Khayter, C., Iafrate, A. J., Le, L. P., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3117 · Cited by 2,268
Complementary Sequence-Mediated Exon Circularization
Zhang, X.-O., Wang, H.-B., Zhang, Y., Lu, X., Chen, L.-L., & Yang, L. (2014) · Cell · doi:10.1016/j.cell.2014.09.001 · Cited by 1,999
CIRI: an efficient and unbiased algorithm for de novo circular RNA identification
Gao, Y., Wang, J., & Zhao, F. (2015) · Genome Biology · doi:10.1186/s13059-014-0571-3 · Cited by 1,112
Szabo, L., Morey, R., Palpant, N. J., Wang, P. L., Afari, N., Jiang, C., Parast, M. M., Murry, C. E., Laurent, L. C., & Salzman, J. (2015) · Genome Biology · doi:10.1186/s13059-015-0690-5 · Cited by 607
Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions
Westermann, A. J., Förstner, K. U., Amman, F., Barquist, L., Chao, Y., Schulte, L. N., Müller, L., Reinhardt, R., Stadler, P. F., & Vogel, J. (2016) · Nature · doi:10.1038/nature16547 · Cited by 499
Self-citation
Metadata
- Authors
- Hoffmann, S., Otto, C., Doose, G., Tanzer, A., Langenberger, D., Christ, S., Kunz, M., Holdt, L. M., Teupser, D., Hackermüller, J., & Stadler, P. F.
- Venue
- Genome Biology
- Published
- 2014-02-10
- Volume
- 15
- Issue
- 2
- Pages
- R34-R34
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2051477788
- Cited by
- 270
- References
- 42
- FWCI
- 9.86
- Type
- journal article
- Language
- en
- Open access
- gold
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- Hoffmann, S., Otto, C., Doose, G., Tanzer, A., Langenberger, D., Christ, S., Kunz, M., Holdt, L. M., Teupser, D., Hackermüller, J., & Stadler, P. F. (2014). A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biology. https://doi.org/10.1186/gb-2014-15-2-r34
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