The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
Open accessAbstract
TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/.
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Cites
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Self-citationMapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
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Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
A cellular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemia
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deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
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Cited by
HISAT: a fast spliced aligner with low memory requirements
Kim, D., Langmead, B., & Salzberg, S. L. (2015) · Nature Methods · doi:10.1038/nmeth.3317 · Cited by 24,112
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Self-citationIntegrative Clinical Genomics of Advanced Prostate Cancer
Robinson, D., Van Allen, E. M., Wu, Y.-M., Schultz, N., Lonigro, R. J., Mosquera, J.-M., Montgomery, B., Taplin, M.-E., Pritchard, C. C., Attard, G., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.001 · Cited by 3,645
“Paired-end transcriptome sequencing reads were aligned to the human reference genome (GRCh37/hg19) using a RNA-seq spliced read mapper Tophat2 (Kim and Salzberg, 2011) (Tophat 2.0.4), with ‘‘–fusion-search’’ option turned on to detect potential gene fusion transcripts.”
MethodInfluentialPacBio Sequencing and its Applications
Rhoads, A., & Au, K. F. (2015) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.08.002 · Cited by 2,135
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
Metadata
- Authors
- Kim, D., & Salzberg, S. L.
- Venue
- Genome Biology
- Published
- 2011-08-11
- Volume
- 12
- Issue
- 8
- Pages
- R72-R72
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2139399606
- Cited by
- 809
- References
- 9
- FWCI
- 16.11
- Type
- journal article
- Language
- en
- Open access
- gold
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