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BioMed Research International
Volume 2013 (2013), Article ID 340620, 6 pages
State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity
1Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126 Torino, Italy
2Department of Computer Science, University of Torino, C.So Svizzera 185, 10149 Torino, Italy
3Unit of Cancer Epidemiology, Department of Biomedical Sciences and Human Oncology, University of Torino, 10126 Torino, Italy
Received 4 October 2012; Revised 11 January 2013; Accepted 15 January 2013
Academic Editor: Tun-Wen Pai
Copyright © 2013 Matteo Carrara et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, “Mapping and quantifying mammalian transcriptomes by RNA-Seq,” Nature Methods, vol. 5, no. 7, pp. 621–628, 2008.
- C. A. Maher, C. Kumar-Sinha, X. Cao et al., “Transcriptome sequencing to detect gene fusions in cancer,” Nature, vol. 458, no. 7234, pp. 97–101, 2009.
- F. Abate, A. Acquaviva, G. Paciello et al., et al., “Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model,” Bioinformatics, vol. 28, no. 16, pp. 2114–2121, 2012.
- M. K. Iyer, A. M. Chinnaiyan, and C. A. Maher, “ChimeraScan: a tool for identifying chimeric transcription in sequencing data,” Bioinformatics, vol. 27, no. 20, pp. 2903–2904, 2011.
- A. McPherson, F. Hormozdiari, A. Zayed et al., et al., “deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data,” PLoS Computational Biology, vol. 7, no. 5, Article ID e1001138, 2011.
- R. W. Francis, K. Thompson-Wicking, K. W. Carter, D. Anderson, U. R. Kees, and A. H. Beesley, “FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data,” PloS One, vol. 7, no. 6, Article ID e39987, 2012.
- Y. Li, J. Chien, D. I. Smith, and J. Ma, “FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq,” Bioinformatics, vol. 27, no. 12, Article ID btr265, pp. 1708–1710, 2011.
- H. Ge, K. Liu, T. Juan, F. Fang, M. Newman, and W. Hoeck, “FusionMap: Detecting fusion genes from next-generation sequencing data at base-pair resolution,” Bioinformatics, vol. 27, no. 14, Article ID btr310, pp. 1922–1928, 2011.
- K. Wang, D. Singh, Z. Zeng et al., “MapSplice: accurate mapping of RNA-seq reads for splice junction discovery,” Nucleic Acids Research, vol. 38, no. 18, p. e178, 2010.
- D. Kim and S. L. Salzberg, “TopHat-Fusion: an algorithm for discovery of novel fusion transcripts,” Genome Biology, vol. 12, no. 8, article R72, 2011.
- H. Edgren, A. Murumagi, S. Kangaspeska et al., “Identification of fusion genes in breast cancer by paired-end RNA-sequencing,” Genome Biology, vol. 12, no. 1, article no. R6, 2011.
- M. F. Berger, J. Z. Levin, K. Vijayendran et al., “Integrative analysis of the melanoma transcriptome,” Genome Research, vol. 20, no. 4, pp. 413–427, 2010.
- M. Carrara, M. Beccuti, F. Cavallo et al., “State of art fusion-finder algorithms are suitable to detect Transcription-Induced Chimeras in normal tissues?” BMC Bioinformatics. In press.
- R. C. Gentleman, V. J. Carey, D. M. Bates et al., “Bioconductor: open software development for computational biology and bioinformatics,” Genome Biology, vol. 5, no. 10, article R80, 2004.
- R. Sanges, F. Cordero, and R. A. Calogero, “oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language,” Bioinformatics, vol. 23, no. 24, pp. 3406–3408, 2007.
- G. R. Grant, M. H. Farkas, A. D. Pizarro et al., “Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM),” Bioinformatics, vol. 27, no. 18, pp. 2518–2528, 2011.