Trapnell, C., L. Pachter, and S.L. Salzberg (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinfor-matics, 25(9): p. 1105-11.
has been cited by the following article:
TITLE: Isoform Inference From RNA-Seq Samples Based on Gene Structures on Chromosomes
AUTHORS: Yan Ji, Jia Wei
KEYWORDS: RNA-Seq; isoform inference; cancer genes; Cufflinks; RSEM
JOURNAL NAME: Journal of Biosciences and Medicines, Vol.1 No.1, February 6, 2013
ABSTRACT: The emerging RNA-Seq technology makes it possible to infer splicing variants from millions of short sequence reads. Here we present a method to identify isoforms by their specific signatures on chromosomes including both exons and junctions. By applying this method to a RNA-Seq dataset of gastric cancer, we showed that our method is more accurate and sensitive than other isoform inference tools such as RSEM and Cufflinks. By constructing a network from gene list identified by our method but missed by other tools, we found that some cancer-related genes enriched in network modules have significant implications for cancer drug discovery.