Genome biology · 2010 · 92 citations · 13 references
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BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 28.9K citations · Full text
TopHat: discovering splice junctions with RNA-Seq
Cole Trapnell, Lior Pachter, Steven L. Salzberg · Bioinformatics · 2009 · 12K citations · Full text
The Human Genome Browser at UCSC
W. James Kent, Charles W. Sugnet, Terrence S. Furey et al. · Genome Research · 2002 · 10.7K citations · Full text
Alternative isoform regulation in human tissue transcriptomes
Eric T. Wang, Rickard Sandberg, Shujun Luo et al. · Nature · 2008 · 5.2K citations · Full text