Identification and functional annotation of lncRNA genes with hypermethylation in colorectal cancer

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder, Steve Horvath · BMC Bioinformatics · 2008 · 29.1K citations · Full text

Life Sciences, Bioinformatics, Systems Biology +15

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang, Tao Liu, Clifford A. Meyer et al. · Genome biology · 2008 · 19.9K citations · Full text

Life Sciences, Bioinformatics, Molecular Biology +11

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Cole Trapnell, Brian A. Williams, Geo Pertea et al. · Nature Biotechnology · 2010 · 16.5K citations

Life Sciences, Cell Biology, Molecular Biology +16

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell, Lior Pachter, Steven L. Salzberg · Bioinformatics · 2009 · 12.1K citations · Full text

Life Sciences, Bioinformatics, Molecular Biology +16

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

Jun-Hao Li, Shun Liu, Hui Zhou et al. · Nucleic Acids Research · 2013 · 6K citations · Full text

Life Sciences, Bioinformatics, Molecular Biology +16