The Lair: a resource for exploratory analysis of published RNA-Seq data

by Pimentel, Harold, Sturmfels, Pascal, Bray, Nicolas, Melsted, Páll, Pachter, Lior
Published 2016

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

by Kim, Daehwan, Pertea, Geo, Trapnell, Cole, Pimentel, Harold, Kelley, Ryan, Salzberg, Steven L
Published 2013

A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

by Pimentel, Harold, Parra, Marilyn, Gee, Sherry L., Mohandas, Narla, Pachter, Lior, Conboy, John G.
Published 2016

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis

by Pimentel, Harold, Parra, Marilyn, Gee, Sherry, Ghanem, Dana, An, Xiuli, Li, Jie, Mohandas, Narla, Pachter, Lior, Conboy, John G.
Published 2014