Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments. - Srinka Ghosh; Heather A. Hirsch; Edward A. Sekinger; Kevin Struhl; Thomas R. Gingeras (BMC Bioinform., 2006)

Differential analysis for high density tiling microarray data. - Srinka Ghosh; Heather A. Hirsch; Edward A. Sekinger; Philipp Kapranov; Kevin Struhl; Thomas R. Gingeras (BMC Bioinform., 2007)

STAR: ultrafast universal RNA-seq aligner. - Alexander Dobin; Carrie A. Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R. Gingeras (Bioinform., 2013)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)