Integrated analysis of the genome and the transcriptome by FANTOM. - Shintaro Katayama; Mutsumi Kanamori; Yoshihide Hayashizaki (Briefings Bioinform., 2004)

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. - Hideya Kawaji; Takeya Kasukawa; Shiro Fukuda; Shintaro Katayama; Chikatoshi Kai; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki (Nucleic Acids Res., 2006)

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization. - Shintaro Katayama; Virpi Töhönen; Sten Linnarsson; Juha Kere (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)

Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods. - Shintaro Katayama; Tiina Skoog; Cilla Söderhäll; Elisabet Einarsdottir; Kaarel Krjutskov; Juha Kere (BMC Bioinform., 2019)