DBTMEE: a database of transcriptome in mouse early embryos. - Sung-Joon Park; Katsuhiko Shirahige; Miho Ohsugi; Kenta Nakai (Nucleic Acids Res., 2015)

Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. - Ryuichiro Nakato; Katsuhiko Shirahige (Briefings Bioinform., 2017)

Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile. - Ryuichiro Nakato; Katsuhiko Shirahige (Bioinform., 2018)

DBTSS/DBKERO for integrated analysis of transcriptional regulation. - Ayako Suzuki; Shin Kawano; Toutai Mituyama; Mikita Suyama; Yae Kanai; Katsuhiko Shirahige; Hiroyuki Sasaki; Katsushi Tokunaga; Katsuya Tsuchihara; Sumio Sugano; Kenta Nakai; Yutaka Suzuki (Nucleic Acids Res., 2018)