siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. - Yuki Naito; Tomoyuki Yamada; Kumiko Ui-Tei; Shinichi Morishita; Kaoru Saigo (Nucleic Acids Res., 2004)

dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference. - Yuki Naito; Tomoyuki Yamada; Takahiro Matsumiya; Kumiko Ui-Tei; Kaoru Saigo; Shinichi Morishita (Nucleic Acids Res., 2005)

siVirus: web-based antiviral siRNA design software for highly divergent viral sequences. - Yuki Naito; Kumiko Ui-Tei; Toru Nishikawa; Yutaka Takebe; Kaoru Saigo (Nucleic Acids Res., 2006)

siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. - Yuki Naito; Jun Yoshimura; Shinichi Morishita; Kumiko Ui-Tei (BMC Bioinform., 2009)

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. - Yuki Naito; Kimihiro Hino; Hidemasa Bono; Kumiko Ui-Tei (Bioinform., 2015)

The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. - Piotr J. Kamola; Yuko Nakano; Tomoko Takahashi; Paul A. Wilson 002; Kumiko Ui-Tei (PLoS Comput. Biol., 2015)