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)