A Parzen window-based approach for the detection of locally enriched transcription factor binding sites. - Alexis Vandenbon; Yutaro Kumagai; Shunsuke Teraguchi; Karlou Mar Amada; Shizuo Akira; Daron M. Standley (BMC Bioinform., 2013)

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies. - Kazuo Yamashita; Kazuyoshi Ikeda; Karlou Mar Amada; Shide Liang; Yuko Tsuchiya; Haruki Nakamura; Hiroki Shirai; Daron M. Standley (Bioinform., 2014)

MAFFT-DASH: integrated protein sequence and structural alignment. - John Rozewicki; Songling Li; Karlou Mar Amada; Daron M. Standley; Kazutaka Katoh (Nucleic Acids Res., 2019)