GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures. - Daron M. Standley; Hiroyuki Toh; Haruki Nakamura (BMC Bioinform., 2005)

ASH structure alignment package: Sensitivity and selectivity in domain classification. - Daron M. Standley; Hiroyuki Toh; Haruki Nakamura (BMC Bioinform., 2007)

Protein structure databases with new web services for structural biology and biomedical research. - Daron M. Standley; Akira R. Kinjo; Kengo Kinoshita; Haruki Nakamura (Briefings Bioinform., 2008)

SeSAW: balancing sequence and structural information in protein functional mapping. - Daron M. Standley; Reiko Yamashita; Akira R. Kinjo; Hiroyuki Toh; Haruki Nakamura (Bioinform., 2010)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. - Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; et al. (J. Biomed. Semant., 2010)

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. - Shide Liang; Dandan Zheng 003; Daron M. Standley; Bo Yao; Martin Zacharias; Chi Zhang 013 (BMC Bioinform., 2010)

Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins. - Shunsuke Teraguchi; Ashwini Patil; Daron M. Standley (BMC Bioinform., 2010)

Fast and accurate prediction of protein side-chain conformations. - Shide Liang; Dandan Zheng 003; Chi Zhang 013; Daron M. Standley (Bioinform., 2011)

Prediction of dinucleotide-specific RNA-binding sites in proteins. - Michael Fernández; Yutaro Kumagai; Daron M. Standley; Akinori Sarai; Kenji Mizuguchi; Shandar Ahmad (BMC Bioinform., 2011)

Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. - Shide Liang; Yaoqi Zhou; Nick V. Grishin; Daron M. Standley (J. Comput. Chem., 2011)

Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator. - Ashwini Patil; Shunsuke Teraguchi; Huy Dinh; Kenta Nakai; Daron M. Standley (Pacific Symposium on Biocomputing, 2012)

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. - Akira R. Kinjo; Hirofumi Suzuki; Reiko Yamashita; Yasuyo Ikegawa; Takahiro Kudou; Reiko Igarashi; Yumiko Kengaku; Hasumi Cho; Daron M. Standley; Atsushi Nakagawa; Haruki Nakamura (Nucleic Acids Res., 2012)

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)

A novel function prediction approach using protein overlap networks. - Shide Liang; Dandan Zheng 003; Daron M. Standley; Huarong Guo; Chi Zhang 013 (BMC Syst. Biol., 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)

A simple method to control over-alignment in the MAFFT multiple sequence alignment program. - Kazutaka Katoh; Daron M. Standley (Bioinform., 2016)

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

Advances in antibody discovery from human BCR repertoires. - Zichang Xu; Hendra S. Ismanto; Hao Zhou; Dianita S. Saputri; Fuminori Sugihara; Daron M. Standley (Frontiers Bioinform., 2022)

Robust detection of infectious disease, autoimmunity, and cancer from the paratope networks of adaptive immune receptors. - Zichang Xu; Hendra S. Ismanto; Dianita S. Saputri; Soichiro Haruna; Guanqun Sun; Jan Wilamowski; Shunsuke Teraguchi; Ayan Sengupta; Songling Li; Daron M. Standley (Briefings Bioinform., 2024)