Daron M. Standley

Publication Activity (10 Years)

Years Active: 2005-2022
Publications (10 Years): 3

Top Topics

Multiple Sequence Alignments

Protein Sequences

Transcription Factor Binding Sites

Computational Biology

Top Venues

BMC Syst. Biol.

Nucleic Acids Res.

Publications

Zichang Xu, Hendra S. Ismanto, Hao Zhou, Dianita S. Saputri, Fuminori Sugihara, Daron M. Standley
Advances in antibody discovery from human BCR repertoires. Frontiers Bioinform. 2 (2022)
John Rozewicki, Songling Li, Karlou Mar Amada, Daron M. Standley, Kazutaka Katoh
MAFFT-DASH: integrated protein sequence and structural alignment. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Kazutaka Katoh, Daron M. Standley
A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinform. 32 (13) (2016)
Kazuo Yamashita, Kazuyoshi Ikeda, Karlou Mar Amada, Shide Liang, Yuko Tsuchiya, Haruki Nakamura, Hiroki Shirai, Daron M. Standley
Kotai Antibody Builder: automated high-resolution structural modeling of antibodies. Bioinform. 30 (22) (2014)
Alexis Vandenbon, Yutaro Kumagai, Shunsuke Teraguchi, Karlou Mar Amada, Shizuo Akira, Daron M. Standley
A Parzen window-based approach for the detection of locally enriched transcription factor binding sites. BMC Bioinform. 14 (2013)
Shide Liang, Dandan Zheng, Daron M. Standley, Huarong Guo, Chi Zhang
A novel function prediction approach using protein overlap networks. BMC Syst. Biol. 7 (2013)
Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, Daron M. Standley
Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator. Pacific Symposium on Biocomputing (2012)
Akira R. Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Daron M. Standley, Atsushi Nakagawa, Haruki Nakamura
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res. 40 (Database-Issue) (2012)
Shide Liang, Yaoqi Zhou, Nick V. Grishin, Daron M. Standley
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. J. Comput. Chem. 32 (8) (2011)
Shide Liang, Dandan Zheng, Chi Zhang, Daron M. Standley
Fast and accurate prediction of protein side-chain conformations. Bioinform. 27 (20) (2011)
Michael Fernández, Yutaro Kumagai, Daron M. Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad
Prediction of dinucleotide-specific RNA-binding sites in proteins. BMC Bioinform. 12 (S-13) (2011)
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, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. 1 (2010)
Shunsuke Teraguchi, Ashwini Patil, Daron M. Standley
Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins. BMC Bioinform. 11 (S-7) (2010)
Daron M. Standley, Reiko Yamashita, Akira R. Kinjo, Hiroyuki Toh, Haruki Nakamura
: balancing sequence and structural information in protein functional mapping. Bioinform. 26 (9) (2010)
Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, Chi Zhang
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinform. 11 (2010)
Daron M. Standley, Akira R. Kinjo, Kengo Kinoshita, Haruki Nakamura
Protein structure databases with new web services for structural biology and biomedical research. Briefings Bioinform. 9 (4) (2008)
Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
ASH structure alignment package: Sensitivity and selectivity in domain classification. BMC Bioinform. 8 (2007)
Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures. BMC Bioinform. 6 (2005)