Towards parallel evaluation and learning of Boolean μ-formulas with molecules. - Masami Hagiya; Masanori Arita; Daisuke Kiga; Kensaku Sakamoto; Shigeyuki Yokoyama (DNA Based Computers, 1997)

Successive State Transitions with I/O Interface by Molecules. - Ken Komiya; Kensaku Sakamoto; Hidetaka Gouzu; Shigeyuki Yokoyama; Masanori Arita; Akio Nishikawa; Masami Hagiya (DNA Computing, 2000)

Improving Sequence Design for DNA Computing. - Masanori Arita; Akio Nishikawa; Masami Hagiya; Ken Komiya; Hidetaka Gouzu; Kensaku Sakamoto (GECCO, 2000)

Complexity analysis of the SAT engine: DNA algorithms as probabilistic algorithms. - Masami Hagiya; John A. Rose; Ken Komiya; Kensaku Sakamoto (Theor. Comput. Sci., 2002)

Branching DNA machines based on transitions of hairpin structures. - Mitsuhiro Kubota; Kazumasa Ohtake; Ken Komiya; Kensaku Sakamoto; Masami Hagiya (IEEE Congress on Evolutionary Computation, 2003)

Conformational Addressing Using the Hairpin Structure of Single-Strand DNA. - Atsushi Kameda; Masahito Yamamoto; Hiroki Uejima; Masami Hagiya; Kensaku Sakamoto; Azuma Ohuchi (DNA, 2003)

Toward "Wet" Implementation of Genetic Algorithm for Protein Engineering. - Kensaku Sakamoto; Masayuki Yamamura; Hiroshi Someya (DNA, 2004)

Development of an In Vivo Computer Based on Escherichia coli. - Hirotaka Nakagawa; Kensaku Sakamoto; Yasubumi Sakakibara (DNA, 2005)

Hairpin-based state machine and conformational addressing: Design and experiment. - Atsushi Kameda; Masahito Yamamoto; Hiroki Uejima; Masami Hagiya; Kensaku Sakamoto; Azuma Ohuchi (Nat. Comput., 2005)

Biologically-implemented genetic algorithm for protein engineering. - Hiroshi Someya; Kensaku Sakamoto; Masayuki Yamamura (GECCO, 2009)

An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes. - Aditya K. Padhi; Ashutosh Kumar 001; Ken-ichi Haruna; Haruna Sato; Hiroko Tamura; Satoru Nagatoishi; Kouhei Tsumoto; Atushi Yamaguchi; Fumie Iraha; Mihoko Takahashi; Kensaku Sakamoto; Kam Y. J. Zhang (Briefings Bioinform., 2021)