DNA implementation of nondeterminism. - Y. Gao; Max H. Garzon; R. C. Murphy; John A. Rose; Russell J. Deaton; Donald R. Franceschetti; Stanley Edward Stevens Jr. (DNA Based Computers, 1997)

A DNA based implementation of an evolutionary search for good encodings for DNA computation. - Russell J. Deaton; R. C. Murphy; John A. Rose; Max H. Garzon; Donald R. Franceschetti; S. E. Stevens (ICEC, 1997)

In Vitro Implementation of Finite-State Machines. - Max H. Garzon; Y. Gao; John A. Rose; R. C. Murphy; Russell J. Deaton; Donald R. Franceschetti; Stanley Edward Stevens Jr. (Workshop on Implementing Automata, 1997)

DNA Compunting: A Review. - Russell J. Deaton; Max H. Garzon; John A. Rose; Donald R. Franceschetti; Stanley Edward Stevens Jr. (Fundam. Informaticae, 1998)

Soft molecular computing. - Max H. Garzon; Russell J. Deaton; John A. Rose (DNA Based Computers, 1999)

The Fidelity of Annealing-Ligation: A Theoretical Analysis. - John A. Rose; Russell J. Deaton (DNA Computing, 2000)

PNA-mediated Whiplash PCR. - John A. Rose; Russell J. Deaton; Masami Hagiya; Akira Suyama (DNA, 2001)

The Fidelity of the Tag-Antitag System. - John A. Rose; Russell J. Deaton; Masami Hagiya; Akira Suyama (DNA, 2001)

A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides. - Russell J. Deaton; Junghuei Chen; Hong Bi; John A. Rose (DNA, 2002)

A PNA-mediated Whiplash PCR-based Program for In Vitro Protein Evolution. - John A. Rose; Mitsunori Takano; Akira Suyama (DNA, 2002)

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

The fidelity of the tag-antitag system II: reconciliation with the stringency picture. - John A. Rose; Masami Hagiya; Akira Suyama (IEEE Congress on Evolutionary Computation, 2003)

A DNA Computing-based Genetic Program for In Vitro Protein Evolution via Constrained Pseudomodule Shuffling. - John A. Rose; Mitsunori Takano; Masami Hagiya; Akira Suyama (Genet. Program. Evolvable Mach., 2003)

Equilibrium Modelling of Oligonucleotide Hybridization, Error, and Efficiency for DNA-Based Computational Systems. - John A. Rose (KES, 2004)

The Fidelity of the Tag-Antitag System III. Robustness in the Excess Limit: The Stringent Temperature. - John A. Rose (KES, 2004)

Editorial. - Max H. Garzon; John A. Rose (Nat. Comput., 2004)

Statistical thermodynamic analysis and designof DNA-based computers. - John A. Rose; Russell J. Deaton; Akira Suyama (Nat. Comput., 2004)

Physical modeling of biomolecular computers: Models, limitations, and experimental validation. - John A. Rose; Akira Suyama (Nat. Comput., 2004)

The fidelity of the tag-antitag system: Characterization of the stringent temperature for robustness in the excess limit. - John A. Rose (Int. J. Knowl. Based Intell. Eng. Syst., 2005)

A New Readout Approach in DNA Computing Based on Real-Time PCR with TaqMan Probes. - Zuwairie Ibrahim; John A. Rose; Yusei Tsuboi; Osamu Ono; Marzuki Khalid (DNA, 2006)

Experimental Validation of the Statistical Thermodynamic Model for Prediction of the Behavior of Autonomous Molecular Computers Based on DNA Hairpin Formation. - Ken Komiya; Satsuki Yaegashi; Masami Hagiya; Akira Suyama; John A. Rose (DNA, 2006)

Displacement Whiplash PCR: Optimized Architecture and Experimental Validation. - John A. Rose; Ken Komiya; Satsuki Yaegashi; Masami Hagiya (DNA, 2006)

An improved readout method of molecular computation based on real-time PCR implemented on DNA Engine Opticon 2 System. - Zuwairie Ibrahim; Muhammad Faiz Mohamed Saaid; Ali S. Paramita; Akira Suyama; John A. Rose (IEEE Congress on Evolutionary Computation, 2007)

Experimental Validation of Signal Dependent Operation in Whiplash PCR. - Ken Komiya; Masayuki Yamamura; John A. Rose (DNA, 2008)

Experimental implementation and analysis of a DNA computing readout method based on real-time PCR with TaqMan probes. - Zuwairie Ibrahim; John A. Rose; Akira Suyama; Marzuki Khalid (Nat. Comput., 2008)

Experimental validation and optimization of signal dependent operation in whiplash PCR. - Ken Komiya; Masayuki Yamamura; John A. Rose (Nat. Comput., 2010)

Analysis and design of a single-molecule DNA nanodevice for thermal band-pass filters. - John A. Rose; Ken Komiya (NEMS, 2016)

Reputation-based Decentralized Autonomous Organization for the non-profit sector: Leveraging blockchain to enhance good governance. - Yoshiro Saito; John A. Rose (Frontiers Blockchain, 2022)