[Aita00JTB]
T. Aita and Y. Husimi.
Theory of an Evolutionary Molecular Engineering using Simultaneous
Accumulation of Advantageous Mutations.
J. Theoret. Biol., Vol.207, 2000,
pp.543--556.
[Aita00JMB]
T. Aita and Y. Husimi.
Adaptive walks by the fittest among finite random mutants
on the Mt.Fuji-type fitness Landscape II: The effect of small nonadditivity.
J. Math. Biol., Vol.41, 2000,
pp.207--231.
[Aita00JME]
T. Aita, S. Urata and Y. Husimi.
From amino acid landscape to protein landscape:
Analysis of genetic codes in terms of fitness landscape.
J. Mol. Evol., Vol.50, 2000,
pp.313--323.
[Aita00Biopolymers]
T. Aita, H. Uchiyama, T. Inaoka, M. Nakajima and Y. Husimi.
Analysis of local fitness landscapes with a model of
the rough Mt.Fuji-type landscape:
Application to prolyl endopeptidase and thermolysin.
Biopolymers, Vol.54, 2000,
pp.64--79.
[Aita98JTB]
A. Aita and Y. Husimi.
Fitness landscape for a biopolymer participating in a multi-step reaction.
J. Theor. Biol., Vol.191, 1998,
pp.337--390.
[Aita98JTB']
A. Aita and Y. Husimi.
Adaptive walks by the fittest among finite random mutants on
the Mt.Fuji-type fitness landscape.
J. Theor. Biol., Vol.193, 1998,
pp.383--405.
[Aita96JTB]
A. Aita and Y. Husimi.
Fitness spectrum among random mutants on Mt.Fuji-type fitness landscape.
J. Theor. Biol., Vol.182, 1996,
pp.469--485.
[Arita00GECCO]
M. Arita, A. Nishikawa, M. Hagiya, K. Komiya H. Gouzu and
K. Sakamoto.
Improving Sequence Design for DNA Computing.
Proceedings of the Gnenetic and Evolutionary Computation Conference
(GECCO 2000), 2000,
pp.875--882. [Arita00GCB]
M. Arita, K. Asai, and T. Nishioka.
Reconstructing Metabolic Pathways with New Enzyme Classification.
German Conference in Bioinformatics (GCB'00), 2000,
pp.99-106.
[Arita00SPT]
M. Arita.
Metabolic Reconstruction using Shortest Paths.
Simulation Practice and Theory, Vol.8, No.2, 2000,
pp.109-125.
[Arita00JSAI]
M. Arita.
Graph Modeling of Metabolism,
Journal of Japanese Society for Artificial Intelligence (JSAI),
Vol.15, No.4, 2000,
pp.703--710.
[Arita99GIW]
M. Arita, K. Asai, and T. Nishioka.
Finding Precursor Compounds in Secondary Metabolism.
Genome Informatics 1999, Genome Informatics Series, No.10,
Universal Academy Press, Inc., Tokyo, Japan, 1999,
pp.113--120.
[Arita97GP]
Masanori Arita, Akira Suyama and Masami Hagiya.
A Heuristic Approach for Hamiltonian Path Problem with Molecules.
Proceedings of 2nd Genetic Programming (GP-97), 1997,
pp.457--462. [Arita97ICEC]
Masanori Arita, Masami Hagiya and Akira Suyama.
Joining and Rotating Data with Molecules,
IEEE International Conference on Evolutionary Computation, 1997,
pp.243--248. [Eli99JB]
P. Eli, K. Nishigaki and Y. Husimi.
Characterization of imidazole as a DNA denaturant by using TGGE of
PCR products from a random pool of DNA.
J. Biochem., Vol.125, 1999,
pp.790--794.
[Eli98CL]
P. Eli and Y. Husimi.
Imidazole improves specificity of PCR by suppressing product-priming outgrowth.
Chem. Lett., Vol.1998, 1998,
pp.683--684.
[Hagiya01LNCS]
Masami Hagiya.
From Molecular Computing to Molecular Programming,
DNA6, Sixth International Meeting on DNA Based Computers,
Lecture Notes in Computer Science, 2001,
to appear. [Hagiya99NGC]
Masami Hagiya.
Perspectives on Molecular Computing.
New Generation Computing, Vol.17, 1999,
pp.131--151. [Hagiya98GP]
Masami Hagiya.
Towards Autonomous Molecular Computers.
Genetic Programming 1998:
Proceedings of the Third Annual Conference, Morgan Kaufmann, 1998,
pp.691-699. [Head99CEC]
T. Head, M. Yamamura, and S. Gal.
Aqueous Computing -- Writing on Molecules.
Proc. CEC'99, 1999,
pp.1006--1010.
[Higuchi00PPSN]
T. Higuchi, S. Tsutsui, and M. Yamamura.
Theoretical Analysis of Simplex Crossover for Real-Coded Genetic Algorithms.
Proc PPSN VI, 2000,
pp.365--374.
[Husimi99EC]
Y. Husimi, T. Aita and S. Urata.
An Evolution of Evolvability: The second coding with correlated mapping.
Preliminary Proceedings of DIMACS Workshop on Evolution as Computation,
1999,
pp.229--234.
[Ito00Gene]
Y. Ito, M. Suzuki and Y. Husimi.
A novel T-vector using green fluorescent protein as an indicator.
Gene, Vol.245, 2000,
pp.67--77.
[Ito99BBRC]
Y. Ito, M. Suzuki and Y. Husimi.
A green fluorescent protein with mutation of enhanced fluorescence at
488nm excitation.
Biophys. Biochem. Res. Comm., Vol.264, 1999,
pp.556--560.
[Kiga98NAR]
D. Kiga, Y. Futamura, K. Sakamoto, S. Yokoyama.
An RNA aptamer to the xanthine/guanine base with a distictive mode of
purine recognition.
Nucleic Acids Res., Vol.26, 1998,
pp.1755-1760.
[Kimoto98FEBS]
M. Kimoto, K. Sakamoto, M. Shirouzu, I. Hirao, S. Yokoyama.
RNA aptamers that specifically bind to the Ras-binding domain of Raf-1.
FEBS Lett., Vol.441, 1998,
pp.322--326.
[Kinoshita97NAR]
Y. Kinoshita, K. Nishigaki and Y. Husimi.
Fluorescence-, isotope- or biotin-labeling of the 5'-end of
single-stranded DNA/RNA using T4 RNA ligase.
Nucleic Acids Res., Vol.25, 1997,
pp.3747--3748.
[Kobayashi01TCS]
S. Kobayashi, V. Mitrana, Gh. Paun and G. Rozenberg.
Formal Properties of PA-Matching.
Theoretical Computer Science,
accepted for publication.
[Kobayashi01TCS']
Satoshi Kobayashi and Yasubumi Sakakibara.
Multiple Splicing Systems and the Universal Computability.
Theoretical Computer Science,
accepted for publication.
[Kobayashi00Multiset]
S. Kobayashi.
Concentration Prediction of Pattern Reaction Systems.
Pre-Proc. of Workshop on Multiset Processing,
CDMTS Research Report Series 140 (Univ. of Auckland),
August, 2000,
pp.112--123. [Kobayashi99JCO]
Satoshi Kobayashi.
Horn Clause Computation with DNA Molecules.
J. of Combinatorial Optimization, Vol.3, 1999,
pp.277--299.
[Kobayashi97ICEC]
Satoshi Kobayashi, Takashi Yokomori,
Gen-ichi Sampei and Kiyoshi Mizobuchi.
DNA Implementation of Simple Horn Clause Computation.
Proc. of IEEE International Conference on
Evolutionary Computation'97, 1997,
pp.213--217. [Komiya00DNA]
Ken Komiya, Kensaku Sakamoto, Hidetaka Gouzu, Shigeyuki Yokoyama,
Masanori Arita, Akio Nishikawa and Masami Hagiya.
Successive State Transitions with I/O Interface by Molecules.
DNA6, Sixth International Meeting on DNA Based Computers,
Preliminary Proceedings, 2000,
pp.21--30.
[Kurata99GIW]
K. Kurata and A. Suyama.
Probe design for DNA chips.
Genome Informatics 1999, Genome Informatics Series, No.10,
Universal Academy Press, Inc., Tokyo, Japan, 1999,
pp.225--226.
[Morimoto99DIMACS]
N. Morimoto, M. Arita and Akira Suyama.
Solid-Phase DNA Solution to the Hamiltonian Path Problem.
DIMACS Series in Discrete Mathematics and Theoretical Computer Science,
Vol.48, 1999,
pp.193--206. [Morimoto97DNA]
N. Morimoto, M. Arita and A. Suyama.
Solid-Phase DNA Solution to the Hamiltonian Path Problem.
Preliminary Proceedings,
3rd DIMACS Workshop on DNA Based Computers,
University of Pennsylvania,
June 23 - June 25, 1997,
pp.83--92.
[Morimoto97BCEC]
N. Morimoto, M. Arita and A. Suyama.
Stepwise Generation of Hamiltonian Path with Molecules.
Proc. of Biocomputing and Emergent Computation, 1997,
pp.184--192.
[Nemoto97FEBS]
N. Nemoto, E. Miyamoto-Sato, Y. Husimi and H. Yanagawa.
In vitro virus: Bonding of mRNA bearing puromycin at the 3'-terminal end
to the C-terminal end of its encoded protein on the ribosome in vitro.
FEBS Lett., Vol.414, 1997,
pp.405--408.
[Nishikawa01SC]
Akio Nishikawa, Masayuki Yamamura and Masami Hagiya.
DNA Computation Simulator Based on Abstract Bases.
Soft Computing, 2001,
in press. [Nishikawa99GECCO]
Akio Nishikawa, Masami Hagiya and Masayuki Yamamura.
Virtual DNA Simulator and Protocol Design by GA.
Proceedings of the Genetic and Evolutionary Computation Conference
(GECCO'99), Vol.2, 1999,
pp.1810--1816.
[Nishikawa99CEC]
Akio Nishikawa and Masami Hagiya.
Towards a System for Simulating DNA Computing with Whiplash PCR.
CEC'99, Congress on Evolutionary Computation, 1999,
pp.960--966.
[Park00BRGS]
S. J. Park, and M. Yamamura.
Using Genetic Algorithm to Detect Structural Similarities in Proteins.
Proc. BRGS2000, Vol.2, 2000,
pp.201--203.
[Paun00JUCS]
G. Paun and T. Yokomori.
Simulating H systems by P systems.
Journal of Universal Computer Science, Vol.6, No.1, 2000,
pp.178--193.
[Paun99DNA]
Gh. Paun and T. Yokomori.
Membrane Computing Based on Splicing.
Proc. of 5th DIMACS Workshop on DNA Based Computers, MIT, USA,
June, 1999,
pp.213--227.
[Rose00MPS]
John A. Rose, Akira Suyama, Masami Hagiya and Russel J. Deaton.
An Antisense Antidote for Whiplash PCR,
IPSJ Symposium Series, Vol.2000, No.16,
Information Processing Society of Japan, 2000,
pp.101--108.
[Rose00DNA]
J. A. Rose, R. J. Deaton.
The fidelity of annealing-ligation: A theoretical analysis.
DNA6, Sixth International Meeting on DNA Based Computers,
Preliminary Proceedings, 2000,
pp.207--221.
[Sakakibara01SC]
Yasubumi Sakakibara and Satoshi Kobayashi.
Sticker Systems with Complex Structures.
Soft Computing,
accepted for publication.
[Sakakibara00GIW]
Yasubumi Sakakibara and Akira Suyama.
Intelligent DNA Chips: Logical operation of gene expression profiles
on DNA computers.
Genome Informatics 2000, Genome Informatics Series, No.11,
Universal Academy Press, Inc., Tokyo, Japan, 2000,
pp.33--42.
[Sakakibara00DNA]
Yasubumi Sakakibara.
Solving computational learning problems of Boolean formulae
on DNA computers.
DNA6, Sixth International Meeting on DNA Based Computers,
Preliminary Proceedings, 2000,
pp.193--204.
[Sakakibara99TCS]
Yasubumi Sakakibara and Claudio Ferretti.
Splicing on Tree-like Structures.
Theoretical Computer Science, Vol.210, 1999,
pp.227--243.
[Sakakibara98JPST]
Yasubumi Sakakibara.
DNA Computers: A New Computing Paradigm.
Journal of Photopolymer Science and Technology, Vol.11, No.4, 1998,
pp.681--686.
[Sakamoto99BioSystems]
Kensaku Sakamoto, Daisuke Kiga, Ken Komiya, Hidetaka Gouzu,
Shigeyuki Yokoyama, Shuji Ikeda, Hiroshi Sugiyama, and
Masami Hagiya.
State Transitions by Molecules.
BioSystems, Vol.52, No.1--3, 1999,
pp.81--91. [Sakamoto98DNA]
Kensaku Sakamoto, Daisuke Kiga, Ken Komiya,
Hidetaka Gouzu, Shigeyuki Yokoyama, Shuji Ikeda, Hiroshi Sugiyama, and
Masami Hagiya.
State Transitions by Molecules.
Preliminary Proceedings,
Fourth International Meeting on DNA Based Computers,
University of Pennsylvania,
June 15 - June 19, 1998,
pp.87-99.
[Someya99GECCO]
H. Someya, and M. Yamamura.
A Genetic Algorithm without Parameters Tuning and its Application on
the Floorplan Design Problem.
Proceedings of the Genetic and Evolutionary Computation Conference
(GECCO'99), Vol.1, 1999,
pp.620--627.
[Suyama00CCMB]
A. Suyama, N. Nishida, K. Kurata and K. Omagari.
Gene Expression Analysis by DNA Computing.
Currents in Computational Molecular Biology, 2000,
pp.12--13.
[Suyama97Micromachine]
A. Suyama.
DNA Chips - Integrated Chemical Circuits for DNA Diagnosis and DNA Computers.
Proc. of Third International Micromachine Symposium,, 1997,
pp.7--12. [Takano99JACS]
M. Takano, T. Yamato, J. Higo, A. Suyama, K. Nagayama.
Molecular dynamics of a 15-residue Poly(L-alanine) in water:
Helix formation and energetics.
J. Amer. Chem. Soc., Vol. 121, 1999,
pp. 605--612.
[Tsutsui99GECCO]
S. Tsutsui, M. Yamamura, and T. Higuchi.
Multi-parent Recombination with Simplex Crossover in
Real Coded Genetic Algorithms.
Proceedings of the Genetic and Evolutionary Computation Conference
(GECCO'99), Vol.1, 1999,
pp.657--664.
[Yamamoto01CL]
Y. Yamamoto, S. Komiya and Y. Husimi.
Stabilized 3SR against evolutionary instability.
Chem. Lett, 2001,
submitted.
[Yamamoto01DIMACS]
Y. Yamamoto, M. Suzuki and Y. Husimi.
Dynamics in a 3SR evolution reactor and its applications.
DIMACS Series in Discrete Mathematics and
Theoretical Computer Science, 2001,
in press.
[Yamamura97JCIS]
M. Yamamura，H. Satoh，and S. Kobayashi.
A Markov Analysis of Generation Alternation Models on
Minimal Deceptive Problems.
Proc. JCIS'97, Vol.1, 1997,
pp.47--50.
[Yamamura96ICEC]
M. Yamamura, I. Ono, and S. Kobayashi.
Emergent Search on Double Circle TSPs using Subtour Exchange Crossover.
Proc. ICEC'96, 1996,
pp.535--540.
[Yokomori00TCS]
C. Ferretti, G. Mauri, S. Kobayashi and T.Yokomori.
On the Universality of Post and Splicing Systems.
Theoretical Computer Science, Vol.231, 2000,
pp.157--170.
[Yokomori99DLT]
T. Yokomori.
Computation = Self-assembly+Conformational Change:
Toward New Computing Paradigms.
Proc. of 4th International Conference on Developments in
Language Theory(DLT'99), Aachen, July, 1999,
pp.21--30. [Yokomori99DNA]
T. Yokomori.
YAC: Yet Another Computation Model of Self-Assembly,
Proc. of 5th DIMACS Workshop on DNA Based Computers, MIT, USA,
June, 1999,
pp.153--167. [Yokomori97DNA]
T. Yokomori and S. Kobayashi.
DNA-EC: A Model of DNA-Computing Based on Equality Checking.
Proc. of 3rd DIMACS Workshop on DNA Based Computers,
Philadelphia, USA, June, 1997,
pp.334--347. [Yokomori97ICEC]
T. Yokomori, S. Kobayashi and C. Ferretti.
On the power of circular splicing systems and DNA computatibility.
Proc. of IEEE Intern. Conference on Evolutionary
Computation, Indianapolis, USA, April, 1997,
pp.219--224. [Yoshida00DIMACS]
H. Yoshida and A. Suyama.
Solution to 3-SAT by breadth first search.
DIMACS Series in Discrete Mathematics and Theoretical Computer Science,
Vol.54, 2000,
pp.9--22.
[Yoshida99DNA]
H. Yoshida and A. Suyama.
Solution to 3-SAT by Breadth First Search,
Proc. of Fifth International Meeting on DNA Based Computers, MIT, USA,
June, 1999,
pp.9--20.
(Arita00GECCO.ps.gz 218k)
(Arita97GP.ps.gz 65k)
(Arita97ICEC.ps.gz 87k )
(Hagiya01LNCS.ps.gz 658k)
(Hagiya99NGC.ps.gz 198k)
(Hagiya98GP.ps.gz 96k)
(Kobayashi00Multiset.ps.gz 66k)
(Kobayashi97ICEC.ps.gz 52k)
(Morimoto99DIMACS.ps.gz 176k)
(Nishikawa01SC.ps.gz 294k)
(Sakamoto99BioSystems.ps.gz 149k)
(Suyama97Micromachine.ps.gz 644k)
(Yokomori99DLT.ps.gz 135k)
(Yokomori99DNA.ps.gz 141k)
(Yokomori97DNA.ps.gz 73k)
(Yokomori97ICEC.ps.gz 63k)
Talks
to index