Degree

• 博士（理学）（）
• Ph.D. (Computer Science)（University of Western Ontario）

Research History

Education

Awards

• LA/EATCS Best Presentation Award（2018-02）
• CIAA 2016 Best Paper Award (Sheng Yu Award)（2016-07）

Others

Papers

• Towards composable computations by RNA co-transcriptional folding: A proof-of-concept demonstration of nested loops in oritatami（2024-06） [DOI] [ResearchMap] [ResearchMap]
• Programmable single-stranded architectures for computing.（2023-09） [DOI] [DBLP] [Othres link]
• Freezing 1-tag systems with states（2023-09） [ResearchMap] [ResearchMap]
• Ok: A kinetic model for locally reconfigurable molecular systems（2023-05） [ResearchMap] [ResearchMap]
• On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding.（2022-12） [DOI] [DBLP] [Othres link] [Othres link]
• Oritatami systems assemble shapes no less complex than tile assembly model (aTAM)（2022-03-09）
• Square network on a word（2021-11） [DOI] [Scopus] [Scopus]
• Simple intrinsic simulation of cellular automata in oritatami molecular folding model（2021-01-05）
• Linear bounds on the size of the conformations in greedy deterministic oritatami（2021） [DOI] [DBLP] [Othres link]
• A general architecture of oritatami systems for simulating arbitrary finite automata（2021）
• Counting infinitely by oritatami co-transcriptional folding（2021） [DOI]
• Transcript design problem of oritatami systems（2020）
• Renewal of the major fields of New Generation Computing Vol. 38（2020） [DOI] [DBLP] [Othres link]
• A General Architecture of Oritatami Systems for Simulating Arbitrary Finite Automata（2019） [DOI]
• Self-attraction removal from oritatami systems（2019）
• On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence.（2019） [DOI] [DBLP] [DBLP] [DBLP]
• Oritatami: a computational model for molecular co-transcriptional folding（2019）
• Single-stranded architectures for computing（2019）
• Nondeterministic seedless oritatami systems and hardness of testing their equivalence（2018）
• Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding（2018）
• Know when to fold 'em: Self-assembly of shapes by folding in oritatami（2018）
• Transcript design problem of oritatami systems（2018）
• Proving the Turing universality of oritatami co-transcriptional folding（2018）
• The Complexity of Fixed-Height Patterned Tile Self-Assembly（2017-08） [DOI] [Web of Scientce]
• Oritatami System; a Survey and the Impossibility of Simple Simulation at Small Delays（2017） [DOI] [Web of Scientce]
• Self-attraction removal from oritatami systems（2017） [DOI]
• The extended equation of Lyndon and Schutzenberger（2016-11-26）
• Rule set design problems for oritatami system（2016-09-22）
• Programming biomolecules that fold greedily during transcription（2016-08-22）
• Binary pattern tile set synthesis is NP-hard（2016-04-26）
• The Complexity of Fixed-Height Patterned Tile Self-assembly（2016） [DOI] [Web of Scientce]
• Nondeterministic seedless oritatami systems and hardness of testing their equivalence（2016） [DOI]
• A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tileset synthesis（2015-11-24）
• Program Size and Temperature in Self-Assembly（2015-07） [DOI] [Web of Scientce]
• Dynamic Simulation of 1D Cellular Automata in the Active aTAM（2015-07） [DOI] [Web of Scientce]
• 3-color bounded patterned self-assembly（2015-06） [DOI] [Web of Scientce]
• Computational complexity of inverse word search problem（2015）
• Square-Density Increasing Mappings（2015） [DOI] [Web of Scientce]
• Semilinear Sets and Counter Machines: a Brief Survey（2015） [DOI] [Web of Scientce]
• Binary Pattern Tile Set Synthesis Is NP-hard（2015） [DOI] [Web of Scientce]
• Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise（2014-03） [DOI] [Web of Scientce]
• A Stronger Square Conjecture on Binary Words（2014） [Web of Scientce]
• Operational State Complexity under Parikh Equivalence（2014） [Web of Scientce]
• Generalised Lyndon-Schutzenberger Equations（2014） [Web of Scientce]
• On computational complexity of graph inference from counting（2013-12） [DOI] [Scopus] [Scopus]
• On the open problem of Ginsburg concerning semilinear sets and related problems（2013-08） [DOI] [Web of Scientce]
• The power of nondeterminism in self-assembly（2013）
• On the behavior of tile assembly system at high temperatures（2013） [DOI]
• Convering nondeterministic automata and context-free grammars into Parikh equivalent one-way and two-way deterministic automata（2013）
• On the boundedness property of semilinear sets（2013）
• Combinatorial optimization in pattern assembly (extended abstract)（2013）
• 3-Color Bounded Patterned Self-assemblyY（2013） [Web of Scientce]
• Computing Minimum Tile Sets to Self-Assemble Color Patterns（2013） [Web of Scientce]
• One-reversal counter machines and multihead automata: Revisited（2012-10） [DOI] [Web of Scientce]
• CHARACTERIZATIONS OF BOUNDED SEMILINEAR LANGUAGES BY ONE-WAY AND TWO-WAY DETERMINISTIC MACHINES（2012-09） [DOI] [Web of Scientce]
• Absoluteness of subword inequality is undecidable（2012-02） [DOI] [Web of Scientce]
• Iterated Hairpin Completions of Non-crossing Words（2012） [Web of Scientce]
• Triangular and hexagonal tile self-assembly systems（2012）
• On the behavior of tile assembly system at high temperatures（2012） [DOI] [DBLP] [Othres link] [Othres link]
• Converting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata（2012）
• SCHEMA FOR PARALLEL INSERTION AND DELETION: REVISITED（2011-11） [DOI] [Web of Scientce]
• An extension of the Lyndon-Schutzenberger result to pseudoperiodic words（2011-04） [DOI] [Web of Scientce]
• Block insertion and deletion on trajectories（2011-03） [DOI] [Web of Scientce]
• PROPERTIES OF PSEUDO-PRIMITIVE WORDS AND THEIR APPLICATIONS（2011-02） [DOI] [Web of Scientce]
• Triangular Tile Self-assembly Systems（2011） [Web of Scientce]
• Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement（2011） [Web of Scientce]
• ORTHOGONAL SHUFFLE ON TRAJECTORIES（2011-01） [DOI] [Web of Scientce]
• K-Comma Codes and Their Generalizations（2011） [DOI] [Web of Scientce]
• On the Regularity of Iterated Hairpin Completion of a Single Word（2011） [DOI] [Web of Scientce]
• The Power of Nondeterminism in Self-Assembly（2011） [Web of Scientce]
• One-Reversal Counter Machines and Multihead Automata: Revisited（2011） [Web of Scientce]
• Characterizations of bounded semilinear languages by one-way and two-way deterministic machines（2011）
• Program Size and Temperature in Self-assembly（2011） [Web of Scientce]
• On a special class of primitive words（2010-01） [DOI] [Web of Scientce]
• An Improved Bound for an Extension of Fine and Wilf's Theorem and Its Optimality（2010） [DOI] [Web of Scientce]
• Schema for Parallel Insertion and Deletion（2010） [Web of Scientce]
• Twin-roots of words and their properties（2009-05） [DOI] [Web of Scientce]
• On pseudoknot-bordered words and their properties（2009-02） [DOI] [Web of Scientce]
• An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots（2009） [Web of Scientce]
• Towards the Sequence Design Preventing Pseudoknot Formation（2009） [Web of Scientce]
• Duplication in DNA Sequences（2009） [DOI] [Web of Scientce]
• On the Reversibility of Parallel Insertion, and Its Relation to Comma Codes（2009） [Web of Scientce]
• An Extension of the Lyndon Schutzenberger Result to Pseudoperiodic Words（2009） [Web of Scientce]
• On a special class of primitive words（2008） [Web of Scientce]
• A grammatical approach to the alignment of structure-annotated strings（2005-12） [DOI] [Web of Scientce]
• Efficient learning of k-reversible context-free grammars from positive structural examples（2004） [Web of Scientce]
• Hierarchical Alignment of RNA secondary structures including pseudoknots（2004）

Misc

• RNA折り紙（2019）
• Cotranscriptional folding: A frontier in molecular engineering a challenge for computer scientists（2017-05-01）

Presentations

• RNA Co-transcriptionality: How can/should we program RNA for computations?（2025-03-19）
• RNA co-transcriptionality: How can/should we program RNA for computations?（2024-12-04）
• RNA co-transcriptionality（2024-11-20）
• Shifts as a driving force for computing by co-transcriptional folding（2024-09-13）
• How complex shapes can RNA fold into?（2023-10-13） [ResearchMap] [ResearchMap]
• Freezing 1-Tag systems with states（2023-09-06） [ResearchMap] [ResearchMap]
• On algorithmic self-assembly of squares by co-transcriptional folding（2022-12-20） [ResearchMap] [ResearchMap]
• Single-stranded architectures for computing by RNA co-transcriptional folding（2022-12-15）
• Single-stranded architectures for RNA co-transcriptional folding（2022-09-19）
• Single-stranded architectures for RNA co-transcriptional folding（2022-09-19）
• Turedo a new computational model for molecular nanobots?（2022-07-14）
• Oritatami systems assemble shapes no less complex than tile assembly model（2022-03-15）
• Algorithmic self-assembly of squares in oritatami（2021-02-01）
• Simple intrinsic simulation of cellular automata in oritatami molecular folding model（2021-01-05）
• Les oritatamis tracent des dessins indécidables（2020-12-04）
• Single-stranded architectures for computing（2020-11-06）
• A single-stranded architecture for infinite counting（2020-01-27）
• Counting infinitely by oritatami co-transcriptional folding（2020-01-20）
• Single-stranded architectures for computing（2019-08-05）
• A general architecture of oritatami systems for simulating arbitrary finite automata（2019-07-22）
• On the power of oritatami cotranscriptional folding with unary bead sequence（2019-04-13）
• Proving the Turing universality of oritatami cotranscriptional folding（2018-12-16）
• Know when to fold 'em: Self-assembly of shapes by folding in oritatami（2018-10-08）
• Transcript desing problem of oritatami systems（2018-10-08）
• Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding（2018-07-30）
• Proving Turing universality of cotranscriptional folding（2018-04-06）
• Self-Assembly of shapes by cotranscriptional folding（2018-04-02）
• Cotranscriptional Folding: A Frontier in Molecular Engineering（2018-02-20）
• Proving Turing universality of cotranscriptional folding（2018-02-05）
• Turing completeness of RNA cotarnsccriptional folding（2018-01-19）
• Self-attraction removal from oritatami systems（2017-07-03）
• Bit string bifurcation by cotranscriptional folding（2017-06-06）
• Bit string bifurcation by cotranscriptional folding（2017-05-13）
• Self-assembly at nano scale by molecular Xerox（2017-05-13）
• Nano-scale self-assembly using molecular Xerox（2016-12-02）
• Oritatami, a novel frontier in molecular self-assembly（2016-11-21）
• Oritatami, a novel mathematical model of RNA cotranscriptional folding（2016-10-20）
• Nondeterministic seedless oritatami systems and hardness of testing their equivalence（2016-09-04）
• Programming biomolecules that fold greedily during transcription（2016-08-22）
• The complexity of fixed-height patterned tile self-assembly（2016-07-19）
• Folding Turing is hard but feasible（2016-06-06）
• Molecular cotranscriptional folding: A novel challenge in theory and applications of self-assembly（2016-01-25）
• Molecular cotranscriptional folding: A novel topic in theory and applications of self-assembly（2015-10-22）
• Square-density increasing mappings（2015-09-14）
• Computational complexity of inverse word search problem（2015-08-21）
• Efficient universal computation by molecular cotranscriptional folding（2015-08-17）
• Binary pattern tile set synthesis is NP-hard（2015-07-04）
• Oritatami, a model of cotranscriptional folding（2015-03-04）
• Generalized Lyndon-Schutzenberger equations（2014-08-25）
• Operational state complexity under Parikh equivalence（2014-08-05）
• DNA pattern self-assembly: Introduction and recent breakthroughs（2014-06-09）
• Stronger square conjecture on binary words（2014-01-25）
• A stronger square conjecture on binary words（2014-01-24）
• Computing minimum tile sets to self-assembly color patterns（2013-12-16）
• How many repetitions can you put on a sequence?（2013-11-07）
• Combinatorial optimization in pattern-assembly（2013-11-06）
• Combinatorial optimization in pattern-assembly（2013-10-13）
• 3-color bounded patterned self-assembly（2013-09-22）
• Combinatorial optimization in pattern assembly (extended abstract)（2013-07-01）
• On the boundedness property of semilinear sets（2013-05-20）
• DNA pattern self-assembly（2013-05-15）
• DNA pattern self-assembly（2013-04-24）
• Roles that temperature plays in self-assembly（2012-11-30）
• Combinatorial optimization in pattern assembly（2012-11-02）
• Descriptional complexity in Parikh equivalence（2012-10-18）
• Conveting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata（2012-08-14）
• On the behavior of tile assembly system at high temperatures（2012-06-18）
• Triangular and hexagonal tile self-assembly systems（2012-02-21）
• On the behavior of tile assembly system at high temperatures（2012-01-30）
• Iterated hairpin completions of non-crossing words（2012-01-21）
• In the century of communication（2011-12-13）
• Program size and temperature in self-assembly（2011-12-05）
• Roles that temperature play in self-assembly（2011-11-10）
• Number theory and computational efficiency in chemoinformatics（2011-11-03）
• Number theory and computational efficiency in chemoinformatics（2011-08-25）
• An introduction to the world of self-assembly（2011-08-24）
• Characterizations of bounded semilinear languages by one-way and two-way deterministic machines（2011-08-20）
• Scalable, time-responsive, digital, energy-efficient, moleculer circuits using DNA strand displacement（2011-06-14）
• One-reversal counter machines and multihead automata: revisited（2011-01-22）
• Power of nondeterminism in self-assembly（2011-01-22）
• Schema for parallel insertion and deletion（2010-08-17）
• Triangular tile self-assembly systems（2010-06-14）
• Schema for parallel insertion and deletion（2009-12-12）
• An extension of fundamental notions in combinatorics on words inspired by DNA information encoding（2009-07-06）
• An extension of the Lyndon-Schutzenberger result to pseudoperiodic words（2009-06-30）
• On the reversibility of parallel insertion, and its relation to comma codes（2009-05-19）
• Duplication in DNA sequences（2008-09-16）
• On a special class of primitive words（2008-08-27）
• Towards the sequence design preventing pseudoknot formation（2007-12-10）
• An efficient multiple alignment method for DNA secondary structures including pseudoknots（2007-12-10）
• Hierarchical alignment of RNA secondary structures including pseudoknots（2004-12-13）
• Efficient learning of k-reversible context-free grammars from positive structural examples（2004-10-11）

Books and Other Publications

• Proceedings of the 30th International Conference on DNA Computing and Molecular Programming（2024-09-09）
• Special issue of New Generation Computing devoted to Hagiya-sensei's 64th birthday.（2022-08）
• Special issue of Natural Computing devoted to the International Conference on Unconventional Computation and Natural Computation (UCNC 2019)（2021）
• Special issue of International Journal of Foundations of Computer Science (IJFCS) devoted to Developments in Language Theory 2018（2020-09）
• Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation (UCNC2019, Tokyo, Japan, June 3-7, 2019)（2019）
• Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation（2019）
• Proceedings of the 22nd International Conference on Developments in Language Theory (DLT2018, Tokyo, Japan, September 10-14, 2018)（2018-08-06）
• Encyclopedia of Algorithms（2016）
• Handbook of Natural Computing（2012）
• Proc. 14th International Conference on Developments in Language Theory（2010）

Works

Research Projects

Media Coverage

Industrial Property Rights

Professional Memberships

Committee Memberships

Teaching Experience

• Formal Language Theory
• MICS実験第2
• 情報領域演習第2
• 大学院技術英語
• Exercise in Informatics 1
• MICS実験第一
• K過程輪講
• 総合コミュニケーション科学
• Combinatorics

Social Contribution

Academic Contribution