学位

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

経歴

学歴

受賞

• LA/EATCS Best Presentation Award
• CIAA 2016 Best Paper Award (Sheng Yu Award)

その他

論文

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

その他業績

• RNA折り紙
• Cotranscriptional folding: A frontier in molecular engineering a challenge for computer scientists

講演・口頭発表等

• RNA co-transcriptionality: How can/should we program RNA for computations?
• RNA co-transcriptionality
• Shifts as a driving force for computing by co-transcriptional folding
• How complex shapes can RNA fold into? [ResearchMap] [ResearchMap]
• Freezing 1-Tag systems with states [ResearchMap] [ResearchMap]
• On algorithmic self-assembly of squares by co-transcriptional folding [ResearchMap] [ResearchMap]
• Single-stranded architectures for computing by RNA co-transcriptional folding
• Single-stranded architectures for RNA co-transcriptional folding
• Single-stranded architectures for RNA co-transcriptional folding
• Turedo a new computational model for molecular nanobots?
• Oritatami systems assemble shapes no less complex than tile assembly model
• Algorithmic self-assembly of squares in oritatami
• Simple intrinsic simulation of cellular automata in oritatami molecular folding model
• Les oritatamis tracent des dessins indécidables
• Single-stranded architectures for computing
• A single-stranded architecture for infinite counting
• Counting infinitely by oritatami co-transcriptional folding
• Single-stranded architectures for computing
• A general architecture of oritatami systems for simulating arbitrary finite automata
• On the power of oritatami cotranscriptional folding with unary bead sequence
• Proving the Turing universality of oritatami cotranscriptional folding
• Know when to fold 'em: Self-assembly of shapes by folding in oritatami
• Transcript desing problem of oritatami systems
• Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding
• Proving Turing universality of cotranscriptional folding
• Self-Assembly of shapes by cotranscriptional folding
• Cotranscriptional Folding: A Frontier in Molecular Engineering
• Proving Turing universality of cotranscriptional folding
• Turing completeness of RNA cotarnsccriptional folding
• Self-attraction removal from oritatami systems
• Bit string bifurcation by cotranscriptional folding
• Bit string bifurcation by cotranscriptional folding
• Self-assembly at nano scale by molecular Xerox
• 分子コピー機を用いたナノスケール自己組織化
• Oritatami, a novel frontier in molecular self-assembly
• Oritatami, a novel mathematical model of RNA cotranscriptional folding
• Nondeterministic seedless oritatami systems and hardness of testing their equivalence
• Programming biomolecules that fold greedily during transcription
• The complexity of fixed-height patterned tile self-assembly
• Folding Turing is hard but feasible
• Molecular cotranscriptional folding: A novel challenge in theory and applications of self-assembly
• Molecular cotranscriptional folding: A novel topic in theory and applications of self-assembly
• Square-density increasing mappings
• Computational complexity of inverse word search problem
• Efficient universal computation by molecular cotranscriptional folding
• Binary pattern tile set synthesis is NP-hard
• 折り畳み：共転写性フォールディングの数理モデル
• 一般化Lyndon-Schutzenberger方程式
• パリキ合同に基づく操作の状態複雑性
• DNA pattern self-assembly: Introduction and recent breakthroughs
• Stronger square conjecture on binary words
• A stronger square conjecture on binary words
• Computing minimum tile sets to self-assembly color patterns
• How many repetitions can you put on a sequence?
• Combinatorial optimization in pattern-assembly
• Combinatorial optimization in pattern-assembly
• 3-color bounded patterned self-assembly
• Combinatorial optimization in pattern assembly (extended abstract)
• On the boundedness property of semilinear sets
• DNA pattern self-assembly
• DNA pattern self-assembly
• Roles that temperature plays in self-assembly
• Combinatorial optimization in pattern assembly
• Descriptional complexity in Parikh equivalence
• Conveting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata
• On the behavior of tile assembly system at high temperatures
• Triangular and hexagonal tile self-assembly systems
• On the behavior of tile assembly system at high temperatures
• Iterated hairpin completions of non-crossing words
• In the century of communication
• Program size and temperature in self-assembly
• Roles that temperature play in self-assembly
• Number theory and computational efficiency in chemoinformatics
• Number theory and computational efficiency in chemoinformatics
• An introduction to the world of self-assembly
• Characterizations of bounded semilinear languages by one-way and two-way deterministic machines
• Scalable, time-responsive, digital, energy-efficient, moleculer circuits using DNA strand displacement
• One-reversal counter machines and multihead automata: revisited
• Power of nondeterminism in self-assembly
• Schema for parallel insertion and deletion
• Triangular tile self-assembly systems
• Schema for parallel insertion and deletion
• An extension of fundamental notions in combinatorics on words inspired by DNA information encoding
• An extension of the Lyndon-Schutzenberger result to pseudoperiodic words
• On the reversibility of parallel insertion, and its relation to comma codes
• Duplication in DNA sequences
• On a special class of primitive words
• Towards the sequence design preventing pseudoknot formation
• An efficient multiple alignment method for DNA secondary structures including pseudoknots
• Hierarchical alignment of RNA secondary structures including pseudoknots
• Efficient learning of k-reversible context-free grammars from positive structural examples

書籍等出版物

• Proceedings of the 30th International Conference on DNA Computing and Molecular Programming
• Special issue of New Generation Computing devoted to Hagiya-sensei's 64th birthday.
• Special issue of Natural Computing devoted to the International Conference on Unconventional Computation and Natural Computation (UCNC 2019)
• Special issue of International Journal of Foundations of Computer Science (IJFCS) devoted to Developments in Language Theory 2018
• Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation (UCNC2019, Tokyo, Japan, June 3-7, 2019)
• Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation
• Proceedings of the 22nd International Conference on Developments in Language Theory (DLT2018, Tokyo, Japan, September 10-14, 2018)
• Encyclopedia of Algorithms
• 自然計算についてのハンドブック
• 言語理論の進展に関する第１４回国際会議紀要

作品等

共同研究・競争的資金等の研究課題

• 文字列の辞書式順序の組合せ論とその応用
• 共転写性フォールディングの本質的計算完全性
• 万能折り畳みシステムの小型化とその限界
• 国際会議UCNC2019への助成
• 国際会議DLT2018への助成
• 共転写性フォールディングによる自己組織化システムの実際的設計と最適化
• 国際会議DLT2018への助成
• 機関選抜のため、研究テーマはなし
• 国際会議DLT2018への助成
• 共転写性フォールディングの数理モデル化とチューリング完全性
• 分子自己組織化システムの実際的な設計とその最適化

メディア報道

産業財産権

所属学協会

委員歴

担当経験のある科目

• 形式言語理論
• MICS実験第2
• 情報領域演習第2
• 大学院技術英語
• 情報領域演習第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

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