Shinnosuke Seki

Max Wiedenhöft

CoRR, April, 2025

Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes.

[BibT_eX]

[DOI]

Pekka Orponen

Antti Elonen

Proceedings of the 31st International Conference on DNA Computing and Molecular Programming, 2025

Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion.

[BibT_eX]

[DOI]

Da-Jung Cho

Max Wiedenhöft

Proceedings of the 31st International Conference on DNA Computing and Molecular Programming, 2025

2024

Towards composable computations by RNA co-transcriptional folding: A proof-of-concept demonstration of nested loops in oritatami.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2024

2023

Programmable single-stranded architectures for computing.

[BibT_eX]

[DOI]

Yu Kihara

Nat. Comput., September, 2023

Freezing 1-Tag Systems with States.

[BibT_eX]

[DOI]

Proceedings of the 16th International Conference on Automata and Formal Languages, 2023

2022

Preface to Hagiya-sensei's 2<sup>6</sup>-th Birthday Special Issue.

[BibT_eX]

[DOI]

Shin-ya Nishizaki

New Gener. Comput., 2022

Oritatami Systems Assemble Shapes No Less Complex Than Tile Assembly Model (ATAM).

[BibT_eX]

[DOI]

Proceedings of the 39th International Symposium on Theoretical Aspects of Computer Science, 2022

On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding.

[BibT_eX]

[DOI]

Proceedings of the 33rd International Symposium on Algorithms and Computation, 2022

2021

Square network on a word.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2021

Preface.

[BibT_eX]

[DOI]

Ian McQuillan

Nat. Comput., 2021

Linear Bounds on the Size of Conformations in Greedy Deterministic Oritatami.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 2021

2020

Renewal of the Major Fields of New Generation Computing Vol. 38 (2020).

[BibT_eX]

[DOI]

Masayuki Numao

Yutaka Matsuo

New Gener. Comput., 2020

Special Issue Developments in Language Theory 2018 - Preface.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 2020

Counting Infinitely by Oritatami Co-transcriptional Folding.

[BibT_eX]

[DOI]

Kohei Maruyama

Proceedings of the SOFSEM 2020: Theory and Practice of Computer Science, 2020

Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model.

[BibT_eX]

[DOI]

Proceedings of the LATIN 2020: Theoretical Informatics, 2020

2019

A General Architecture of Oritatami Systems for Simulating Arbitrary Finite Automata.

[BibT_eX]

[DOI]

Proceedings of the Implementation and Application of Automata, 2019

On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence.

[BibT_eX]

[DOI]

Kohei Maruyama

Reoto Morita

Proceedings of the Theory and Applications of Models of Computation, 2019

Single-Stranded Architectures for Computing.

[BibT_eX]

[DOI]

Proceedings of the Developments in Language Theory - 23rd International Conference, 2019

2018

Towards the Algorithmic Molecular Self-assembly of Fractals by Cotranscriptional Folding.

[BibT_eX]

[DOI]

Yusei Masuda

Yuki Ubukata

Proceedings of the Implementation and Application of Automata, 2018

Proving the Turing Universality of Oritatami Co-Transcriptional Folding.

[BibT_eX]

[DOI]

Cody W. Geary

Pierre-Étienne Meunier

Nicolas Schabanel

Proceedings of the 29th International Symposium on Algorithms and Computation, 2018

Transcript Design Problem of Oritatami Systems.

[BibT_eX]

[DOI]

Yo-Sub Han

Hwee Kim

Proceedings of the DNA Computing and Molecular Programming - 24th International Conference, 2018

Know When to Fold 'Em: Self-assembly of Shapes by Folding in Oritatami.

[BibT_eX]

[DOI]

Proceedings of the DNA Computing and Molecular Programming - 24th International Conference, 2018

2017

Rule set design problems for oritatami systems.

[BibT_eX]

[DOI]

Makoto Ota

Theor. Comput. Sci., 2017

The extended equation of Lyndon and Schützenberger.

[BibT_eX]

[DOI]

J. Comput. Syst. Sci., 2017

A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tileset synthesis.

[BibT_eX]

[DOI]

J. Comb. Optim., 2017

Oritatami System; a Survey and the Impossibility of Simple Simulation at Small Delays.

[BibT_eX]

[DOI]

Trent A. Rogers

Fundam. Informaticae, 2017

Self-attraction Removal from Oritatami Systems.

[BibT_eX]

[DOI]

Proceedings of the Descriptional Complexity of Formal Systems, 2017

2016

Patterned Self-Assembly Tile Set Synthesis.

[BibT_eX]

[DOI]

Encyclopedia of Algorithms, 2016

The Complexity of Fixed-Height Patterned Tile Self-assembly.

[BibT_eX]

[DOI]

Andrew Winslow

Proceedings of the Implementation and Application of Automata, 2016

Programming Biomolecules That Fold Greedily During Transcription.

[BibT_eX]

[DOI]

Cody W. Geary

Pierre-Etienne Meunier

Nicolas Schabanel

Proceedings of the 41st International Symposium on Mathematical Foundations of Computer Science, 2016

Nondeterministic Seedless Oritatami Systems and Hardness of Testing Their Equivalence.

[BibT_eX]

[DOI]

Proceedings of the DNA Computing and Molecular Programming - 22nd International Conference, 2016

2015

Dynamic Simulation of 1D Cellular Automata in the Active aTAM.

[BibT_eX]

[DOI]

Natasa Jonoska

Daria Karpenko

New Gener. Comput., 2015

3-color bounded patterned self-assembly.

[BibT_eX]

[DOI]

Nat. Comput., 2015

Semilinear Sets and Counter Machines: a Brief Survey.

[BibT_eX]

[DOI]

Fundam. Informaticae, 2015

Efficient Universal Computation by Greedy Molecular Folding.

[BibT_eX]

[DOI]

Cody W. Geary

Pierre-Étienne Meunier

Nicolas Schabanel

CoRR, 2015

Binary Pattern Tile Set Synthesis Is NP-hard.

[BibT_eX]

[DOI]

Pierre-Étienne Meunier

Matthew J. Patitz

Proceedings of the Automata, Languages, and Programming - 42nd International Colloquium, 2015

Square-Density Increasing Mappings.

[BibT_eX]

[DOI]

Florin Manea

Proceedings of the Combinatorics on Words - 10th International Conference, 2015

2014

A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tile set synthesis.

[BibT_eX]

[DOI]

CoRR, 2014

Computing Minimum Tile Sets to Self-Assemble Colors Patterns.

[BibT_eX]

[DOI]

CoRR, 2014

A Stronger Square Conjecture on Binary Words.

[BibT_eX]

[DOI]

Natasa Jonoska

Florin Manea

Proceedings of the SOFSEM 2014: Theory and Practice of Computer Science, 2014

Generalised Lyndon-Schützenberger Equations.

[BibT_eX]

[DOI]

Proceedings of the Mathematical Foundations of Computer Science 2014, 2014

Operational State Complexity under Parikh Equivalence.

[BibT_eX]

[DOI]

Giovanna J. Lavado

Giovanni Pighizzini

Proceedings of the Descriptional Complexity of Formal Systems, 2014

2013

On the open problem of Ginsburg concerning semilinear sets and related problems.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2013

On computational complexity of graph inference from counting.

[BibT_eX]

[DOI]

Nat. Comput., 2013

Converting nondeterministic automata and context-free grammars into Parikh equivalent one-way and two-way deterministic automata.

[BibT_eX]

[DOI]

Giovanna J. Lavado

Giovanni Pighizzini

Inf. Comput., 2013

Combinatorial Optimization in Pattern Assembly

[BibT_eX]

[DOI]

CoRR, 2013

Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise.

[BibT_eX]

[DOI]

Rémi Lemoy

Alexander Mozeika

CoRR, 2013

Combinatorial Optimization in Pattern Assembly - (Extended Abstract).

[BibT_eX]

[DOI]

Proceedings of the Unconventional Computation and Natural Computation, 2013

On the Boundedness Property of Semilinear Sets.

[BibT_eX]

[DOI]

Proceedings of the Theory and Applications of Models of Computation, 2013

Computing Minimum Tile Sets to Self-Assemble Color Patterns.

[BibT_eX]

[DOI]

Proceedings of the Algorithms and Computation - 24th International Symposium, 2013

3-Color Bounded Patterned Self-assembly - (Extended Abstract).

[BibT_eX]

[DOI]

Proceedings of the DNA Computing and Molecular Programming - 19th International Conference, 2013

2012

DNA Computing - Foundations and Implications.

[BibT_eX]

[DOI]

Petr Sosík

Proceedings of the Handbook of Natural Computing, 2012

Absoluteness of subword inequality is undecidable.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2012

Iterated Hairpin Completions of Non-crossing Words.

[BibT_eX]

[DOI]

Proceedings of the SOFSEM 2012: Theory and Practice of Computer Science, 2012

Converting Nondeterministic Automata and Context-Free Grammars into Parikh Equivalent Deterministic Automata.

[BibT_eX]

[DOI]

Giovanna J. Lavado

Giovanni Pighizzini

Proceedings of the Developments in Language Theory - 16th International Conference, 2012

On the Behavior of Tile Assembly System at High Temperatures.

[BibT_eX]

[DOI]

Yasushi Okuno

Proceedings of the How the World Computes, 2012

Triangular and Hexagonal Tile Self-assembly Systems.

[BibT_eX]

[DOI]

Zhi Xu

Proceedings of the Computation, Physics and Beyond, 2012

2011

Block insertion and deletion on trajectories.

[BibT_eX]

[DOI]

Bo Cui

Theor. Comput. Sci., 2011

Schema for Parallel Insertion and Deletion: Revisited.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 2011

Properties of Pseudo-Primitive Words and their Applications.

[BibT_eX]

[DOI]

Benoît Masson

Int. J. Found. Comput. Sci., 2011

Orthogonal Shuffle on Trajectories.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 2011

On the Regularity of Iterated Hairpin Completion of a Single Word.

[BibT_eX]

[DOI]

Fundam. Informaticae, 2011

K-Comma Codes and Their Generalizations.

[BibT_eX]

[DOI]

Bo Cui

Fundam. Informaticae, 2011

One-Reversal Counter Machines and Multihead Automata: Revisited.

[BibT_eX]

[DOI]

Proceedings of the SOFSEM 2011: Theory and Practice of Computer Science, 2011

The Power of Nondeterminism in Self-Assembly.

[BibT_eX]

[DOI]

Proceedings of the Twenty-Second Annual ACM-SIAM Symposium on Discrete Algorithms, 2011

Program Size and Temperature in Self-Assembly.

[BibT_eX]

[DOI]

Ho-Lin Chen

David Doty

Proceedings of the Algorithms and Computation - 22nd International Symposium, 2011

Characterizations of Bounded Semilinear Languages by One-Way and Two-way Deterministic Machines.

[BibT_eX]

Proceedings of the Automata and Formal Languages, 13th International Conference, 2011

2010

An Improved Bound for an Extension of Fine and Wilf's Theorem and Its Optimality.

[BibT_eX]

[DOI]

Fundam. Informaticae, 2010

Parallelism, Program Size, Time, and Temperature in Self-Assembly.

[BibT_eX]

[DOI]

Electron. Colloquium Comput. Complex., 2010

Triangular Self-Assembly

[BibT_eX]

[DOI]

Zhi Xu

CoRR, 2010

Triangular Tile Self-assembly Systems.

[BibT_eX]

[DOI]

Zhi Xu

Proceedings of the DNA Computing and Molecular Programming - 16th International Conference, 2010

Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement.

[BibT_eX]

[DOI]

Proceedings of the DNA Computing and Molecular Programming - 16th International Conference, 2010

Schema for Parallel Insertion and Deletion.

[BibT_eX]

[DOI]

Proceedings of the Developments in Language Theory, 14th International Conference, 2010

2009

Twin-roots of words and their properties.

[BibT_eX]

[DOI]

Kalpana Mahalingam

Theor. Comput. Sci., 2009

On pseudoknot-bordered words and their properties.

[BibT_eX]

[DOI]

J. Comput. Syst. Sci., 2009

An Extension of the Lyndon Schützenberger Result to Pseudoperiodic Words.

[BibT_eX]

[DOI]

Proceedings of the Developments in Language Theory, 13th International Conference, 2009

On the Reversibility of Parallel Insertion, and Its Relation to Comma Codes.

[BibT_eX]

[DOI]

Bo Cui

Proceedings of the Algebraic Informatics, Third International Conference, 2009

2008

On a Special Class of Primitive Words.

[BibT_eX]

[DOI]

Elena Czeizler

Proceedings of the Mathematical Foundations of Computer Science 2008, 2008

Duplication in DNA Sequences.

[BibT_eX]

[DOI]

Proceedings of the Developments in Language Theory, 12th International Conference, 2008

2007

An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots.

[BibT_eX]

[DOI]

Satoshi Kobayashi

Proceedings of the Natural Computing, 2007

Towards the Sequence Design Preventing Pseudoknot Formation.

[BibT_eX]

[DOI]

Proceedings of the Natural Computing, 2007

2005

A Grammatical Approach to the Alignment of Structure-Annotated Strings.

[BibT_eX]

[DOI]

Satoshi Kobayashi

IEICE Trans. Inf. Syst., 2005

2004

Efficient Learning of <i>k</i>-Reversible Context-Free Grammars from Positive Structural Examples.

[BibT_eX]

[DOI]