Shinnosuke Seki

120 papers A* 1A 1B 20C 13Journal 68Unranked 14

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A Formalization of Co-Transcriptional Splicing as an Operation on Formal Languages. CoRR Da-Jung Cho, Szilárd Zsolt Fazekas, Shinnosuke Seki, Max Wiedenhöft
2025	J	`jnl`	A formalization of co-transcriptional splicing as an operation on formal languages. Nat. Comput. Da-Jung Cho, Szilárd Zsolt Fazekas, Shinnosuke Seki, Max Wiedenhöft
2025	J	`jnl`	Programmable Co-Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion. CoRR Da-Jung Cho, Szilárd Zsolt Fazekas, Shinnosuke Seki, Max Wiedenhöft
2025	B	`conf`	Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion. DNA Da-Jung Cho, Szilárd Zsolt Fazekas, Shinnosuke Seki, Max Wiedenhöft
2025	B	`conf`	Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes. DNA Pekka Orponen, Shinnosuke Seki, Antti Elonen
2024	B	`ed.`	30th International Conference on DNA Computing and Molecular Programming, DNA 2024, Baltimore, Maryland, USA, September 16-20, 2024 DNA 30 Shinnosuke Seki, Jaimie Marie Stewart
2024	J	`jnl`	Towards composable computations by RNA co-transcriptional folding: A proof-of-concept demonstration of nested loops in oritatami. Theor. Comput. Sci. Szilárd Zsolt Fazekas, Naoya Iwano, Yu Kihara, Ryuichi Matsuoka, Shinnosuke Seki, Hinano Takeuchi
2023	—	`conf`	Freezing 1-Tag Systems with States. AFL Szilárd Zsolt Fazekas, Shinnosuke Seki
2023	J	`jnl`	Programmable single-stranded architectures for computing. Nat. Comput. Yu Kihara, Shinnosuke Seki
2022	B	`conf`	On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding. ISAAC Szilárd Zsolt Fazekas, Hwee Kim, Ryuichi Matsuoka, Shinnosuke Seki, Hinano Takeuchi
2022	A	`conf`	Oritatami Systems Assemble Shapes No Less Complex Than Tile Assembly Model (ATAM). STACS Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Guillaume Theyssier
2022	J	`jnl`	Preface to Hagiya-sensei's 2 New Gener. Comput. Shin-ya Nishizaki, Shinnosuke Seki
2021	J	`jnl`	A general architecture of oritatami systems for simulating arbitrary finite automata. Theor. Comput. Sci. Yo-Sub Han, Hwee Kim, Yusei Masuda, Shinnosuke Seki
2021	J	`jnl`	Counting infinitely by oritatami co-transcriptional folding. Nat. Comput. Kohei Maruyama, Shinnosuke Seki
2021	J	`jnl`	Linear Bounds on the Size of Conformations in Greedy Deterministic Oritatami. Int. J. Found. Comput. Sci. Szilárd Zsolt Fazekas, Hwee Kim, Ryuichi Matsuoka, Reoto Morita, Shinnosuke Seki
2021	J	`jnl`	Preface. Nat. Comput. Ian McQuillan, Shinnosuke Seki
2021	J	`jnl`	Square network on a word. Theor. Comput. Sci. Szilárd Zsolt Fazekas, Shinnosuke Seki
2020	B	`conf`	Counting Infinitely by Oritatami Co-transcriptional Folding. SOFSEM Kohei Maruyama, Shinnosuke Seki
2020	J	`jnl`	Renewal of the Major Fields of New Generation Computing Vol. 38 (2020). New Gener. Comput. Masayuki Numao, Yutaka Matsuo, Shinnosuke Seki
2020	B	`conf`	Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model. LATIN Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Yuki Ubukata
2020	J	`jnl`	Special Issue Developments in Language Theory 2018 - Preface. Int. J. Found. Comput. Sci. Shinnosuke Seki
2020	J	`jnl`	Transcript design problem of oritatami systems. Nat. Comput. Yo-Sub Han, Hwee Kim, Shinnosuke Seki
2019	C	`conf`	A General Architecture of Oritatami Systems for Simulating Arbitrary Finite Automata. CIAA Yo-Sub Han, Hwee Kim, Yusei Masuda, Shinnosuke Seki
2019	J	`jnl`	A general architecture of oritatami systems for simulating arbitrary finite automata. CoRR Yo-Sub Han, Hwee Kim, Yusei Masuda, Shinnosuke Seki
2019	C	`conf`	On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence. TAMC Szilárd Zsolt Fazekas, Kohei Maruyama, Reoto Morita, Shinnosuke Seki
2019	J	`jnl`	Self-Attraction Removal from Oritatami Systems. Int. J. Found. Comput. Sci. Yo-Sub Han, Hwee Kim, Trent A. Rogers, Shinnosuke Seki
2019	C	`conf`	Single-Stranded Architectures for Computing. DLT Shinnosuke Seki
2019	—	`ed.`	Unconventional Computation and Natural Computation - 18th International Conference, UCNC 2019, Tokyo, Japan, June 3-7, 2019, Proceedings UCNC Ian McQuillan, Shinnosuke Seki
2018	C	`ed.`	Developments in Language Theory - 22nd International Conference, DLT 2018, Tokyo, Japan, September 10-14, 2018, Proceedings DLT Mizuho Hoshi, Shinnosuke Seki
2018	J	`jnl`	Know When to Fold 'Em: Self-Assembly of Shapes by Folding in Oritatami. CoRR Erik D. Demaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, Hadley Thomas
2018	B	`conf`	Know When to Fold 'Em: Self-assembly of Shapes by Folding in Oritatami. DNA Erik D. Demaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, Hadley Thomas
2018	J	`jnl`	Nondeterministic seedless oritatami systems and hardness of testing their equivalence. Nat. Comput. Yo-Sub Han, Hwee Kim, Makoto Ota, Shinnosuke Seki
2018	B	`conf`	Proving the Turing Universality of Oritatami Co-Transcriptional Folding. ISAAC Cody W. Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki
2018	C	`conf`	Towards the Algorithmic Molecular Self-assembly of Fractals by Cotranscriptional Folding. CIAA Yusei Masuda, Shinnosuke Seki, Yuki Ubukata
2018	B	`conf`	Transcript Design Problem of Oritatami Systems. DNA Yo-Sub Han, Hwee Kim, Shinnosuke Seki
2017	J	`jnl`	A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tileset synthesis. J. Comb. Optim. Aleck C. Johnsen, Ming-Yang Kao, Shinnosuke Seki
2017	J	`jnl`	Binary Pattern Tile Set Synthesis Is NP-Hard. Algorithmica Lila Kari, Steffen Kopecki, Pierre-Étienne Meunier, Matthew J. Patitz, Shinnosuke Seki
2017	J	`jnl`	Oritatami System; a Survey and the Impossibility of Simple Simulation at Small Delays. Fundam. Informaticae Trent A. Rogers, Shinnosuke Seki
2017	J	`jnl`	Rule set design problems for oritatami systems. Theor. Comput. Sci. Makoto Ota, Shinnosuke Seki
2017	—	`conf`	Self-attraction Removal from Oritatami Systems. DCFS Yo-Sub Han, Hwee Kim, Trent A. Rogers, Shinnosuke Seki
2017	J	`jnl`	The Complexity of Fixed-Height Patterned Tile Self-Assembly. Int. J. Found. Comput. Sci. Shinnosuke Seki, Andrew Winslow
2017	J	`jnl`	The extended equation of Lyndon and Schützenberger. J. Comput. Syst. Sci. Florin Manea, Mike Müller, Dirk Nowotka, Shinnosuke Seki
2016	B	`conf`	Nondeterministic Seedless Oritatami Systems and Hardness of Testing Their Equivalence. DNA Yo-Sub Han, Hwee Kim, Makoto Ota, Shinnosuke Seki
2016	—	`ch.`	Patterned Self-Assembly Tile Set Synthesis. Encyclopedia of Algorithms Shinnosuke Seki
2016	B	`conf`	Programming Biomolecules That Fold Greedily During Transcription. MFCS Cody W. Geary, Pierre-Etienne Meunier, Nicolas Schabanel, Shinnosuke Seki
2016	J	`jnl`	The Complexity of Fixed-Height Patterned Tile Self-Assembly. CoRR Shinnosuke Seki, Andrew Winslow
2016	C	`conf`	The Complexity of Fixed-Height Patterned Tile Self-assembly. CIAA Shinnosuke Seki, Andrew Winslow
2015	J	`jnl`	3-color bounded patterned self-assembly. Nat. Comput. Lila Kari, Steffen Kopecki, Shinnosuke Seki
2015	—	`conf`	Binary Pattern Tile Set Synthesis Is NP-hard. ICALP (1) Lila Kari, Steffen Kopecki, Pierre-Étienne Meunier, Matthew J. Patitz, Shinnosuke Seki
2015	J	`jnl`	Dynamic Simulation of 1D Cellular Automata in the Active aTAM. New Gener. Comput. Natasa Jonoska, Daria Karpenko, Shinnosuke Seki
2015	J	`jnl`	Efficient Universal Computation by Greedy Molecular Folding. CoRR Cody W. Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki
2015	J	`jnl`	Program Size and Temperature in Self-Assembly. Algorithmica Ho-Lin Chen, David Doty, Shinnosuke Seki
2015	J	`jnl`	Semilinear Sets and Counter Machines: a Brief Survey. Fundam. Informaticae Oscar H. Ibarra, Shinnosuke Seki
2015	—	`conf`	Square-Density Increasing Mappings. WORDS Florin Manea, Shinnosuke Seki
2014	B	`conf`	A Stronger Square Conjecture on Binary Words. SOFSEM Natasa Jonoska, Florin Manea, Shinnosuke Seki
2014	J	`jnl`	A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tile set synthesis. CoRR Aleck C. Johnsen, Ming-Yang Kao, Shinnosuke Seki
2014	J	`jnl`	Binary pattern tile set synthesis is NP-hard. CoRR Lila Kari, Steffen Kopecki, Pierre-Étienne Meunier, Matthew J. Patitz, Shinnosuke Seki
2014	J	`jnl`	Computing Minimum Tile Sets to Self-Assemble Colors Patterns. CoRR Aleck C. Johnsen, Ming-Yang Kao, Shinnosuke Seki
2014	—	`conf`	Generalised Lyndon-Schützenberger Equations. MFCS (1) Florin Manea, Mike Müller, Dirk Nowotka, Shinnosuke Seki
2014	—	`conf`	Operational State Complexity under Parikh Equivalence. DCFS Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki
2013	B	`conf`	3-Color Bounded Patterned Self-assembly - (Extended Abstract). DNA Lila Kari, Steffen Kopecki, Shinnosuke Seki
2013	J	`jnl`	3-color Bounded Patterned Self-assembly. CoRR Lila Kari, Steffen Kopecki, Shinnosuke Seki
2013	J	`jnl`	Combinatorial Optimization in Pattern Assembly CoRR Shinnosuke Seki
2013	—	`conf`	Combinatorial Optimization in Pattern Assembly - (Extended Abstract). UCNC Shinnosuke Seki
2013	B	`conf`	Computing Minimum Tile Sets to Self-Assemble Color Patterns. ISAAC Aleck C. Johnsen, Ming-Yang Kao, Shinnosuke Seki
2013	J	`jnl`	Converting nondeterministic automata and context-free grammars into Parikh equivalent one-way and two-way deterministic automata. Inf. Comput. Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki
2013	J	`jnl`	On computational complexity of graph inference from counting. Nat. Comput. Szilárd Zsolt Fazekas, Hiro Ito, Yasushi Okuno, Shinnosuke Seki, Kei Taneishi
2013	J	`jnl`	On the Behavior of Tile Assembly System at High Temperatures. Comput. Shinnosuke Seki, Yasushi Okuno
2013	C	`conf`	On the Boundedness Property of Semilinear Sets. TAMC Oscar H. Ibarra, Shinnosuke Seki
2013	J	`jnl`	On the open problem of Ginsburg concerning semilinear sets and related problems. Theor. Comput. Sci. Oscar H. Ibarra, Shinnosuke Seki
2013	J	`jnl`	The Power of Nondeterminism in Self-Assembly. Theory Comput. Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2013	J	`jnl`	Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise. CoRR Rémi Lemoy, Alexander Mozeika, Shinnosuke Seki
2012	J	`jnl`	Absoluteness of subword inequality is undecidable. Theor. Comput. Sci. Shinnosuke Seki
2012	J	`jnl`	Characterizations of Bounded semilinear Languages by One-Way and Two-Way Deterministic Machines. Int. J. Found. Comput. Sci. Oscar H. Ibarra, Shinnosuke Seki
2012	C	`conf`	Converting Nondeterministic Automata and Context-Free Grammars into Parikh Equivalent Deterministic Automata. Developments in Language Theory Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki
2012	J	`jnl`	Converting Nondeterministic Automata and Context-Free Grammars into Parikh Equivalent One-Way and Two-Way Deterministic Automata CoRR Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki
2012	—	`ch.`	DNA Computing - Foundations and Implications. Handbook of Natural Computing Lila Kari, Shinnosuke Seki, Petr Sosík
2012	B	`conf`	Iterated Hairpin Completions of Non-crossing Words. SOFSEM Lila Kari, Steffen Kopecki, Shinnosuke Seki
2012	C	`conf`	On the Behavior of Tile Assembly System at High Temperatures. CiE Shinnosuke Seki, Yasushi Okuno
2012	J	`jnl`	On the behavior of tile assembly system at high temperatures CoRR Shinnosuke Seki, Yasushi Okuno
2012	J	`jnl`	One-reversal counter machines and multihead automata: Revisited. Theor. Comput. Sci. Ehsan Chiniforooshan, Mark Daley, Oscar H. Ibarra, Lila Kari, Shinnosuke Seki
2012	—	`conf`	Triangular and Hexagonal Tile Self-assembly Systems. Computation, Physics and Beyond Lila Kari, Shinnosuke Seki, Zhi Xu
2011	J	`jnl`	Absoluteness of subword inequality is undecidable CoRR Shinnosuke Seki
2011	J	`jnl`	An extension of the Lyndon-Schützenberger result to pseudoperiodic words. Inf. Comput. Elena Czeizler, Eugen Czeizler, Lila Kari, Shinnosuke Seki
2011	J	`jnl`	Block insertion and deletion on trajectories. Theor. Comput. Sci. Bo Cui, Lila Kari, Shinnosuke Seki
2011	—	`conf`	Characterizations of Bounded Semilinear Languages by One-Way and Two-way Deterministic Machines. AFL Oscar H. Ibarra, Shinnosuke Seki
2011	J	`jnl`	Iterated Hairpin Completions of Non-crossing Words CoRR Lila Kari, Steffen Kopecki, Shinnosuke Seki
2011	J	`jnl`	K-Comma Codes and Their Generalizations. Fundam. Informaticae Bo Cui, Lila Kari, Shinnosuke Seki
2011	J	`jnl`	On the Regularity of Iterated Hairpin Completion of a Single Word. Fundam. Informaticae Lila Kari, Shinnosuke Seki, Steffen Kopecki
2011	J	`jnl`	On the regularity of iterated hairpin completion of a single word CoRR Lila Kari, Steffen Kopecki, Shinnosuke Seki
2011	B	`conf`	One-Reversal Counter Machines and Multihead Automata: Revisited. SOFSEM Ehsan Chiniforooshan, Mark Daley, Oscar H. Ibarra, Lila Kari, Shinnosuke Seki
2011	J	`jnl`	Orthogonal Shuffle on Trajectories. Int. J. Found. Comput. Sci. Mark Daley, Lila Kari, Shinnosuke Seki, Petr Sosík
2011	B	`conf`	Program Size and Temperature in Self-Assembly. ISAAC Ho-Lin Chen, David Doty, Shinnosuke Seki
2011	J	`jnl`	Properties of Pseudo-Primitive Words and their Applications. Int. J. Found. Comput. Sci. Lila Kari, Benoît Masson, Shinnosuke Seki
2011	J	`jnl`	Schema for Parallel Insertion and Deletion: Revisited. Int. J. Found. Comput. Sci. Lila Kari, Shinnosuke Seki
2011	A*	`conf`	The Power of Nondeterminism in Self-Assembly. SODA Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2010	J	`jnl`	An Improved Bound for an Extension of Fine and Wilf's Theorem and Its Optimality. Fundam. Informaticae Lila Kari, Shinnosuke Seki
2010	C	`ed.`	Developments in Language Theory, 14th International Conference, DLT 2010, London, ON, Canada, August 17-20, 2010. Proceedings Developments in Language Theory Yuan Gao, Hanlin Lu, Shinnosuke Seki, Sheng Yu
2010	J	`jnl`	On a special class of primitive words. Theor. Comput. Sci. Elena Czeizler, Lila Kari, Shinnosuke Seki
2010	J	`jnl`	Parallelism, Program Size, Time, and Temperature in Self-Assembly CoRR Ho-Lin Chen, David Doty, Shinnosuke Seki, David Soloveichik
2010	J	`jnl`	Parallelism, Program Size, Time, and Temperature in Self-Assembly. Electron. Colloquium Comput. Complex. Ho-Lin Chen, David Doty, Shinnosuke Seki, David Soloveichik
2010	J	`jnl`	Properties of Pseudo-Primitive Words and their Applications CoRR Lila Kari, Benoît Masson, Shinnosuke Seki
2010	B	`conf`	Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement. DNA Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2010	J	`jnl`	Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits using DNA Strand Displacement CoRR Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2010	C	`conf`	Schema for Parallel Insertion and Deletion. Developments in Language Theory Lila Kari, Shinnosuke Seki
2010	J	`jnl`	The Power of Nondeterminism in Self-Assembly CoRR Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2010	J	`jnl`	The Power of Nondeterminism in Self-Assembly. Electron. Colloquium Comput. Complex. Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
2010	J	`jnl`	Triangular Self-Assembly CoRR Lila Kari, Shinnosuke Seki, Zhi Xu
2010	B	`conf`	Triangular Tile Self-assembly Systems. DNA Lila Kari, Shinnosuke Seki, Zhi Xu
2009	C	`conf`	An Extension of the Lyndon Schützenberger Result to Pseudoperiodic Words. Developments in Language Theory Elena Czeizler, Eugen Czeizler, Lila Kari, Shinnosuke Seki
2009	—	`conf`	Duplication in DNA Sequences. Algorithmic Bioprocesses Masami Ito, Lila Kari, Zachary Kincaid, Shinnosuke Seki
2009	J	`jnl`	On pseudoknot-bordered words and their properties. J. Comput. Syst. Sci. Lila Kari, Shinnosuke Seki
2009	—	`conf`	On the Reversibility of Parallel Insertion, and Its Relation to Comma Codes. CAI Bo Cui, Lila Kari, Shinnosuke Seki
2009	J	`jnl`	Twin-roots of words and their properties. Theor. Comput. Sci. Lila Kari, Kalpana Mahalingam, Shinnosuke Seki
2008	C	`conf`	Duplication in DNA Sequences. Developments in Language Theory Masami Ito, Lila Kari, Zachary Kincaid, Shinnosuke Seki
2008	B	`conf`	On a Special Class of Primitive Words. MFCS Elena Czeizler, Lila Kari, Shinnosuke Seki
2007	—	`conf`	An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots. IWNC Shinnosuke Seki, Satoshi Kobayashi
2007	—	`conf`	Towards the Sequence Design Preventing Pseudoknot Formation. IWNC Lila Kari, Shinnosuke Seki
2005	J	`jnl`	A Grammatical Approach to the Alignment of Structure-Annotated Strings. IEICE Trans. Inf. Syst. Shinnosuke Seki, Satoshi Kobayashi
2004	—	`conf`	Efficient Learning of ICGI Shinnosuke Seki, Satoshi Kobayashi