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2020 – today
- 2024
[j43]Szilárd Zsolt Fazekas, Naoya Iwano, Yu Kihara, Ryuichi Matsuoka, Shinnosuke Seki, Hinano Takeuchi:
Towards composable computations by RNA co-transcriptional folding: A proof-of-concept demonstration of nested loops in oritatami. Theor. Comput. Sci. 999: 114550 (2024)- [e4]Shinnosuke Seki
, Jaimie Marie Stewart:
30th International Conference on DNA Computing and Molecular Programming, DNA 30, September 16-20, 2024, Baltimore, Maryland, USA. LIPIcs 314, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2024, ISBN 978-3-95977-344-7 [contents] - 2023
- [j42]Yu Kihara, Shinnosuke Seki:
Programmable single-stranded architectures for computing. Nat. Comput. 22(3): 563-585 (2023) - [c44]Szilárd Zsolt Fazekas, Shinnosuke Seki:
Freezing 1-Tag Systems with States. AFL 2023: 82-95 - 2022
- [j41]Shin-ya Nishizaki, Shinnosuke Seki:
Preface to Hagiya-sensei's 26-th Birthday Special Issue. New Gener. Comput. 40(2): 399-402 (2022) - [c43]Szilárd Zsolt Fazekas, Hwee Kim, Ryuichi Matsuoka, Shinnosuke Seki, Hinano Takeuchi:
On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding. ISAAC 2022: 37:1-37:15 - [c42]Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Guillaume Theyssier:
Oritatami Systems Assemble Shapes No Less Complex Than Tile Assembly Model (ATAM). STACS 2022: 51:1-51:23 - 2021
- [j40]Szilárd Zsolt Fazekas, Hwee Kim, Ryuichi Matsuoka, Reoto Morita, Shinnosuke Seki:
Linear Bounds on the Size of Conformations in Greedy Deterministic Oritatami. Int. J. Found. Comput. Sci. 32(5): 575-596 (2021) - [j39]Ian McQuillan, Shinnosuke Seki:
Preface. Nat. Comput. 20(2): 191-192 (2021) - [j38]Kohei Maruyama, Shinnosuke Seki:
Counting infinitely by oritatami co-transcriptional folding. Nat. Comput. 20(2): 329-340 (2021) - [j37]Yo-Sub Han, Hwee Kim, Yusei Masuda, Shinnosuke Seki:
A general architecture of oritatami systems for simulating arbitrary finite automata. Theor. Comput. Sci. 870: 29-52 (2021) - [j36]Szilárd Zsolt Fazekas, Shinnosuke Seki:
Square network on a word. Theor. Comput. Sci. 894: 121-134 (2021) - 2020
- [j35]Shinnosuke Seki:
Special Issue Developments in Language Theory 2018 - Preface. Int. J. Found. Comput. Sci. 31(6): 663-665 (2020) - [j34]Yo-Sub Han, Hwee Kim, Shinnosuke Seki:
Transcript design problem of oritatami systems. Nat. Comput. 19(2): 323-335 (2020) - [j33]Masayuki Numao, Yutaka Matsuo, Shinnosuke Seki:
Renewal of the Major Fields of New Generation Computing Vol. 38 (2020). New Gener. Comput. 38(1): 1-3 (2020) - [c41]Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Yuki Ubukata:
Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model. LATIN 2020: 425-436 - [c40]Kohei Maruyama, Shinnosuke Seki:
Counting Infinitely by Oritatami Co-transcriptional Folding. SOFSEM 2020: 566-575
2010 – 2019
- 2019
- [j32]Yo-Sub Han, Hwee Kim, Trent A. Rogers, Shinnosuke Seki:
Self-Attraction Removal from Oritatami Systems. Int. J. Found. Comput. Sci. 30(6-7): 1047-1067 (2019) - [c39]Shinnosuke Seki:
Single-Stranded Architectures for Computing. DLT 2019: 41-56 - [c38]Szilárd Zsolt Fazekas, Kohei Maruyama, Reoto Morita, Shinnosuke Seki:
On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence. TAMC 2019: 188-207 - [c37]Yo-Sub Han, Hwee Kim, Yusei Masuda, Shinnosuke Seki:
A General Architecture of Oritatami Systems for Simulating Arbitrary Finite Automata. CIAA 2019: 146-157 - [e3]Ian McQuillan, Shinnosuke Seki:
Unconventional Computation and Natural Computation - 18th International Conference, UCNC 2019, Tokyo, Japan, June 3-7, 2019, Proceedings. Lecture Notes in Computer Science 11493, Springer 2019, ISBN 978-3-030-19310-2 [contents] - [i22]Yo-Sub Han, Hwee Kim, Yusei Masuda, Shinnosuke Seki:
A general architecture of oritatami systems for simulating arbitrary finite automata. CoRR abs/1904.10174 (2019) - 2018
- [j31]Yo-Sub Han, Hwee Kim, Makoto Ota, Shinnosuke Seki:
Nondeterministic seedless oritatami systems and hardness of testing their equivalence. Nat. Comput. 17(1): 67-79 (2018) - [c36]Erik D. Demaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, Hadley Thomas:
Know When to Fold 'Em: Self-assembly of Shapes by Folding in Oritatami. DNA 2018: 19-36 - [c35]Yo-Sub Han, Hwee Kim, Shinnosuke Seki:
Transcript Design Problem of Oritatami Systems. DNA 2018: 139-154 - [c34]Cody W. Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki:
Proving the Turing Universality of Oritatami Co-Transcriptional Folding. ISAAC 2018: 23:1-23:13 - [c33]Yusei Masuda, Shinnosuke Seki, Yuki Ubukata:
Towards the Algorithmic Molecular Self-assembly of Fractals by Cotranscriptional Folding. CIAA 2018: 261-273 - [e2]Mizuho Hoshi, Shinnosuke Seki:
Developments in Language Theory - 22nd International Conference, DLT 2018, Tokyo, Japan, September 10-14, 2018, Proceedings. Lecture Notes in Computer Science 11088, Springer 2018, ISBN 978-3-319-98653-1 [contents] - [i21]Erik D. Demaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, Hadley Thomas:
Know When to Fold 'Em: Self-Assembly of Shapes by Folding in Oritatami. CoRR abs/1807.04682 (2018) - 2017
- [j30]Lila Kari, Steffen Kopecki, Pierre-Étienne Meunier, Matthew J. Patitz, Shinnosuke Seki:
Binary Pattern Tile Set Synthesis Is NP-Hard. Algorithmica 78(1): 1-46 (2017) - [j29]Trent A. Rogers, Shinnosuke Seki:
Oritatami System; a Survey and the Impossibility of Simple Simulation at Small Delays. Fundam. Informaticae 154(1-4): 359-372 (2017) - [j28]Shinnosuke Seki, Andrew Winslow:
The Complexity of Fixed-Height Patterned Tile Self-Assembly. Int. J. Found. Comput. Sci. 28(5): 465-482 (2017) - [j27]Aleck C. Johnsen, Ming-Yang Kao, Shinnosuke Seki:
A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tileset synthesis. J. Comb. Optim. 33(2): 496-529 (2017) - [j26]Florin Manea, Mike Müller, Dirk Nowotka, Shinnosuke Seki:
The extended equation of Lyndon and Schützenberger. J. Comput. Syst. Sci. 85: 132-167 (2017) - [j25]Makoto Ota, Shinnosuke Seki:
Rule set design problems for oritatami systems. Theor. Comput. Sci. 671: 26-35 (2017) - [c32]Yo-Sub Han, Hwee Kim, Trent A. Rogers, Shinnosuke Seki:
Self-attraction Removal from Oritatami Systems. DCFS 2017: 164-176 - 2016
- [c31]Yo-Sub Han, Hwee Kim, Makoto Ota, Shinnosuke Seki:
Nondeterministic Seedless Oritatami Systems and Hardness of Testing Their Equivalence. DNA 2016: 19-34 - [c30]Cody W. Geary, Pierre-Etienne Meunier, Nicolas Schabanel, Shinnosuke Seki:
Programming Biomolecules That Fold Greedily During Transcription. MFCS 2016: 43:1-43:14 - [c29]Shinnosuke Seki, Andrew Winslow:
The Complexity of Fixed-Height Patterned Tile Self-assembly. CIAA 2016: 248-259 - [r1]Shinnosuke Seki:
Patterned Self-Assembly Tile Set Synthesis. Encyclopedia of Algorithms 2016: 1542-1545 - [i20]Shinnosuke Seki, Andrew Winslow:
The Complexity of Fixed-Height Patterned Tile Self-Assembly. CoRR abs/1604.07190 (2016) - 2015
- [j24]Ho-Lin Chen, David Doty, Shinnosuke Seki:
Program Size and Temperature in Self-Assembly. Algorithmica 72(3): 884-899 (2015) - [j23]Oscar H. Ibarra, Shinnosuke Seki:
Semilinear Sets and Counter Machines: a Brief Survey. Fundam. Informaticae 138(1-2): 61-76 (2015) - [j22]Lila Kari, Steffen Kopecki, Shinnosuke Seki:
3-color bounded patterned self-assembly. Nat. Comput. 14(2): 279-292 (2015) - [j21]Natasa Jonoska, Daria Karpenko, Shinnosuke Seki:
Dynamic Simulation of 1D Cellular Automata in the Active aTAM. New Gener. Comput. 33(3): 271-295 (2015) - [c28]Florin Manea, Shinnosuke Seki:
Square-Density Increasing Mappings. WORDS 2015: 160-169 - [c27]Lila Kari, Steffen Kopecki, Pierre-Étienne Meunier, Matthew J. Patitz, Shinnosuke Seki:
Binary Pattern Tile Set Synthesis Is NP-hard. ICALP (1) 2015: 1022-1034 - [i19]Cody W. Geary, Pierre-Étienne Meunier, Nicolas Schabanel, Shinnosuke Seki:
Efficient Universal Computation by Greedy Molecular Folding. CoRR abs/1508.00510 (2015) - 2014
- [c26]Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki:
Operational State Complexity under Parikh Equivalence. DCFS 2014: 294-305 - [c25]Florin Manea, Mike Müller, Dirk Nowotka, Shinnosuke Seki:
Generalised Lyndon-Schützenberger Equations. MFCS (1) 2014: 402-413 - [c24]Natasa Jonoska, Florin Manea, Shinnosuke Seki:
A Stronger Square Conjecture on Binary Words. SOFSEM 2014: 339-350 - [i18]Lila Kari, Steffen Kopecki, Pierre-Étienne Meunier, Matthew J. Patitz, Shinnosuke Seki:
Binary pattern tile set synthesis is NP-hard. CoRR abs/1404.0967 (2014) - [i17]Aleck C. Johnsen, Ming-Yang Kao, Shinnosuke Seki:
Computing Minimum Tile Sets to Self-Assemble Colors Patterns. CoRR abs/1404.2962 (2014) - [i16]Aleck C. Johnsen, Ming-Yang Kao, Shinnosuke Seki:
A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tile set synthesis. CoRR abs/1409.1619 (2014) - 2013
- [j20]Shinnosuke Seki, Yasushi Okuno:
On the Behavior of Tile Assembly System at High Temperatures. Comput. 2(2): 107-124 (2013) - [j19]Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki:
Converting nondeterministic automata and context-free grammars into Parikh equivalent one-way and two-way deterministic automata. Inf. Comput. 228: 1-15 (2013) - [j18]Szilárd Zsolt Fazekas, Hiro Ito, Yasushi Okuno, Shinnosuke Seki, Kei Taneishi:
On computational complexity of graph inference from counting. Nat. Comput. 12(4): 589-603 (2013) - [j17]Oscar H. Ibarra, Shinnosuke Seki:
On the open problem of Ginsburg concerning semilinear sets and related problems. Theor. Comput. Sci. 501: 11-19 (2013) - [j16]Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
The Power of Nondeterminism in Self-Assembly. Theory Comput. 9: 1-29 (2013) - [c23]Lila Kari, Steffen Kopecki, Shinnosuke Seki:
3-Color Bounded Patterned Self-assembly - (Extended Abstract). DNA 2013: 105-117 - [c22]Aleck C. Johnsen, Ming-Yang Kao, Shinnosuke Seki:
Computing Minimum Tile Sets to Self-Assemble Color Patterns. ISAAC 2013: 699-710 - [c21]Oscar H. Ibarra, Shinnosuke Seki:
On the Boundedness Property of Semilinear Sets. TAMC 2013: 156-168 - [c20]Shinnosuke Seki:
Combinatorial Optimization in Pattern Assembly - (Extended Abstract). UCNC 2013: 220-231 - [i15]Shinnosuke Seki:
Combinatorial Optimization in Pattern Assembly. CoRR abs/1301.3771 (2013) - [i14]Lila Kari, Steffen Kopecki, Shinnosuke Seki:
3-color Bounded Patterned Self-assembly. CoRR abs/1306.3257 (2013) - [i13]Rémi Lemoy, Alexander Mozeika, Shinnosuke Seki:
Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise. CoRR abs/1311.4388 (2013) - 2012
- [j15]Oscar H. Ibarra, Shinnosuke Seki:
Characterizations of Bounded semilinear Languages by One-Way and Two-Way Deterministic Machines. Int. J. Found. Comput. Sci. 23(6): 1291-1306 (2012) - [j14]Shinnosuke Seki:
Absoluteness of subword inequality is undecidable. Theor. Comput. Sci. 418: 116-120 (2012) - [j13]Ehsan Chiniforooshan, Mark Daley, Oscar H. Ibarra, Lila Kari, Shinnosuke Seki:
One-reversal counter machines and multihead automata: Revisited. Theor. Comput. Sci. 454: 81-87 (2012) - [c19]Lila Kari, Shinnosuke Seki, Zhi Xu:
Triangular and Hexagonal Tile Self-assembly Systems. Computation, Physics and Beyond 2012: 357-375 - [c18]Shinnosuke Seki, Yasushi Okuno:
On the Behavior of Tile Assembly System at High Temperatures. CiE 2012: 549-559 - [c17]Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki:
Converting Nondeterministic Automata and Context-Free Grammars into Parikh Equivalent Deterministic Automata. Developments in Language Theory 2012: 284-295 - [c16]Lila Kari, Steffen Kopecki, Shinnosuke Seki:
Iterated Hairpin Completions of Non-crossing Words. SOFSEM 2012: 337-348 - [p1]Lila Kari, Shinnosuke Seki, Petr Sosík:
DNA Computing - Foundations and Implications. Handbook of Natural Computing 2012: 1073-1127 - [i12]Shinnosuke Seki, Yasushi Okuno:
On the behavior of tile assembly system at high temperatures. CoRR abs/1211.4949 (2012) - [i11]Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki:
Converting Nondeterministic Automata and Context-Free Grammars into Parikh Equivalent One-Way and Two-Way Deterministic Automata. CoRR abs/1212.1346 (2012) - 2011
- [j12]Bo Cui, Lila Kari, Shinnosuke Seki:
K-Comma Codes and Their Generalizations. Fundam. Informaticae 107(1): 1-18 (2011) - [j11]Lila Kari, Shinnosuke Seki, Steffen Kopecki:
On the Regularity of Iterated Hairpin Completion of a Single Word. Fundam. Informaticae 110(1-4): 201-215 (2011) - [j10]Elena Czeizler, Eugen Czeizler, Lila Kari, Shinnosuke Seki:
An extension of the Lyndon-Schützenberger result to pseudoperiodic words. Inf. Comput. 209(4): 717-730 (2011) - [j9]Mark Daley, Lila Kari, Shinnosuke Seki, Petr Sosík:
Orthogonal Shuffle on Trajectories. Int. J. Found. Comput. Sci. 22(1): 213-222 (2011) - [j8]Lila Kari, Benoît Masson, Shinnosuke Seki:
Properties of Pseudo-Primitive Words and their Applications. Int. J. Found. Comput. Sci. 22(2): 447-471 (2011) - [j7]Lila Kari, Shinnosuke Seki:
Schema for Parallel Insertion and Deletion: Revisited. Int. J. Found. Comput. Sci. 22(7): 1655-1668 (2011) - [j6]Bo Cui, Lila Kari, Shinnosuke Seki:
Block insertion and deletion on trajectories. Theor. Comput. Sci. 412(8-10): 714-728 (2011) - [c15]Oscar H. Ibarra, Shinnosuke Seki:
Characterizations of Bounded Semilinear Languages by One-Way and Two-way Deterministic Machines. AFL 2011: 211-224 - [c14]Ho-Lin Chen, David Doty, Shinnosuke Seki:
Program Size and Temperature in Self-Assembly. ISAAC 2011: 445-453 - [c13]Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
The Power of Nondeterminism in Self-Assembly. SODA 2011: 590-602 - [c12]Ehsan Chiniforooshan, Mark Daley, Oscar H. Ibarra, Lila Kari, Shinnosuke Seki:
One-Reversal Counter Machines and Multihead Automata: Revisited. SOFSEM 2011: 166-177 - [i10]Lila Kari, Steffen Kopecki, Shinnosuke Seki:
On the regularity of iterated hairpin completion of a single word. CoRR abs/1104.2385 (2011) - [i9]Shinnosuke Seki:
Absoluteness of subword inequality is undecidable. CoRR abs/1108.2758 (2011) - [i8]Lila Kari, Steffen Kopecki, Shinnosuke Seki:
Iterated Hairpin Completions of Non-crossing Words. CoRR abs/1110.0760 (2011) - 2010
- [j5]Lila Kari, Shinnosuke Seki:
An Improved Bound for an Extension of Fine and Wilf's Theorem and Its Optimality. Fundam. Informaticae 101(3): 215-236 (2010) - [j4]Elena Czeizler, Lila Kari, Shinnosuke Seki:
On a special class of primitive words. Theor. Comput. Sci. 411(3): 617-630 (2010) - [c11]Lila Kari, Shinnosuke Seki:
Schema for Parallel Insertion and Deletion. Developments in Language Theory 2010: 267-278 - [c10]Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement. DNA 2010: 25-36 - [c9]Lila Kari, Shinnosuke Seki, Zhi Xu:
Triangular Tile Self-assembly Systems. DNA 2010: 89-99 - [e1]Yuan Gao, Hanlin Lu, Shinnosuke Seki, Sheng Yu:
Developments in Language Theory, 14th International Conference, DLT 2010, London, ON, Canada, August 17-20, 2010. Proceedings. Lecture Notes in Computer Science 6224, Springer 2010, ISBN 978-3-642-14454-7 [contents] - [i7]Lila Kari, Benoît Masson, Shinnosuke Seki:
Properties of Pseudo-Primitive Words and their Applications. CoRR abs/1002.4084 (2010) - [i6]Lila Kari, Shinnosuke Seki, Zhi Xu:
Triangular Self-Assembly. CoRR abs/1002.4996 (2010) - [i5]Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits using DNA Strand Displacement. CoRR abs/1003.3275 (2010) - [i4]Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
The Power of Nondeterminism in Self-Assembly. CoRR abs/1006.2897 (2010) - [i3]Ho-Lin Chen, David Doty, Shinnosuke Seki, David Soloveichik:
Parallelism, Program Size, Time, and Temperature in Self-Assembly. CoRR abs/1011.3493 (2010) - [i2]Nathaniel Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki:
The Power of Nondeterminism in Self-Assembly. Electron. Colloquium Comput. Complex. TR10 (2010) - [i1]Ho-Lin Chen, David Doty, Shinnosuke Seki, David Soloveichik:
Parallelism, Program Size, Time, and Temperature in Self-Assembly. Electron. Colloquium Comput. Complex. TR10 (2010)
2000 – 2009
- 2009
- [j3]Lila Kari, Shinnosuke Seki:
On pseudoknot-bordered words and their properties. J. Comput. Syst. Sci. 75(2): 113-121 (2009) - [j2]Lila Kari, Kalpana Mahalingam, Shinnosuke Seki:
Twin-roots of words and their properties. Theor. Comput. Sci. 410(24-25): 2393-2400 (2009) - [c8]Masami Ito, Lila Kari, Zachary Kincaid, Shinnosuke Seki:
Duplication in DNA Sequences. Algorithmic Bioprocesses 2009: 43-61 - [c7]Bo Cui, Lila Kari, Shinnosuke Seki:
On the Reversibility of Parallel Insertion, and Its Relation to Comma Codes. CAI 2009: 204-219 - [c6]Elena Czeizler, Eugen Czeizler, Lila Kari, Shinnosuke Seki:
An Extension of the Lyndon Schützenberger Result to Pseudoperiodic Words. Developments in Language Theory 2009: 183-194 - 2008
- [c5]Masami Ito, Lila Kari, Zachary Kincaid, Shinnosuke Seki:
Duplication in DNA Sequences. Developments in Language Theory 2008: 419-430 - [c4]Elena Czeizler, Lila Kari, Shinnosuke Seki:
On a Special Class of Primitive Words. MFCS 2008: 265-277 - 2007
- [c3]Lila Kari, Shinnosuke Seki:
Towards the Sequence Design Preventing Pseudoknot Formation. IWNC 2007: 101-110 - [c2]Shinnosuke Seki, Satoshi Kobayashi:
An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots. IWNC 2007: 179-188 - 2005
- [j1]Shinnosuke Seki, Satoshi Kobayashi:
A Grammatical Approach to the Alignment of Structure-Annotated Strings. IEICE Trans. Inf. Syst. 88-D(12): 2727-2737 (2005) - 2004
- [c1]Shinnosuke Seki, Satoshi Kobayashi:
Efficient Learning of k-Reversible Context-Free Grammars from Positive Structural Examples. ICGI 2004: 285-287
Coauthor Index
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