Published papers
Number of published data : 68
No. Classification Refereed paper Title Authorship Author Journal Volume/issue/page Publication date ISSN DOI URL
1 Paper
Yes
Nondeterministic seedless oritatami systems and hardness of testing their equivalence
Joint
Yo-Sub Han, Hwee Kim, Makoto Ota, Shinnosuke Seki
Natural Computing
17/ 1, 67-79
2018



2 Paper
Yes
The complexity of fixed-height patterned tile self-assembly
Joint
Shinnosuke Seki, Andrew Winslow
International Journal of Foundations of Computer Science
28/ 5, 465-482
2017



3 Paper
Yes
Oritatami system: a survey and the impossibility of simple simulation at small delays
Joint
Trent A. Rogers, Shinnosuke Seki
Fundamenta Informaticae
154, Not assigned yet-
2017



4 Paper
Yes
The extended equation of Lyndon and Schutzenberger
Joint
Florin Manea, Mike Muller, Dirk Nowotka, Shinnosuke Seki
Journal of Computer and System Sciences
85, 132-167
2016/11/26



5 Paper
Yes
Rule set design problems for oritatami system
Joint
Makoto Ota and Shinnosuke Seki
Theoretical Computer Science
671, 26-35
2016/09/22



6 Paper
Yes
Binary pattern tile set synthesis is NP-hard
Joint
Lila Kari, Steffen Kopecki, Pierre-Etienne Meunier, Matthew J. Patitz, and Shinnosuke Seki
Algorithmica
78/ 1, 1-46
2016/04/26



7 Paper
Yes
Semilinear sets and counter machines: a brief survey
Joint
Oscar Ibarra, Shinnosuke Seki
Fundamenta Informaticae
138/ 1-2, 61-76
2015



8 Paper
Yes
A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tileset synthesis
Joint
Aleck Johnsen, Ming-Yang Kao, Shinnosuke Seki
Journal of Combinatorial Optimization
33/ 2, 496-529
2015/11/24



9 Paper
Yes
Dynamic simulation of 1D cellular automata in the Active aTAM
Joint
Natasa Jonoska, Daria Karpenko, Shinnosuke Seki
New Generation Computing
33/ 3, 271-295
2015/07/01



10 Paper
Yes
Program size and temperature in self-assembly
Joint
Ho-Lin Chen, David Doty, Shinnosuke Seki
Algorithmica
72/ 3, 884-899
2015/07/01



11 Paper
Yes
3-color bounded patterned self-assembly
Joint
Lila Kari, Steffen Kopecki, Shinnosuke Seki
Natural Computing
14/ 2, 279-292
2015/06/01



12 Paper
Yes
Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise
Joint
Remi Lemoy, Alexander Mozeika, Shinnosuke Seki
Journal of Physics A: Mathematical and Theoretical
47/ 10, 105001-105001
2014



13 Paper
Yes
On the open problem of Ginsburg concerning semilinear sets and related problems
Joint
Oscar H. Ibarra, Shinnosuke Seki
Theoretical Computer Science
501, 11-19
2013



14 Paper
Yes
Convering nondeterministic automata and context-free grammars into Parikh equivalent one-way and two-way deterministic automata
Joint
Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki
Information and Computation
228-229, 1-15
2013



15 Paper
Yes
On the behavior of tile assembly model at high temperatures
Joint
Shinnosuke Seki, Yasushi Okuno
Computability
2/ 2, 107-124
2013



16 Paper
Yes
The power of nondeterminism in self-assembly
Joint
Nathan Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
Theory of Computing
9, 1-29
2013



17 Paper
Yes
On computational complexity of graph inference from counting
Joint
Szilard Zholt Fazekas, Hiro Ito, Yasushi Okuno, Shinnosuke Seki, Kei Taneishi
Natural Computing
12/ 4, 589-603
2013



18 Paper
Yes
Characterizations of bounded semilinear languages by one-way and two-way deterministic machines
Joint
Oscar H. Ibarra, Shinnosuke Seki
International Journal of Foundations of Computer Science
23/ 6, 1291-1305
2012



19 Paper
Yes
One-reversal counter machines and multihead automata: revisited
Joint
Ehsan Chiniforooshan, Mark Daley, Oscar H. Ibarra, Lila Kari, Shinnosuke Seki
Theoretical Computer Science
454, 81-87
2012



20 Paper
Yes
Absoluteness of subowrd inequality is undecidable
Only
Shinnosuke Seki
Theoretical Computer Science
419, 116-120
2012



21 Paper
Yes
On the regularity of iterated hairpin completion of a single word
Joint
Lila Kari, Steffen Kopecki, Shinnosuke Seki
Fundamenta Informaticae
110/ 1-4, 201-215
2011



22 Paper
Yes
Schema for parallel insertion and deletion: revisited
Joint
Lila Kari, Shinnosuke Seki
International Journal of Foundations of Computer Science
22/ 7, 1655-1668
2011



23 Paper
Yes
An extension of Lyndon-Schutzenberger result to pseudoperiodic words
Joint
Elena Czeizler, Eugen Czeizler, Lila Kari, Shinnosuke Seki
Information and Computation
209, 717-730
2011



24 Paper
Yes
Properties of pseudo-primitive words and their applications
Joint
Benoit Masson, Lila Kari, Shinnosuke Seki
International Journal of Foundations of Computer Science
22/ 2, 447-471
2011



25 Paper
Yes
K-comma codes and their generalizations
Joint
Bo Cui, Lila Kari, Shinnosuke Seki
Fundamenta Informaticae
107, 1-18
2011



26 Paper
Yes
Orthogonal shuffle on trajectories
Joint
Mark Daley, Lila Kari, Shinnosuke Seki, Petr Sosik
International Journal of Foundations of Computer Science
22/ 1, 213-222
2011



27 Paper
Yes
Block insertion and deletion on trajectories
Joint
Bo Cui, Lila Kari, Shinnosuke Seki
Theoretical Computer Science
412/ 8-10, 714-728
2011



28 Paper
Yes
An improved bound for an extension of Fine and Wilf's theorem and its optimality
Joint
Lila Kari, Shinnosuke Seki
Fundamenta Informaticae
101/ 3, 215-236
2010



29 Paper
Yes
On a special class of primitive words
Joint
Elena Czeizler, Lila Kari, Shinnosuke Seki
Theoretical Computer Science
411, 617-630
2010



30 Paper
Yes
On pseudoknot-bordered words and their properties
Joint
Lila Kari, Shinnosuke Seki
Journal of Computer and System Sciences
75, 113-121
2009



31 Paper
Yes
Twin-roots of words and their properties
Joint
Lila Kari, Kalpana Mahalingam, Shinnosuke Seki
Theoretical Computer Science
410, 2393-2400
2009



32 Paper
Yes
A grammatical approach to the alignment of structure-annotated strings
Joint
Shinnosuke Seki, Satoshi Kobayashi
IEICE Transactions on Information and Systems
E88-D/ 12, 2727-2737
2005



33 Invited paper
Yes
Cotranscriptional folding: A frontier in molecular engineering a challenge for computer scientists
Only
Shinnosuke Seki
SIAM News
Not assigned yet
2017/05/01



34 International conference proceedings, etc.
Yes
Transcript design problem of oritatami systems
Joint
Yo-Sub Han, Hwee Kim, and Shinnosuke Seki
Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA 24)
LNCS/ 11145, 139-154
2018



35 International conference proceedings, etc.
Yes
Know when to fold 'em: Self-assembly of shapes by folding in oritatami
Joint
Erik Demaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, and Hadley Thoams
Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA 24)
LNCS/ 11145, 19-36
2018



36 International conference proceedings, etc.
Yes
Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding
Joint
Yusei Masuda, Shinnosuke Seki, and Yuki Ubukata
Proceedings of the 23rd International Conference on Implementation and Applications of Automata
LNCS/ 10977, 261-273
2018



37 International conference proceedings, etc.
Yes
Self-attraction removal from oritatami systems
Joint
Yo-Sub Han, Hwee Kim, Trent A. Rogers, and Shinnosuke Seki
Proc. 19th International Conference on Descriptional Complexity of Formal Systems (DCFS 2017)
LNCS 10316, 164-176
2017/06/26



38 International conference proceedings, etc.
Yes
Programming biomolecules that fold greedily during transcription
Joint
Cody Geary, Pierre-Etienne Meunier, Nicolas Schabanel, and Shinnosuke Seki
MFCS 2016: 41st International Symposium on Mathematical Foundations of Computer Science
LIPIcs 58, 43:1-43:14
2016/08/22



39 International conference proceedings, etc.
Yes
Nondeterministic seedless oritatami systems and hardness of testing their equivalence
Joint
Yo-Sub Han, Hwee Kim, Makoto Ota, Shinnosuke Seki
DNA22: 22nd International Conference on DNA Computing and Molecular Programming
LNCS 9818, 19-34
2016/08/17



40 International conference proceedings, etc.
Yes
The complexity of fixed-height patterned tile self-assembly
Joint
Shinnosuke Seki and Andrew Winslow
CIAA 2016: 21st International Conference on Implementation and Application of Automata
LNCS 9705, 248-259
2016/07/01



41 International conference proceedings, etc.
Yes
Binary pattern tile set synthesis is NP-hard
Joint
Lila Kari, Steffen Kopecki, Pierre-Etienne Meunier, Matthew J. Patitz, Shinnosuke Seki
ICALP 2015: Proceedings of the 42nd International Colloquium on Automata, Languages, and Programming
LNCS 9134, 1022-1034
2015



42 International conference proceedings, etc.
Yes
Square-density increasing mappings
Joint
Florin Manea and Shinnosuke Seki
Proc. 10th International Conference on Combinatorics on Words (WORDS 2015)
LNCS 9304, 160-169
2015/09/01



43 International conference proceedings, etc.
Yes
Generalized Lyndon-Schutzenberger equations
Joint
Florin Manea, Mike Muller, Dirk Nowotka, Shinnosuke Seki
MFCS 2014: Proceedings of the 39th International Symposium on Mathematical Foundations of Computer Science
LNCS 8634, 402-413
2014



44 International conference proceedings, etc.
Yes
Operational state complexity under Parikh equivalence
Joint
Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki
DCSF 2014: Proceedings of the 16th International Workshop on Descriptional Complexity of Formal Systems
LNCS 8614, 294-305
2014



45 International conference proceedings, etc.
Yes
Stronger square conjecture on binary words
Joint
Natasha Jonoska, Florin Manea, Shinnosuke Seki
SOFSEM 2014: Proceedings of the 40th International Conference on Current Trends in Theory and Practice of Computer Science
LNCS 8327, 339-350
2014



46 International conference proceedings, etc.
Yes
Computing minimum tile sets to self-assemble color patterns
Joint
Aleck Johnsen, Ming-Yang Kao, Shinnosuke Seki
ISAAC 2013: Proceedings of the 24th International Symposium on Algorithms and Computation
LNCS 8283, 699-710
2013



47 International conference proceedings, etc.
Yes
3-color bounded patterned self-assembly
Joint
Lila Kari, Steffen Kopecki, Shinnosuke Seki
DNA 19: Proceedings of the 19th International Conference on DNA Computing and Molecular Programming
LNCS 8141, 105-117
2013



48 International conference proceedings, etc.
Yes
Combinatorial optimization in pattern assembly (extended abstract)
Only
Shinnosuke Seki
UCNC 2013: Proceedings of the Unconventional Computation and Natural Computation - 12th International Conference
LNCS 7956, 220-231
2013



49 International conference proceedings, etc.
Yes
On the boundedness property of semilinear sets
Joint
Oscar H. Ibarra, Shinnosuke Seki
TAMC 2013: Proceedings of the 10th Annual Conference on Theory and Applications of Models of Computation
LNCS 7876, 156-168
2013



50 International conference proceedings, etc.
Yes
Converting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata
Joint
Giovanna J. Lavado, Giovanni Pighizzini, Shinnosuke Seki
DLT 2012: Proceedings of the 16th International Conference on Developments in Language Theory
LNCS 7410, 284-295
2012



51 International conference proceedings, etc.
Yes
On the behavior of tile assembly system at high temperatures
Joint
Shinnosuke Seki, Yasushi Okuno
CiE 2012: Proceedings of the Turing Centenary Conference - How the World Computes
LNCS 7318, 549-559
2012



52 International conference proceedings, etc.
Yes
Triangular and hexagonal tile self-assembly systems
Joint
Lila Kari, Shinnosuke Seki, Zhi Xu
WTCS 2012: Proceedings of the International Workshop on Theoretical Computer Science
LNCS 7160, 357-375
2012



53 International conference proceedings, etc.
Yes
Iterated hairpin completions of non-crossing words
Joint
Lila Kari, Steffen Kopecki, Shinnosuke Seki
SOFSEM 2012: Proceedings of the 38th International Conference on Current Trends in Theory and Practice of Computer Science
LNCS 7174, 337-348
2012



54 International conference proceedings, etc.
Yes
Program size and temperature in self-assembly
Joint
Ho-Lin Chen, David Doty, Shinnosuke Seki
ISAAC 2011: Proceedings of the 22nd International Symposium on Algorithms and Computation
LNCS 7074, 445-453
2011



55 International conference proceedings, etc.
Yes
Characterizations of bounded semilinear languages by one-way and two-way deterministic machines
Joint
Oscar H. Ibarra, Shinnosuke Seki
AFL 2011: Proceedings of the 13th International Conference on Automata and Formal Languages
211-224
2011



56 International conference proceedings, etc.
Yes
One-reversal counter machines and multihead automata: revisited
Joint
Ehsan Chiniforooshan, Mark Daley, Oscar H. Ibarra, Lila Kari, Shinnosuke Seki
SOFSEM 2011: Proceedings of the 37th International Conference on Current Trends in Theory and Practice of Computer Science
LNCS 6543, 166-177
2011



57 International conference proceedings, etc.
Yes
The power of nondeterminism in self-assembly
Joint
Nathan Bryans, Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
SODA 2011: Proceedings of ACM-SIAM Symposium on Discrete Algorithms
590-602
2011



58 International conference proceedings, etc.
Yes
Schema for parallel insertion and deletion
Joint
Lila Kari, Shinnosuke Seki
DLT 2010: Proceedings of the 14th International Conference on Developments in Language Theory
LNCS 6224, 267-278
2010



59 International conference proceedings, etc.
Yes
Time-responsive, digital, energy-efficient, molecular circuits using DNA strand displacement
Joint
Ehsan Chiniforooshan, David Doty, Lila Kari, Shinnosuke Seki
DNA 16: Proceedings of the 16th International Conference on DNA Computing and Molecular Programming
LNCS 6518, 25-36
2010



60 International conference proceedings, etc.
Yes
Triangular tile self-assembly systems
Joint
Lila Kari, Shinnosuke Seki, Zhi Xu
DNA 16: Proceedings of the 16th International Conference on DNA Computing and Molecular Programming
LNCS 6518, 89-99
2010



61 International conference proceedings, etc.
Yes
An extension of the Lyndon-Schutzenberger result to pseudoperiodic words
Joint
Elena Czeizler, Eugen Czeizler, Lila Kari, Shinnosuke Seki
DLT 2009: Proceedings of the 13th International Conference on Developments in Language Theory
LNCS 5583, 183-194
2009



62 International conference proceedings, etc.
Yes
On the reversibility of parallel insertion, and its relation to comma codes
Joint
Bo Cui, Lila Kari, Shinnosuke Seki
CAI 2009: Proceedings of the 3rd International Conference on Algebraic Informatics
LNCS 5725, 204-219
2009



63 International conference proceedings, etc.
Yes
Duplication in DNA sequences
Joint
Masami Ito, Lila Kari, Zachary Kincaid, Shinnosuke Seki
DLT 2008: Proceedings of the 12th International Conference on Developments in Language Theory
LNCS 5257, 419-430
2008



64 International conference proceedings, etc.
Yes
On a special class of primitive words
Joint
Elena Czeizler, Lila Kari, Shinnosuke Seki
MFCS 2008: Proceedings of the Mathematical Foundations of Computer Science
LNCS 5162, 265-277
2008



65 International conference proceedings, etc.
Yes
Towards the sequence desing preventing pseudoknot formation
Joint
Lila Kari, Shinnosuke Seki
IWNC 2007: Proceedings of the 2nd International Workshop on Natural Computing
PICT 1, 101-110
2007



66 International conference proceedings, etc.
Yes
An efficient multiple alignment method for RNA secondary structures including pseudoknots
Joint
Shinnosuke Seki, Satoshi Kobayashi
IWNC 2007: Proceedings of the 2nd International Workshop on Natural Computing
PICT 1, 179-188
2007



67 International conference proceedings, etc.
Yes
Hierarchical Alignment of RNA secondary structures including pseudoknots
Joint
Shinnosuke Seki, Atsushi Kijima, Satoshi Kobayashi, Genichi Sanpei
GIW 2004: Proceedings of the 15th International Conference on Genome Informatics
117-1-117-2
2004



68 International conference proceedings, etc.
Yes
Efficient learning of k-reversible context-free grammars from positive structural examples
Joint
Shinnosuke Seki, Satoshi Kobayashi
ICGI 2004: Proceedings of the 7th International Colloquium on Grammatical Inference
LNAI 3264, 285-287
2004