Published papers
Number of published data : 66
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
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, N/A-N/A
2018



35 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



36 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



37 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



38 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



39 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



40 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



41 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



42 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



43 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



44 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



45 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



46 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



47 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



48 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



49 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



50 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



51 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



52 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



53 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



54 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



55 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



56 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



57 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



58 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



59 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



60 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



61 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



62 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



63 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



64 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



65 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



66 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