Publications
Here is a list of publications from our lab.For those by Seki, see his dblp.
Books
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Mizuho Hoshi and Shinnosuke Seki
Proceedings of the 22nd International Conference on Developments in Language Theory (DLT 2018, Tokyo, Japan, Sept. 10-14, 2018)
LNCS 11088, Springer, 2018.
Book chapters
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Shinnosuke Seki
Patterned Self-Assembly Tile Set Synthesis
Encyclopedia of Algorithms 2016, Springer, pp.1542-1545, 2016
Conferences
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Cody Geary, Pierre-Etienne Meunier, Nicolas Schabanel, and Shinnosuke Seki
Proving the Turing universality of oritatami co-transcriptional folding
ISAAC 2018: Proc. 28th International Symposium on Algorithms and Computation (Jiaoxi, Taiwan, Dec. 16-19, 2018), LIPIcs 123, pp. 23:1-23:13, 2018
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Erik D. Domaine, Jacob Hendricks, Meagan Olsen, Matthew J. Patitz, Trent A. Rogers, Nicolas Schabanel, Shinnosuke Seki, and Hadley Thomas
Know when to fold 'em: self-assembly of shapes by folding in oritatami
DNA 24: Proc. 24th International Conference on DNA Computing and Molecular Programming (Jinan, China, Oct. 8-12, 2018), LNCS 11145, pp. 19-36, 2018
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Yo-Sub Han, Hwee Kim, and Shinnosuke Seki
Transcription design problems of oritatami systems
DNA 24: Proc. 24th International Conference on DNA Computing and Molecular Programming (Jinan, China, Oct. 8-12, 2018), LNCS 11145, pp. 139-154, 2018
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Yusei Masuda, Shinnosuke Seki, and Yuki Ubukata
Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding
CIAA 2018: Proc. 23rd International Conference on Implementation and Applications of Automata (Charlottetown, Canada, July 30 - Aug. 2, 2018), LNCS 10977, 261-273, 2018
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Yo-Sub Han, Hwee Kim, Trent A. Rogers, and Shinnosuke Seki
Self-attraction removal from oritatami systems
DCFS 2017: Proc. 19th International Conference on Descriptional Complexity of Formal Systems (Milan, Italy, July 3-5, 2017), LNCS 10316, pp.164-176, 2017
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Yo-Sub Han, Hwee Kim, Makoto Ota, and Shinnosuke Seki
Nondeterministic seedless oritatami systems and hardness of their equivalence
DNA 22: Proc. 22nd International Conference on DNA Computing and Molecular Programming (Munich, Germany, Sept. 4-8, 2016), LNCS 9818, pp.19-34, 2016
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Cody Geary, Pierre-Etienne Meunier, Nicolas Schabanel, and Shinnosuke Seki
Programming biomolecules that fold greedily during transcription
MFCS 2016: Proc. 41st International Symposium on Mathematical Foundations of Computer Science (Krakow, Poland, Aug. 22-26, 2016), Leibniz International Proceedings in Informatics (LIPIcs), pp.43:1-43:14, 2016
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Shinnosuke Seki and Andrew Winslow
The complexity of fixed-height patterned tile self-assembly
CIAA 2016: Proc. 21st International Conference on Implementation and Application of Automata (Seoul, Republic of Korea, July 19-22, 2016), LNCS 9705, pp.248-259, 2016
arXiv, Presentation (PDF) -
Florin Manea and Shinnosuke Seki
Square-density increasing mappings
WORDS 2015: Proc. 10th International Conference on Combinatorics on Words (Kiel, Germany, Sept. 14-17, 2015), LNCS 9304, pp.160-169, 2015 -
Lila Kari, Steffen Kopecki, Pierre-Etienne Meunier, Matthew J. Patitz, and Shinnosuke Seki
Binary pattern tile set synthesis is NP-hard
ICALP 2015: Proc. 42nd International Colloquium on Automata, Languages, and Programming (Kyoto, Japan, July 6-10, 2015), LNCS 9134, pp.1022-1034, 2015
arXiv, Publisher's website
Journals
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Yo-Sub Han, Hwee Kim, Makoto Ota, and Shinnosuke Seki
Nondeterministic seedless oritatami systems and hardness of testing their equivalence
Natural Computing 17(1), pp.67-79, 2018 -
Shinnosuke Seki and Andrew Winslow
The complexity of fixed-height patterned tile self-assembly
International Journal of Foundations of Computer Science 28(5), pp. 465-482, 2017 -
Shinnosuke Seki
Cotranscriptional Folding: A Frontier in Molecular Engineering A challenge for computer scientists
SIAM News May 01, 2017
Publisher's website -
Trent A. Rogers and Shinnosuke Seki
Oritatami system: a survey and the impossibility of simple simulation at small delays
Fundamenta Informaticae 154(1-4), pp.359-372, 2017 -
Florin Manea, Mike Müller, Dirk Nowotka, and Shinnosuke Seki
The extended equation of Lyndon and Schützenberger
Journal of Computer and System Sciences 85, pp.132-167, 2017 -
Makoto Ota and Shinnosuke Seki
Rule set design problems for oritatami system
Theoretical Computer Science 671, pp.26-35, 2017
Publishder's website -
Lila Kari, Steffen Kopecki, Pierre-Etienne Meunier, Matthew J. Patitz, and Shinnosuke Seki
Binary pattern tile set synthesis is NP-hard
Algorithmica 78(1), pp.1-46, 2017
arXiv, Publisher's website -
Aleck Johnsen, Ming-Yang Kao, and Shinnosuke Seki
A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tile set synthesis
Journal of Combinatorial Optimization 33(2), pp.496-529, 2017
arXiv, Publisher's website