Publications

Here is a list of publications from our lab.
For those by Seki, see his dblp.

Books

  1. 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

  1. Shinnosuke Seki
    Patterned Self-Assembly Tile Set Synthesis
    Encyclopedia of Algorithms 2016, Springer, pp.1542-1545, 2016

Conferences

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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)
  9. 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
  10. 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

  1. 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
  2. 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
  3. Shinnosuke Seki
    Cotranscriptional Folding: A Frontier in Molecular Engineering A challenge for computer scientists
    SIAM News May 01, 2017
    Publisher's website
  4. 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
  5. 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
  6. Makoto Ota and Shinnosuke Seki
    Rule set design problems for oritatami system
    Theoretical Computer Science 671, pp.26-35, 2017
    Publishder's website
  7. 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
  8. 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