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

Book chapters

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


  1. 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
  2. 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
  3. 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
  4. 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)
  5. 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
  6. 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


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