Shinnosuke SEKI

Department of Computer and Network EngineeringAssociate Professor
Cluster I (Informatics and Computer Engineering)Associate Professor

Degree

  • 博士(理学)
  • Ph.D. (Computer Science), University of Western Ontario

Research Keyword

  • Theory of self-assembly

Field Of Study

  • Informatics, Computational science
  • Nanotechnology/Materials, Nano/micro-systems
  • Informatics, Information theory

Career

  • Sep. 2018 - Present
    Ecole Normale Superieure de Lyon, Invited Professor, France
  • Sep. 2013 - Mar. 2015
    Academy of Finland, Postdoctoral Researcher, Principal Investigator, Finland
  • Feb. 2012 - Aug. 2013
    Aalto University, Department of Information and Computer Science, Postdoctoral Researcher, Finland
  • 01 May 2011 - 15 Feb. 2012
    Kyoto University, 薬学研究科, 博士研究員
  • Sep. 2010 - Apr. 2011
    University of Western Ontario, Department of Computer Science, Postdoctoral Researcher, Canada

Educational Background

  • 01 Sep. 2006 - 31 Aug. 2010
    The University of Western Ontario, Department of Computer Science, Canada
  • 01 Apr. 2004 - 31 Mar. 2006
    The University of Electro-Communications, 情報工学専攻

Member History

  • Feb. 2024 - Present
    Member, Program Committee of the IEEE 3rd Conference on Information Technology and Data Science (CITDS 2024)
  • Nov. 2023 - Present
    Member, Program Committee of the 26th International Conference on Descriptional Complexity of Formal Systems (DCFS 2024), Society
  • Sep. 2023 - Present
    Co-chair, Program Committee of the 30th International Conference on DNA Computing and Molecular Programming (DNA30), Society
  • Aug. 2023 - Present
    Member, Organizing Committee of the 28th International Conference on Implementation and Application of Automata (CIAA 2024), Society
  • Jul. 2023 - Present
    Member, Organizing Committee of the 21st International Conference on Unconventional Computation and Natural Computation (UCNC 2024), Society
  • Sep. 2022 - Present
    Member, Steering Committee of the International Conference on Machines, Computations, and Universality (MCU), Society
  • Oct. 2021 - Present
    Co-chair, Steering Committee of the International Conference on Unconventional Computation and Natural Computation (UCNC), Co-chair
  • Sep. 2019 - Present
    Area Editor, New Generation Computing, Editorial Board, Society
  • Apr. 2018 - Present
    Advisory Board, Springer Natural Computing Book-Series, Society
  • Aug. 2017 - Present
    Member, Steering Committee of International Conference on Developments in Language Theory (DLT), Society
  • Sep. 2022 - Sep. 2023
    Member, Program Committee of the 29th International Conference on DNA Computing and Molecular Programming (DNA29), Society
  • Sep. 2022 - Sep. 2023
    Member, Program Committee of the 27th International Conference on Implementation and Application of Automata (CIAA2023), Society
  • Jul. 2022 - Jul. 2023
    Member, Program Committee of the 25th International Conference on Descriptional Complexity of Formal Systems (DCFS 2023), Society
  • Apr. 2022 - Jul. 2023
    Member, Program Committee of the 19th Conference on Computability in Europe (CiE2023), Society
  • 01 Apr. 2018
    専門委員, 情報処理学会アルゴリズム研究会
  • 01 Apr. 2018
    関 新之助, 情報処理学会アルゴリズム研究会
  • 01 Oct. 2014
    関 新之助, 情報処理学会論文誌「数理モデル化と応用」編集委員会, Society

Award

  • Feb. 2018
    European Association for Theoretical Computer Science (EATCS)
    LA/EATCS Best Presentation Award
    International society
  • Jul. 2016
    CIAA 2016 Best Paper Award (Sheng Yu Award), Shinnosuke Seki;Andrew Winslow
    International society

Paper

  • Towards composable computations by RNA co-transcriptional folding: A proof-of-concept demonstration of nested loops in oritatami
    Szilárd Zsolt Fazekas; Naoya Iwano; Yu Kihara; Ryuichi Matsuoka; Shinnosuke Seki; Hinano Takeuchi
    Corresponding, Theoretical Computer Science, Elsevier BV, 999, 114550-114550, Jun. 2024, Peer-reviwed, Invited
    Scientific journal, English
  • Programmable single-stranded architectures for computing.
    Yu Kihara; Shinnosuke Seki
    Corresponding, Natural Computing, 22, 3, 563-585, Sep. 2023, Peer-reviwed, Invited
    Scientific journal, English
  • Freezing 1-tag systems with states
    Szilard Zsolt Fazekas; Shinnosuke Seki
    Corresponding, Electronic Proceedings in Theoretical Computer Science (EPTCS), Proceedings of the 16th International Conference on Automata and Formal Languages (AFL 2023), 386, 82-95, Sep. 2023, Peer-reviwed
    International conference proceedings, English
  • Ok: A kinetic model for locally reconfigurable molecular systems
    Pierre Marcus; Nicolas Schabanel; Shinnosuke Seki
    Corresponding, Visions of DNA Nanotechnology at 40 for the Next 40, 229-240, May 2023, Peer-reviwed, Invited
    Scientific journal, English
  • On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding.
    Szilárd Zsolt Fazekas; Hwee Kim; Ryuichi Matsuoka; Shinnosuke Seki; Hinano Takeuchi
    Proc. ISAAC2022, LIPIcs 248, 37:1-37:15, Dec. 2022, Peer-reviwed
    International conference proceedings, English
  • Oritatami systems assemble shapes no less complex than tile assembly model (aTAM)
    Daria Pchelina; Nicolas Schabanel; Shinnosuke Seki; Guillaume Theyssier
    Proceedings of the 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022), LIPIcs 219, 51:1-51:23, 09 Mar. 2022, Peer-reviwed
    International conference proceedings, English
  • Square network on a word
    Szilard Zsolt Fazekas; Shinnosuke Seki
    Theoretical Computer Science, Elsevier, 894, 26, 121-134, Nov. 2021, Peer-reviwed
    Scientific journal, English
  • Simple intrinsic simulation of cellular automata in oritatami molecular folding model
    Daria Pchelina; Nicolas Schabanel; Shinnosuke Seki; Yuki Ubukata
    Proceedings of the 14th Latin American Theoretical Informatics Symposium (LATIN 2020), Springer, LNCS 12118, 425-436, 05 Jan. 2021, Peer-reviwed
    International conference proceedings, English
  • Linear bounds on the size of the conformations in greedy deterministic oritatami
    Szilard Zsolt Fazekas; Hwee Kim; Ryuichi Matsuoka; Reoto Morita; Shinnosuke Seki
    International Journal of Foundations of Computer Science, World Scientific Publishing Company, 32, 5, 575-596, 2021, Peer-reviwed
    Scientific journal, English
  • A general architecture of oritatami systems for simulating arbitrary finite automata
    Yo-Sub Han; Hwee Kim; Yusei Masuda; Shinnosuke Seki
    Theoretical Computer Science, Springer, 870, 16, 29-52, 2021, Peer-reviwed
    Scientific journal, English
  • Counting infinitely by oritatami co-transcriptional folding
    Kohei Maruyama; Shinnosuke Seki
    Natural Computing, Springer, 20, 2, 329-340, 2021, Peer-reviwed
    Scientific journal, English
  • Transcript design problem of oritatami systems
    Yo-Sub Han; Hwee Kim; Shinnosuke Seki
    Natural Computing, Springer, 19, 2, 323-335, 2020, Peer-reviwed
    Scientific journal, English
  • Renewal of the major fields of New Generation Computing Vol. 38
    Masayuki Numao; Yutaka Matsuo; Shinnosuke Seki
    New Generation Computing, 38, 1, 1-3, 2020, Peer-reviwed
    Scientific journal, English
  • A General Architecture of Oritatami Systems for Simulating Arbitrary Finite Automata
    Yo-Sub Han; Hwee Kim; Yusei Masuda; Shinnosuke Seki
    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Verlag, 11601, 146-157, 2019
    International conference proceedings, English
  • Self-attraction removal from oritatami systems
    Yo-Sub Han; Hwee Kim; Trent A. Rogers; Shinnosuke Seki
    International Journal of Foundations of Computer Science, 30, 6-7, 1047-1067, 2019, Peer-reviwed
    Scientific journal, English
  • On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence.
    Szilárd Zsolt Fazekas; Kohei Maruyama; Reoto Morita; Shinnosuke Seki
    Proceedings of the 15th International Conference on Theory and Applications of Models of Computation (TAMC 2019), Springer, LNCS 11436, 188-207, 2019, Peer-reviwed
    International conference proceedings, English
  • Oritatami: a computational model for molecular co-transcriptional folding
    Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki
    International Journal of Molecular Sciences, MDPI, 20, 9, 2259, 2019, Peer-reviwed
    Scientific journal, English
  • Single-stranded architectures for computing
    Shinnosuke Seki
    Proceedings of the 23rd International Conference on Developments in Language Theory (DLT 2019), Springer, LNCS 11647, 41-56, 2019, Peer-reviwed, Invited
    International conference proceedings, English
  • Nondeterministic seedless oritatami systems and hardness of testing their equivalence
    Yo-Sub Han; Hwee Kim; Makoto Ota; Shinnosuke Seki
    Natural Computing, Springer, 17, 1, 67-79, 2018, Peer-reviwed
    Scientific journal, English
  • Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding
    Yusei Masuda; Shinnosuke Seki; Yuki Ubukata
    Proceedings of the 23rd International Conference on Implementation and Applications of Automata (CIAA2018), Springer, LNCS, 10977, 261-273, 2018, Peer-reviwed
    International conference proceedings, English
  • Know when to fold 'em: Self-assembly of shapes by folding in oritatami
    Erik Demaine; Jacob Hendricks; Meagan Olsen; Matthew J. Patitz; Trent A. Rogers; Nicolas Schabanel; Shinnosuke Seki; Hadley Thoams
    Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA 24), Springer, LNCS, 11145, 19-36, 2018, Peer-reviwed
    International conference proceedings, English
  • Transcript design problem of oritatami systems
    Yo-Sub Han; Hwee Kim; Shinnosuke Seki
    Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA 24), Springer, LNCS, 11145, 139-154, 2018, Peer-reviwed
    International conference proceedings, English
  • Proving the Turing universality of oritatami co-transcriptional folding
    Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki
    Proceedings of the 29th International Symposium on Algorithms and Computation (ISAAC2018), Schloss Dagstuhl, LIPIcs 123, 23:1-23:13, 2018, Peer-reviwed
    International conference proceedings, English
  • The Complexity of Fixed-Height Patterned Tile Self-Assembly
    Shinnosuke Seki; Andrew Winslow
    INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, 28, 5, 465-482, Aug. 2017, Peer-reviwed
    Scientific journal, English
  • Oritatami System; a Survey and the Impossibility of Simple Simulation at Small Delays
    Trent A. Rogers; Shinnosuke Seki
    FUNDAMENTA INFORMATICAE, 154, 1-4, 359-372, 2017, Peer-reviwed
    Scientific journal, English
  • Self-attraction removal from oritatami systems
    Yo-Sub Han; Hwee Kim; Trent A. Rogers; Shinnosuke Seki
    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Verlag, 10316, 164-176, 2017, Peer-reviwed
    International conference proceedings, English
  • The extended equation of Lyndon and Schutzenberger
    Florin Manea; Mike Muller; Dirk Nowotka; Shinnosuke Seki
    Journal of Computer and System Sciences, Elsevier, 85, 132-167, 26 Nov. 2016, Peer-reviwed
    Scientific journal, English
  • Rule set design problems for oritatami system
    Makoto Ota; Shinnosuke Seki
    Theoretical Computer Science, Elsevier, 671, 26-35, 22 Sep. 2016, Peer-reviwed
    Scientific journal, English
  • Programming biomolecules that fold greedily during transcription
    Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki
    MFCS 2016: 41st International Symposium on Mathematical Foundations of Computer Science, LIPIcs 58, 43:1-43:14, 22 Aug. 2016, Peer-reviwed
    International conference proceedings, English
  • Binary pattern tile set synthesis is NP-hard
    Lila Kari; Steffen Kopecki; Pierre-Etienne Meunier; Matthew J. Patitz; Shinnosuke Seki
    Algorithmica, Springer, 78, 1, 1-46, 26 Apr. 2016, Peer-reviwed
    Scientific journal, English
  • The Complexity of Fixed-Height Patterned Tile Self-assembly
    Shinnosuke Seki; Andrew Winslow
    Implementation and Application of Automata, 9705, LNCS 9705, 248-259, 2016, Peer-reviwed
    International conference proceedings, English
  • Nondeterministic seedless oritatami systems and hardness of testing their equivalence
    Yo-Sub Han; Hwee Kim; Makoto Ota; Shinnosuke Seki
    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Verlag, 9818, 19-34, 2016, Peer-reviwed
    International conference proceedings, English
  • A manually-checkable proof for the NP-hardness of 11-color pattern self-assembly tileset synthesis
    Aleck Johnsen; Ming-Yang Kao; Shinnosuke Seki
    Journal of Combinatorial Optimization, Springer, 33, 2, 496-529, 24 Nov. 2015, Peer-reviwed
    Scientific journal, English
  • Program Size and Temperature in Self-Assembly
    Ho-Lin Chen; David Doty; Shinnosuke Seki
    ALGORITHMICA, 72, 3, 884-899, Jul. 2015, Peer-reviwed
    Scientific journal, English
  • Dynamic Simulation of 1D Cellular Automata in the Active aTAM
    Natasa Jonoska; Daria Karpenko; Shinnosuke Seki
    NEW GENERATION COMPUTING, 33, 3, 271-295, Jul. 2015, Peer-reviwed
    Scientific journal, English
  • 3-color bounded patterned self-assembly
    Lila Kari; Steffen Kopecki; Shinnosuke Seki
    NATURAL COMPUTING, 14, 2, 279-292, Jun. 2015, Peer-reviwed
    Scientific journal, English
  • Computational complexity of inverse word search problem
    Hiro Ito; Shinnosuke Seki
    IET Conference Publications, Institution of Engineering and Technology, 2015, 673, 41-44, 2015
    International conference proceedings, English
  • Square-Density Increasing Mappings
    Florin Manea; Shinnosuke Seki
    COMBINATORICS ON WORDS, WORDS 2015, 9304, 160-169, 2015, Peer-reviwed
    International conference proceedings, English
  • Semilinear Sets and Counter Machines: a Brief Survey
    Oscar H. Ibarra; Shinnosuke Seki
    FUNDAMENTA INFORMATICAE, 138, 1-2, 61-76, 2015, Peer-reviwed
    Scientific journal, English
  • Binary Pattern Tile Set Synthesis Is NP-hard
    Lila Kari; Steffen Kopecki; Pierre-Etienne Meunier; Matthew J. Patitz; Shinnosuke Seki
    Automata, Languages, and Programming, Pt I, 9134, 1022-1034, 2015, Peer-reviwed
    International conference proceedings, English
  • Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise
    Remi Lemoy; Alexander Mozeika; Shinnosuke Seki
    JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, 47, 10, 105001-105001, Mar. 2014, Peer-reviwed
    Scientific journal, English
  • A Stronger Square Conjecture on Binary Words
    Natasa Jonoska; Florin Manea; Shinnosuke Seki
    SOFSEM 2014: THEORY AND PRACTICE OF COMPUTER SCIENCE, 8327, 339-350, 2014, Peer-reviwed
    International conference proceedings, English
  • Operational State Complexity under Parikh Equivalence
    Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki
    DESCRIPTIONAL COMPLEXITY OF FORMAL SYSTEMS, DCFS 2014, 8614, 294-305, 2014, Peer-reviwed
    International conference proceedings, English
  • Generalised Lyndon-Schutzenberger Equations
    Florin Manea; Mike Mueller; Dirk Nowotka; Shinnosuke Seki
    MATHEMATICAL FOUNDATIONS OF COMPUTER SCIENCE 2014, PT I, 8634, 402-+, 2014, Peer-reviwed
    International conference proceedings, English
  • On computational complexity of graph inference from counting
    Szilárd Zsolt Fazekas; Hiro Ito; Yasushi Okuno; Shinnosuke Seki; Kei Taneishi
    Natural Computing, Springer, 12, 4, 589-603, Dec. 2013, Peer-reviwed
    Scientific journal, English
  • On the open problem of Ginsburg concerning semilinear sets and related problems
    Oscar H. Ibarra; Shinnosuke Seki
    THEORETICAL COMPUTER SCIENCE, 501, 11-19, Aug. 2013, Peer-reviwed
    Scientific journal, English
  • The power of nondeterminism in self-assembly
    Nathan Bryans; Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki
    Theory of Computing, 9, 1-29, 2013, Peer-reviwed
    Scientific journal, English
  • On the behavior of tile assembly system at high temperatures
    Shinnosuke Seki; Yasushi Okuno
    Computability, IOS Press, 2, 2, 107-124, 2013, Peer-reviwed
    Scientific journal, English
  • Convering nondeterministic automata and context-free grammars into Parikh equivalent one-way and two-way deterministic automata
    Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki
    Information and Computation, Elsevier, 228-229, 1-15, 2013, Peer-reviwed
    Scientific journal, English
  • On the boundedness property of semilinear sets
    Oscar H. Ibarra; Shinnosuke Seki
    TAMC 2013: Proceedings of the 10th Annual Conference on Theory and Applications of Models of Computation, Springer, LNCS 7876, 156-168, 2013, Peer-reviwed
    International conference proceedings, English
  • Combinatorial optimization in pattern assembly (extended abstract)
    Shinnosuke Seki
    UCNC 2013: Proceedings of the Unconventional Computation and Natural Computation - 12th International Conference, Springer, LNCS 7956, 220-231, 2013, Peer-reviwed
    International conference proceedings, English
  • 3-Color Bounded Patterned Self-assemblyY
    Lila Kari; Steffen Kopecki; Shinnosuke Seki
    DNA COMPUTING AND MOLECULAR PROGRAMMING, DNA 2013, 8141, 105-117, 2013, Peer-reviwed
    International conference proceedings, English
  • Computing Minimum Tile Sets to Self-Assemble Color Patterns
    Aleck C. Johnsen; Ming-Yang Kao; Shinnosuke Seki
    ALGORITHMS AND COMPUTATION, 8283, 699-710, 2013, Peer-reviwed
    International conference proceedings, English
  • One-reversal counter machines and multihead automata: Revisited
    Ehsan Chiniforooshan; Mark Daley; Oscar H. Ibarra; Lila Kari; Shinnosuke Seki
    THEORETICAL COMPUTER SCIENCE, 454, 81-87, Oct. 2012, Peer-reviwed
    Scientific journal, English
  • CHARACTERIZATIONS OF BOUNDED SEMILINEAR LANGUAGES BY ONE-WAY AND TWO-WAY DETERMINISTIC MACHINES
    Oscar H. Ibarra; Shinnosuke Seki
    INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, 23, 6, 1291-1305, Sep. 2012, Peer-reviwed
    Scientific journal, English
  • Absoluteness of subword inequality is undecidable
    Shinnosuke Seki
    THEORETICAL COMPUTER SCIENCE, 418, 116-120, Feb. 2012, Peer-reviwed
    Scientific journal, English
  • Iterated Hairpin Completions of Non-crossing Words
    Lila Kari; Steffen Kopecki; Shinnosuke Seki
    SOFSEM 2012: THEORY AND PRACTICE OF COMPUTER SCIENCE, 7147, 337-+, 2012, Peer-reviwed
    International conference proceedings, English
  • Triangular and hexagonal tile self-assembly systems
    Lila Kari; Shinnosuke Seki; Zhi Xu
    WTCS 2012: Proceedings of the International Workshop on Theoretical Computer Science, Springer, LNCS 7160, 357-375, 2012, Peer-reviwed
    International conference proceedings, English
  • On the behavior of tile assembly system at high temperatures
    Shinnosuke Seki; Yasushi Okuno
    CiE 2012: Proceedings of the Turing Centenary Conference - How the World Computes, LNCS 7318, 549-559, 2012, Peer-reviwed
    International conference proceedings, English
  • Converting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata
    Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki
    DLT 2012: Proceedings of the 16th International Conference on Developments in Language Theory, Springer, LNCS 7410, 284-295, 2012, Peer-reviwed
    International conference proceedings, English
  • SCHEMA FOR PARALLEL INSERTION AND DELETION: REVISITED
    Lila Kari; Shinnosuke Seki
    INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, 22, 7, 1655-1668, Nov. 2011, Peer-reviwed
    Scientific journal, English
  • An extension of the Lyndon-Schutzenberger result to pseudoperiodic words
    Elena Czeizler; Eugen Czeizler; Lila Kari; Shinnosuke Seki
    INFORMATION AND COMPUTATION, 209, 4, 717-730, Apr. 2011, Peer-reviwed
    Scientific journal, English
  • Block insertion and deletion on trajectories
    Bo Cui; Lila Kari; Shinnosuke Seki
    THEORETICAL COMPUTER SCIENCE, 412, 8-10, 714-728, Mar. 2011, Peer-reviwed
    Scientific journal, English
  • PROPERTIES OF PSEUDO-PRIMITIVE WORDS AND THEIR APPLICATIONS
    Lila Kari; Benoit Masson; Shinnosuke Seki
    INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, 22, 2, 447-471, Feb. 2011, Peer-reviwed
    Scientific journal, English
  • Triangular Tile Self-assembly Systems
    Lila Kari; Shinnosuke Seki; Zhi Xu
    DNA COMPUTING AND MOLECULAR PROGRAMMING, 6518, 89-99, 2011, Peer-reviwed
    International conference proceedings, English
  • Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement
    Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki
    DNA COMPUTING AND MOLECULAR PROGRAMMING, 6518, 25-36, 2011, Peer-reviwed
    International conference proceedings, English
  • ORTHOGONAL SHUFFLE ON TRAJECTORIES
    Mark Daley; Lila Kari; Shinnosuke Seki; Petr Sosik
    INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, 22, 1, 213-222, Jan. 2011, Peer-reviwed
    Scientific journal, English
  • K-Comma Codes and Their Generalizations
    Bo Cui; Lila Kari; Shinnosuke Seki
    FUNDAMENTA INFORMATICAE, 107, 1, 1-18, 2011, Peer-reviwed
    Scientific journal, English
  • On the Regularity of Iterated Hairpin Completion of a Single Word
    Lila Kari; Shinnosuke Seki; Steffen Kopecki
    FUNDAMENTA INFORMATICAE, 110, 1-4, 201-215, 2011, Peer-reviwed
    Scientific journal, English
  • The Power of Nondeterminism in Self-Assembly
    Nathaniel Bryans; Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki
    PROCEEDINGS OF THE TWENTY-SECOND ANNUAL ACM-SIAM SYMPOSIUM ON DISCRETE ALGORITHMS, 590-602, 2011, Peer-reviwed
    International conference proceedings, English
  • One-Reversal Counter Machines and Multihead Automata: Revisited
    Ehsan Chiniforooshan; Mark Daley; Oscar H. Ibarra; Lila Kari; Shinnosuke Seki
    SOFSEM 2011: THEORY AND PRACTICE OF COMPUTER SCIENCE, 6543, 166-177, 2011, Peer-reviwed
    International conference proceedings, English
  • Characterizations of bounded semilinear languages by one-way and two-way deterministic machines
    Oscar H. Ibarra; Shinnosuke Seki
    AFL 2011: Proceedings of the 13th International Conference on Automata and Formal Languages, 211-224, 2011, Peer-reviwed
    International conference proceedings, English
  • Program Size and Temperature in Self-assembly
    Ho-Lin Chen; David Doty; Shinnosuke Seki
    ALGORITHMS AND COMPUTATION, 7074, 445-+, 2011, Peer-reviwed
    International conference proceedings, English
  • On a special class of primitive words
    Elena Czeizler; Lila Kari; Shinnosuke Seki
    THEORETICAL COMPUTER SCIENCE, 411, 3, 617-630, Jan. 2010, Peer-reviwed
    Scientific journal, English
  • An Improved Bound for an Extension of Fine and Wilf's Theorem and Its Optimality
    Lila Kari; Shinnosuke Seki
    FUNDAMENTA INFORMATICAE, 101, 3, 215-236, 2010, Peer-reviwed
    Scientific journal, English
  • Schema for Parallel Insertion and Deletion
    Lila Kari; Shinnosuke Seki
    DEVELOPMENTS IN LANGUAGE THEORY, 6224, 267-278, 2010, Peer-reviwed
    International conference proceedings, English
  • Twin-roots of words and their properties
    Lila Kari; Kalpana Mahalingam; Shinnosuke Seki
    THEORETICAL COMPUTER SCIENCE, 410, 24-25, 2393-2400, May 2009, Peer-reviwed
    Scientific journal, English
  • On pseudoknot-bordered words and their properties
    Lila Kari; Shinnosuke Seki
    JOURNAL OF COMPUTER AND SYSTEM SCIENCES, 75, 2, 113-121, Feb. 2009, Peer-reviwed
    Scientific journal, English
  • An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots
    Shinnosuke Seki; Satoshi Kobayashi
    NATURAL COMPUTING, PROCEEDINGS, 1, 179-+, 2009, Peer-reviwed
    International conference proceedings, English
  • Towards the Sequence Design Preventing Pseudoknot Formation
    Lila Kari; Shinnosuke Seki
    NATURAL COMPUTING, PROCEEDINGS, 1, 101-110, 2009, Peer-reviwed
    International conference proceedings, English
  • Duplication in DNA Sequences
    Masami Ito; Lila Kari; Zachary Kincaid; Shinnosuke Seki
    ALGORITHMIC BIOPROCESSES, LNCS 5257, 43-+, 2009, Peer-reviwed
    International conference proceedings, English
  • On the Reversibility of Parallel Insertion, and Its Relation to Comma Codes
    Bo Cui; Lila Kari; Shinnosuke Seki
    ALGEBRAIC INFORMATICS, 5725, 204-219, 2009, Peer-reviwed
    International conference proceedings, English
  • An Extension of the Lyndon Schutzenberger Result to Pseudoperiodic Words
    Elena Czeizler; Eugen Czeizler; Lila Kari; Shinnosuke Seki
    DEVELOPMENTS IN LANGUAGE THEORY, PROCEEDINGS, 5583, 183-+, 2009, Peer-reviwed
    International conference proceedings, English
  • On a special class of primitive words
    Elena Czeizler; Lila Kari; Shinnosuke Seki
    MATHEMATICAL FOUNDATIONS OF COMPUTER SCIENCE 2008, PROCEEDINGS, 5162, 265-277, 2008, Peer-reviwed
    International conference proceedings, English
  • A grammatical approach to the alignment of structure-annotated strings
    S Seki; S Kobayashi
    IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, E88D, 12, 2727-2737, Dec. 2005, Peer-reviwed
    Scientific journal, English
  • Efficient learning of k-reversible context-free grammars from positive structural examples
    S Seki; S Kobayashi
    GRAMMATICAL INFERENCE: ALGORITHMS AND APPLICATIONS, PROCEEDINGS, 3264, 285-287, 2004, Peer-reviwed
    Scientific journal, English
  • Hierarchical Alignment of RNA secondary structures including pseudoknots
    Shinnosuke Seki; Atsushi Kijima; Satoshi Kobayashi; Genichi Sanpei
    GIW 2004: Proceedings of the 15th International Conference on Genome Informatics, 117-1-117-2, 2004, Peer-reviwed
    International conference proceedings, English

MISC

  • RNA折り紙
    関 新之助
    Lead, 2019, 電子情報通信学会誌, 102, 4, 330-334, Japanese, Peer-reviwed, Invited
  • Cotranscriptional folding: A frontier in molecular engineering a challenge for computer scientists
    Shinnosuke Seki
    SIAM (Society for Industrial and Applied Mathematics), 01 May 2017, SIAM News, Not assigned yet, English, Peer-reviwed, Introduction scientific journal

Books and other publications

  • Proceedings of the 30th International Conference on DNA Computing and Molecular Programming
    Jaimie Marie Stewar; Shinnosuke Seki
    Joint editor, Schloss Dagstuhl, 09 Sep. 2024, 9783959773447
  • Special issue of New Generation Computing devoted to Hagiya-sensei's 64th birthday.
    English, Joint editor, Springer, Aug. 2022
  • Special issue of Natural Computing devoted to the International Conference on Unconventional Computation and Natural Computation (UCNC 2019)
    Ian McQuillan; Shinnosuke Seki
    English, Joint editor, Springer, 2021
  • Special issue of International Journal of Foundations of Computer Science (IJFCS) devoted to Developments in Language Theory 2018
    Shinnosuke Seki
    English, Editor, World Scientific, Sep. 2020
  • Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation (UCNC2019, Tokyo, Japan, June 3-7, 2019)
    English, Joint editor, Springer, 2019
  • Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation
    English, Joint editor, Springer, 2019
  • Proceedings of the 22nd International Conference on Developments in Language Theory (DLT2018, Tokyo, Japan, September 10-14, 2018)
    Scholarly book, English, Joint editor, Springer, 06 Aug. 2018
  • Encyclopedia of Algorithms
    Shinnosuke Seki
    Dictionary or encycropedia, English, Single work, Patterned Self-Assembly Tile Set Synthesis, Springer, 2016
  • Handbook of Natural Computing
    Lila Kari; Shinnosuke Seki; Petr Sosik
    Scholarly book, English, Contributor, Springer, 2012
  • Proc. 14th International Conference on Developments in Language Theory
    Yuan Gao; Hanlin Lu; Shinnosuke Seki; Sheng Yu
    Scholarly book, English, Editor, Springer, 2010

Lectures, oral presentations, etc.

  • RNA Co-transcriptionality: How can/should we program RNA for computations?
    Shinnosuke Seki
    Public discourse, English, Aalto Theory Seminar, Invited
    19 Mar. 2025
  • RNA co-transcriptionality: How can/should we program RNA for computations?
    Shinnosuke Seki
    Public discourse, English, Hamilton Institute Seminar, Invited
    04 Dec. 2024
  • RNA co-transcriptionality
    Shinnosuke Seki
    Public discourse, English, One FLAT seminar, Invited
    20 Nov. 2024
  • Shifts as a driving force for computing by co-transcriptional folding
    Shinnosuke Seki
    Public discourse, English, Seminar at California Institute of Technology, Invited
    13 Sep. 2024
  • How complex shapes can RNA fold into?
    Shinnosuke Seki
    Invited oral presentation, English, 17th International Conference on Reachability Problems (RP 2023), Invited, Peer-reviewed
    13 Oct. 2023
    11 Oct. 2023- 13 Oct. 2023
  • Freezing 1-Tag systems with states
    Szilard Zsolf Fazekas
    Oral presentation, English, 16th International Conference on Automata and Formal Languages (AFL 2023), Peer-reviewed
    06 Sep. 2023
    05 Sep. 2023- 07 Sep. 2023
  • On algorithmic self-assembly of squares by co-transcriptional folding
    Ryuichi Matsuoka
    Oral presentation, English, The 33rd International Symposium on Algorithms and Computation (ISAAC 2022), Hanyang University, Seoul, Republic of Korea, Peer-reviewed
    20 Dec. 2022
    19 Dec. 2022- 21 Dec. 2022
  • Single-stranded architectures for computing by RNA co-transcriptional folding
    Shinnosuke Seki
    Public discourse, English, Invited, Ajou University, Suwon, Republic of Korea
    15 Dec. 2022
  • Single-stranded architectures for RNA co-transcriptional folding
    Shinnosuke Seki
    Invited oral presentation, English, Moving and Computing 2022 (MaC2022), Invited, University of Pisa, Pisa, Italy, International conference
    19 Sep. 2022
  • Single-stranded architectures for RNA co-transcriptional folding
    Shinnosuke Seki
    Invited oral presentation, English, Dagstuhl seminar 22381: Rational Design of Ribonucleic Acids, Invited, Schloss Dagstuhl, Dagstuhl, Germany, International conference
    19 Sep. 2022
  • Turedo a new computational model for molecular nanobots?
    Nicolas Schabanel
    Invited oral presentation, English, Computability in Europe (CiE 2022), Invited, Swansea University, International conference
    14 Jul. 2022
  • Oritatami systems assemble shapes no less complex than tile assembly model
    Nicolas Schabanel
    Oral presentation, English, 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022), International conference
    15 Mar. 2022
  • Algorithmic self-assembly of squares in oritatami
    松岡 龍一
    Oral presentation, English, 2021年度 冬のLAシンポジウム, 京都大学数理解析研究所, Domestic conference
    01 Feb. 2021
  • Simple intrinsic simulation of cellular automata in oritatami molecular folding model
    Daria Pchelina
    Oral presentation, English, 14th Latin American Symposium on Theoretical Informatics (LATIN 2020), Invited, International conference
    05 Jan. 2021
  • Les oritatamis tracent des dessins indécidables
    Nicolas Schabanel
    Oral presentation, French, Journées SDA2 2020: Systèmes Dynamiques, Automates et Algorithmes, Caen, France, International conference
    04 Dec. 2020
  • Single-stranded architectures for computing
    Shinnosuke Seki
    Oral presentation, English, 1st International Conference on Information Technology and Data Science, Invited, University of Debrecen, Debrecen, Hungary, International conference
    06 Nov. 2020
  • A single-stranded architecture for infinite counting
    Shinnosuke Seki
    Public discourse, English, Invited, Politecnico di Torino (Torino, Italy)
    27 Jan. 2020
  • Counting infinitely by oritatami co-transcriptional folding
    Kohei Maruyama
    Oral presentation, English, SOFSEM2020: 46th International Conference on Current Trends in Theory and Practice of Informatics, Limassol, Cyprus, International conference
    20 Jan. 2020
  • Single-stranded architectures for computing
    Shinnosuke Seki
    Invited oral presentation, English, 23rd International Conference on Developments in Language Theory (DLT 2019), Invited, University of Warsaw, Warsaw, Poland, International conference
    05 Aug. 2019
  • A general architecture of oritatami systems for simulating arbitrary finite automata
    Shinnosuke Seki
    Oral presentation, English, CIAA2019: 24th International Conference on Implementation and Application of Automata, Slovak Academy of Science, Kosice, Slovakia, International conference
    22 Jul. 2019
  • On the power of oritatami cotranscriptional folding with unary bead sequence
    Kohei Maruyama; Reoto Morita
    Oral presentation, English, TAMC2019: 15th Annual Conference on Theory and Applications of Models of Computation, International conference
    13 Apr. 2019
  • Proving the Turing universality of oritatami cotranscriptional folding
    Nicolas Schabanel
    Oral presentation, English, 29th International Symposium on Algorithms and Computation (ISAAC2018), International conference
    16 Dec. 2018
  • Know when to fold 'em: Self-assembly of shapes by folding in oritatami
    Nicolas Schabanel
    Oral presentation, English, DNA24: 24th International Conference on DNA Computing and Molecular Programming, International conference
    08 Oct. 2018
  • Transcript desing problem of oritatami systems
    Hwee Kim
    Oral presentation, English, DNA24: 24th International Conference on DNA Computing and Molecular Programming, International conference
    08 Oct. 2018
  • Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding
    Yusei Masuda; Yuki Ubukata
    Oral presentation, English, 23rd International Conference on Implementation and Application of Automata (CIAA 2018), International conference
    30 Jul. 2018
  • Proving Turing universality of cotranscriptional folding
    Shinnosuke Seki
    Oral presentation, English, 2018 Zassenhaus Groups and Friends Conference, Invited, University of South Florida, Tampa, FL, USA, International conference
    06 Apr. 2018
  • Self-Assembly of shapes by cotranscriptional folding
    Shinnosuke Seki
    Oral presentation, English, Invited, Department of Mathematics and Statistics, University of South Florida
    02 Apr. 2018
  • Cotranscriptional Folding: A Frontier in Molecular Engineering
    Shinnosuke Seki
    Oral presentation, English, 京都大学数理解析研究所RIMS共同研究(公開型)「代数系、論理、言語とその周辺領域」, Domestic conference
    20 Feb. 2018
  • Proving Turing universality of cotranscriptional folding
    Shinnosuke Seki
    Oral presentation, Japanese, 京都大学数理解析研究所RIMS共同研究(公開型)「アルゴリズムと計算理論の基礎と応用」, Domestic conference
    05 Feb. 2018
  • Turing completeness of RNA cotarnsccriptional folding
    Shinnosuke Seki
    Invited oral presentation, English, SICE Molecular Robotics Seminar, 4th JST Seminar on Ethical Issues for Molecular Robots, Invited, Hakata, Japan, Domestic conference
    19 Jan. 2018
  • Self-attraction removal from oritatami systems
    Hwee Kim
    Oral presentation, English, 19th International Conference on Descriptional Complexity of Formal Systems, Milan, Italy, International conference
    03 Jul. 2017
  • Bit string bifurcation by cotranscriptional folding
    Yusei Masuda; Yuki Ubukata
    Oral presentation, English, 1st International Workshop on Oritatami, Shinnosuke Seki, University of Arkansas, International conference
    06 Jun. 2017
  • Bit string bifurcation by cotranscriptional folding
    Yusei Masuda; Yuki Ubukata
    Oral presentation, English, 11th International Workshop on Natural Computing, Akita International University, International conference
    13 May 2017
  • Self-assembly at nano scale by molecular Xerox
    Shinnosuke Seki
    Invited oral presentation, English, 11th International Workshop on Natural Computing, Invited, Akita International University, Akita, Japan, International conference
    13 May 2017
  • Nano-scale self-assembly using molecular Xerox
    Shinnosuke Seki
    Oral presentation, Japanese, 第2回 若手研究者のための熱利用・環境技術ワークショップ, Invited, 化学工学会エネルギー部会熱利用分科会, 東京都八王子市, Domestic conference
    02 Dec. 2016
  • Oritatami, a novel frontier in molecular self-assembly
    Shinnosuke Seki
    Invited oral presentation, English, Invited, Yonsei University
    21 Nov. 2016
  • Oritatami, a novel mathematical model of RNA cotranscriptional folding
    Shinnosuke Seki
    Public discourse, English, Invited, Akita University, Akita, Japan
    20 Oct. 2016
  • Nondeterministic seedless oritatami systems and hardness of testing their equivalence
    Hwee Kim
    Oral presentation, English, The 22nd International Conference on DNA Computing and Molecular Programming (DNA 22), Munich, Germany, International conference
    04 Sep. 2016
  • Programming biomolecules that fold greedily during transcription
    Pierre-Etienne Meunier
    Oral presentation, English, 41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016), International conference
    22 Aug. 2016
  • The complexity of fixed-height patterned tile self-assembly
    Shinnosuke Seki
    Oral presentation, English, 21st International Conference on Implementation and Application of Automata (CIAA 2016), Seoul, Republic of Korea, International conference
    19 Jul. 2016
  • Folding Turing is hard but feasible
    Nicolas Schabanel
    Oral presentation, English, Highlights of Algorithms (HALG 2016), Paris, France, International conference
    06 Jun. 2016
  • Molecular cotranscriptional folding: A novel challenge in theory and applications of self-assembly
    Shinnosuke Seki
    Public discourse, English, Invited, University of South Florida, Tampa, Florida, USA
    25 Jan. 2016
  • Molecular cotranscriptional folding: A novel topic in theory and applications of self-assembly
    Shinnosuke Seki
    Invited oral presentation, English, 5th Interdisciplinary Research and Global Outlook (IRAGO2015)
    22 Oct. 2015
  • Square-density increasing mappings
    Shinnosuke Seki
    Oral presentation, English, 10th International Conference on Combinatorics on Words (WORDS2015), International conference
    14 Sep. 2015
  • Computational complexity of inverse word search problem
    Hiro Ito
    Oral presentation, English, 12th International Symposium on Operations Research and Its Applications (ISORA2015), International conference
    21 Aug. 2015
  • Efficient universal computation by molecular cotranscriptional folding
    Shinnosuke Seki
    Oral presentation, English, 21st International Conference on DNA Computing and Molecular Programming (DNA21), Wyss Institute for Biologically inspired Engineering at Harvard University, International conference
    17 Aug. 2015
  • Binary pattern tile set synthesis is NP-hard
    Shinnosuke Seki
    Oral presentation, English, 42nd International Colloquium on Automata, Languages, and Programming (ICALP2015), International conference
    04 Jul. 2015
  • Oritatami, a model of cotranscriptional folding
    Shinnosuke Seki
    Public discourse, English, Invited, Turku, Finland, International conference
    04 Mar. 2015
  • Generalized Lyndon-Schutzenberger equations
    Florin Manea
    Oral presentation, English, MFCS2014: 39th International Symposium on Mathematical Foundations of Computer Science, Budapest, Hungary, International conference
    25 Aug. 2014
  • Operational state complexity under Parikh equivalence
    Shinnosuke Seki
    Public symposium, English, DCFS2014: 16th International Workshop on Descriptional Complexity of Formal Systems, Turku, Finland, International conference
    05 Aug. 2014
  • DNA pattern self-assembly: Introduction and recent breakthroughs
    Nicolas Schabanel
    Invited oral presentation, English, Complexite et Algorithmes: Algorithmes naturels, Invited, Universite Paris Diderot, LIAFA, Paris, France, International conference
    09 Jun. 2014
  • Stronger square conjecture on binary words
    Shinnosuke Seki
    Oral presentation, English, SOFSEM2014: 40th International Conference on Current Trends in Theory and Practice of Computer Science, International conference
    25 Jan. 2014
  • A stronger square conjecture on binary words
    Shinnosuke Seki
    Invited oral presentation, English, Invited, Slovak Academy of Science, Kosice, Slovakia
    24 Jan. 2014
  • Computing minimum tile sets to self-assembly color patterns
    Aleck Johnson
    Oral presentation, English, ISAAC2013: 24th International Symposium on Algorithms and Computation, Hong Kong, International conference
    16 Dec. 2013
  • How many repetitions can you put on a sequence?
    Shinnosuke Seki
    Invited oral presentation, English, Invited, University of North Florida, Jacksonville, FL, USA
    07 Nov. 2013
  • Combinatorial optimization in pattern-assembly
    Shinnosuke Seki
    Invited oral presentation, English, Invited, University of North Florida, Jacksonville, FL, USA
    06 Nov. 2013
  • Combinatorial optimization in pattern-assembly
    Shinnosuke Seki
    Invited oral presentation, English, Invited, Northwestern University, Evanston, IL, USA
    13 Oct. 2013
  • 3-color bounded patterned self-assembly
    Steffen Kopecki
    Oral presentation, English, DNA 19: 19th International Conference on DNA Computing and Molecular Programming, Tempe, Arizona, USA, International conference
    22 Sep. 2013
  • Combinatorial optimization in pattern assembly (extended abstract)
    Shinnosuke Seki
    Oral presentation, English, UCNC2013: 12th International Conference on Unconventional Computation and Natural Computation, Milan, Italy, International conference
    01 Jul. 2013
  • On the boundedness property of semilinear sets
    Shinnosuke Seki
    Oral presentation, English, TAMC2013: 10th Annual Conference on Theory and Applications of Models of Computation, Hong Kong, International conference
    20 May 2013
  • DNA pattern self-assembly
    Shinnosuke Seki
    Invited oral presentation, English, Invited, Yonsei University, Seoul, Republic of Korea
    15 May 2013
  • DNA pattern self-assembly
    Shinnosuke Seki
    Invited oral presentation, English, Helsinki Institute for Information Technology (HIIT), Helsinki, Finland
    24 Apr. 2013
  • Roles that temperature plays in self-assembly
    Shinnosuke Seki
    Invited oral presentation, English, Invited, University of South Florida, Tampa, FL, USA
    30 Nov. 2012
  • Combinatorial optimization in pattern assembly
    Shinnosuke Seki
    Invited oral presentation, English, Invited, California Institute of Technology, Pasadena, California, USA
    02 Nov. 2012
  • Descriptional complexity in Parikh equivalence
    Shinnosuke Seki
    Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada
    18 Oct. 2012
  • Conveting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata
    Giovanni Pighizzini
    Oral presentation, English, DLT2012: 16th International Conference on Developments in Language Theory, Taipei, Taiwan, International conference
    14 Aug. 2012
  • On the behavior of tile assembly system at high temperatures
    Shinnosuke Seki
    Oral presentation, English, CiE2012: Turing Centenary Conference - How the World Computes, Cambridge, UK, International conference
    18 Jun. 2012
  • Triangular and hexagonal tile self-assembly systems
    Zhi Xu
    Oral presentation, English, WTCS2012: International Workshop on Theoretical Computer Science, Auckland, New Zealand, International conference
    21 Feb. 2012
  • On the behavior of tile assembly system at high temperatures
    Shinnosuke Seki
    Invited oral presentation, English, Slovak Academy of Science, Kosice, Slovakia
    30 Jan. 2012
  • Iterated hairpin completions of non-crossing words
    Shinnosuke Seki
    Oral presentation, English, SOFSEM2012: 38th International Conference on Current Trends in Theory and Practice of Computer Science, Spindleruv Mlyn, Czech Republic, International conference
    21 Jan. 2012
  • In the century of communication
    Shinnosuke Seki
    Invited oral presentation, English, Invited, 島根大学, 松江、日本
    13 Dec. 2011
  • Program size and temperature in self-assembly
    David Doty
    Oral presentation, English, ISAAC2011: 22nd International Symposium on Algorithms and Computation, Yokohama, Japan, International conference
    05 Dec. 2011
  • Roles that temperature play in self-assembly
    Shinnosuke Seki
    Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada
    10 Nov. 2011
  • Number theory and computational efficiency in chemoinformatics
    Shinnosuke Seki
    Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada
    03 Nov. 2011
  • Number theory and computational efficiency in chemoinformatics
    Shinnosuke Seki
    Invited oral presentation, English, Invited, University of Pavol Jozef Safarik, Kosice, Slovakia
    25 Aug. 2011
  • An introduction to the world of self-assembly
    Shinnosuke Seki
    Invited oral presentation, English, Invited, Slovak Academy of Science, Kosice, Slovakia
    24 Aug. 2011
  • Characterizations of bounded semilinear languages by one-way and two-way deterministic machines
    Shinnosuke Seki
    Oral presentation, English, AFL2011: 13th International Conference on Automata and Formal Languages, Debrecen, Hungary, International conference
    20 Aug. 2011
  • Scalable, time-responsive, digital, energy-efficient, moleculer circuits using DNA strand displacement
    David Doty
    Poster presentation, English, DNA16: 16th International Conference on DNA Computing and Molecular Programming, Hong Kong, International conference
    14 Jun. 2011
  • One-reversal counter machines and multihead automata: revisited
    Shinnosuke Seki
    Oral presentation, English, SOFSEM2011: 37th International Conference on Current Trends in Theory and Practice of Computer Science, High Tatras, Slovakia, International conference
    22 Jan. 2011
  • Power of nondeterminism in self-assembly
    David Doty
    Oral presentation, English, SODA2011: ACM-SIAM Symposium on Discrete Algorithms, San Fransisco, California, USA, International conference
    22 Jan. 2011
  • Schema for parallel insertion and deletion
    Shinnosuke Seki
    Oral presentation, English, DLT2010: 14th International Conference on Developments in Language Theory, London, ON, Canada, International conference
    17 Aug. 2010
  • Triangular tile self-assembly systems
    Shinnosuke Seki
    Poster presentation, English, DNA16: 16th International Conference on DNA Computing and Molecular Programming, Hong Kong, International conference
    14 Jun. 2010
  • Schema for parallel insertion and deletion
    Shinnosuke Seki
    Invited oral presentation, English, Workshop on Formal Languages and Automata III, Invited, Kyoto Sangyo University, Kyoto, Japan, International conference
    12 Dec. 2009
  • An extension of fundamental notions in combinatorics on words inspired by DNA information encoding
    Shinnosuke Seki
    Invited oral presentation, English, Invited, Universitate Potsdam, Potsdam, Germany
    06 Jul. 2009
  • An extension of the Lyndon-Schutzenberger result to pseudoperiodic words
    Shinnosuke Seki
    Oral presentation, English, DLT2009: 13th International Conference on Developments in Language Theory, Stuttgard, Germany, International conference
    30 Jun. 2009
  • On the reversibility of parallel insertion, and its relation to comma codes
    Bo Cui
    Oral presentation, English, CAI2009: 3rd International Conference on Algebraic Informatics, Thessaloniki, Greece, International conference
    19 May 2009
  • Duplication in DNA sequences
    Zachary Kincaid
    Oral presentation, English, DLT2008: 12th International Conference on Developments in Language Theory, Kyoto, Japan, International conference
    16 Sep. 2008
  • On a special class of primitive words
    Elena Czeizler
    Oral presentation, English, MFCS2008: 33rd International Symposium on Mathematical Foundations of Computer Science, Torun, Poland, International conference
    27 Aug. 2008
  • Towards the sequence design preventing pseudoknot formation
    Shinnosuke Seki
    Oral presentation, English, IWNC2007: 2nd International Workshop on Natural Computing, Nagoya, Japan, International conference
    10 Dec. 2007
  • An efficient multiple alignment method for DNA secondary structures including pseudoknots
    Shinnosuke Seki
    Oral presentation, English, IWNC2007: 2nd International Workshop on Natural Computing, Nagoya, Japan, International conference
    10 Dec. 2007
  • Hierarchical alignment of RNA secondary structures including pseudoknots
    Shinnosuke Seki
    Poster presentation, English, GIW2004: 15th International Workshop on Genome Informatics, Yokohama, Japan, International conference
    13 Dec. 2004
  • Efficient learning of k-reversible context-free grammars from positive structural examples
    Shinnosuke Seki
    Poster presentation, English, ICGI: 7th International Colloquium on Grammatical Inferences, Athens, Greece, International conference
    11 Oct. 2004

Courses

  • Formal Language Theory
    Oct. 2021 - Present
    The University of Electro-Communications
  • MICS実験第2
    Oct. 2020 - Present
    The University of Electro-Communications
  • 情報領域演習第2
    Apr. 2020 - Present
    The University of Electro-Communications
  • 大学院技術英語
    Apr. 2020 - Present
    The University of Electro-Communications
  • Exercise in Informatics 1
    Oct. 2017 - Mar. 2023
    The University of Electro-Communications
  • MICS実験第一
    The University of Electro-Communications
  • K過程輪講
    The University of Electro-Communications
  • 総合コミュニケーション科学
    The University of Electro-Communications
  • Combinatorics
    Aalto University

Research Themes

  • Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes
    Pekka Orponen; Shinnosuke Seki
    Aalto Science Institute (AScI), AScI Visiting Researcher Funding, Aalto University, Principal investigator
    Mar. 2025
  • 文字列の辞書式順序の組合せ論とその応用
    坂内 英夫
    01 Apr. 2020 - 31 Mar. 2024
  • 共転写性フォールディングの本質的計算完全性
    01 Apr. 2020 - 31 Mar. 2023
  • 万能折り畳みシステムの小型化とその限界
    29 Jun. 2018 - 31 Mar. 2020
  • 国際会議UCNC2019への助成
    Shinnosuke Seki
    Tateishi Science and Technology Foundation
    25 Sep. 2018 - 07 Jun. 2019
  • 国際会議DLT2018への助成
    Shinnosuke Seki
    National Institute of Information and Communications Technology (NICT), Support for the 22nd International Conference on Developments in Language Theory (DLT 2018), Principal investigator
    01 Apr. 2018
  • 共転写性フォールディングによる自己組織化システムの実際的設計と最適化
    01 Apr. 2016 - 31 Mar. 2018
  • 国際会議DLT2018への助成
    Shinnosuke Seki
    The Telecommunications Advancement Foundation, シンポジウム・セミナー 振興普及援助
    01 Sep. 2017
  • 機関選抜のため、研究テーマはなし
    Shinnosuke Seki
    Japan Science and Technology Agency, Principal investigator
    06 Aug. 2015 - 31 Mar. 2017
  • 国際会議DLT2018への助成
    (株)久保田情報技研, 国際会議DLT2018開催支援寄付金
    2017
  • 共転写性フォールディングの数理モデル化とチューリング完全性
    Shinnosuke Seki
    Principal investigator
    01 Apr. 2015 - 31 Mar. 2016
  • Practical designs of molecular self-assembly systems and their optimization
    Shinnosuke Seki
    Academy of Finland, Principal investigator
    01 Sep. 2013 - 31 Mar. 2015