博士（理学）

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

Theory of self-assembly

Informatics, Computational science

Nanotechnology/Materials, Nano/micro-systems

Informatics, Information theory

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, Afghanistan

Sep. 2010 - Apr. 2011
University of Western Ontario, Department of Computer Science, Postdoctoral Researcher, Canada

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, Afghanistan

Sep. 2023 - Present
Co-chair, Program Committee of the 30th International Conference on DNA Computing and Molecular Programming (DNA30), 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), Society, Co-chair

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

Nov. 2024 - Sep. 2025
Member, Program Committee of the 29th International Conference on Implementation and Application of Automata (CIAA2025), Others

Nov. 2024 - Aug. 2025
Member, Program Committee of the 31st International Conference on DNA Computing and Molecular Programming (DNA31), Others

Nov. 2024 - Jul. 2025
Member, Program Committee of the 26th International Conference on Descriptional Complexity of Formal Systems (DCFS 2025), Others

Sep. 2019 - Mar. 2025
Area Editor, New Generation Computing, Editorial Board, Society

Feb. 2024 - Nov. 2024
Member, Program Committee of the IEEE 3rd Conference on Information Technology and Data Science (CITDS 2024), Society

Aug. 2023 - Aug. 2024
Member, Organizing Committee of the 28th International Conference on Implementation and Application of Automata (CIAA 2024), Society

Nov. 2023 - Jul. 2024
Member, Program Committee of the 26th International Conference on Descriptional Complexity of Formal Systems (DCFS 2024), Society

Jul. 2023 - Jun. 2024
Member, Organizing Committee of the 21st International Conference on Unconventional Computation and Natural Computation (UCNC 2024), 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, Society

01 Apr. 2018
関 新之助, 情報処理学会アルゴリズム研究会, Society

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

Aug. 2025
International Society for Nanoscale Science, Computation and Engineering (ISNSCE)
Programmable co‑transcriptional splicing: Realizing regular languages via hairpin deletion
Excellent Student Paper Award, Max Wiedenhöft
International academic award, Afghanistan

Feb. 2018
European Association for Theoretical Computer Science (EATCS)
LA/EATCS Best Presentation Award
International society, Afghanistan

Jul. 2016
CIAA 2016 Best Paper Award (Sheng Yu Award), Shinnosuke Seki;Andrew Winslow
International society, Afghanistan

A formalization of co-transcriptional splicing as an operation on formal languages
Da-Jung Cho; Szilárd Zsolt Fazekas; Shinnosuke Seki; Max Wiedenhöft
Corresponding, Natural Computing, Springer Science and Business Media LLC, 23 Aug. 2025, Peer-reviwed, Invited, Null
Scientific journal, English

Secondary structure design for cotranscriptional 3D RNA origami wireframes.
Pekka Orponen; Shinnosuke Seki; Antti Elonen
Corresponding, Proceedings of the 31st International Conference on DNA Computing and Molecular Programming (DNA31), 347, 6:1-6:18, Aug. 2025, Peer-reviwed, Null
International conference proceedings, English

Programmable co‑transcriptional splicing: Realizing regular languages via hairpin deletion
Da-Jung Cho; Szilárd Zsolt Fazekas; Shinnosuke Seki; Max Wiedenhöf
Corresponding, Proceedings of the 31st International Conference on DNA Computing and Molecular Programming (DNA31), 347, 5:1-5:22, Aug. 2025, Peer-reviwed, Null
International conference proceedings, English

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, Null
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, Null
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, Null
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, Null
Scientific journal, English

On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding.
Szilárd Zsolt Fazekas; Hwee Kim; Ryuichi Matsuoka; Shinnosuke Seki; Hinano Takeuchi
Lead, Proc. ISAAC2022, LIPIcs 248, 37:1-37:15, Dec. 2022, Peer-reviwed, Null
International conference proceedings, English

Oritatami systems assemble shapes no less complex than tile assembly model (aTAM)
Daria Pchelina; Nicolas Schabanel; Shinnosuke Seki; Guillaume Theyssier
Lead, 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, Null
International conference proceedings, English

Square network on a word
Szilard Zsolt Fazekas; Shinnosuke Seki
Lead, Theoretical Computer Science, Elsevier, 894, 26, 121-134, Nov. 2021, Peer-reviwed, Null
Scientific journal, English

Simple intrinsic simulation of cellular automata in oritatami molecular folding model
Daria Pchelina; Nicolas Schabanel; Shinnosuke Seki; Yuki Ubukata
Lead, Proceedings of the 14th Latin American Theoretical Informatics Symposium (LATIN 2020), Springer, LNCS 12118, 425-436, 05 Jan. 2021, Peer-reviwed, Null
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
Lead, International Journal of Foundations of Computer Science, World Scientific Publishing Company, 32, 5, 575-596, 2021, Peer-reviwed, Null
Scientific journal, English

A general architecture of oritatami systems for simulating arbitrary finite automata
Yo-Sub Han; Hwee Kim; Yusei Masuda; Shinnosuke Seki
Lead, Theoretical Computer Science, Springer, 870, 16, 29-52, 2021, Peer-reviwed, Null
Scientific journal, English

Counting infinitely by oritatami co-transcriptional folding
Kohei Maruyama; Shinnosuke Seki
Lead, Natural Computing, Springer, 20, 2, 329-340, 2021, Peer-reviwed, Null
Scientific journal, English

Transcript design problem of oritatami systems
Yo-Sub Han; Hwee Kim; Shinnosuke Seki
Lead, Natural Computing, Springer, 19, 2, 323-335, 2020, Peer-reviwed, Null
Scientific journal, English

Renewal of the major fields of New Generation Computing Vol. 38
Masayuki Numao; Yutaka Matsuo; Shinnosuke Seki
Lead, New Generation Computing, 38, 1, 1-3, 2020, Peer-reviwed, Null
Scientific journal, English

A General Architecture of Oritatami Systems for Simulating Arbitrary Finite Automata
Yo-Sub Han; Hwee Kim; Yusei Masuda; Shinnosuke Seki
Lead, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Verlag, 11601, 146-157, 2019, Null
International conference proceedings, English

Self-attraction removal from oritatami systems
Yo-Sub Han; Hwee Kim; Trent A. Rogers; Shinnosuke Seki
Lead, International Journal of Foundations of Computer Science, 30, 6-7, 1047-1067, 2019, Peer-reviwed, Null
Scientific journal, English

On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence.
Szilárd Zsolt Fazekas; Kohei Maruyama; Reoto Morita; Shinnosuke Seki
Lead, Proceedings of the 15th International Conference on Theory and Applications of Models of Computation (TAMC 2019), Springer, LNCS 11436, 188-207, 2019, Peer-reviwed, Null
International conference proceedings, English

Oritatami: a computational model for molecular co-transcriptional folding
Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki
Lead, International Journal of Molecular Sciences, MDPI, 20, 9, 2259, 2019, Peer-reviwed, Null
Scientific journal, English

Single-stranded architectures for computing
Shinnosuke Seki
Lead, Proceedings of the 23rd International Conference on Developments in Language Theory (DLT 2019), Springer, LNCS 11647, 41-56, 2019, Peer-reviwed, Invited, Null
International conference proceedings, English

Nondeterministic seedless oritatami systems and hardness of testing their equivalence
Yo-Sub Han; Hwee Kim; Makoto Ota; Shinnosuke Seki
Lead, Natural Computing, Springer, 17, 1, 67-79, 2018, Peer-reviwed, Null
Scientific journal, English

Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding
Yusei Masuda; Shinnosuke Seki; Yuki Ubukata
Lead, Proceedings of the 23rd International Conference on Implementation and Applications of Automata (CIAA2018), Springer, LNCS, 10977, 261-273, 2018, Peer-reviwed, Null
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
Lead, Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA 24), Springer, LNCS, 11145, 19-36, 2018, Peer-reviwed, Null
International conference proceedings, English

Transcript design problem of oritatami systems
Yo-Sub Han; Hwee Kim; Shinnosuke Seki
Lead, Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA 24), Springer, LNCS, 11145, 139-154, 2018, Peer-reviwed, Null
International conference proceedings, English

Proving the Turing universality of oritatami co-transcriptional folding
Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki
Lead, Proceedings of the 29th International Symposium on Algorithms and Computation (ISAAC2018), Schloss Dagstuhl, LIPIcs 123, 23:1-23:13, 2018, Peer-reviwed, Null
International conference proceedings, English

The Complexity of Fixed-Height Patterned Tile Self-Assembly
Shinnosuke Seki; Andrew Winslow
Lead, INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, 28, 5, 465-482, Aug. 2017, Peer-reviwed, Null
Scientific journal, English

Oritatami System; a Survey and the Impossibility of Simple Simulation at Small Delays
Trent A. Rogers; Shinnosuke Seki
Lead, FUNDAMENTA INFORMATICAE, 154, 1-4, 359-372, 2017, Peer-reviwed, Null
Scientific journal, English

Self-attraction removal from oritatami systems
Yo-Sub Han; Hwee Kim; Trent A. Rogers; Shinnosuke Seki
Lead, 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, Null
International conference proceedings, English

The extended equation of Lyndon and Schutzenberger
Florin Manea; Mike Muller; Dirk Nowotka; Shinnosuke Seki
Lead, Journal of Computer and System Sciences, Elsevier, 85, 132-167, 26 Nov. 2016, Peer-reviwed, Null
Scientific journal, English

Rule set design problems for oritatami system
Makoto Ota; Shinnosuke Seki
Lead, Theoretical Computer Science, Elsevier, 671, 26-35, 22 Sep. 2016, Peer-reviwed, Null
Scientific journal, English

Programming biomolecules that fold greedily during transcription
Cody Geary; Pierre-Etienne Meunier; Nicolas Schabanel; Shinnosuke Seki
Lead, MFCS 2016: 41st International Symposium on Mathematical Foundations of Computer Science, LIPIcs 58, 43:1-43:14, 22 Aug. 2016, Peer-reviwed, Null
International conference proceedings, English

Binary pattern tile set synthesis is NP-hard
Lila Kari; Steffen Kopecki; Pierre-Etienne Meunier; Matthew J. Patitz; Shinnosuke Seki
Lead, Algorithmica, Springer, 78, 1, 1-46, 26 Apr. 2016, Peer-reviwed, Null
Scientific journal, English

The Complexity of Fixed-Height Patterned Tile Self-assembly
Shinnosuke Seki; Andrew Winslow
Lead, Implementation and Application of Automata, 9705, LNCS 9705, 248-259, 2016, Peer-reviwed, Null
International conference proceedings, English

Nondeterministic seedless oritatami systems and hardness of testing their equivalence
Yo-Sub Han; Hwee Kim; Makoto Ota; Shinnosuke Seki
Lead, 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, Null
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
Lead, Journal of Combinatorial Optimization, Springer, 33, 2, 496-529, 24 Nov. 2015, Peer-reviwed, Null
Scientific journal, English

Program Size and Temperature in Self-Assembly
Ho-Lin Chen; David Doty; Shinnosuke Seki
Lead, ALGORITHMICA, 72, 3, 884-899, Jul. 2015, Peer-reviwed, Null
Scientific journal, English

Dynamic Simulation of 1D Cellular Automata in the Active aTAM
Natasa Jonoska; Daria Karpenko; Shinnosuke Seki
Lead, NEW GENERATION COMPUTING, 33, 3, 271-295, Jul. 2015, Peer-reviwed, Null
Scientific journal, English

3-color bounded patterned self-assembly
Lila Kari; Steffen Kopecki; Shinnosuke Seki
Lead, NATURAL COMPUTING, 14, 2, 279-292, Jun. 2015, Peer-reviwed, Null
Scientific journal, English

Computational complexity of inverse word search problem
Hiro Ito; Shinnosuke Seki
Lead, IET Conference Publications, Institution of Engineering and Technology, 2015, 673, 41-44, 2015, Null
International conference proceedings, English

Square-Density Increasing Mappings
Florin Manea; Shinnosuke Seki
Lead, COMBINATORICS ON WORDS, WORDS 2015, 9304, 160-169, 2015, Peer-reviwed, Null
International conference proceedings, English

Semilinear Sets and Counter Machines: a Brief Survey
Oscar H. Ibarra; Shinnosuke Seki
Lead, FUNDAMENTA INFORMATICAE, 138, 1-2, 61-76, 2015, Peer-reviwed, Null
Scientific journal, English

Binary Pattern Tile Set Synthesis Is NP-hard
Lila Kari; Steffen Kopecki; Pierre-Etienne Meunier; Matthew J. Patitz; Shinnosuke Seki
Lead, Automata, Languages, and Programming, Pt I, 9134, 1022-1034, 2015, Peer-reviwed, Null
International conference proceedings, English

Transfer matrix analysis of one-dimensional majority cellular automata with thermal noise
Remi Lemoy; Alexander Mozeika; Shinnosuke Seki
Lead, JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, 47, 10, 105001-105001, Mar. 2014, Peer-reviwed, Null
Scientific journal, English

A Stronger Square Conjecture on Binary Words
Natasa Jonoska; Florin Manea; Shinnosuke Seki
Lead, SOFSEM 2014: THEORY AND PRACTICE OF COMPUTER SCIENCE, 8327, 339-350, 2014, Peer-reviwed, Null
International conference proceedings, English

Operational State Complexity under Parikh Equivalence
Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki
Lead, DESCRIPTIONAL COMPLEXITY OF FORMAL SYSTEMS, DCFS 2014, 8614, 294-305, 2014, Peer-reviwed, Null
International conference proceedings, English

Generalised Lyndon-Schutzenberger Equations
Florin Manea; Mike Mueller; Dirk Nowotka; Shinnosuke Seki
Lead, MATHEMATICAL FOUNDATIONS OF COMPUTER SCIENCE 2014, PT I, 8634, 402-+, 2014, Peer-reviwed, Null
International conference proceedings, English

On computational complexity of graph inference from counting
Szilárd Zsolt Fazekas; Hiro Ito; Yasushi Okuno; Shinnosuke Seki; Kei Taneishi
Lead, Natural Computing, Springer, 12, 4, 589-603, Dec. 2013, Peer-reviwed, Null
Scientific journal, English

On the open problem of Ginsburg concerning semilinear sets and related problems
Oscar H. Ibarra; Shinnosuke Seki
Lead, THEORETICAL COMPUTER SCIENCE, 501, 11-19, Aug. 2013, Peer-reviwed, Null
Scientific journal, English

The power of nondeterminism in self-assembly
Nathan Bryans; Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki
Lead, Theory of Computing, 9, 1-29, 2013, Peer-reviwed, Null
Scientific journal, English

On the behavior of tile assembly system at high temperatures
Shinnosuke Seki; Yasushi Okuno
Lead, Computability, IOS Press, 2, 2, 107-124, 2013, Peer-reviwed, Null
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
Lead, Information and Computation, Elsevier, 228-229, 1-15, 2013, Peer-reviwed, Null
Scientific journal, English

On the boundedness property of semilinear sets
Oscar H. Ibarra; Shinnosuke Seki
Lead, TAMC 2013: Proceedings of the 10th Annual Conference on Theory and Applications of Models of Computation, Springer, LNCS 7876, 156-168, 2013, Peer-reviwed, Null
International conference proceedings, English

Combinatorial optimization in pattern assembly (extended abstract)
Shinnosuke Seki
Lead, UCNC 2013: Proceedings of the Unconventional Computation and Natural Computation - 12th International Conference, Springer, LNCS 7956, 220-231, 2013, Peer-reviwed, Null
International conference proceedings, English

3-Color Bounded Patterned Self-assemblyY
Lila Kari; Steffen Kopecki; Shinnosuke Seki
Lead, DNA COMPUTING AND MOLECULAR PROGRAMMING, DNA 2013, 8141, 105-117, 2013, Peer-reviwed, Null
International conference proceedings, English

Computing Minimum Tile Sets to Self-Assemble Color Patterns
Aleck C. Johnsen; Ming-Yang Kao; Shinnosuke Seki
Lead, ALGORITHMS AND COMPUTATION, 8283, 699-710, 2013, Peer-reviwed, Null
International conference proceedings, English

One-reversal counter machines and multihead automata: Revisited
Ehsan Chiniforooshan; Mark Daley; Oscar H. Ibarra; Lila Kari; Shinnosuke Seki
Lead, THEORETICAL COMPUTER SCIENCE, 454, 81-87, Oct. 2012, Peer-reviwed, Null
Scientific journal, English

CHARACTERIZATIONS OF BOUNDED SEMILINEAR LANGUAGES BY ONE-WAY AND TWO-WAY DETERMINISTIC MACHINES
Oscar H. Ibarra; Shinnosuke Seki
Lead, INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, 23, 6, 1291-1305, Sep. 2012, Peer-reviwed, Null
Scientific journal, English

Absoluteness of subword inequality is undecidable
Shinnosuke Seki
Lead, THEORETICAL COMPUTER SCIENCE, 418, 116-120, Feb. 2012, Peer-reviwed, Null
Scientific journal, English

Iterated Hairpin Completions of Non-crossing Words
Lila Kari; Steffen Kopecki; Shinnosuke Seki
Lead, SOFSEM 2012: THEORY AND PRACTICE OF COMPUTER SCIENCE, 7147, 337-+, 2012, Peer-reviwed, Null
International conference proceedings, English

Triangular and hexagonal tile self-assembly systems
Lila Kari; Shinnosuke Seki; Zhi Xu
Lead, WTCS 2012: Proceedings of the International Workshop on Theoretical Computer Science, Springer, LNCS 7160, 357-375, 2012, Peer-reviwed, Null
International conference proceedings, English

On the behavior of tile assembly system at high temperatures
Shinnosuke Seki; Yasushi Okuno
Lead, CiE 2012: Proceedings of the Turing Centenary Conference - How the World Computes, LNCS 7318, 549-559, 2012, Peer-reviwed, Null
International conference proceedings, English

Converting nondeterministic automata and context-free grammars into Parikh equivalent deterministic automata
Giovanna J. Lavado; Giovanni Pighizzini; Shinnosuke Seki
Lead, DLT 2012: Proceedings of the 16th International Conference on Developments in Language Theory, Springer, LNCS 7410, 284-295, 2012, Peer-reviwed, Null
International conference proceedings, English

SCHEMA FOR PARALLEL INSERTION AND DELETION: REVISITED
Lila Kari; Shinnosuke Seki
Lead, INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, 22, 7, 1655-1668, Nov. 2011, Peer-reviwed, Null
Scientific journal, English

An extension of the Lyndon-Schutzenberger result to pseudoperiodic words
Elena Czeizler; Eugen Czeizler; Lila Kari; Shinnosuke Seki
Lead, INFORMATION AND COMPUTATION, 209, 4, 717-730, Apr. 2011, Peer-reviwed, Null
Scientific journal, English

Block insertion and deletion on trajectories
Bo Cui; Lila Kari; Shinnosuke Seki
Lead, THEORETICAL COMPUTER SCIENCE, 412, 8-10, 714-728, Mar. 2011, Peer-reviwed, Null
Scientific journal, English

PROPERTIES OF PSEUDO-PRIMITIVE WORDS AND THEIR APPLICATIONS
Lila Kari; Benoit Masson; Shinnosuke Seki
Lead, INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, 22, 2, 447-471, Feb. 2011, Peer-reviwed, Null
Scientific journal, English

Triangular Tile Self-assembly Systems
Lila Kari; Shinnosuke Seki; Zhi Xu
Lead, DNA COMPUTING AND MOLECULAR PROGRAMMING, 6518, 89-99, 2011, Peer-reviwed, Null
International conference proceedings, English

Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement
Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki
Lead, DNA COMPUTING AND MOLECULAR PROGRAMMING, 6518, 25-36, 2011, Peer-reviwed, Null
International conference proceedings, English

ORTHOGONAL SHUFFLE ON TRAJECTORIES
Mark Daley; Lila Kari; Shinnosuke Seki; Petr Sosik
Lead, INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE, 22, 1, 213-222, Jan. 2011, Peer-reviwed, Null
Scientific journal, English

K-Comma Codes and Their Generalizations
Bo Cui; Lila Kari; Shinnosuke Seki
Lead, FUNDAMENTA INFORMATICAE, 107, 1, 1-18, 2011, Peer-reviwed, Null
Scientific journal, English

On the Regularity of Iterated Hairpin Completion of a Single Word
Lila Kari; Shinnosuke Seki; Steffen Kopecki
Lead, FUNDAMENTA INFORMATICAE, 110, 1-4, 201-215, 2011, Peer-reviwed, Null
Scientific journal, English

The Power of Nondeterminism in Self-Assembly
Nathaniel Bryans; Ehsan Chiniforooshan; David Doty; Lila Kari; Shinnosuke Seki
Lead, PROCEEDINGS OF THE TWENTY-SECOND ANNUAL ACM-SIAM SYMPOSIUM ON DISCRETE ALGORITHMS, 590-602, 2011, Peer-reviwed, Null
International conference proceedings, English

One-Reversal Counter Machines and Multihead Automata: Revisited
Ehsan Chiniforooshan; Mark Daley; Oscar H. Ibarra; Lila Kari; Shinnosuke Seki
Lead, SOFSEM 2011: THEORY AND PRACTICE OF COMPUTER SCIENCE, 6543, 166-177, 2011, Peer-reviwed, Null
International conference proceedings, English

Characterizations of bounded semilinear languages by one-way and two-way deterministic machines
Oscar H. Ibarra; Shinnosuke Seki
Lead, AFL 2011: Proceedings of the 13th International Conference on Automata and Formal Languages, 211-224, 2011, Peer-reviwed, Null
International conference proceedings, English

Program Size and Temperature in Self-assembly
Ho-Lin Chen; David Doty; Shinnosuke Seki
Lead, ALGORITHMS AND COMPUTATION, 7074, 445-+, 2011, Peer-reviwed, Null
International conference proceedings, English

On a special class of primitive words
Elena Czeizler; Lila Kari; Shinnosuke Seki
Lead, THEORETICAL COMPUTER SCIENCE, 411, 3, 617-630, Jan. 2010, Peer-reviwed, Null
Scientific journal, English

An Improved Bound for an Extension of Fine and Wilf's Theorem and Its Optimality
Lila Kari; Shinnosuke Seki
Lead, FUNDAMENTA INFORMATICAE, 101, 3, 215-236, 2010, Peer-reviwed, Null
Scientific journal, English

Schema for Parallel Insertion and Deletion
Lila Kari; Shinnosuke Seki
Lead, DEVELOPMENTS IN LANGUAGE THEORY, 6224, 267-278, 2010, Peer-reviwed, Null
International conference proceedings, English

Twin-roots of words and their properties
Lila Kari; Kalpana Mahalingam; Shinnosuke Seki
Lead, THEORETICAL COMPUTER SCIENCE, 410, 24-25, 2393-2400, May 2009, Peer-reviwed, Null
Scientific journal, English

On pseudoknot-bordered words and their properties
Lila Kari; Shinnosuke Seki
Lead, JOURNAL OF COMPUTER AND SYSTEM SCIENCES, 75, 2, 113-121, Feb. 2009, Peer-reviwed, Null
Scientific journal, English

An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots
Shinnosuke Seki; Satoshi Kobayashi
Lead, NATURAL COMPUTING, PROCEEDINGS, 1, 179-+, 2009, Peer-reviwed, Null
International conference proceedings, English

Towards the Sequence Design Preventing Pseudoknot Formation
Lila Kari; Shinnosuke Seki
Lead, NATURAL COMPUTING, PROCEEDINGS, 1, 101-110, 2009, Peer-reviwed, Null
International conference proceedings, English

Duplication in DNA Sequences
Masami Ito; Lila Kari; Zachary Kincaid; Shinnosuke Seki
Lead, ALGORITHMIC BIOPROCESSES, LNCS 5257, 43-+, 2009, Peer-reviwed, Null
International conference proceedings, English

On the Reversibility of Parallel Insertion, and Its Relation to Comma Codes
Bo Cui; Lila Kari; Shinnosuke Seki
Lead, ALGEBRAIC INFORMATICS, 5725, 204-219, 2009, Peer-reviwed, Null
International conference proceedings, English

An Extension of the Lyndon Schutzenberger Result to Pseudoperiodic Words
Elena Czeizler; Eugen Czeizler; Lila Kari; Shinnosuke Seki
Lead, DEVELOPMENTS IN LANGUAGE THEORY, PROCEEDINGS, 5583, 183-+, 2009, Peer-reviwed, Null
International conference proceedings, English

On a special class of primitive words
Elena Czeizler; Lila Kari; Shinnosuke Seki
Lead, MATHEMATICAL FOUNDATIONS OF COMPUTER SCIENCE 2008, PROCEEDINGS, 5162, 265-277, 2008, Peer-reviwed, Null
International conference proceedings, English

A grammatical approach to the alignment of structure-annotated strings
S Seki; S Kobayashi
Lead, IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, E88D, 12, 2727-2737, Dec. 2005, Peer-reviwed, Null
Scientific journal, English

Efficient learning of k-reversible context-free grammars from positive structural examples
S Seki; S Kobayashi
Lead, GRAMMATICAL INFERENCE: ALGORITHMS AND APPLICATIONS, PROCEEDINGS, 3264, 285-287, 2004, Peer-reviwed, Null
Scientific journal, English

Hierarchical Alignment of RNA secondary structures including pseudoknots
Shinnosuke Seki; Atsushi Kijima; Satoshi Kobayashi; Genichi Sanpei
Lead, GIW 2004: Proceedings of the 15th International Conference on Genome Informatics, 117-1-117-2, 2004, Peer-reviwed, Null
International conference proceedings, English

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, Report scientific journal, Null

Cotranscriptional folding: A frontier in molecular engineering a challenge for computer scientists
Shinnosuke Seki
Lead, SIAM (Society for Industrial and Applied Mathematics), 01 May 2017, SIAM News, Not assigned yet, English, Peer-reviwed, Introduction scientific journal, Null

Proceedings of the 30th International Conference on DNA Computing and Molecular Programming
Jaimie Marie Stewar; Shinnosuke Seki
Scholarly book, Abkhazian, Joint editor, Schloss Dagstuhl, 09 Sep. 2024, 9783959773447

Special issue of New Generation Computing devoted to Hagiya-sensei's 64th birthday.
Scholarly book, 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
Scholarly book, 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
Scholarly book, 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)
Scholarly book, English, Joint editor, Springer, 2019

Proceedings of the 18th International Conference on Unconventional Computation and Natural Computation
Scholarly book, 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

Programmable co‑transcriptional splicing: Realizing regular languages via hairpin deletion
Max Wiedenhof
Oral presentation, English, DNA31: The 31st International Conference on DNA Computing and Molecular Programming, Peer-reviewed, Afghanistan, Domestic conference
27 Aug. 2025
25 Aug. 2025- 29 Aug. 2025

Secondary structure design for cotranscriptional 3D RNA origami wireframes
Pekka Orponen
Oral presentation, English, DNA31: The 31st International Conference on DNA Computing and Molecular Programming, Peer-reviewed, Afghanistan, Domestic conference
27 Aug. 2025
25 Aug. 2025- 29 Aug. 2025

RNA Co-transcriptionality: How can/should we program RNA for computations?
Shinnosuke Seki
Public discourse, English, Aalto Theory Seminar, Invited, Afghanistan, Domestic conference
19 Mar. 2025

RNA co-transcriptionality: How can/should we program RNA for computations?
Shinnosuke Seki
Public discourse, English, Hamilton Institute Seminar, Invited, Afghanistan, Domestic conference
04 Dec. 2024

RNA co-transcriptionality
Shinnosuke Seki
Public discourse, English, One FLAT seminar, Invited, Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, Domestic conference
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, Afghanistan, Domestic conference
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, Afghanistan, Domestic conference
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, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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), Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, International conference
06 Nov. 2020

A single-stranded architecture for infinite counting
Shinnosuke Seki
Public discourse, English, Invited, Politecnico di Torino (Torino, Italy), Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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), Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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), Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, Domestic conference
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」, Peer-reviewed, Afghanistan, 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」, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, Domestic conference
02 Dec. 2016

Oritatami, a novel frontier in molecular self-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, Yonsei University, Peer-reviewed, Afghanistan, Domestic conference
21 Nov. 2016

Oritatami, a novel mathematical model of RNA cotranscriptional folding
Shinnosuke Seki
Public discourse, English, Invited, Akita University, Akita, Japan, Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, 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), Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, International conference
19 Jul. 2016

Folding Turing is hard but feasible
Nicolas Schabanel
Oral presentation, English, Highlights of Algorithms (HALG 2016), Paris, France, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, Domestic conference
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), Peer-reviewed, Afghanistan, Domestic conference
22 Oct. 2015

Square-density increasing mappings
Shinnosuke Seki
Oral presentation, English, 10th International Conference on Combinatorics on Words (WORDS2015), Peer-reviewed, Afghanistan, 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), Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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), Peer-reviewed, Afghanistan, International conference
04 Jul. 2015

Oritatami, a model of cotranscriptional folding
Shinnosuke Seki
Public discourse, English, Invited, Turku, Finland, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, Domestic conference
07 Nov. 2013

Combinatorial optimization in pattern-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, University of North Florida, Jacksonville, FL, USA, Peer-reviewed, Afghanistan, Domestic conference
06 Nov. 2013

Combinatorial optimization in pattern-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, Northwestern University, Evanston, IL, USA, Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, International conference
20 May 2013

DNA pattern self-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, Yonsei University, Seoul, Republic of Korea, Peer-reviewed, Afghanistan, Domestic conference
15 May 2013

DNA pattern self-assembly
Shinnosuke Seki
Invited oral presentation, English, Helsinki Institute for Information Technology (HIIT), Helsinki, Finland, Peer-reviewed, Afghanistan, Domestic conference
24 Apr. 2013

Roles that temperature plays in self-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, University of South Florida, Tampa, FL, USA, Peer-reviewed, Afghanistan, Domestic conference
30 Nov. 2012

Combinatorial optimization in pattern assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, California Institute of Technology, Pasadena, California, USA, Peer-reviewed, Afghanistan, Domestic conference
02 Nov. 2012

Descriptional complexity in Parikh equivalence
Shinnosuke Seki
Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada, Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, Domestic conference
10 Nov. 2011

Number theory and computational efficiency in chemoinformatics
Shinnosuke Seki
Invited oral presentation, English, Invited, University of Western Ontario, London, ON, Canada, Peer-reviewed, Afghanistan, Domestic conference
03 Nov. 2011

Number theory and computational efficiency in chemoinformatics
Shinnosuke Seki
Invited oral presentation, English, Invited, University of Pavol Jozef Safarik, Kosice, Slovakia, Peer-reviewed, Afghanistan, Domestic conference
25 Aug. 2011

An introduction to the world of self-assembly
Shinnosuke Seki
Invited oral presentation, English, Invited, Slovak Academy of Science, Kosice, Slovakia, Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, Domestic conference
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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, 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, Peer-reviewed, Afghanistan, International conference
11 Oct. 2004

Formal Language Theory
Oct. 2021 - Present
The University of Electro-Communications, Undergraduate liberal arts, Afghanistan

MICS実験第2
Oct. 2020 - Present
The University of Electro-Communications, Undergraduate liberal arts, Afghanistan

情報領域演習第2
Apr. 2020 - Present
The University of Electro-Communications, Undergraduate liberal arts, Afghanistan

大学院技術英語
Apr. 2020 - Present
The University of Electro-Communications, Undergraduate liberal arts, Afghanistan

Exercise in Informatics 1
Oct. 2017 - Mar. 2023
The University of Electro-Communications, Undergraduate liberal arts, Afghanistan

MICS実験第一
The University of Electro-Communications, Undergraduate liberal arts, Afghanistan

K過程輪講
The University of Electro-Communications, Undergraduate liberal arts, Afghanistan

総合コミュニケーション科学
The University of Electro-Communications, Undergraduate liberal arts, Afghanistan

Combinatorics
Aalto University, Undergraduate liberal arts, Afghanistan

Rokam: RNA Origami Kinetic Assembly Model
Nicolas Schabanel; Shinnosuke Seki
Auvergne-Rhône-Alpes, Bourse Region Ambition Internationale de Auvergne-Rhone-Alpes, ENS Lyon, Health Science, Principal investigator
Sep. 2025 - Aug. 2028

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
Principal investigator
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
Principal investigator
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
Principal investigator
29 Jun. 2018 - 31 Mar. 2020

国際会議UCNC2019への助成
Shinnosuke Seki
Tateishi Science and Technology Foundation, Principal investigator
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
Principal investigator
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, Principal investigator
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, Principal investigator
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