Preprints

  1. Kashin Sugishita, Noha Abdel-Mottaleb, Qiong Zhang, Naoki Masuda.
    A growth model for water distribution networks with loops.
    Preprint: arXiv:2106.13519

  2. Kazuki Nakajima, Kazuyuki Shudo, Naoki Masuda.
    Randomizing hypergraphs preserving degree correlation and local clustering.
    Preprint: arXiv:2106.12162

  3. Elohim Fonseca dos Reis, Naoki Masuda.
    Metapopulation models imply non-Poissonian statistics of interevent times.
    Preprint: arXiv:2106.10348

  4. Lingqi Meng, Naoki Masuda.
    Epidemic dynamics on metapopulation networks with node2vec mobility.
    Preprint: arXiv:2106.08080

  5. Arthur P. C. Spencer, Jonathan C. W. Brooks, Naoki Masuda, Hollie Byrne, Richard Lee-Kelland, Sally Jary, Marianne Thoresen, Marc Goodfellow, Frances M. Cowan, Ela Chakkarapani.
    Motor function and white matter connectivity in children treated with therapeutic hypothermia for neonatal encephalopathy.
    Preprint: https://doi.org/10.1101/2021.04.30.21256369

  6. Marie Saitou, Naoki Masuda, Omer Gokcumen.
    Network-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants.
    Preprint: https://doi.org/10.1101/2021.01.25.428140

Journal papers (refereed papers only)

  1. Takahiro Ezaki, Yu Himeno, Takamitsu Watanabe, Naoki Masuda.
    Modeling state-transition dynamics in resting-state brain signals by the hidden Markov and Gaussian mixture models.
    European Journal of Neuroscience, 54, 5404-5416 (2021). [open access]
    Preprint: arXiv:2001.08369
    Python codes

  2. Hang-Hyun Jo, Naoki Masuda.
    Finite-size effects on the convergence time in continuous-opinion dynamics.
    Physical Review E, 104, 014309 (2021).
    Preprint: arXiv:2103.06055

  3. Kashin Sugishita, Mason A. Porter, Mariano Beguerisse-Díaz, Naoki Masuda.
    Opinion dynamics on tie-decay networks.
    Physical Review Research, 3, 023249 (2021). [open access]
    Preprint: arXiv:2010.00143

  4. Naoki Masuda, Joel C. Miller, Petter Holme.
    Concurrency measures in the era of temporal network epidemiology: A review.
    Journal of the Royal Society Interface, 18, 20210019 (2021). [open access]
    Preprint: arXiv:2012.13317

  5. Christos Ellinas, Christos Nicolaides, Naoki Masuda.
    Mitigation strategies against cascading failures within a project activity network.
    Journal of Computational Social Science, published online (2021).
    Preprint: arXiv:1810.07561

  6. Sadamori Kojaku, Giacomo Livan, Naoki Masuda.
    Detecting citation cartels in journal networks.
    Scientific Reports, 11, 14524 (2021). [open access]
    Preprint: arXiv:2009.09097
    Python codes


  7. Kashin Sugishita, Naoki Masuda.
    Recurrence in the evolution of air transport networks.
    Scientific Reports, 11, 5514 (2021). [open access]
    Preprint: arXiv:2005.14392

  8. Arthur P. C. Spencer, Jonathan C. W. Brooks, Naoki Masuda, Hollie Byrne, Richard Lee-Kelland, Sally Jary, Marianne Thoresen, James Tonks, Marc Goodfellow, Frances M. Cowan, Ela Chakkarapani.
    Disrupted brain connectivity in children treated with therapeutic hypothermia for neonatal encephalopathy.
    NeuroImage: Clinical, 30, 102582 (2021). [open access]
    Preprint: https://doi.org/10.1101/2020.09.23.20200014

  9. Elohim Fonseca dos Reis, Mark Viney, Naoki Masuda.
    Network analysis of the immune state of mice.
    Scientific Reports, 11, 4306 (2021). [open access]
    Preprint: https://doi.org/10.1101/638445

  10. Marinho A Lopes, Dominik Krzemiński, Khalid Hamandi, Krish D. Singh, Naoki Masuda, John R. Terry, Jiaxiang Zhang.
    A computational biomarker of juvenile myoclonic epilepsy from resting-state MEG.
    Clinical Neurophysiology, 132, 922-927 (2021). [open access]
    Preprint: https://doi.org/10.1101/2020.05.18.20102681

  11. Lingqi Meng, Naoki Masuda.
    Analysis of node2vec random walks on networks.
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 476, 20200447 (2020). [open access]
    Preprint: arXiv:2006.04904

  12. Shun Kodate, Ryusuke Chiba, Shunya Kimura, Naoki Masuda.
    Detecting problematic transactions in a consumer-to-consumer e-commerce network.
    Applied Network Science, 5, 90 (2020). [open access]
    Preprint: arXiv:1906.07974
    Featured by Ledge.ai (in Japanese)
    Featured by impress (in Japanese)
    Press release (in Japanese; メルカリ)
    Press release (in Japanese; 東北大学)

  13. Elohim Fonseca dos Reis, Aming Li, Naoki Masuda.
    Generative models of simultaneously heavy-tailed distributions of inter-event times on nodes and edges.
    Physical Review E, 102, 052303 (2020). [open access]
    Preprint: arXiv:2008.13034

  14. Shogo Kajimura, Naoki Masuda, Johnny King L. Lau, Kou Murayama.
    Focused attention meditation changes the boundary and configuration of functional networks in the brain.
    Scientific Reports, 10, 18426 (2020). [open access]
    Preprint: https://doi.org/10.1101/664573

  15. Xiu-Xiu Zhan, Ziyu Li, Naoki Masuda, Petter Holme, Huijuan Wang.
    Susceptible-infected-spreading-based network embedding in static and temporal networks.
    EPJ Data Science, 9, 30 (2020). [open access]
    Preprint: arXiv:2004.06750

  16. Mengqiao Xu, Qian Pan, Haoxiang Xia, Naoki Masuda.
    Estimating international trade status of countries from global liner shipping networks.
    Royal Society Open Science, 7, 200386 (2020). [open access]
    Preprint: arXiv:2001.07688
    Data and Python codes

  17. Marinho A. Lopes, Jiaxiang Zhang, Dominik Krzemiński, Khalid Hamandi, Qi Chen, Lorenzo Livi, Naoki Masuda.
    Recurrence quantification analysis of dynamic brain networks.
    European Journal of Neuroscience, 53, 1040-1059 (2021). [open access]
    Preprint: arXiv:2001.03761

  18. Irene Malvestio, Alessio Cardillo, Naoki Masuda.
    Interplay between k-core and community structure in complex networks.
    Scientific Reports, 10, 14702 (2020). [open access]
    Preprint: arXiv:2005.01147

  19. Genki Ichinose, Daiki Miyagawa, Junji Ito, Naoki Masuda.
    Winning by hiding behind others: An analysis of speed skating data.
    PLOS ONE, 15, e0237470 (2020). [open access]
    Preprint: arXiv:2004.06464
    日本語の研究紹介(Qiita)(in Japanese)
    研究ナビの記事 (in Japanese)(Qiita の記事と内容は同一)

  20. Naoki Masuda, Takayuki Hiraoka.
    Waiting-time paradox in 1922.
    Northeast Journal of Complex Systems, 2, 1 (2020). [open access]
    Preprint: arXiv:2004.14081

  21. Alessio Cardillo, Naoki Masuda.
    Critical mass effect in evolutionary games triggered by zealots.
    Physical Review Research, 2, 023305 (2020). [open access]
    Preprint: arXiv:1912.00400

  22. Naoki Masuda, Petter Holme.
    Small inter-event times govern epidemic spreading on networks.
    Physical Review Research, 2, 023163 (2020). [open access]
    Preprint: arXiv:1911.04040

  23. Takayuki Hiraoka, Naoki Masuda, Aming Li, Hang-Hyun Jo.
    Modeling temporal networks with bursty activity patterns of nodes and links.
    Physical Review Research, 2, 023073 (2020). [open access]
    Preprint: arXiv:1912.11212

  24. Gabriele Valentini, Naoki Masuda, Zachary Shaffer, Jake R. Hanson, Takao Sasaki, Sara Imari Walker, Theodore P. Pavlic, Stephen C. Pratt.
    Division of labor promotes the spread of information in colony emigrations by the ant Temnothorax rugatulus.
    Proceedings of the Royal Society B: Biological Sciences, 287, 20192950 (2020).
    Preprint: https://doi.org/10.1101/791996
    Featured by ASU Now
    Video

  25. Makoto Okada, Kenji Yamanishi, Naoki Masuda.
    Long-tailed distributions of inter-event times as mixtures of exponential distributions.
    Royal Society Open Science, 7, 191643 (2020). [open access]
    Preprint: arXiv:1905.00699
    Python codes

  26. Naoki Masuda, Victor M. Preciado, Masaki Ogura.
    Analysis of the susceptible-infected-susceptible epidemic dynamics in networks via the non-backtracking matrix.
    IMA Journal of Applied Mathematics, 85, 214-230 (2020). [open access]
    Preprint: arXiv:1906.04269

  27. Takahiro Ezaki, Elohim Fonseca dos Reis, Takamitsu Watanabe, Michiko Sakaki, Naoki Masuda.
    Closer to critical resting-state neural dynamics in individuals with higher fluid intelligence.
    Communications Biology, 3, 52 (2020). [open access]
    Preprint: https://doi.org/10.1101/688655
    C code (the code to gather outputs stored in different files is in Python)

  28. Dominik Krzemiński, Naoki Masuda, Khalid Hamandi, Krish D. Singh, Bethany Routley, Jiaxiang Zhang.
    Energy landscape of resting magnetoencephalography reveals fronto-parietal network impairments in epilepsy.
    Network Neuroscience, 4, 374-396 (2020).
    Preprint: https://doi.org/10.1101/703074

  29. Sadamori Kojaku, Naoki Masuda.
    Constructing networks by filtering correlation matrices: A null model approach.
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 475, 20190578 (2019).
    Preprint: arXiv:1903.10805
    Python codes

  30. Naoki Masuda, Fanlin Meng.
    Dynamical stability of water distribution networks.
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 475, 20190291 (2019).
    Preprint: arXiv:1905.06132
    MATLAB code and water distribution network data

  31. Masaki Ogura, Victor M. Preciado, Naoki Masuda.
    Optimal containment of epidemics over temporal activity-driven networks.
    SIAM Journal on Applied Mathematics, 79, 986-1006 (2019).
    Preprint: arXiv:1802.08961

  32. Takamitsu Watanabe, Geraint Rees, Naoki Masuda.
    Atypical intrinsic neural timescale in autism.
    eLife, 8, e42256 (2019). [open access]
    Download presentation slides
    Related insight article by Leonardo L. Gollo

  33. Naoki Masuda, Petter Holme.
    Detecting sequences of system states in temporal networks.
    Scientific Reports, 9, 795 (2019). [open access]
    Preprint: arXiv:1803.04755
    Python and MATLAB codes
    Short introduction to this research
    日本語の研究紹介 (in Japanese)

  34. Sadamori Kojaku, Mengqiao Xu, Haoxiang Xia, Naoki Masuda.
    Multiscale core-periphery structure in a global liner shipping network.
    Scientific Reports, 9, 404 (2019). [open access]
    Preprint: arXiv:1808.04549
    Python codes

  35. Naoki Masuda, Sadamori Kojaku, Yukie Sano.
    Configuration model for correlation matrices preserving the node strength.
    Physical Review E, 98, 012312 (2018). [open access]
    Typo
    Preprint: arXiv:1806.08709
    MATLAB codes

  36. Sadamori Kojaku, Giulio Cimini, Guido Caldarelli, Naoki Masuda.
    Structural changes in the interbank market across the financial crisis from multiple core-periphery analysis.
    Journal of Network Theory in Finance, 4, 33-51 (2018).
    Preprint: arXiv:1802.05139

  37. Takuya Sekiguchi, Kohei Tamura, Naoki Masuda.
    Population changes in residential clusters in Japan.
    PLOS ONE, 13, e0197144 (2018). [open access]
    Preprint: arXiv:1706.09439

  38. Sadamori Kojaku, Naoki Masuda.
    A generalised significance test for individual communities in networks.
    Scientific Reports, 8, 7351 (2018). [open access]
    Preprint: arXiv:1712.00298
    Python codes

  39. Sadamori Kojaku, Naoki Masuda.
    Core-periphery structure requires something else in the network.
    New Journal of Physics, 20, 043012 (2018). [open access]
    Preprint: arXiv:1710.07076
    C++ and MATLAB codes

  40. Takahiro Ezaki, Michiko Sakaki, Takamitsu Watanabe, Naoki Masuda.
    Age-related changes in the ease of dynamical transitions in human brain activity.
    Human Brain Mapping, 39, 2673-2688 (2018). [open access]

  41. Naoki Masuda, Michiko Sakaki, Takahiro Ezaki, Takamitsu Watanabe.
    Clustering coefficients for correlation networks.
    Frontiers in Neuroinformatics, 12, 7 (2018). [open access]
    Typo
    Preprint: arXiv:1806.10228
    Download presentation slides
    C++ codes

  42. Genki Ichinose, Naoki Masuda.
    Zero-determinant strategies in finitely repeated games.
    Journal of Theoretical Biology, 438, 61-77 (2018). [open access]
    Preprint: arXiv:1707.03097

  43. Naoki Masuda, Luis E. C. Rocha.
    A Gillespie algorithm for non-Markovian stochastic processes.
    SIAM Review, 60, 95-115 (2018). [open access]
    Preprint: arXiv:1601.01490
    C/C++ codes for the Laplace Gillespie algorithm, one to generate positively correlated inter-event times etc.
    Short introduction to this research
    日本語の研究紹介 (in Japanese)

  44. Takahiro Ezaki, Naoki Masuda.
    Reinforcement learning account of network reciprocity.
    PLOS ONE, 12, e0189220 (2017). [open access]
    Preprint: arXiv:1706.04310

  45. Sadamori Kojaku, Naoki Masuda.
    Finding multiple core-periphery pairs in networks.
    Physical Review E, 96, 052313 (2017). [open access]
    Preprint: arXiv:1702.06903
    MATLAB codes
    日本語の研究紹介 (in Japanese)

  46. Luis E. C. Rocha, Naoki Masuda, Petter Holme.
    Sampling of temporal networks: Methods and biases.
    Physical Review E, 96, 052302 (2017). [open access]
    Preprint: arXiv:1707.02108

  47. Tomokatsu Onaga, James P. Gleeson, Naoki Masuda.
    Concurrency-induced transitions in epidemic dynamics on temporal networks.
    Physical Review Letters, 119, 108301 (2017). [open access]
    Preprint: arXiv:1702.05054
    Download presentation slides

  48. Naoki Masuda, Mason A. Porter, Renaud Lambiotte.
    Random walks and diffusion on networks.
    Physics Reports, 716-717, 1-58 (2017). [open access]

    Corrigendum to ``Random walks and diffusion on networks'' [Phys. Rep. 716-717 (2017) 1-58].
    Physics Reports, 745, 96 (2018).

    Second corrigendum to ``Random walks and diffusion on networks'' [Phys. Rep. 716-717 (2017) 1-58].
    Physics Reports, 851, 37-39 (2020).

    Preprint: arXiv:1612.03281
    Download presentation slides

  49. Kohei Tamura, Naoki Masuda.
    Effects of the distant population density on spatial patterns of demographic dynamics.
    Royal Society Open Science, 4, 170391 (2017). [open access]
    Typo
    Preprint: arXiv:1704.07523

  50. Takahiro Ezaki, Takamitsu Watanabe, Masayuki Ohzeki, Naoki Masuda.
    Energy landscape analysis of neuroimaging data.
    Philosophical Transactions of the Royal Society A, 375, 20160287 (2017). [open access]
    Preprint: arXiv:1611.05137
    MATLAB code for calculating and visualizing energy landscapes is availble here.
    MATLAB code to calculate the maximum-likelihood estimator is also available as the supplementary material of the paper.

  51. Thomas A. O'Shea-Wheller, Naoki Masuda, Ana Sendova-Franks, Nigel R. Franks.
    Variability in individual assessment behaviour and its implications for collective decision-making.
    Proceedings of the Royal Society B: Biological Sciences, 284, 20162237 (2017).
    Featured by New Scientist

  52. Yutaka Horita, Masanori Takezawa, Keigo Inukai, Toshimasa Kita, Naoki Masuda.
    Reinforcement learning accounts for moody conditional cooperation behavior: experimental results.
    Scientific Reports, 7, 39275 (2017). [open access]

  53. Teruyoshi Kobayashi, Naoki Masuda.
    Fragmenting networks by targeting collective influencers at a mesoscopic level.
    Scientific Reports, 6, 37778 (2016). [open access]
    Preprint: arXiv:1605.03694
    MATLAB codes for the immunization algorithm

  54. Luis E. C. Rocha, Naoki Masuda.
    Individual-based approach to epidemic processes on arbitrary dynamic contact networks.
    Scientific Reports, 6, 31456 (2016). [open access]
    Preprint: arXiv:1510.09179

  55. Takahiro Ezaki, Yutaka Horita, Masanori Takezawa, Naoki Masuda.
    Reinforcement learning explains conditional cooperation and its moody cousin.
    PLOS Computational Biology, 12, e1005034 (2016). [open access]
    日本語の研究紹介 (in Japanese)

  56. Leo Speidel, Konstantin Klemm, Víctor M. Eguíluz, Naoki Masuda.
    Temporal interactions facilitate endemicity in the susceptible-infected-susceptible epidemic model.
    New Journal of Physics, 18, 073013 (2016). [open access]
    Typos
    Preprint: arXiv:1602.00859
    Download presentation slides

  57. Ryosuke Nishi, Taro Takaguchi, Keigo Oka, Takanori Maehara, Masashi Toyoda, Ken-ichi Kawarabayashi, Naoki Masuda.
    Reply trees in Twitter: data analysis and branching process models.
    Social Network Analysis and Mining, 6, 26 (2016). [open access]

  58. Naoki Masuda.
    Accelerating coordination in temporal networks by engineering the link order.
    Scientific Reports, 6, 22105 (2016). [open access]
    Preprint: arXiv:1510.09085

  59. Yutaka Horita, Masanori Takezawa, Takuji Kinjo, Yo Nakawake, Naoki Masuda.
    Transient nature of cooperation by pay-it-forward reciprocity.
    Scientific Reports, 6, 19471 (2016). [open access]

  60. Jens Malmros, Naoki Masuda, Tom Britton.
    Random walks on directed networks: Inference and respondent-driven sampling.
    Journal of Official Statistics, 32, 433-459 (2016). [open access]
    Preprint: arXiv:1308.3600

  61. Leo Speidel, Taro Takaguchi, Naoki Masuda.
    Community detection in directed acyclic graphs.
    European Physical Journal B, 88, 203 (2015). [open access]
    Preprint: arXiv:1503.05641
    Featured by Advances in Engineering

  62. Kohei Tamura, Naoki Masuda.
    Win-stay lose-shift strategy in formation changes in football.
    EPJ Data Science, 4, 9 (2015). [open access]
    Preprint: arXiv:1503.02484
    Short introduction to this research
    日本語の研究紹介 (in Japanese)

  63. Nigel Franks, Jonathan Stuttard, Carolina Doran, Julian Esposito, Maximillian Master, Ana Sendova-Franks, Naoki Masuda, Nicholas Britton.
    How ants use quorum sensing to estimate the average quality of a fluctuating resource.
    Scientific Reports, 5, 11890 (2015). [open access]

  64. Naoki Masuda, Thomas A. O'Shea-Wheller, Carolina Doran, Nigel R. Franks.
    Computational model of collective nest selection by ants with heterogeneous acceptance thresholds.
    Royal Society Open Science, 2, 140533 (2015). [open access]

  65. Naoki Masuda, Feng Fu.
    Evolutionary models of in-group favoritism.
    F1000Prime Reports, 7, 27 (2015). [open access]

  66. Naoki Masuda.
    Opinion control in complex networks.
    New Journal of Physics, 17, 033031 (2015). [open access]
    Preprint: arXiv:1412.2170

  67. Petter Holme, Naoki Masuda.
    The basic reproduction number as a predictor for epidemic outbreaks in temporal networks.
    PLOS ONE, 10, e0120567 (2015). [open access]
    Preprint: arXiv:1407.6598

  68. Víctor M. Eguíluz, Naoki Masuda, Juan Fernández-Gracia.
    Bayesian decision making in human collectives with binary choices.
    PLOS ONE, 10, e0121332 (2015). [open access]
    Preprint: arXiv:1502.01055
    Also available at SSRN

  69. Leo Speidel, Renaud Lambiotte, Kazuyuki Aihara, Naoki Masuda.
    Steady state and mean recurrence time for random walks on stochastic temporal networks.
    Physical Review E, 91, 012806 (2015). [open access]
    Preprint: arXiv:1407.4582

  70. Yohei Nakajima, Naoki Masuda.
    Evolutionary dynamics in finite populations with zealots.
    Journal of Mathematical Biology, 70, 465-484 (2015). [open access]
    Preprint:
    arXiv:1308.2273

  71. Takamitsu Watanabe, Naoki Masuda, Fukuda Megumi, Ryota Kanai, Geraint Rees.
    Energy landscape and dynamics of brain activity during human bistable perception.
    Nature Communications, 5, 4765 (2014). [open access]
    MATLAB code for calculating and visualizing energy landscapes is availble here.
    MATLAB code to calculate the maximum-likelihood estimator is also available as the supplementary material of one of our papers.
    日本語の研究紹介 (in Japanese)

  72. Hiroyuki Shimoji, Masato S. Abe, Kazuki Tsuji, Naoki Masuda.
    Global network structure of dominance hierarchy of ant workers.
    Journal of the Royal Society Interface, 11, 20140599 (2014). [open access]
    Preprint: arXiv:1407.4277
    Download presentation slides
    Dominance network data are available at the journal's website.
    日本語の研究紹介 (in Japanese)

  73. Ryosuke Nishi, Naoki Masuda.
    Dynamics of social balance under temporal interaction.
    EPL, 107, 48003 (2014). [open access]
    Preprint: arXiv:1403.4891

  74. Yuni Iwamasa, Naoki Masuda.
    Networks maximizing the consensus time of voter models.
    Physical Review E, 90, 012816 (2014).
    Preprint: arXiv:1404.6360

  75. Naoki Masuda.
    Voter model on the two-clique graph.
    Physical Review E, 90, 012802 (2014). [open access]
    Preprint: arXiv:1403.4763

  76. Takamitsu Watanabe, Shigeyuki Kan, Takahiko Koike, Masaya Misaki, Seiki Konishi, Satoru Miyauchi, Yasushi Miyashita, Naoki Masuda.
    Network-dependent modulation of brain activity during sleep.
    NeuroImage, 98, 1-10 (2014). [open access]

  77. Luis E. C. Rocha, Naoki Masuda.
    Random walk centrality for temporal networks.
    New Journal of Physics, 16, 063023 (2014). [open access]
    Preprint: arXiv:1401.5648

  78. Takamitsu Watanabe, Masanori Takezawa, Yo Nakawake, Akira Kunimatsu, Hidenori Yamasue, Mitsuhiro Nakamura, Yasushi Miyashita, Naoki Masuda.
    Two distinct neural mechanisms underlying indirect reciprocity.
    Proceedings of the National Academy of Sciences of the United States of America, 111, 3990-3995 (2014). [open access]
    Featured by Le Scienze (in Italian)
    Press release (in Japanese)

  79. Naoki Masuda.
    Evolution via imitation among like-minded individuals.
    Journal of Theoretical Biology, 349, 100-108 (2014). [open access]
    Preprint: arXiv:1307.4141

  80. Koji Oishi, Manuel Cebrian, Andres Abeliuk, Naoki Masuda.
    Iterated crowdsourcing dilemma game.
    Scientific Reports, 4, 4100 (2014). [open access]
    Preprint: arXiv:1401.4267

  81. Takamitsu Watanabe, Satoshi Hirose, Hiroyuki Wada, Yoshio Imai, Toru Machida, Ichiro Shirouzu, Seiki Konishi, Yasushi Miyashita, Naoki Masuda.
    Energy landscapes of resting-state brain networks.
    Frontiers in Neuroinformatics, 8, 12 (2014). [open access]

  82. Kodai Saito, Naoki Masuda.
    Two types of well followed users in the followership networks of Twitter.
    PLOS ONE, 9, e84265 (2014). [open access]
    Preprint: arXiv:1302.0677

  83. Shoma Tanabe, Naoki Masuda.
    Complex dynamics of a nonlinear voter model with contrarian agents.
    Chaos, 23, 043136 (2013). [open access]
    Preprint: arXiv:1308.2795

  84. Naoki Masuda, Konstantin Klemm, Víctor M. Eguíluz.
    Temporal networks: slowing down diffusion by long lasting interactions.
    Physical Review Letters, 111, 188701 (2013). [open access]
    Preprint: arXiv:1305.2938

  85. Naoki Masuda.
    Voter models with contrarian agents.
    Physical Review E, 88, 052803 (2013). [open access]
    Preprint: arXiv:1306.4401

  86. Takehisa Hasegawa, Taro Takaguchi, Naoki Masuda.
    Observability transitions in correlated networks.
    Physical Review E, 88, 042809 (2013). [open access]
    Preprint: arXiv:1309.1862

  87. Makoto Hiroi, Masamichi Ohkura, Junichi Nakai, Naoki Masuda, Koichi Hashimoto, Kiichi Inoue, André Fiala, Tetsuya Tabata.
    Principal component analysis of odor coding at the level of third order olfactory neurons in Drosophila.
    Genes to Cells, 18, 1070-1081 (2013).

  88. Ryosuke Nishi, Naoki Masuda.
    Collective opinion formation model under Bayesian updating and confirmation bias.
    Physical Review E, 87, 062123 (2013). [open access]
    Preprint: arXiv:1302.3949

  89. Taro Takaguchi, Naoki Masuda, Petter Holme.
    Bursty communication patterns facilitate spreading in a threshold-based epidemic dynamics.
    PLOS ONE, 8, e68629 (2013). [open access]
    Preprint: arXiv:1206.2097

  90. Naoki Masuda, Issei Kurahashi, Hiroko Onari.
    Suicide ideation of individuals in online social networks.
    PLOS ONE, 8, e62262 (2013). [open access]
    Preprint: arXiv:1207.0561
    Featured by Psychological Progress
    Featured by MIT Technology Review
    Featured by I Programmer news
    Featured by The Japan Daily Press
    日本語の研究紹介 (in Japanese)

  91. Masayoshi Ito, Naoki Masuda, Kazunori Shinomiya, Keita Endo, Kei Ito.
    Systematic analysis of neural projections reveals clonal composition of the Drosophila brain.
    Current Biology, 23, 644-655 (2013).

  92. Naoki Masuda, Petter Holme.
    Predicting and controlling infectious disease epidemics using temporal networks.
    F1000Prime Reports, 5, 6 (2013). [open access]

  93. Shun-ichi Amari, Hiroyasu Ando, Taro Toyoizumi, Naoki Masuda.
    State concentration exponent as a measure of quickness in Kauffman-type networks.
    Physical Review E, 87, 022814 (2013). [open access]
    Preprint: arXiv:1202.6526

  94. Takamitsu Watanabe, Satoshi Hirose, Hiroyuki Wada, Yoshio Imai, Toru Machida, Ichiro Shirouzu, Seiki Konishi, Yasushi Miyashita, Naoki Masuda.
    A pairwise maximum entropy model accurately describes resting-state human brain networks.
    Nature Communications, 4, 1370 (2013). [open access]
    Unofficial errata
    MATLAB code to calculate the maximum-likelihood estimator is also available as the supplementary material of one of our papers.

  95. Ryo Fujie, Kazuyuki Aihara, Naoki Masuda.
    A model of competition among more than two languages.
    Journal of Statistical Physics, 151, 289-303 (2013). [open access]
    Preprint: arXiv:1206.4557

  96. Shoma Tanabe, Hideyuki Suzuki, Naoki Masuda.
    Indirect reciprocity with trinary reputations.
    Journal of Theoretical Biology, 317, 338-347 (2013). [open access]
    Preprint: arXiv:1205.3547

  97. Mitsuhiro Nakamura, Naoki Masuda.
    Groupwise information sharing promotes ingroup favoritism in indirect reciprocity.
    BMC Evolutionary Biology, 12, 213 (2012). [open access]
    Preprint: arXiv:1207.5663
    Download presentation slides

  98. Shun Motegi, Naoki Masuda.
    A network-based dynamical ranking system for competitive sports.
    Scientific Reports, 2, 904 (2012). [open access]
    Featured by Nature Japan (in Japanese)
    Preprint: arXiv:1203.2228
    Download presentation slides (in Japanese)

  99. Naoki Masuda.
    Evolution of cooperation driven by zealots.
    Scientific Reports, 2, 646 (2012). [open access]
    Featured by Nature Japan (in Japanese)
    Preprint: arXiv:1207.2548

  100. Taro Takaguchi, Nobuo Sato, Kazuo Yano, Naoki Masuda.
    Importance of individual events in temporal networks.
    New Journal of Physics, 14, 093003 (2012). [open access]
    Preprint: arXiv:1205.4808
    Download presentation slides

  101. Naoki Masuda, Mitsuhiro Nakamura.
    Coevolution of trustful buyers and cooperative sellers in the trust game.
    PLOS ONE,7(9), e44169 (2012). [open access]
    Preprint: arXiv:1103.2648

  102. Naoki Masuda.
    Ingroup favoritism and intergroup cooperation under indirect reciprocity based on group reputation.
    Journal of Theoretical Biology, 311, 8-18 (2012). [open access]
    Preprint: arXiv:1205.2825

  103. Taro Ueno, Naoki Masuda, Shoen Kume, Kazuhiko Kume.
    Dopamine modulates the rest period length without perturbation of its power law distribution in Drosophila melanogaster.
    PLOS ONE, 7 (2), e32007 (2012). [open access]

  104. Hiroshi Kori, Yoji Kawamura, Naoki Masuda.
    Structure of cell networks critically determines oscillation regularity.
    Journal of Theoretical Biology, 297, 61-72 (2012). [open access]
    Preprint: arXiv:1108.4790

  105. Shoma Tanabe, Naoki Masuda.
    Evolution of cooperation facilitated by reinforcement learning with adaptive aspiration levels.
    Journal of Theoretical Biology, 293, 151-160 (2012). [open access]
    Preprint: arXiv:1106.6107

  106. Naoki Masuda.
    Clustering in large networks does not promote upstream reciprocity.
    PLOS ONE, 6 (10), e25190 (2011). [open access]
    Preprint: arXiv:1108.1440

  107. Taro Takaguchi, Naoki Masuda.
    Voter model with non-Poissonian inter-event intervals.
    Physical Review E, 84, 036115 (2011). [open access]
    Preprint: arXiv:1011.4445

  108. Takehisa Hasegawa, Naoki Masuda.
    Robustness of networks against propagating attacks under vaccination strategies.
    Journal of Statistical Mechanics, P09014 (2011).
    Preprint: arXiv:1102.4878

  109. Taro Takaguchi, Mitsuhiro Nakamura, Nobuo Sato, Kazuo Yano, Naoki Masuda.
    Predictability of conversation partners.
    Physical Review X, 1, 011008 (2011). [open access]
    Preprint: arXiv:1104.5344
    Download presentation slides

  110. Mitsuhiro Nakamura, Naoki Masuda.
    Indirect reciprocity under incomplete observation.
    PLOS Computational Biology, 7 (7), e1002113 (2011). [open access]

  111. C.-K. Yun, N. Masuda, B. Kahng.
    Diversity and critical behavior in prisoner's dilemma game.
    Physical Review E, 83, 057102 (2011).
    Preprint: arXiv:1006.3607

  112. Naoki Masuda, Mitsuhiro Nakamura.
    Numerical analysis of a reinforcement learning model with the dynamic aspiration level in the iterated Prisoner's Dilemma.
    Journal of Theoretical Biology, 278, 55-62 (2011). [open access]
    Preprint: arXiv:1012.0121

  113. Takehisa Hasegawa, Norio Konno, Naoki Masuda.
    Numerical study of a three-state host-parasite system on the square lattice.
    Physical Review E, 83, 046102 (2011).
    Preprint: arXiv:1006.4428

  114. Yuri Ogiso, Kazuhide Tsuneizumi, Naoki Masuda, Makoto Sato, Tetsuya Tabata.
    Robustness of the Dpp morphogen activity gradient depends on negative feedback regulation by the inhibitory Smad, Dad.
    Development Growth and Differentiation, 53, 668-678 (2011).

  115. Naoki Masuda, S. Redner.
    Can partisan voting lead to truth?
    Journal of Statistical Mechanics, L02002 (2011). [open access]
    Preprint: arXiv:1012.2462

  116. Naoki Masuda, Hiroshi Kori.
    Dynamics-based centrality for directed networks.
    Physical Review E, 82, 056107 (2010).
    Preprint: arXiv:1006.3138
    Selected for Virtual Journal of Biological Physics Research, 20(10) (2010).

  117. Takamitsu Watanabe, Naoki Masuda.
    Enhancing the spectral gap of networks by node removal.
    Physical Review E, 82, 046102 (2010).
    Preprint: arXiv:1003.4340
    Download presentation slides [pdf only]

  118. Jun Ohkubo, Kazushi Yoshida, Yuichi Iino, Naoki Masuda.
    Long-tail behavior in locomotion of Caenorhabditis elegans.
    Journal of Theoretical Biology, 267, 213-222 (2010).
    Preprint: arXiv:1008.3014
    日本語の研究紹介 (in Japanese)

  119. Naoki Masuda.
    Effects of diffusion rates on epidemic spreads in metapopulation networks.
    New Journal of Physics, 12, 093009 (2010). [open access]
    Preprint: arXiv:1004.2391

  120. Naoki Masuda, Yoji Kawamura, Hiroshi Kori.
    Collective fluctuations in networks of noisy components.
    New Journal of Physics, 12, 093007 (2010). [open access]
    Preprint: arXiv:0911.5013

  121. Ralf Tönjes, Naoki Masuda, Hiroshi Kori.
    Synchronization transition of identical phase oscillators in a directed small-world network.
    Chaos, 20, 033108 (2010). [open access]
    Preprint: arXiv:1003.2020

  122. Naoki Masuda, N. Gibert, S. Redner.
    Heterogeneous voter models.
    Physical Review E, 82, 010103(R) (2010).
    Preprint: arXiv:1003.0768

  123. Akio Iwagami, Naoki Masuda.
    Upstream reciprocity in heterogeneous networks.
    Journal of Theoretical Biology, 265, 297-305 (2010). [open access]
    Preprint: arXiv:0905.4007

  124. Yusuke Ide, Norio Konno, Naoki Masuda.
    Statistical properties of a generalized threshold network model.
    Methodology & Computing in Applied Probability, 12, 361-377 (2010).
    Preprint: arXiv:0707.1744
    Download presentation slides

  125. Naoki Masuda.
    Immunization of networks with community structure.
    New Journal of Physics, 11, 123018 (2009). [open access]
    Preprint: arXiv:0909.1945

  126. Naoki Masuda, Yoji Kawamura, Hiroshi Kori.
    Impact of hierarchical modular structure on ranking of individual nodes in directed networks.
    New Journal of Physics, 11, 113002 (2009). [open access]
    Preprint: arXiv:0907.0900

  127. Naoki Masuda, Yoji Kawamura, Hiroshi Kori.
    Analysis of relative influence of nodes in directed networks.
    Physical Review E, 80, 046114 (2009).
    Preprint: arXiv:0907.0901

  128. Naoki Masuda, Hisashi Ohtsuki.
    A theoretical analysis of temporal difference learning in the iterated Prisoner's Dilemma game.
    Bulletin of Mathematical Biology, 71, 1818-1850 (2009).

  129. Naoki Masuda.
    Selective population rate coding: a possible computational role of gamma oscillations in selective attention.
    Neural Computation, 21, 3335-3362 (2009).

  130. Yuko K. Takahashi, Hiroshi Kori, Naoki Masuda.
    Self-organization of feedforward structure and entrainment in excitatory neural networks with spike-timing-dependent plasticity.
    Physical Review E, 79, 051904 (2009).
    Preprint: arXiv:0809.1127
    Selected for Virtual Journal of Biological Physics Research, 17(10) (2009).

  131. Naoki Masuda, Hisashi Ohtsuki.
    Evolutionary dynamics and fixation probabilities in directed networks.
    New Journal of Physics, 11, 033012 (2009). [open access]
    Preprint: arXiv:0812.1075

  132. Naoki Masuda.
    Directionality of contact networks suppresses selection pressure in evolutionary dynamics.
    Journal of Theoretical Biology, 258, 323-334 (2009). [open access]
    Preprint: arXiv:0812.1076

  133. N. Masuda, J. S. Kim, B. Kahng.
    Priority queues with bursty arrivals of incoming tasks.
    Physical Review E, 79, 036106 (2009).
    Preprint: arXiv:0805.0841

  134. Taro Ueno, Naoki Masuda.
    Controlling nosocomial infection based on structure of hospital social networks.
    Journal of Theoretical Biology, 254, 655-666 (2008). [open access]
    Preprint: arXiv:0803.1879
    Download presentation slides

  135. Naoki Masuda.
    Oscillatory dynamics in evolutionary games are suppressed by heterogeneous adaptation rates of players.
    Journal of Theoretical Biology, 251,181-189 (2008). [open access]
    Preprint: arXiv:0803.1023

  136. Naoki Masuda, Shun-ichi Amari.
    A computational study of synaptic mechanisms of partial memory transfer in cerebellar vestibulo-ocular-reflex learning.
    Journal of Computational Neuroscience, 24, 137-156 (2008).

  137. Nobuaki Sugimine, Naoki Masuda, Norio Konno, Kazuyuki Aihara.
    On global and local critical points of extended contact process on homogeneous trees.
    Mathematical Biosciences, 213, 13-17 (2008).

  138. Naoki Masuda, Brent Doiron.
    Gamma oscillations of spiking neural populations enhance signal discrimination.
    PLOS Computational Biology, 3 (11), e236, 2348-2355 (2007). [open access]

  139. Naoki Masuda.
    Participation costs dismiss the advantage of heterogeneous networks in evolution of cooperation.
    Proceedings of the Royal Society B: Biological Sciences, 274, 1815-1821 (2007). [open access]
    Preprint: arXiv:physics/0702017
    Download presentation slides

  140. Naoki Masuda, Hiroshi Kori.
    Formation of feedforward networks and frequency synchrony by spike-timing-dependent plasticity.
    Journal of Computational Neuroscience, 22, 327-345 (2007).
    Preprint: arXiv:1207.2816

  141. Naoki Masuda, Masato Okada, Kazuyuki Aihara.
    Filtering of spatial bias and noise inputs by spatially structured neural networks.
    Neural Computation, 19, 1854-1870 (2007).

  142. Naoki Masuda, Kazuyuki Aihara.
    Dual coding hypotheses for neural information representation.
    Mathematical Biosciences, 207, 312-321 (2007).

  143. Naoki Masuda, Hisashi Ohtsuki.
    Tag-based indirect reciprocity by incomplete social information.
    Proceedings of the Royal Society B: Biological Sciences, 274, 689-695 (2007). [open access]
    Download presentation slides

  144. Yong-Yeol Ahn, Hawoong Jeong, Naoki Masuda, Jae Dong Noh.
    Epidemic dynamics of two species of interacting particles on scale-free networks.
    Physical Review E, 74, 066113 (2006).
    Preprint: arXiv:cont-mat/0608461

  145. Naoki Masuda, Norio Konno.
    Networks with dispersed degrees save stable coexistence of species in cyclic competition.
    Physical Review E, 74, 066102 (2006).
    Preprint: arXiv:cond-mat/0603114

  146. Yuichi Katori, Naoki Masuda, Kazuyuki Aihara.
    Dynamic switching of optimal neural codes in networks with gap junctions.
    Neural Networks, 19, 1463-1466 (2006).

  147. Naoki Masuda, Norio Konno.
    Multi-state epidemic processes on complex networks.
    Journal of Theoretical Biology, 243, 64-75 (2006).
    Preprint: arXiv:cond-mat/0504329

  148. Kazumichi Ohtsuka, Norio Konno, Naoki Masuda, Kazuyuki Aihara.
    Phase diagrams and correlation inequalities of a three-state stochastic epidemic model on the square lattice.
    International Journal of Bifurcation and Chaos, 16(12), 3687-3693 (2006).

  149. Naoki Masuda, Goce Jakimoski, Kazuyuki Aihara, Ljupco Kocarev.
    Chaotic block ciphers: from theory to practical algorithms.
    IEEE Transactions on Circuits and Systems Part I, 53(6), 1341-1352 (2006).

  150. Naoki Masuda, Norio Konno.
    VIP-club phenomenon: emergence of elites and masterminds in social networks.
    Social Networks, 28, 297-309 (2006).
    Preprint: arXiv:cond-mat/0501129
    Download presentation slides

  151. Naoki Masuda.
    Simultaneous rate-synchrony codes in populations of spiking neurons.
    Neural Computation, 18, 45-59 (2006).

  152. N. Masuda, K.-I. Goh, B. Kahng.
    Extremal dynamics on complex networks: analytic solutions.
    Physical Review E, 72, 066106 (2005).
    Preprint: arXiv:cond-mat/0508623

  153. Norio Konno, Naoki Masuda, Rahul Roy, Anish Sarkar.
    Rigorous results on the threshold network model.
    Journal of Physics A: Mathematical and General, 38, 6277-6291 (2005).
    Preprint: arXiv:math.PR/0505681
    Download presentation slides

  154. Naoki Masuda, Brent Doiron, André Longtin, Kazuyuki Aihara.
    Coding of temporally varying signals in networks of spiking neurons with global delayed feedback.
    Neural Computation, 17, 2139-2175 (2005).

  155. Naoki Masuda, Hiroyoshi Miwa, Norio Konno.
    Geographical threshold graphs with small-world and scale-free properties.
    Physical Review E, 71, 036108 (2005).
    Preprint: arXiv:cond-mat/0409378
    Download presentation slides

  156. Naoki Masuda, Hiroyoshi Miwa, Norio Konno.
    Analysis of scale-free networks based on a threshold graph with intrinsic vertex weights.
    Physical Review E, 70, 036124 (2004).
    Preprint: arXiv:cond-mat/0403524
    Download presentation slides

  157. Naoki Masuda, Norio Konno.
    Subcritical behavior in the alternating supercritical Domany-Kinzel dynamics.
    European Physical Journal B, 40, 313-319 (2004).
    Preprint: arXiv:cond-mat/0407745

  158. Naoki Masuda, Norio Konno.
    Return times of random walk on generalized random graphs.
    Physical Review E, 69, 066113 (2004).
    Preprint: arXiv:cond-mat/0401255
    Selected for Virtual Journal of Biological Physics Research, 7(12) (2004).
    Download presentation slides

  159. Naoki Masuda, Kazuyuki Aihara.
    Dual coding and effects of global feedback in multilayered neural networks.
    Neurocomputing, 58-60, 33-39 (2004).

  160. Naoki Masuda, Norio Konno, Kazuyuki Aihara.
    Transmission of severe acute respiratory syndrome in dynamical small-world networks.
    Physical Review E, 69, 031917 (2004).
    Preprint: arXiv:cond-mat/0401598
    Selected for Virtual Journal of Biological Physics Research, 7(7) (2004).

  161. Naoki Masuda, Kazuyuki Aihara.
    Self-organizing dual coding based on spike-time-dependent plasticity.
    Neural Computation, 16, 627-663 (2004).

  162. Naoki Masuda, Kazuyuki Aihara.
    Global and local synchrony of coupled neurons in small-world networks.
    Biological Cybernetics, 90, 302-309 (2004).

  163. Naoki Masuda, Kazuyuki Aihara.
    Spatial prisoner's dilemma optimally played in small-world networks.
    Physics Letters A, 313, 55-61 (2003).
    Download presentation slides

  164. Naoki Masuda, Kazuyuki Aihara.
    Filtered interspike interval encoding by class II neurons.
    Physics Letters A, 311, 485-490 (2003).

  165. Naoki Masuda, Kazuyuki Aihara.
    Ergodicity of spike trains: when does trial averaging make sense
    Neural Computation, 15, 1341-1372 (2003).

  166. Naoki Masuda, Kazuyuki Aihara.
    Duality of rate coding and temporal spike coding in multilayered feedforward networks.
    Neural Computation, 15, 103-125 (2003).

  167. Naoki Masuda, Kazuyuki Aihara.
    Bridging rate coding and temporal spike coding by effect of noise.
    Physical Review Letters, 88, 248101 (2002).
    Selected for Virtual Journal of Biological Physics Research, 3(11) (2002).

  168. Naoki Masuda, Kazuyuki Aihara.
    Spatiotemporal spike encoding of a continuous external signal.
    Neural Computation, 14, 1599-1628 (2002).

  169. Naoki Masuda, Kazuyuki Aihara.
    Dynamical characteristics of discretized chaotic permutations.
    International Journal of Bifurcation and Chaos, 12, 2087-2103 (2002).

  170. Naoki Masuda, Kazuyuki Aihara.
    Cryptosystems with discretized chaotic maps.
    IEEE Transactions on Circuits and Systems Part I, 49, 28-40 (2002).

  171. Naoki Masuda, Kazuyuki Aihara.
    Synchronization of pulse-coupled excitable neurons.
    Physical Review E, 64, 051906 (2001).
    Selected for Virtual Journal of Biological Physics Research, 2(11) (2001).

  172. Henry D. I. Abarbanel, Naoki Masuda, M. I. Rabinovich, Evren Tumer.
    Distribution of mutual information.
    Physics Letters A, 281, 368-373 (2001).
    Preprint: arXiv:nlin/0011016

  173. Naoki Masuda, Yasunori Okabe.
    Time series analysis with wavelet coefficients.
    Japan Journal of Industrial and Applied Mathematics, 18, 129-158 (2001).

  174. The following copyright notices apply to the papers published in Physical Review Letters, Physical Review E, and Chaos, which can be downloaded on this webpage: Copyright American Institute of Physics as of the publication year. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.

Refereed conference papers

  1. Masaki Ogura, Junpei Tagawa, Naoki Masuda.
    Distributed agreement on activity driven networks.
    Preprint: arXiv:1801.07412
    To be presented in: 2018 American Control Conference.
    Wisconsin Center, Milwaukee, USA, June 27-29, 2018.

  2. Xia Cui, Sadamori Kojaku, Naoki Masuda, Danushka Bollegala.
    Solving feature spareness in text classification using core-periphery decomposition.
    The Seventh Joint Conference on Lexical and Computational Semantics (*SEM 2018).
    New Orleans, USA, June 5-6 (2018).
    In: Proceedings, 255-264.

  3. Naoki Masuda, Konstantin Klemm, Víctor M. Eguíluz.
    Slowing down of linear consensus dynamics on temporal networks: some theoretical extensions.
    4th IFAC Conference on Analysis and Control of Chaotic Systems.
    Tokyo, Japan, August 26-28 (2015).
    In: IFAC-PapersOnLine, 48-18, 187-192 (2015). [open access]
    Typos

  4. Kodai Saito, Naoki Masuda.
    Two types of Twitter users with equally many followers.
    The 2013 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2013).
    Niagara, Canada, August 25-28 (2013).
    In: Proceedings, 1425-1426.

  5. Naoki Masuda, Tetsuya Fujie, Kazuo Murota.
    Application of semidefinite programming to maximize the spectral gap produced by node removal.
    4th Workshop on Complex Networks (CompleNet 2013).
    Berlin, March 13-15 (2013).
    In: Complex Networks IV, Studies in Computational Intelligence, 476, 155-163 (2013).
    Preprint: arXiv:1301.1503
    Download presentation slides [pdf only]

  6. Jin Seop Kim, Naoki Masuda, Byungnam Kahng.
    A priority queue model of human dynamics with bursty input tasks.
    First International Conference on Complex Sciences: Theory and Applications (Complex' 2009).
    Shanghai, China, February 23-25 (2009).
    In: Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, 5, 2402-2410 (2009).

  7. Naoki Masuda, Hiroshi Kori.
    STDP enhances frequency synchrony in neural networks with a pacemaker.
    International Joint Conference on Neural Networks (IJCNN 2007).
    Orlando, Florida, USA, August 12-17 (2007).
    In: Proceedings of International Joint Conference on Neural Networks, 96-101 (2007).

  8. Naoki Masuda, Shun-ichi Amari.
    Modeling memory transfer and savings in cerebellar motor learning.
    Neural Information Processing Systems (NIPS) 2005.
    Vancouver, Canada, December 5-10 (2005).
    In: Advances in Neural Information Processing Systems (Eds. Y. Weiss, B. Scholkopf, J. Platt), 18, 859-866 (2006).

  9. Naoki Masuda, Kazuyuki Aihara.
    Collective behavior of pulse-coupled FitzHugh-Nagumo neurons.
    The 8th International Conference on Neural Information Processing (ICONIP 2001).
    Shanghai, China, November 14-18 (2001).
    In: Proceedings of ICONIP2001, Vol. 2, 910-915.

  10. Naoki Masuda, Kazuyuki Aihara.
    Cryptosystems based on space-discretization of chaotic maps.
    The IEEE International Symposium on Circuits and Systems, 2001 (ISCAS 2001).
    Sydney, Australia, May 6-9 (2001).
    In: Proceedings of ISCAS 2001, III, 321-324.

  11. Naoki Masuda, Kazuyuki Aihara.
    Cryptosystem based on a finite-state baker's map and its security analysis.
    1999 International Symposium on Nonlinear Theory and its Applications (NOLTA99).
    Hilton Waikoloa Village, Waikoloa, Hawaii, USA, November 28 - December 2 (1999).
    In: Proceedings of NOLTA'99, 613-616.

Books

  1. Naoki Masuda, Renaud Lambiotte.
    A Guide to Temporal Networks.
    World Scientific, Singapore (2020).
    (The first edition was published in 2016.)

  2. Naoki Masuda, Kwang-Il Goh, Tao Jia, Junichi Yamanoi, Hiroki Sayama. (Editors)
    Proceedings of NetSci-X 2020: Sixth International Winter School and Conference on Network Science.
    Springer, Cham, Switzerland (2020).
    On Amazon

  3. Naoki Masuda, Petter Holme. (Editors)
    Temporal Network Epidemiology.
    Springer, Singapore (2017).

    On Amazon

Book chapters

  1. Tomokatsu Onaga, James P. Gleeson, Naoki Masuda.
    The effect of concurrency on epidemic threshold in time-varying networks.
    In: Temporal Network Theory, Petter Holme and Jari Saramäki (Eds.), Springer, Cham (2019), pp. 253--267.

  2. Naoki Masuda, Petter Holme.
    Introduction to temporal network epidemiology.
    In: Temporal Network Epidemiology, Naoki Masuda and Petter Holme (Eds.), Springer, Singapore (2017), pp. 1-16.

  3. Leo Speidel, Konstantin Klemm, Víctor M. Eguíluz, Naoki Masuda.
    Epidemic threshold in temporally-switching networks.
    In: Temporal Network Epidemiology, Naoki Masuda and Petter Holme (Eds.), Springer, Singapore (2017), pp. 161-177.

  4. Naoki Masuda, Taro Takaguchi, Nobuo Sato, Kazuo Yano.
    Self-exciting point process modeling of conversation event sequences.
    In: Temporal Networks, Petter Holme and Jari Saramäki (Eds.), Springer-Verlag, Berlin (2013), pp. 245-264.
    Preprint: arXiv:1205.5109

Editorials, commentaries, papers in institutional journals, papers for young adults, reports, English translation of Japanese papers, etc.

  1. Naoki Masuda, Mason A. Porter.
    The waiting-time paradox.
    Frontiers for Young Minds, 8, 582433 (2021). [open access]
    Preprint: arXiv:2007.05883
    Also posted to: https://doi.org/10.31235/osf.io/uem6d

  2. Teruyoshi Kobayashi, Naoki Masuda.
    Introduction to the special issue “Economics and Complex Networks”.
    Japanese Economic Review,72, 1-4 (2021). [open access]

  3. Naoki Masuda, Francisco C. Santos.
    A mathematical look at empathy.
    eLife, 8, e47036 (2019). [open access]

  4. Yoshimi Yoshino, Naoki Masuda.
    Evolution of cooperation is a robust outcome in the prisoner's dilemma on dynamic networks.
    Preprint: arXiv:1006.5791
    Presented in a domestic workshop on networks in Japan.

  5. Akihiro Fujihara, Yusuke Ide, Norio Konno, Naoki Masuda, Hiroyoshi Miwa, Masato Uchida.
    Limit theorems for the average distance and the degree distribution of the threshold network model.
    Interdisciplinary Information Sciences, 15, 361-366 (2010). [open access]

  6. Yusuke Ide, Norio Konno, Naoki Masuda.
    Limit theorems for some statistics of a generalized threshold network model.
    RIMS Kôkyûroku, 1551, 81-86 (2007). [open access]

  7. Naoki Masuda, Kazuyuki Aihara.
    The prediction of chaotic time series with wavelet coefficients.
    Electronics and Communications in Japan, Part III (Fundamental Electronic Science), 84(6), 50-59 (2001).

Referee activities (論文査読者としての活動)

  1. American Journal of Physical Anthropology
  2. American Naturalist
  3. Animal Behaviour
  4. Annals of Applied Probability
  5. Artificial Life and Robotics
  6. Automatica
  7. Behavioral Ecology
  8. Biological Cybernetics
  9. Biology Letters
  10. BMC Evolutionary Biology
  11. BMC Infectious Diseases
  12. Brain and Cognition
  13. Bulletin of Mathematical Biology
  14. Cerebral Cortex
  15. Chaos
  16. Chaos, Solitons & Fractals
  17. Cognitive Neurodynamics
  18. Communications Biology
  19. Communications Physics
  20. Communications in Nonlinear Science and Numerical Simulation
  21. Complexity
  22. Computational Social Networks
  23. Current Zoology
  24. Dynamic Games and Applications
  25. Ecological Modelling
  26. Ecological Research
  27. Ecology and Evolution
  28. eLife
  29. Entropy
  30. European Journal of Applied Mathematics
  31. European Journal of Combinatorics
  32. European Journal of Neuroscience
  33. European Physical Journal B
  34. Europhysics Letters
  35. Evolutionary Bioinformatics
  36. Fractals
  37. Frontiers in Physics
  38. Human Brain Mapping
  39. IEEE Journal on Selected Areas in Communications
  40. IEEE Transactions on Circuits and Systems I
  41. IEEE Transactions on Circuits and Systems II
  42. IEEE Transactions on Control of Network Systems
  43. IEEE Transactions on Evolutionary Computation
  44. IEEE Transactions on Information Theory
  45. IEEE Transactions on Network Science and Engineering
  46. IEICE (an elec. engg. journal issued in Japan)
  47. IET Control Theory & Applications
  48. IET Systems Biology
  49. International Journal of Behavioral Development
  50. International Journal of Bifurcation and Chaos
  51. International Journal of Environmental Research and Public Health
  52. International Journal of Modern Physics C
  53. Journal of Circuits, Systems, and Computers
  54. Journal of Complex Networks
  55. Journal of Conflict Resolution
  56. Journal of Mathematical Biology
  57. Journal of Neurophysiology
  58. Journal of Physics A
  59. Journal of Quantitative Analysis of Sports
  60. Journal of Signal Transduction
  61. Journal of Statistical Mechanics
  62. Journal of Systems and Software
  63. Journal of the Physical Society of Japan
  64. Journal of the Royal Society Interface
  65. Journal of Theoretical Biology
  66. Mathematical Biosciences
  67. Mathematical Problems in Engineering
  68. Methods in Ecology and Evolution
  69. Myrmecological News
  70. Nature Communications
  71. Nature Physics
  72. Neural Networks
  73. Neurocomputing
  74. Neuropsychologia
  75. New Journal of Physics
  76. Nonlinearity
  77. Physica A
  78. Physica D
  79. Physical Review E
  80. Physical Review Letters
  81. Physical Review Research
  82. Physical Review X
  83. Physics Letters A
  84. PLOS Biology
  85. PLOS Computational Biology
  86. PLOS ONE
  87. Proceedings of the National Academy of Sciences of the United States of America
  88. Proceedings of the Royal Society A
  89. Proceedings of the Royal Society B
  90. Royal Society Open Science
  91. Science Advances
  92. Scientific Reports
  93. SIAM Journal on Applied Mathematics
  94. SIAM Review
  95. Social Network Analysis and Mining
  96. Sociological Methodology
  97. Stochastic Processes and their Applications
  98. Trends in Neurosciences