1. Sadamori Kojaku, Naoki Masuda.
    Core-periphery structure requires something else in the network.
    Preprint: arXiv:1710.07076
    C++ and MATLAB codes

  2. Genki Ichinose, Naoki Masuda.
    Zero-determinant strategies in finitely repeated games.
    Preprint: arXiv:1707.03097

  3. Takuya Sekiguchi, Kohei Tamura, Naoki Masuda.
    Population changes in residential clusters in Japan.
    Preprint: arXiv:1706.09439

  4. Takahiro Ezaki, Naoki Masuda.
    Reinforcement learning account of network reciprocity.
    Preprint: arXiv:1706.04310

Journal papers (refereed papers only)

  1. Sadamori Kojaku, Naoki Masuda.
    Finding multiple core-periphery pairs in networks.
    Physical Review E, in press (2017).
    Preprint: arXiv:1702.06903
    MATLAB codes

  2. Luis E. C. Rocha, Naoki Masuda, Petter Holme.
    Sampling of temporal networks: Methods and biases.
    Physical Review E, in press (2017).
    Preprint: arXiv:1707.02108

  3. Tomokatsu Onaga, James P. Gleeson, Naoki Masuda.
    Concurrency-induced transitions in epidemic dynamics on temporal networks.
    Physical Review Letters, 119, 108301 (2017).
    Preprint: arXiv:1702.05054

  4. Naoki Masuda, Mason A. Porter, Renaud Lambiotte.
    Random walks and diffusion on networks.
    Physics Reports, in press (2017).
    Preprint: arXiv:1612.03281

  5. 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]
    Preprint: arXiv:1704.07523

  6. 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 (maintained by the first author of the paper).
    MATLAB code to calculate the maximum-likelihood estimator is also available as the supplementary material of the paper.

  7. Naoki Masuda, Luis E. C. Rocha.
    A Gillespie algorithm for non-Markovian stochastic processes.
    SIAM Review, in press (2017).
    Preprint: arXiv:1601.01490
    C/C++ codes used for producing the results in the paper

  8. 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

  9. 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]

  10. 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

  11. 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

  12. 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]

  13. 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]
    Preprint: arXiv:1602.00859

  14. 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]

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

  16. 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]

  17. 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

  18. 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

  19. 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

  20. 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]

  21. 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]

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

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

  24. 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

  25. 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

  26. 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

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

  28. 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]

  29. 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.

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

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

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

  33. 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]

  34. 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

  35. 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)

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

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

  38. 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]

  39. 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

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

  41. 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

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

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

  44. 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).

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

  46. 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

  47. 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

  48. 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).

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

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

  51. 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

  52. 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

  53. 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

  54. 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

  55. 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)

  56. 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

  57. 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

  58. 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

  59. 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

  60. 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]

  61. 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

  62. 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

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

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

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

  66. 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

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

  68. 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

  69. 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

  70. 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

  71. 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).

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

  73. 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).

  74. 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]

  75. 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

  76. 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

  77. 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

  78. 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

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

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

  81. 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

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

  83. 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

  84. 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

  85. 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).

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

  87. 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).

  88. 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

  89. 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

  90. 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

  91. 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

  92. 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

  93. 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).

  94. 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).

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

  96. 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

  97. 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

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

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

  100. 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

  101. 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

  102. 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

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

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

  105. 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).

  106. 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).

  107. 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

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

  109. 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

  110. 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

  111. 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).

  112. 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

  113. 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

  114. 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

  115. 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

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

  117. 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).

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

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

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

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

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

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

  124. 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).

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

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

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

  128. 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).

  129. 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

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

  131. 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.


  1. Naoki Masuda, Petter Holme. (Editors)
    Temporal Network Epidemiology.
    Springer (2017).
    On Amazon

  2. Naoki Masuda, Renaud Lambiotte.
    A Guide to Temporal Networks.
    World Scientific, Singapore (2016).
    On Amazon

Book chapters

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

Papers in institutional journals, translation of Japanese papers, etc.

  1. 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.

  2. 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]

  3. 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).

Presentation in international conferences, post-conference proceedings (assorted ones only)

  1. 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]

  2. 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). [poster]
    In: Complex Networks IV, Studies in Computational Intelligence, 476, 155-163 (2013).
    Preprint: arXiv:1301.1503
    Download presentation slides [pdf only]

  3. Naoki Masuda.
    Temporal networks: Introduction.
    School. NetSci2013.
    Danish Technical University, Lyngby, Denmark, June 3-7 (2013).

  4. 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).

  5. 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). [poster]
    In: Advances in Neural Information Processing Systems (Eds. Y. Weiss, B. Scholkopf, J. Platt), 18, 859-866 (2006).

  6. 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.

  7. 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.

Referee activities (論文査読者としての活動)

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