1. Christos Ellinas, Naoki Masuda.
    Modelling project failure and its mitigation in a time-stamped network of interrelated tasks.
    Preprint: arXiv:1810.07561

  2. Naoki Masuda, Petter Holme.
    Detecting sequences of system states in temporal networks.
    Preprint: arXiv:1803.04755
    Python and MATLAB codes

  3. Masaki Ogura, Victor M. Preciado, Naoki Masuda.
    Optimal containment of epidemics over temporal activity-driven networks.
    Preprint: arXiv:1802.08961

Journal papers (refereed papers only)

  1. Sadamori Kojaku, Mengqiao Xu, Haoxiang Xia, Naoki Masuda.
    Multiscale core-periphery structure in a global liner shipping network.
    Scientific Reports, in press (2018). [open access]
    Preprint: arXiv:1808.04549
    Python codes

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

  3. 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

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

  5. 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

  6. 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

  7. 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]

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

  9. 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

  10. 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.

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

  12. 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

  13. 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

  14. 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

  15. Naoki Masuda, Mason A. Porter, Renaud Lambiotte.
    Random walks and diffusion on networks.
    Physics Reports, 716-717, 1-58 (2017). [open access]
    Preprint: arXiv:1612.03281

  16. 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

  17. 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.

  18. 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

  19. 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]

  20. 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

  21. 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

  22. 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]

  23. 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

  24. 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]

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

  26. 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]

  27. 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

  28. 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

  29. 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

  30. 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]

  31. 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]

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

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

  34. 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

  35. 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

  36. 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

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

  38. 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.

  39. 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.

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

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

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

  43. 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]

  44. 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

  45. 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)

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

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

  48. 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]

  49. 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

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

  51. 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

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

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

  54. 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).

  55. 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

  56. 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

  57. 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

  58. 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).

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

  60. 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

  61. 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.

  62. 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

  63. 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

  64. 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

  65. 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)

  66. 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

  67. 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

  68. 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

  69. 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

  70. 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]

  71. 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

  72. 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

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

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

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

  76. 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

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

  78. 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

  79. 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

  80. 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

  81. 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).

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

  83. 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).

  84. 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]

  85. 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

  86. 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

  87. 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

  88. 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

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

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

  91. 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

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

  93. 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

  94. 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

  95. 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).

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

  97. 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).

  98. 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

  99. 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

  100. 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

  101. 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

  102. 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

  103. 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).

  104. 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).

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

  106. 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

  107. 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

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

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

  110. 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

  111. 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

  112. 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

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

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

  115. 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).

  116. 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).

  117. 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

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

  119. 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

  120. 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

  121. 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).

  122. 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

  123. 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

  124. 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

  125. 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

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

  127. 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).

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

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

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

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

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

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

  134. 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).

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

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

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

  138. 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).

  139. 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

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

  141. 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]

  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.


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

    On Amazon

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

Book chapters

  1. 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.

  2. 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.

  3. 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

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).

Referee activities (論文査読者としての活動)

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