業績 

(see also Google Citation, ORCID and ResearchMap)

65. Kondo Y*, Naoki H

      Spatially resolved mapping of tau amplification rates via differentiable simulation of prion-like propagation.

      bioRxiv  (2026) [Link] # preprint

64. Kaneko T, Sakaguchi S*, Fujioka S, Yada Y, Kojima R, Naoki H*

       Monju: Multi-criteria clustering in single-cell omics.

      bioRxiv  (2026) [Link] # preprint

63. Ando Y, Yada Y*, Kashima M, Bessho Y, Hirata H, Naoki H, Matsui T*

      hB-PAC: A non-invasive aging clock for quantifying individual differences in aging.     

      bioRxiv  (2026) [Link] # preprint

62. Inutsuka K, Nishioka T, Macpherson T, Fujiwara M, Hikida T*, Naoki H*

      Inside insight: decoding how insight emerges from competing world models.       

      bioRxiv  (2026) [Link] # preprint

61. Tsutsumi M, Kubo T, Kato TA*, Naoki H*

      Mind the gap: quantifying population–individual gap in depressive symptom dynamics through energy landscapes.       

      bioRxiv  (2026) [Link] # preprint

60. Terada K, Kondo Y*

      Elasticity of a three-dimensional cell vertex model of epithelia.       

      bioRxiv  (2026) [Link] # preprint

59. Higashino I, Ito R, Okochi Y, Inutsuka K, Yokoyama H, Kato R, Yada Y, Amemori K, Naoki H*

      Decoding how optimism-pessimism bias dynamically shapes risk-taking behavior.       

      bioRxiv  (2026) [Link] # preprint

58. Okochi Y, Sawazaki Y,  Kondo Y*, Naoki H*

      Inferring division-associated stochasticity from time-series single-cell transcriptomes.

      bioRxiv  (2026) [Link] # preprint

57. Fukui M, Kondo Y, Saito N*, Naoki H*

      Filament-resolved simulations reproduce self-organization of lamellipodia and filopodia.       

      bioRxiv  (2026) [Link] # preprint

56. Ota R*, Sakamoto M, Aoki W, Naoki H*

      Prediction of quantitative function of artificially-designed protein from structural information.       

      bioRxiv  (2025) [Link] # preprint

55. Itoh T,  Kondo Y*,  Nakayama T, Shinomiya A, Aoki K, Yoshimura T, Naoki H* 

      Inverse signal importance in real exposome: How do biological systems dynamically prioritize multiple environmental signals?.       

      bioRxiv  (2025) [Link] # preprint

54. Takeuchi RF, Sato AY, Ito KN, Yokoyama H, Miyata R, Ueda R, Kitajima K,  Kamaguchi R, Suzuki T, Isobe K, Naoki H,  Osakada F* 

      Posteromedial cortical networks encode visuomotor prediction errors.      

      bioRxiv  (2024) [Link] # preprint

53. Naoki H*, Uegaki K and Ishii S

      Self-organization mechanism of microtubule orientation patterns in axons and dendrites.       

      bioRxiv 163014 (2017) [Link] # preprint

2024~present (at Nagoya U)

52. 

      Spatiotemporal Trajectories of ....

      ACCEPTED  (2026)

51. Sakaguchi S*, Tsutsumi M (Co-first), Nishi K,  Naoki H*

      Disentanglement of batch effects and biological signals across conditions in the single-cell transcriptome.       

      ACCEPTED  (2026) [Link]

50. Nagashima T, Higashino I, Arima-Yoshida F, Hiyoshi K, Nagase M, Yada Y, Naoki H, Watabe AM*

      Optogenetic LTP manipulation and mathematical modeling to investigate value plasticity of the instructive signal in mice.       

      Bio-protocol journal  (2026) [Link]

49. Yada Y*, Naoki H*

      Decomposing Heterogeneity in Disease Progression Speeds and Pathways.       

      npj Digital Medicine  (2026) [Link]

48. Yoneshiro T, Kumagai Y, Nohara K, Iwami S, Honda N, Ohno N, Nishida M*

      Toward the promotion of One Health – Part II: Interdisciplinary research cooperation between Digital Transformation and Exposome.       

      Journal of Physiological Sciences 76, 100078 (2026) [Link] 

47. Okochi Y*,  Matsui T, Sakaguchi S,  Kondo T,  Naoki H*

      Zero-shot reconstruction of mutant spatial transcriptomes.     

      Patterns 7, 101521 (2026) [Link] 

46. Koike J, Nakae K, Yada Y , Hira R,  Naoki H*

      A data-driven framework linking the connectome to spatial gene expression gradients inspired by chemoaffinity theory.       

      Proceedings of the National Academy of Sciences of the United States of America 123(10), e2516572123 (2026) [Link] 

45. Fujiwara M*, Naoki H*

      Gradual proactive regulation of body state by reinforcement learning of homeostasis.      

      Neuroscience Research 223, 105021 (2026) [Link]

44. Kikuchi Y, Asakura Y,  Aoki K, Kondo Y*,  Naoki N*

      Inverse modeling unveils governing law of mechano-chemical dynamics of epithelial migration.      

      PLoS Computional Biology 21(12): e1013854 (2025) [Link]

43. Kikuchi Y*, Naoki H, Iwamoto M

      Intermediate interaction strategies for collective behavior.       

      Physica A: Statistical Mechanics and its Applications 8:1002 (2025) [Link] 

42. Tohyama S , Nagashima T, Higashino I, Arima-Yoshida F, Hiyoshi K , Nagase M, Yada Y, Honda N, Watabe AM*

      Aversive experiences induce valence plasticity of instructive signals to change future learning rules in mice.       

      Communications Biology 8:1002 (2025) [Link]  [Press]

41. Cao Z, Setoyama D, Monica-Natsumi D, Matsushima T, Yada Y, Watabe M, Hikida T, Kato AT, Naoki H* 

      Leveraging Machine Learning to Uncover the Hidden Links between Trusting Behavior and Biological Markers.      

      Dialogues in Clinical Neuroscience 27, 1, 201–215 (2025) [Link] 

40. Ju H, Skibbe H, Fukui M, Yoshimura SH, Naoki H* 

      Machine learning-guided reconstruction of cytoskeleton network from Live-cell AFM Images.      

      iScience 27, 10110907  (2024) [Link]

2021~2023 (at Hiroshima U)

39. Nakayama T, Tanikawa M, Okushi Y, Itoh T, Shimmura T, Maruyama M, Yamaguchi T, Matsumiya A, Shinomiya A, Guh YJ, Chen J, Naruse K,        Kudoh H, Kondo Y, Naoki H, Aoki K, Nagano AJ, Yoshimura T

      A transcriptional program underlying the circannual rhythms of gonadal development in medaka.

      Proceedings of the National Academy of Sciences of the United States of America 120, 52 e2313514120 (2023) [Link] [Press]

38. Yada Y*, Naoki H*

      Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates.      

      npj Systems Biology and Applications 9, 59 (2023)  [Link] 

37. Sakaguchi S, Okochi Y, Tanegashima C, Nishimura O, Uemura T, Kadota M, Naoki H, Kondo T*

      Single-cell transcriptome atlas of Drosophila gastrula 2.0.      

      Cell Reports 42, 112707 (2023) [Link] [Press]

36. Konaka Y, Naoki H*

      Decoding reward–curiosity coflict in decision-making from irrational behaviors.      

      Nature Computational Science 3, 418–432 (2023) [Link] [Press]

35. Hatakeyama Y, Saito N, Mii Y Shinozuka T, Takemoto T, Honda N, Takada S

      Intercellular exchange of Wnt ligands reduces cell population heterogeneity in embryogenesis.      

      Nature Communications 14, 1924 (2023)  [Link]  [Press]

34. Ishino S, Kamada T, Sarpong G, Kitano J, Tsukasa R, Mukohira H, Sun F, Li Y, Kobayashi K, Naoki H, Oishi N, Ogawa M* 

      Dopamine error signal to actively cope with lack of expected reward.      

      Science Advances 9 (10), eade5420 (2023) [Link] [Press]

33. Ju H, Honda N, Yoshimura SH, Kaneko M, Shigematsu T, Kiyono K* 

      Multidimensional fractal scaling analysis using higher order moving average polynomials and its fast algorithm.      

      Signal Processing 208, 108997  (2023) [Link] 

32. Onishi T*, Naoki H*, Igarashi Y*

      Optimal COVID-19 testing strategy on limited resources.      

      PLoS ONE 18(2): e0281319 (2023) [Link] 

31. Yoshido K, Naoki H*

      Adaptive discrimination of antigen risk by predictive coding in immune system.      

      iScience 26, 105754 (2023)  [Link] [Press]

30. Nakamuta S, Yoshido K, Naoki H*

      Stem cell homeostasis regulated by hierarchy and neutral competition.      

      Communication Biology 5, 1268 (2022) [Link] [Press]

29. Kanatsu-Shinohara M, Naoki H , Tanaka T, Tatehana M, Kikkawa T, Osumi N, Shinohara T*

      Regulation of male germline transmission patterns by the Trp53-Cdkn1a pathway.      

      Stem Cell Reports 17: 1-18 (2022) [Link]

28. Okochi Y, Sakaguchi S, Nakae K, Kondo T, Naoki H*

      Model-based prediction of spatial gene expression via generative linear mapping.      

      Nature Communications 12: 3731 (2021) [Link] [Press]

before 2021 (at Kyoto U)

27. Asakura Y, Kondo Y, Aoki K, Naoki H*

      Hierarchical modeling of mechano-chemical dynamics of epithelial sheets across cells and tissue.      

      Scientific Reports 11, 4069 (2021) [LINK] 

26. Naoki H* and Matsui T

      Somite boundary determination in normal and clock-less vertebrate embryos. 

      Development, Growth & Differentiation  62:177–187 (2020) [Link]

25. Naoki H*, Akiyama R, Sari DWK, Ishii S, Bessho Y and Matsui T

      Noise-resistant developmental reproducibility in vertebrate somite formation.       

      PLoS Computational Biology 15(2): e1006579 (2019) [Link] [Press]

24. Sari DWK, Akiyama R, Naoki H, Ishijima H, Bessho Y and Matsui T*

      Time-lapse observation of stepwise regression of Erk activity in zebrafish presomitic mesoderm.      

      Scientific Reports 8, 4335 (2018) [Link] 

23. Yamaguchi S, Naoki H*, Ikeda M, Tsukada Y, Nakano S, Mori I and Ishii S 

      Identification of animal behavioral strategies by inverse reinforcement learning.      

      PLoS Computational Biology 14(5): e1006122 (2018) [Link] [Press]

22. Kanatsu-Shinohara M*, Naoki H and Shinohara T

      Nonrandom contribution of left and right testes to germline transmission from mouse spermatogonial stem cells.      

      Biology of Reproduction 97(6), 902-910 (2017) [Link]

21. Aoki K*, Kondo Y, Naoki H, Hiratsuka T, Ito RE and Matsuda M

      Propagating wave of ERK activation orients collective cell migration.      

      Developmental Cell 43, 305–317 (2017) [Link] [Press]

20. Naoki H* 

      Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection      

      PLoS Computational Biology 13(8), e1005702 (2017) [Link]

19. Takano T, Wu M, Nakamuta S, Naoki H, Ishizawa N, Namba T, Watanabe T, Xu C, Hamaguchi T, Yura Y, Amano M, Hahn KM and 

      Kaibuchi K*

      Discovery of long-range inhibitory signaling to ensure single axon formation.      

      Nature Communications 8, 33 (2017) [Link]

18. Naoki H*, Nishiyama M, Togashi K, Igarashi Y, Hong K* and Ishii S

      Multi-phasic bi-directional chemotactic responses of the growth cone.      

      Scientific Reports 6, 36256 (2016) [Link]

17. Yamao M, Aoki K, Yukinawa N, Ishii S, Matsuda M and Naoki H*

      Two new FRET imaging measures: linearly proportional to and highly contrasting the fraction of active molecules.      

      PLoS One 11(10), e0164254 (2016) [Link]

16. Li Y, Nakae K, Ishii S and Naoki H*

      Uncertainty-dependent extinction of fear memory in an amygdala-mPFC neural circuit model.      

      PLoS Computational Biology 12(9), e1005099 (2016) [Link]

15. Kanatsu-Shinohara M*, Naoki H and Shinohara T

      Nonrandom germline transmission of mouse spermatogonial stem cells.      

      Developmental Cell 38, 248–261(2016) [Link] [Press]

14. Tsukada Y, Yamao M, Naoki H, Shimowada T, Ohnishi N, Kuhara A, Ishii S and Mori I* 

      Reconstruction of spatial thermal gradient encoded in thermosensory neuron AFD in Caenorhabditis elegans.      

      Journal of Neuroscience 36(9), 2571-2581 (2016) [Link] [Press]

13. Yamao M, Naoki H (Co-first), Kunida K, Aoki K, Matsuda M and Ishii S*

      Distinct predictive performance of Rac1 and Cdc42 in cell migration.      

      Scientific Reports 5, 17527 (2015) [Link]

12. Kumagai Y, Naoki H, Nakasyo E, Kamioka Y, Kiyokawa E and Matsuda M*

      Heterogeneity in ERK activity as visualized by in vivo FRET imaging of mammary tumor cells developed in MMTV-Neu mice.      

      Oncogene 34(8), 1051–1057 (2015) [Link]

11. Hiratsuka T, Fujita Y, Naoki H, Aoki K, Kamioka Y and Matsuda M* 

      Intercellular propagation of extracellular signal-regulated kinase activation revealed by in vivo imaging of mouse skin.      

     eLIFE 4, e05178 (2015) [Link] [Press]

2005~2014

10. Yukinaga H, Shionyu C, Hirata E, Ui-Tei K, Nagashima T, Kondo S, Okada-Hatakeyama M, Naoki H and Matsuda M*

      Fluctuation of Rac1 activity is associated with the phenotypic and transcriptional heterogeneity of glioma cells.      

      Journal of Cell Science 127(8), 1805-1815 (2014) [Link]

9.  Naoki H* and Ishii S 

      Mathematical Modeling of Neuronal Polarization During Development.      

      Progress in Molecular Biology and Translational Science 123, 127-141 (2014) [Link]

8.   Kaneko-Kawano T*, Takasu F, Naoki H, Sakumura Y, Ishii S, Ueba T, Eiyama A, Okada A, Kawano Y and Suzuki K 

      Dynamic Regulation of Myosin Light Chain Phosphorylation by Rho-kinase.      

      PLoS One 7(6), e39269 (2012) [Link]

7.  Yamao M, Naoki H* and Ishii S 

      Multi-cellular logistics of collective cell migration.      

      PLoS One 6(12), e27950 (2011) [Link] 

6.  Nonaka S, Naoki H (Co-first)* and Ishii S 

      A multiphysical model of cell migration integrating  reaction-diffusion, membrane and cytoskeleton.      

      Neural Networks 24, 979-989 (2011) [Link] 

5.  Naoki H*, Nakamuta S, Kaibuchi K and Ishii S 

      Flexible Search for Single-Axon Morphology during Neuronal Spontaneous Polarization.      

      PLoS One 6(4), e19034 (2011) [Link] 

4.  Yamao M, Naoki H and Ishii S 

      Noise-Induced collective migration for neural crest cells.       

      Lecture Notes in Computer Science 6352, 155-163 (2010) [Link]

before 2009 (at Kyushu U)

3.  Naoki H*, Sakumura Y and Ishii S 

      Stochastic control of spontaneous signal generation for gradient sensing in chemotaxis.       

      Journal of Theoretical Biology 255, 259-266 (2008) [Link] 

2. Tamura H, Ng DC, Tokuda T, Naoki H, Nakagawa T, Mizuno T, Hatanaka Y, Ishikawa Y, Ohta J and Shiosaka S*

      One-chip sensing device (biomedical photonic LSI) enabled to assess hippocampal steep and gradual up-regulated proteolytic 

      activities.      

      Journal of Neuroscience Methods 173, 114-120 (2008) [Link]

1. Naoki H, Sakumura Y and Ishii S* 

      Local signaling with molecular diffusion as a decoder of Ca2+ signals in synaptic plasticity.     

      Molecular Systems Biology 1, 2005.0027 (2005) [Link] 

7. 心の揺らぎ・非合理性のデータ駆動的解読 

     本田直樹:

     メディカル・サイエンス・ダイジェスト「特集：ひきこもりと精神疾患」49(3) 12-15 (2023) [Link] 

6. データ駆動生物学 〜データに根ざした数理モデリング〜 

     本田直樹:

     数理科学 9月号 「特集：数理モデリングと生命科学」(2021) [Link] 

5. 強化学習・逆強化学習に基づく動物行動のモデリングとデータ解析 

     本田直樹:

     実験医学増刊「機械学習を生命科学に使う！！」 38(20) 202-209 (2020) [Link] 

4. scRNA-seqデータから空間的遺伝子発現パターンを再構成する機械学習 

     大河内康之, 坂口峻太, 本田直樹:

     実験医学増刊「機械学習を生命科学に使う！！」 38(20) 63-69 (2020) [Link] 

3. 軸索の走化性から神経回路形成に至る配線原理 

     本田直樹:

     生物物理 59(3)  141-143 (2019) [Link] 

2. 精子幹細胞の機能的寿命の維持機構

     篠原美都, 本田直樹, 篠原隆司:

     実験医学 35(8) 1297-1302 (2017)

1. 細胞運動のシステム同定

     本田直樹, 山尾 将隆, 石井信:

     生体の科学65(5) 468-469 (2014)

3. 4-2 Gephi─マウスの脳内神経ネットワーク構造をわかりやすくレイアウト

    本田直樹:

    プロ直伝 伝わるデータ・ビジュアル術 ――Excelだけでは作れないデータ可視化レシピ（監修：五十嵐 康伸）（2019）

2. 第７章：定量データに基づく生体情報処理の同定

    本田直樹:

    AI導入によるバイオテクノロジーの発展（監修：植田充美）（2018）

1. Chapter 11: Collective cell migration 

    Yamao M, Honda N and Ishii S:

    Trends in Biophysics: From Cell Dynamics Toward Multicellular Growth Phenomena (Edited by Pavel Kraikivski) 205-235 (2013)

2015~2019