業績 

(see also Google Citation, ORCID and ResearchMap)

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

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

      bioRxiv  (2025) [Link] # preprint

49. Sperrfy the brain: A data-driven realization of Sperry's Chemoaffinity theory in the neural connectome.

       Koike J, Yada Y , Hira R,  Naoki H*

      bioRxiv  (2025) [Link] # preprint

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

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

      bioRxiv  (2025) [Link] # preprint

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

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

      bioRxiv  (2025) [Link] # preprint

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

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

      bioRxiv  (2025) [Link] # preprint

45. Posteromedial cortical networks encode visuomotor prediction errors.

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

      bioRxiv  (2024) [Link] # preprint

44. Zero-shot reconstruction of mutant spatial transcriptomes.

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

      bioRxiv  (2022) [Link] # preprint

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

      Naoki H*, Uegaki K and Ishii S

      bioRxiv 163014 (2017) [Link] # preprint

2024~present (at Nagoya U)

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

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

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

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

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

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

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

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

      iScience 27, 10110907  (2024) [Link]

2021~2024 (at Hiroshima U)

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

      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

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

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

      Yada Y*, Naoki H*

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

37. Single-cell transcriptome atlas of Drosophila gastrula 2.0.

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

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

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

      Konaka Y, Naoki H*

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

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

      Hatakeyama Y, Saito N, Mii Y Shinozuka T, Takemoto T, Naoki H, Takada S

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

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

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

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

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

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

      Signal Processing, 208, 108997  (2023) [Link] 

32. Optimal COVID-19 testing strategy on limited resources.

      Onishi T*, Naoki H*, Igarashi Y*

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

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

      Yoshido K, Naoki H*

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

30. Stem cell homeostasis regulated by hierarchy and neutral competition.

      Nakamuta S, Yoshido K, Naoki H*

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

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

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

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

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

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

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

before 2021 (at Kyoto U)

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

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

      Scientific Reports 11, 4069 (2021) [LINK] 

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

      Naoki H* and Matsui T

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

25. Noise-resistant developmental reproducibility in vertebrate somite formation. 

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

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

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

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

      Scientific Reports 8, 4335 (2018) [Link] 

23. Identification of animal behavioral strategies by inverse reinforcement learning.

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

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

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

      Kanatsu-Shinohara M*, Naoki H and Shinohara T

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

21. Propagating wave of ERK activation orients collective cell migration.

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

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

20. Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection

      Naoki H* 

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

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

      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*

      Nature Communications 8, 33 (2017) [Link]

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

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

      Scientific Reports 6, 36256 (2016) [Link]

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

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

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

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

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

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

15. Nonrandom germline transmission of mouse spermatogonial stem cells.

      Kanatsu-Shinohara M*, Naoki H and Shinohara T

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

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

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

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

13. Distinct predictive performance of Rac1 and Cdc42 in cell migration.

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

      Scientific Reports 5, 17527 (2015) [Link]

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

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

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

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

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

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

2005~2014

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

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

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

9.  Mathematical Modeling of Neuronal Polarization During Development.

      Naoki H* and Ishii S 

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

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

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

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

7.  Multi-cellular logistics of collective cell migration.

      Yamao M, Naoki H* and Ishii S 

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

6.  Noise-Induced collective migration for neural crest cells. 

      Yamao M, Naoki H and Ishii S 

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

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

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

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

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

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

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

before 2009 (at Kyushu U)

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

      Naoki H*, Sakumura Y and Ishii S 

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

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

      activities. 

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

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

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

    Naoki H, Sakumura Y and Ishii S* 

    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