Publications
業績
(see also Google Citation, ORCID and ResearchMap)
プレプリント論文(Preprint Papers)
* and _ indicates the corresponding author and lab members, respectively.
43. Machine learning-guided reconstruction of cytoskeleton network from Live-cell AFM Images.
Ju H, Skibbe H, Fukui M, Yoshimura SH, Honda N*
bioRxiv (2024) [Link] # preprint
42. 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, Honda N*
bioRxiv (2023) [Link] # preprint
41. Zero-shot reconstruction of mutant spatial transcriptomes.
Okochi Y*, Matsui T, Honda N*
bioRxiv (2022) [Link] # preprint
40. Self-organization mechanism of microtubule orientation patterns in axons and dendrites.
Honda N*, Uegaki K and Ishii S
bioRxiv 163014 (2017) [Link] # preprint
学術論文(Peer-reviewed papers)
* indicates the corresponding author.
2021~present (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, Honda N, 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*, Honda N*
npj Systems Biology and Applications 9, 59 (2023) [Link]
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*, Honda N*, Igarashi Y*
PLoS ONE 18(2): e0281319 (2023) [Link]
29. Regulation of male germline transmission patterns by the Trp53-Cdkn1a pathway.
Kanatsu-Shinohara M, Honda N , Tanaka T, Tatehana M, Kikkawa T, Osumi N, Shinohara T*
Stem Cell Reports, 17: 1-18 (2022) [Link]
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, Honda N*
Scientific Reports 11, 4069 (2021) [LINK]
26. Somite boundary determination in normal and clock-less vertebrate embryos.
Honda N* and Matsui T
Development, Growth & Differentiation 62:177–187 (2020) [Link]
24. Time-lapse observation of stepwise regression of Erk activity in zebrafish presomitic mesoderm.
Sari DWK, Akiyama R, Honda N, Ishijima H, Bessho Y and Matsui T*
Scientific Reports 8, 4335 (2018) [Link]
22. Nonrandom contribution of left and right testes to germline transmission from mouse spermatogonial stem cells.
Kanatsu-Shinohara M*, Honda N and Shinohara T
Biology of Reproduction 97(6), 902-910 (2017) [Link]
20. Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection
Honda N*
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, Honda N, 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.
Honda N*, 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 Honda N*
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 Honda N*
PLoS Computational Biology 12(9), e1005099 (2016) [Link]
13. Distinct predictive performance of Rac1 and Cdc42 in cell migration.
Yamao M, Honda N (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, Honda N, Nakasyo E, Kamioka Y, Kiyokawa E and Matsuda M*
Oncogene 34(8), 1051–1057 (2015) [Link]
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, Honda N and Matsuda M*
Journal of Cell Science 127(8), 1805-1815 (2014) [Link]
9. Mathematical Modeling of Neuronal Polarization During Development.
Honda N* 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, Honda N, 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, Honda N* and Ishii S
PLoS One 6(12), e27950 (2011) [Link]
6. Noise-Induced collective migration for neural crest cells.
Yamao M, Honda N 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, Honda N (Co-first)* and Ishii S
Neural Networks 24, 979-989 (2011) [Link]
4. Flexible Search for Single-Axon Morphology during Neuronal Spontaneous Polarization.
Honda N*, 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.
Honda N*, 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, Honda N, 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.
Honda N, Sakumura Y and Ishii S*
Molecular Systems Biology 1, 2005.0027 (2005) [Link]
総説(Reviews)
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]
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)
著書(Books)
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)