NAOKI HONDA

Last Updated :2022/08/02

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Professor
Web Site
E-mail
nhondahiroshima-u.ac.jp
Self-introduction
Data-driven biology, Theoretical biology

Basic Information

Major Professional Backgrounds

  • 2021/04/01, Graduate School of Biostudies, Kyoto University, Specially-appointed Professor
  • 2021/04/01, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Guest Professor (PI)
  • 2020/02/01, 2021/03/31, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Guest Associate Professor (PI)
  • 2018/04/01, 2021/03/31, Kyoto University, Graduate School of Biostudies, Associate professor
  • 2017/04/01, 2018/03/31, Kyoto University, Graduate School of Biostudies, Project associate professor
  • 2013/05/01, 2017/03/31, Kyoto University, Graduate School of Medicine, Project Associate Professor
  • 2012/04/01, 2013/04/30, Kyoto University, Graduate School of Informatics, Project assistant professor
  • 2009/02/01, 2012/03/31, Kyoto University, Graduate School of Informatics, Postdoctoral researcher
  • 2008/04/01, 2009/01/31, Kyushu University, Graduate School of Science, JSPS postdoctoral fellowship
  • 2007/04/01, 2008/03/31, Nara Institute of Science and Technology, Graduate School of Information Science, JSPS research fellow

Academic Degrees

  • Nara Institute of Science and Technology
  • Nara Institute of Science and Technology

Research Fields

  • Biological Sciences;Genome science;System genome science
  • Biology;Biological Science;Developmental biology
  • Informatics;Frontiers of informatics;Life / Health / Medical informatics
  • Informatics;Human informatics;Cognitive science

Affiliated Academic Societies

  • The molecular biology society of japan
  • Japanese Neural Network Society
  • Japanese Society of Developmental Biologists
  • The biophysical society of japan
  • Japan Neuroscience Society
  • Japanese Society for Mathematical Biology

Educational Activity

Course in Charge

  1. 2022, Undergraduate Education, 2Term, Theory of Complex Systems
  2. 2022, Undergraduate Education, 4Term, Mathematics for Modeling and Simulation
  3. 2022, Undergraduate Education, First Semester, Special Study of Mathematics and Informatics for Graduation
  4. 2022, Undergraduate Education, Second Semester, Special Study of Mathematics and Informatics for Graduation
  5. 2022, Undergraduate Education, 2Term, English Seminar for Globalization A
  6. 2022, Undergraduate Education, 2Term, Special Lectures in Mathematics(Network Biology)
  7. 2022, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Mathematical and Life Sciences
  8. 2022, Graduate Education (Master's Program) , 1Term, Exercises in Applied Mathematics and Computational Science A
  9. 2022, Graduate Education (Master's Program) , 2Term, Exercises in Applied Mathematics and Computational Science A
  10. 2022, Graduate Education (Master's Program) , 3Term, Exercises in Applied Mathematics and Computational Science B
  11. 2022, Graduate Education (Master's Program) , 4Term, Exercises in Applied Mathematics and Computational Science B
  12. 2022, Graduate Education (Master's Program) , 1Term, Computational Mathematics A
  13. 2022, Graduate Education (Master's Program) , 2Term, Special Lecture on Mathematical and Life Sciences C
  14. 2022, Graduate Education (Doctoral Program) , 2Term, Special Lecture on Mathematical and Life Sciences G

Research Activities

Academic Papers

  1. Decoding reward–curiosity conflict in decision-making from irrational behaviors., bioRxiv, 2022
  2. Stem cell homeostasis regulated by hierarchy and neutral competition., bioRxiv, 2022
  3. Intercellular exchange of Wnt ligands reduces cell population heterogeneity in embryogenesis., Research Square, 2022
  4. Single-cell transcriptome atlas of Drosophila gastrula 2.0., bioRxiv, 2021
  5. Adaptive discrimination of antigen risk by predictive coding in immune system., bioRxiv, 2021
  6. Optimal and worst examination strategies for COVID-19., medRxiv, 2021
  7. Self-organization mechanism of microtubule orientation patterns in axons and dendrites., bioRxiv, 2017
  8. ★, Model-based prediction of spatial gene expression via generative linear mapping., Nature Communications, 12, 3731, 2021
  9. Hierarchical modeling of mechano-chemical dynamics of epithelial sheets across cells and tissue., Scientific Reports, 11, 4069, 2021
  10. Somite boundary determination in normal and clock-less vertebrate embryos., Development, Growth & Differentiation, 62, 177-187, 2020
  11. ★, Noise-resistant developmental reproducibility in vertebrate somite formation., PLoS Computational Biology, 15(2), e1006579, 2019
  12. Time-lapse observation of stepwise regression of Erk activity in zebrafish presomitic mesoderm, Scientific Reports, 8, 4335, 2018
  13. ★, Identification of animal behavioral strategies by inverse reinforcement learning., PLoS Computational Biology, 14(5), e1006122, 2018
  14. Nonrandom contribution of left and right testes to germline transmission from mouse spermatogonial stem cells., Biology of Reproduction, 97(6), 902-910, 2017
  15. Propagating wave of ERK activation orients collective cell migration., Developmental Cell, 43, 305-317, 2017
  16. ★, Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection, PLoS Computational Biology, 13(8), e1005702, 2017
  17. Discovery of long-range inhibitory signaling to ensure single axon formation., Nature Communications, 8, 33, 2017
  18. Multi-phasic bi-directional chemotactic responses of the growth cone., Scientific Reports, 6, 36256, 2016
  19. Two new FRET imaging measures: linearly proportional to and highly contrasting the fraction of active molecules., PLoS One, 11(10), e0164254, 2016
  20. ★, Uncertainty-dependent extinction of fear memory in an amygdala-mPFC neural circuit model., PLoS Computational Biology, 12(9), e1005099, 2016
  21. Nonrandom germline transmission of mouse spermatogonial stem cells., Developmental Cell, 38, 248-261, 2016
  22. Reconstruction of spatial thermal gradient encoded in thermosensory neuron AFD in Caenorhabditis elegans., Journal of Neuroscience, 36(9), 2571-2581, 2016
  23. ★, Distinct predictive performance of Rac1 and Cdc42 in cell migration., 5, 17527, 2015
  24. 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
  25. Intercellular propagation of extracellular signal-regulated kinase activation revealed by in vivo imaging of mouse skin., eLIFE, 4, e05178, 2015
  26. Fluctuation of Rac1 activity is associated with the phenotypic and transcriptional heterogeneity of glioma cells., Journal of Cell Science, 127(8), 1805-1815, 2014
  27. Mathematical Modeling of Neuronal Polarization During Development., Progress in Molecular Biology and Translational Science, 123, 127-141, 2014
  28. Dynamic Regulation of Myosin Light Chain Phosphorylation by Rho-kinase., PLoS One, 7(6), e39269, 2012
  29. Multi-cellular logistics of collective cell migration., PLoS One, 6(12), e27950, 2011
  30. Noise-Induced collective migration for neural crest cells., Lecture Notes in Computer Science, 6352, 155-163, 2010
  31. A multiphysical model of cell migration integrating reaction-diffusion, membrane and cytoskeleton., Neural Networks, 24, 979-989, 2011
  32. Flexible Search for Single-Axon Morphology during Neuronal Spontaneous Polarization., PLoS One, 6(4), e19034, 2011
  33. Stochastic control of spontaneous signal generation for gradient sensing in chemotaxis., Journal of Theoretical Biology, 255, 259-266, 2008
  34. 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
  35. Local signaling with molecular diffusion as a decoder of Ca2+ signals in synaptic plasticity., Molecular Systems Biology, 1, 2005.0027, 2005

External Funds

Acceptance Results of Competitive Funds

  1. 2021/10, 2024/03
  2. 2021/10, 2024/03
  3. 2021/08, 2024/03
  4. 2021/08, 2024/03
  5. 2021/07, 2025/03
  6. 2021/04, 2025/03
  7. 2020/12, 2025/03
  8. 2020/02, 2025/01
  9. 2019/04, 2021/03
  10. 2019/06, 2021/03
  11. 2018/06, 2020/01
  12. 2016/04, 2020/03
  13. 2013/04, 2016/03
  14. 2007/04, 2008/03