NAOKI HONDA

Last Updated :2023/09/04

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Professor
Web Site
https://sites.google.com/view/data-driven-biology/
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

Educational Backgrounds

  • Nara Institute of Science and Technology, Japan, 2005/04, 2008/03
  • Nara Institute of Science and Technology, Japan, 2003/07, 2005/03
  • Nara Institute of Science and Technology, Japan, 2003/04, 2003/06
  • Doshisha University, Graduate School of Engineering , Japan, 2002/04, 2002/08
  • Doshisha University, School of Engineering , Japan, 1998/04, 2002/03

Academic Degrees

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

Educational Activity

  • [Bachelor Degree Program] School of Science : Mathematics : Mathematics
  • [Master's Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Mathematical and Life Sciences
  • [Doctoral Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Mathematical and Life Sciences

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

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

Educational Activity

Course in Charge

  1. 2023, Liberal Arts Education Program1, 1Term, Seminar in Linear AlgebraI
  2. 2023, Undergraduate Education, 3Term, English Seminar on Mathematics
  3. 2023, Undergraduate Education, 4Term, Mathematics for Modeling and Simulation
  4. 2023, Undergraduate Education, First Semester, Special Study of Mathematics and Informatics for Graduation
  5. 2023, Undergraduate Education, Second Semester, Special Study of Mathematics and Informatics for Graduation
  6. 2023, Undergraduate Education, 1Term, English Seminar for Globalization A
  7. 2023, Undergraduate Education, First Semester, Application of principal component analysis based- and tensor decomposition based- unsupervised feature extraction to bioinformatics
  8. 2023, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Mathematical and Life Sciences
  9. 2023, Graduate Education (Master's Program) , 1Term, Computational Mathematics A
  10. 2023, Graduate Education (Master's Program) , First Semester, Special Lecture on Mathematical and Life Sciences A
  11. 2023, Graduate Education (Master's Program) , First Semester, Exercises in Applied Mathematics and Computational Science A
  12. 2023, Graduate Education (Master's Program) , Second Semester, Exercises in Applied Mathematics and Computational Science B
  13. 2023, Graduate Education (Doctoral Program) , Academic Year, Research for Academic Degree Dissertation in Integrated Life Sciences
  14. 2023, Graduate Education (Doctoral Program) , First Semester, Special Lecture on Mathematical and Life Sciences E

Research Activities

Academic Papers

  1. Single-cell transcriptome atlas of Drosophila gastrula 2.0., Cell Reports, 20230710
  2. Multidimensional fractal scaling analysis using higher order moving average polynomials and its fast algorithm, Signal Processing, 208(108997), 20230701
    Link to Paper Search Results by DOI
  3. ★, Decoding reward–curiosity conflict in decision-making from irrational behaviors., Nature Computational Science, 3, 418-432, 20230515
    Link to Paper Search Results by DOI
  4. Intercellular exchange of Wnt ligands reduces cell population heterogeneity in embryogenesis, Nature Communications, 14(1924), 20230406
    Link to Paper Search Results by DOI
  5. Dopamine error signal to actively cope with lack of expected reward, Science Advances, 9(10), 20230310
    Link to Paper Search Results by DOI
  6. Optimal COVID-19 testing strategy on limited resources, PLoS One, 18(2), 20230224
    Link to Paper Search Results by DOI
  7. ★, Adaptive discrimination between harmful and harmless antigens in the immune system by predictive coding, iScience, 26(1), 20230120
    Link to Paper Search Results by DOI
  8. Zero-shot reconstruction of mutant spatial transcriptomes., bioRxiv, 20221219
  9. ★, Stem cell homeostasis regulated by hierarchy and neutral competition, Communications Biology, 5(1), 20221118
    Link to Paper Search Results by DOI
  10. Prediction of amyloid beta accumulation from multiple biomarkers using a hierarchical Bayesian model., bioRxiv, 20221024
    Link to Paper Search Results by DOI
  11. Regulation of male germline transmission patterns by the Trp53-Cdkn1a pathway, Stem Cell Reports, 17(9), 1924-1941, 20220913
    Link to Paper Search Results by DOI
  12. ★, Model-based prediction of spatial gene expression via generative linear mapping., Nature Communications, 12, 3731, 20210617
    Link to Paper Search Results by DOI
  13. Hierarchical modeling of mechano-chemical dynamics of epithelial sheets across cells and tissue., Scientific Reports, 11, 4069, 20210218
    Link to Paper Search Results by DOI
  14. Somite boundary determination in normal and clock-less vertebrate embryos., Development, Growth & Differentiation, 62, 177-187, 20200228
    Link to Paper Search Results by DOI
  15. ★, Noise-resistant developmental reproducibility in vertebrate somite formation., PLoS Computational Biology, 15(2), e1006579, 20190204
    Link to Paper Search Results by DOI
  16. ★, Identification of animal behavioral strategies by inverse reinforcement learning., PLoS Computational Biology, 14(5), e1006122, 20180502
    Link to Paper Search Results by DOI
  17. Time-lapse observation of stepwise regression of Erk activity in zebrafish presomitic mesoderm, Scientific Reports, 8, 4335, 20180312
    Link to Paper Search Results by DOI
  18. Nonrandom contribution of left and right testes to germline transmission from mouse spermatogonial stem cells., Biology of Reproduction, 97(6), 902-910, 20171109
    Link to Paper Search Results by DOI
  19. Propagating wave of ERK activation orients collective cell migration., Developmental Cell, 43, 305-317, 20171106
    Link to Paper Search Results by DOI
  20. ★, Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection., PLoS Computational Biology, 13(8), e1005702, 20170808
    Link to Paper Search Results by DOI
  21. Self-organization mechanism of microtubule orientation patterns in axons and dendrites., bioRxiv, 20170723
    Link to Paper Search Results by DOI
  22. Discovery of long-range inhibitory signaling to ensure single axon formation., Nature Communications, 8, 33, 20170626
    Link to Paper Search Results by DOI
  23. ★, Multi-phasic bi-directional chemotactic responses of the growth cone., Scientific Reports, 6, 36256, 20161103
    Link to Paper Search Results by DOI
  24. Two new FRET imaging measures: linearly proportional to and highly contrasting the fraction of active molecules., PLoS One, 11(10), e0164254, 20161025
    Link to Paper Search Results by DOI
  25. ★, Uncertainty-dependent extinction of fear memory in an amygdala-mPFC neural circuit model., PLoS Computational Biology, 12(9), e1005099, 20160912
    Link to Paper Search Results by DOI
  26. ★, Nonrandom germline transmission of mouse spermatogonial stem cells., Developmental Cell, 38, 248-261, 20160808
    Link to Paper Search Results by DOI
  27. Reconstruction of spatial thermal gradient encoded in thermosensory neuron AFD in Caenorhabditis elegans., Journal of Neuroscience, 36(9), 2571-2581, 20160302
    Link to Paper Search Results by DOI
  28. ★, Distinct predictive performance of Rac1 and Cdc42 in cell migration., Scientific Reports, 5, 17527, 20151204
    Link to Paper Search Results by DOI
  29. 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, 20150317
    Link to Paper Search Results by DOI
  30. Intercellular propagation of extracellular signal-regulated kinase activation revealed by in vivo imaging of mouse skin., eLIFE, 4, e05178, 20150210
    Link to Paper Search Results by DOI
  31. Fluctuation of Rac1 activity is associated with the phenotypic and transcriptional heterogeneity of glioma cells., Journal of Cell Science, 127(8), 1805-1815, 20140415
    Link to Paper Search Results by DOI
  32. Mathematical Modeling of Neuronal Polarization During Development., Progress in Molecular Biology and Translational Science, 123, 127-141, 20140218
    Link to Paper Search Results by DOI
  33. Dynamic Regulation of Myosin Light Chain Phosphorylation by Rho-kinase., PLoS One, 7(6), e39269, 20120619
    Link to Paper Search Results by DOI
  34. Multi-cellular logistics of collective cell migration., PLoS One, 6(12), e27950, 20111221
    Link to Paper Search Results by DOI
  35. A multiphysical model of cell migration integrating reaction-diffusion, membrane and cytoskeleton., Neural Networks, 24, 979-989, 20110622
    Link to Paper Search Results by DOI
  36. Flexible Search for Single-Axon Morphology during Neuronal Spontaneous Polarization., PLoS One, 6(4), e19034, 20110429
    Link to Paper Search Results by DOI
  37. Noise-Induced collective migration for neural crest cells., Lecture Notes in Computer Science, 6352, 155-163, 20100101
    Link to Paper Search Results by DOI
  38. Stochastic control of spontaneous signal generation for gradient sensing in chemotaxis., Journal of Theoretical Biology, 255, 259-266, 20080822
    Link to Paper Search Results by DOI
  39. 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, 20080815
    Link to Paper Search Results by DOI
  40. ★, Local signaling with molecular diffusion as a decoder of Ca2+ signals in synaptic plasticity., Molecular Systems Biology, 1, 2005.0027, 20051213
    Link to Paper Search Results by DOI

Invited Lecture, Oral Presentation, Poster Presentation

  1. Prediction of Mutant Spatial Transcriptomes by Zero-shot Learning, Honda Naoki, Okochi Yasushi, Takaaki Matsui, International Symposium on Neural Development and Diseases, 2023/03, With Invitation, English, Kyoto University
  2. Decoding mental conflict between reward and curiosity from irrational behaviors., Honda Naoki, The 14th Prediction Science Seminar, 2023/01, With Invitation, English, Online
  3. Multi-modal Data Integration for Predicting Spatial Transcriptome, Honda Naoki, The 30th Hot Spring Harbor International Symposium, 2022/11, With Invitation, English, Online
  4. Data-Driven Decoding of Psychological Conflict., Honda Naoki, Yuki Konaka, NEURO2022, 2022/07, With Invitation, English, Okinawa convention center
  5. Data-driven decoding of decision-making and mental conflict by machine learning, Honda Naoki, HU-RIKEN-OIST Joint workshop, 2022/06, With Invitation, English, Hiroshima University
  6. Decoding reward-curiosity conflict in probabilistic bandit task, N. Honda, International workshop: The free energy principle of the brain: experiments and verification, 2021/12, With Invitation, English
  7. Deciphering Mental Conflict in Decision-Making from Animal Behavioral Data, N. Honda, ASHBi Seminar, 2021/11, With Invitation, English, online
  8. Data-driven hierarchical modeling of collective cell migration, H. Naoki, Society for Mathematical Biology, Minisymposium: Diverse quantitative approaches integrating data and modelling in development and medicine., 2021/06, With Invitation, English, online
  9. Decoding animal behavioral strategy by inverse reinforcement learning, Honda N, The 43rd Annual Meeting of the Japan Neuroscience Society, Symposium: Neuroscience meets ecology: sensing and AI technologies, 2020/07, With Invitation, English, online
  10. Identification of animal behavioral strategies by inverse reinforcement learning, Honda N, Neuroscience Institute workshop 2019 "Neural mechanisms underlying behavior", 2019/11, With Invitation, English, Nagoya University
  11. System Identification of mechano-chemical dynamics in epithelial collective cell migration, Honda N, Annual Meeting of Korean Society for Mathematical Biology, 2019/06, With Invitation, English, Jeju Island, Korea
  12. Identification of animal behavioral strategies by inverse reinforcement learning., Honda N, The A3 Workshop on Mathematical Life Science, 2019/05, With Invitation, English, Peking University, China
  13. Noise-resistant developmental reproducibility in vertebrate somite formation, Honda N, BDR symposium 2019 'Control and Design of Biosystems', 2019/03, With Invitation, English, RIKEN, Kobe
  14. Identification of animal behavioral strategies by inverse reinforcement learning, Honda N, Workshop for Reinforcement Learning & Biological Intelligence, 2019/03, With Invitation, English, University of Tokyo
  15. Mechano-chemical dynamics of collective cell migration in epithelial sheet., Honda N, Seminar for ANM/Collective Dynamics/Mathematical Biology, 2019/02, With Invitation, English, University of Bristol, UK
  16. Noise-resistant developmental reproducibility in vertebrate somite formation, Honda N, The 17th NTU-Kyoto-Tsukuba Joint Symposium, 2018/06, With Invitation, English, Kyoto University
  17. Neural wiring regulated by bi-directional chemotaxis of the growth cone., Honda N, The 4th Cell, Developmental, and Systems Biology Course Meeting, 2017/01, With Invitation, English, Kyoto University
  18. Mathematical modeling in stem cell dynamics., Honda N, The 6th Ritsumeikan-Monash Symposium on Probability and Related Fields, 2016/11, With Invitation, English, Ritsumeikan University
  19. Decoding of intracellular signal transfer from FRET imaging: distinct functions of Rac1 and Cdc42 in cell migration., Honda N, Yamao M, Ishii S, The 11th AIMS Conference on Dynamical Systems, Differential Equations and Applications, 2016/07, With Invitation, English, Orland, USA
  20. Mathematical model for development of neural circuit based on chemotaxis of growth cone., Honda N, Joint Meeting of JSMB and CJK Colloquium on Mathematical Biology, 2015/08, With Invitation, English, Doshisha University
  21. Predictive computational approach on FRET imaging of Rac1 and Cdc42 in cell migration., Honda N, The 3rd Cell, Developmental, and Systems Biology Course Meeting, 2015/04, With Invitation, English, Kyoto University
  22. Theoretical modelling for neuronal polarization and axon guidance., Honda N, Symposium on Multi-dimensional Quantitative Imaging and Mathematical Modeling, 2013/05, With Invitation, English, Kyoto University
  23. Theoretical modeling for axon guidance and polarization., Honda N, Nishiyama M, Hong K, Ishii S, The 34th anual meeting of the japan neuroscience society, Symposium: Gradients of guidance cues in axon and dendrite patterning, 2011/09, With Invitation, English

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, 2009/03