NAOKI HONDA
Last Updated :2023/09/04
- Affiliations, Positions
- Graduate School of Integrated Sciences for Life, Professor
- Web Site
- E-mail
- nhonda
hiroshima-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
- 2023, Liberal Arts Education Program1, 1Term, Seminar in Linear AlgebraI
- 2023, Undergraduate Education, 3Term, English Seminar on Mathematics
- 2023, Undergraduate Education, 4Term, Mathematics for Modeling and Simulation
- 2023, Undergraduate Education, First Semester, Special Study of Mathematics and Informatics for Graduation
- 2023, Undergraduate Education, Second Semester, Special Study of Mathematics and Informatics for Graduation
- 2023, Undergraduate Education, 1Term, English Seminar for Globalization A
- 2023, Undergraduate Education, First Semester, Application of principal component analysis based- and tensor decomposition based- unsupervised feature extraction to bioinformatics
- 2023, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Mathematical and Life Sciences
- 2023, Graduate Education (Master's Program) , 1Term, Computational Mathematics A
- 2023, Graduate Education (Master's Program) , First Semester, Special Lecture on Mathematical and Life Sciences A
- 2023, Graduate Education (Master's Program) , First Semester, Exercises in Applied Mathematics and Computational Science A
- 2023, Graduate Education (Master's Program) , Second Semester, Exercises in Applied Mathematics and Computational Science B
- 2023, Graduate Education (Doctoral Program) , Academic Year, Research for Academic Degree Dissertation in Integrated Life Sciences
- 2023, Graduate Education (Doctoral Program) , First Semester, Special Lecture on Mathematical and Life Sciences E
Research Activities
Academic Papers
- Single-cell transcriptome atlas of Drosophila gastrula 2.0., Cell Reports, 20230710
- Multidimensional fractal scaling analysis using higher order moving average polynomials and its fast algorithm, Signal Processing, 208(108997), 20230701
- ★, Decoding reward–curiosity conflict in decision-making from irrational behaviors., Nature Computational Science, 3, 418-432, 20230515
- Intercellular exchange of Wnt ligands reduces cell population heterogeneity in embryogenesis, Nature Communications, 14(1924), 20230406
- Dopamine error signal to actively cope with lack of expected reward, Science Advances, 9(10), 20230310
- Optimal COVID-19 testing strategy on limited resources, PLoS One, 18(2), 20230224
- ★, Adaptive discrimination between harmful and harmless antigens in the immune system by predictive coding, iScience, 26(1), 20230120
- Zero-shot reconstruction of mutant spatial transcriptomes., bioRxiv, 20221219
- ★, Stem cell homeostasis regulated by hierarchy and neutral competition, Communications Biology, 5(1), 20221118
- Prediction of amyloid beta accumulation from multiple biomarkers using a hierarchical Bayesian model., bioRxiv, 20221024
- Regulation of male germline transmission patterns by the Trp53-Cdkn1a pathway, Stem Cell Reports, 17(9), 1924-1941, 20220913
- ★, Model-based prediction of spatial gene expression via generative linear mapping., Nature Communications, 12, 3731, 20210617
- Hierarchical modeling of mechano-chemical dynamics of epithelial sheets across cells and tissue., Scientific Reports, 11, 4069, 20210218
- Somite boundary determination in normal and clock-less vertebrate embryos., Development, Growth & Differentiation, 62, 177-187, 20200228
- ★, Noise-resistant developmental reproducibility in vertebrate somite formation., PLoS Computational Biology, 15(2), e1006579, 20190204
- ★, Identification of animal behavioral strategies by inverse reinforcement learning., PLoS Computational Biology, 14(5), e1006122, 20180502
- Time-lapse observation of stepwise regression of Erk activity in zebrafish presomitic mesoderm, Scientific Reports, 8, 4335, 20180312
- Nonrandom contribution of left and right testes to germline transmission from mouse spermatogonial stem cells., Biology of Reproduction, 97(6), 902-910, 20171109
- Propagating wave of ERK activation orients collective cell migration., Developmental Cell, 43, 305-317, 20171106
- ★, Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection., PLoS Computational Biology, 13(8), e1005702, 20170808
- Self-organization mechanism of microtubule orientation patterns in axons and dendrites., bioRxiv, 20170723
- Discovery of long-range inhibitory signaling to ensure single axon formation., Nature Communications, 8, 33, 20170626
- ★, Multi-phasic bi-directional chemotactic responses of the growth cone., Scientific Reports, 6, 36256, 20161103
- Two new FRET imaging measures: linearly proportional to and highly contrasting the fraction of active molecules., PLoS One, 11(10), e0164254, 20161025
- ★, Uncertainty-dependent extinction of fear memory in an amygdala-mPFC neural circuit model., PLoS Computational Biology, 12(9), e1005099, 20160912
- ★, Nonrandom germline transmission of mouse spermatogonial stem cells., Developmental Cell, 38, 248-261, 20160808
- Reconstruction of spatial thermal gradient encoded in thermosensory neuron AFD in Caenorhabditis elegans., Journal of Neuroscience, 36(9), 2571-2581, 20160302
- ★, Distinct predictive performance of Rac1 and Cdc42 in cell migration., Scientific Reports, 5, 17527, 20151204
- 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
- Intercellular propagation of extracellular signal-regulated kinase activation revealed by in vivo imaging of mouse skin., eLIFE, 4, e05178, 20150210
- Fluctuation of Rac1 activity is associated with the phenotypic and transcriptional heterogeneity of glioma cells., Journal of Cell Science, 127(8), 1805-1815, 20140415
- Mathematical Modeling of Neuronal Polarization During Development., Progress in Molecular Biology and Translational Science, 123, 127-141, 20140218
- Dynamic Regulation of Myosin Light Chain Phosphorylation by Rho-kinase., PLoS One, 7(6), e39269, 20120619
- Multi-cellular logistics of collective cell migration., PLoS One, 6(12), e27950, 20111221
- A multiphysical model of cell migration integrating reaction-diffusion, membrane and cytoskeleton., Neural Networks, 24, 979-989, 20110622
- Flexible Search for Single-Axon Morphology during Neuronal Spontaneous Polarization., PLoS One, 6(4), e19034, 20110429
- Noise-Induced collective migration for neural crest cells., Lecture Notes in Computer Science, 6352, 155-163, 20100101
- Stochastic control of spontaneous signal generation for gradient sensing in chemotaxis., Journal of Theoretical Biology, 255, 259-266, 20080822
- 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
- ★, Local signaling with molecular diffusion as a decoder of Ca2+ signals in synaptic plasticity., Molecular Systems Biology, 1, 2005.0027, 20051213
Invited Lecture, Oral Presentation, Poster Presentation
- 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
- Decoding mental conflict between reward and curiosity from irrational behaviors., Honda Naoki, The 14th Prediction Science Seminar, 2023/01, With Invitation, English, Online
- Multi-modal Data Integration for Predicting Spatial Transcriptome, Honda Naoki, The 30th Hot Spring Harbor International Symposium, 2022/11, With Invitation, English, Online
- Data-Driven Decoding of Psychological Conflict., Honda Naoki, Yuki Konaka, NEURO2022, 2022/07, With Invitation, English, Okinawa convention center
- 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
- 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
- Deciphering Mental Conflict in Decision-Making from Animal Behavioral Data, N. Honda, ASHBi Seminar, 2021/11, With Invitation, English, online
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Noise-resistant developmental reproducibility in vertebrate somite formation, Honda N, The 17th NTU-Kyoto-Tsukuba Joint Symposium, 2018/06, With Invitation, English, Kyoto University
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 2021/10, 2024/03
- 2021/10, 2024/03
- 2021/08, 2024/03
- 2021/08, 2024/03
- 2021/07, 2025/03
- 2021/04, 2025/03
- 2020/12, 2025/03
- 2020/02, 2025/01
- 2019/04, 2021/03
- 2019/06, 2021/03
- 2018/06, 2020/01
- 2016/04, 2020/03
- 2013/04, 2016/03
- 2007/04, 2009/03