NAOKI HONDA
Last Updated :2023/03/03
- 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
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
- 2022, Undergraduate Education, 2Term, Theory of Complex Systems
- 2022, Undergraduate Education, 4Term, Mathematics for Modeling and Simulation
- 2022, Undergraduate Education, First Semester, Special Study of Mathematics and Informatics for Graduation
- 2022, Undergraduate Education, Second Semester, Special Study of Mathematics and Informatics for Graduation
- 2022, Undergraduate Education, 2Term, English Seminar for Globalization A
- 2022, Undergraduate Education, 2Term, Special Lectures in Mathematics(Network Biology)
- 2022, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Mathematical and Life Sciences
- 2022, Graduate Education (Master's Program) , 1Term, Exercises in Applied Mathematics and Computational Science A
- 2022, Graduate Education (Master's Program) , 2Term, Exercises in Applied Mathematics and Computational Science A
- 2022, Graduate Education (Master's Program) , 3Term, Exercises in Applied Mathematics and Computational Science B
- 2022, Graduate Education (Master's Program) , 4Term, Exercises in Applied Mathematics and Computational Science B
- 2022, Graduate Education (Master's Program) , 3Term, Mathematical Modeling C
- 2022, Graduate Education (Master's Program) , 1Term, Computational Mathematics A
- 2022, Graduate Education (Master's Program) , 2Term, Special Lecture on Mathematical and Life Sciences C
- 2022, Graduate Education (Doctoral Program) , Academic Year, Research for Academic Degree Dissertation in Integrated Life Sciences
- 2022, Graduate Education (Doctoral Program) , 2Term, Special Lecture on Mathematical and Life Sciences G
Research Activities
Academic Papers
- Decoding reward–curiosity conflict in decision-making from irrational behaviors., bioRxiv, 2022
- Stem cell homeostasis regulated by hierarchy and neutral competition., bioRxiv, 2022
- Intercellular exchange of Wnt ligands reduces cell population heterogeneity in embryogenesis., Research Square, 2022
- Single-cell transcriptome atlas of Drosophila gastrula 2.0., bioRxiv, 2021
- Adaptive discrimination of antigen risk by predictive coding in immune system., bioRxiv, 2021
- Optimal and worst examination strategies for COVID-19., medRxiv, 2021
- Self-organization mechanism of microtubule orientation patterns in axons and dendrites., bioRxiv, 2017
- ★, Model-based prediction of spatial gene expression via generative linear mapping., Nature Communications, 12, 3731, 2021
- Hierarchical modeling of mechano-chemical dynamics of epithelial sheets across cells and tissue., Scientific Reports, 11, 4069, 2021
- Somite boundary determination in normal and clock-less vertebrate embryos., Development, Growth & Differentiation, 62, 177-187, 2020
- ★, Noise-resistant developmental reproducibility in vertebrate somite formation., PLoS Computational Biology, 15(2), e1006579, 2019
- Time-lapse observation of stepwise regression of Erk activity in zebrafish presomitic mesoderm, Scientific Reports, 8, 4335, 2018
- ★, Identification of animal behavioral strategies by inverse reinforcement learning., PLoS Computational Biology, 14(5), e1006122, 2018
- Nonrandom contribution of left and right testes to germline transmission from mouse spermatogonial stem cells., Biology of Reproduction, 97(6), 902-910, 2017
- Propagating wave of ERK activation orients collective cell migration., Developmental Cell, 43, 305-317, 2017
- ★, Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection, PLoS Computational Biology, 13(8), e1005702, 2017
- Discovery of long-range inhibitory signaling to ensure single axon formation., Nature Communications, 8, 33, 2017
- Multi-phasic bi-directional chemotactic responses of the growth cone., Scientific Reports, 6, 36256, 2016
- Two new FRET imaging measures: linearly proportional to and highly contrasting the fraction of active molecules., PLoS One, 11(10), e0164254, 2016
- ★, Uncertainty-dependent extinction of fear memory in an amygdala-mPFC neural circuit model., PLoS Computational Biology, 12(9), e1005099, 2016
- Nonrandom germline transmission of mouse spermatogonial stem cells., Developmental Cell, 38, 248-261, 2016
- Reconstruction of spatial thermal gradient encoded in thermosensory neuron AFD in Caenorhabditis elegans., Journal of Neuroscience, 36(9), 2571-2581, 2016
- ★, Distinct predictive performance of Rac1 and Cdc42 in cell migration., 5, 17527, 2015
- 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
- Intercellular propagation of extracellular signal-regulated kinase activation revealed by in vivo imaging of mouse skin., eLIFE, 4, e05178, 2015
- Fluctuation of Rac1 activity is associated with the phenotypic and transcriptional heterogeneity of glioma cells., Journal of Cell Science, 127(8), 1805-1815, 2014
- Mathematical Modeling of Neuronal Polarization During Development., Progress in Molecular Biology and Translational Science, 123, 127-141, 2014
- Dynamic Regulation of Myosin Light Chain Phosphorylation by Rho-kinase., PLoS One, 7(6), e39269, 2012
- Multi-cellular logistics of collective cell migration., PLoS One, 6(12), e27950, 2011
- Noise-Induced collective migration for neural crest cells., Lecture Notes in Computer Science, 6352, 155-163, 2010
- A multiphysical model of cell migration integrating reaction-diffusion, membrane and cytoskeleton., Neural Networks, 24, 979-989, 2011
- Flexible Search for Single-Axon Morphology during Neuronal Spontaneous Polarization., PLoS One, 6(4), e19034, 2011
- Stochastic control of spontaneous signal generation for gradient sensing in chemotaxis., Journal of Theoretical Biology, 255, 259-266, 2008
- 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
- 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
- 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, 2008/03