Naoki Honda

Profile Information

Affiliation: Hiroshima University
: Kyoto University
: National Institutes of Natural Sciences

Degree: 奈良先端科学技術大学院大学

J-GLOBAL ID: 200901011515136622
researchmap Member ID: 5000091530

理論生物学、データ駆動生物学に関する研究を行っております。

Research Interests

Research Areas

Research History

Jul, 2021 - Present

National Institutes of Natural Sciences
Jul, 2021 - Present

Hiroshima University
Apr, 2018 - Mar, 2021

准教授, 生命科学研究科, 京都大学大学院
Apr, 2017 - Mar, 2018

特定准教授, 生命科学研究科, 京都大学大学院
May, 2013 - Mar, 2017

特定准教授, 医学研究科生命動態システム科学推進拠点, 京都大学大学院
Apr, 2012 - Apr, 2013

特任助教, 情報学研究科, 京都大学大学院
Feb, 2009 - Mar, 2012

特定研究員, 情報学研究科, 京都大学大学院
Apr, 2008 - Jan, 2009

学術振興会特別研究員PD, 理学研究院, 九州大学大学院
Apr, 2003 - Mar, 2008

Graduate School of Information Science, Nara Institute of Science and Technology

Papers

A transcriptional program underlying the circannual rhythms of gonadal development in medaka

Tomoya Nakayama, Miki Tanikawa, Yuki Okushi, Thoma Itoh, Tsuyoshi Shimmura, Michiyo Maruyama, Taiki Yamaguchi, Akiko Matsumiya, Ai Shinomiya, Ying-Jey Guh …

Proceedings of the National Academy of Sciences, 120(52), Dec 18, 2023
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates

Yuichiro Yada, Honda Naoki

npj Systems Biology and Applications, 9(1), Nov 23, 2023
Single-cell transcriptome atlas of Drosophila gastrula 2.0.

Shunta Sakaguchi, Sonoko Mizuno, Yasushi Okochi, Chiharu Tanegashima, Osamu Nishimura, Tadashi Uemura, Mitsutaka Kadota, Honda Naoki, Takefumi Kondo

Cell reports, 112707-112707, Jul 3, 2023
Single-cell transcriptome atlas of Drosophila gastrula 2.0

Shunta Sakaguchi, Sonoko Mizuno, Yasushi Okochi, Chiharu Tanegashima, Osamu Nishimura, Tadashi Uemura, Mitsutaka Kadota, Honda Naoki, Takefumi Kondo

Cell Reports, 112707-112707, Jul, 2023
Intercellular exchange of Wnt ligands reduces cell population heterogeneity during embryogenesis

Yudai Hatakeyama, Nen Saito, Yusuke Mii, Ritsuko Takada, Takuma Shinozuka, Tatsuya Takemoto, Honda Naoki, Shinji Takada

Nature Communications, 14(1), Apr 6, 2023
Dopamine error signal to actively cope with lack of expected reward

Seiya Ishino, Taisuke Kamada, Gideon Sarpong, Julia Kitano, Reo Tsukasa, Hisa Mukohira, Fangmiao Sun, Yulong Li, Kenta Kobayashi, Naoki Honda …

Science advances, 9(10) eade5420, Mar 10, 2023 Peer-reviewed
Zero-shot reconstruction of mutant spatial transcriptomes

Yasushi Okochi, Takaaki Matsui, Honda Naoki

Dec 19, 2022
Prediction of amyloid β accumulation from multiple biomarkers using a hierarchical Bayesian model

Yuichiro Yada, Honda Naoki

Oct 24, 2022
Regulation of male germline transmission patterns by the Trp53-Cdkn1a pathway.

Mito Kanatsu-Shinohara, Honda Naoki, Takashi Tanaka, Misako Tatehana, Takako Kikkawa, Noriko Osumi, Takashi Shinohara

Stem cell reports, 17(9) 1924-1941, Aug 1, 2022
Model-based prediction of spatial gene expression via generative linear mapping.

Yasushi Okochi, Shunta Sakaguchi, Ken Nakae, Takefumi Kondo, Honda Naoki

Nature communications, 12(1) 3731-3731, Jun 17, 2021
Hierarchical modeling of mechano-chemical dynamics of epithelial sheets across cells and tissue.

Yoshifumi Asakura, Yohei Kondo, Kazuhiro Aoki, Honda Naoki

Scientific reports, 11(1) 4069-4069, Feb 18, 2021
Somite boundary determination in normal and clock-less vertebrate embryos.

Honda Naoki, Takaaki Matsui

Development, growth & differentiation, Feb 28, 2020 Peer-reviewed
Noise-resistant developmental reproducibility in vertebrate somite formation.

Honda Naoki, Ryutaro Akiyama, Dini Wahyu Kartika Sari, Shin Ishii, Yasumasa Bessho, Takaaki Matsui

PLoS computational biology, 15(2) e1006579, Feb, 2019 Peer-reviewed
Time-lapse observation of stepwise regression of Erk activity in zebrafish presomitic mesoderm.

Dini Wahyu Kartika Sari, Ryutaro Akiyama, Honda Naoki, Hannosuke Ishijima, Yasumasa Bessho, Takaaki Matsui

Scientific reports, 8(1) 4335-4335, Mar 12, 2018 Peer-reviewed
Thermotactic behavioral strategy of C. elegans identified using inverse reinforcement learning

Yamaguchi, S, Naoki, H, Ikeda, M, Tsukada, Y, Nakano, S, Mori, I, Ishii, S

PLoS Computational Biology, 2018 Peer-reviewed
Identification of animal behavioral strategy by inverse reinforcement learning

Yamaguchi S, Honda N, Ikeda M, Tsukada Y, Nakano S, Mori I, Ishii S

PLoS Computational Biology, 14(5) e1006122, 2018 Peer-reviewed
Propagating Wave of ERK Activation Orients Collective Cell Migration

Kazuhiro Aoki, Yohei Kondo, Honda Naoki, Toru Hiratsuka, Reina E. Itoh, Michiyuki Matsuda

DEVELOPMENTAL CELL, 43(3) 305-+, Nov, 2017 Peer-reviewed
Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection

Honda Naoki

PLOS COMPUTATIONAL BIOLOGY, 13(8) e1005702, Aug, 2017 Peer-reviewed
Self-organization mechanism of microtubule orientation patterns in axons and dendrites.

Honda N, Uegaki K, Ishii S

bioRxiv, 163014, Jul, 2017
Discovery of long-range inhibitory signaling to ensure single axon formation

Tetsuya Takano, Mengya Wu, Shinichi Nakamuta, Honda Naoki, Naruki Ishizawa, Takashi Namba, Takashi Watanabe, Chundi Xu, Tomonari Hamaguchi, Yoshimitsu Yura …

NATURE COMMUNICATIONS, 8(33), Jun, 2017 Peer-reviewed

Misc.

細胞間コミュニケーションによるがん進展制御

榎本将人, 本田直樹, 武本花奈美, 竹本大策, 井垣達吏

2017年度生命科学系学会合同年次大会, Dec, 2017 Peer-reviewed
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, May, 2017 Invited
Mathematical model for collective cell migration regulated by external molecular signal

MURASE Akio, Honda NAOKI, ISHII Shin

IEICE technical report. ME and bio cybernetics, 114(514) 245-248, Mar 16, 2015
システム神経科学スプリングスクール2015開催報告

中江健, 松田道行, 石井信, 本田直樹, 浦久保秀俊, 山尾将隆, 近藤洋平, 塚田祐基, 小山雅典, 村上陽平 …

日本神経回路学会誌, 22(2) 78-81, 2015
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, Oct, 2014 Invited
システム神経科学スプリングスクール2014開催報告

中江健, 本田直樹, 浦久保秀俊, 山尾将隆, 近藤洋平, 塚田祐基, 石井信

日本神経回路学会誌, 21(2) 101-104, 2014
システム神経科学スプリングスクール2013開催報告

中江健, 本田直樹, 浦久保秀俊, 山尾将隆, 塚田祐基, 石井信

日本神経回路学会誌 = The Brain & neural networks, 20(2) 84-87, Jun 5, 2013
システム神経生物学スプリングスクール2012開催報告

本田直樹, 中江健, 行縄直人, 山尾将隆, 石井信

日本神経回路学会誌 = The Brain & neural networks, 19(2) 97-100, Jun 5, 2012
Theoretical modeling for axon guidance and polarization

Naoki Honda, Makoto Nishiyama, Kyonsoo Hong, Shin Ishii

NEUROSCIENCE RESEARCH, 71 E11-E11, 2011
Multi-physical full-scale simulation for neuronal morphogenesis

Seigo Nonaka, Naoki Honda, Shin Ishii

NEUROSCIENCE RESEARCH, 68 E105-E105, 2010

Books and Other Publications

AI導入によるバイオテクノロジーの発展

本田直樹 (Role: Contributor, 第７章：定量データに基づく生体情報処理の同定)

シーエムシー出版, Feb, 2018
Trends in Biophysics: From Cell Dynamics Toward Multicellular Growth Phenomena

Yamao M, Honda N, Ishii S (Role: Contributor, Chapter 11: Collective cell migration)

Apple Academic Press, Apr, 2013

Teaching Experience

計算・統計・数理生物学 (京都大学生命科学研究科)

Professional Memberships

Research Projects

多細胞動態を司る支配方程式のデータ駆動的解読

科学研究費助成事業基盤研究(B), 基盤研究(B), 日本学術振興会, Apr, 2021 - Mar, 2025

本田直樹, 青木一洋
あいまい環境に対峙する脳・生命体の情報獲得戦略研究の推進

科学研究費助成事業, 学術変革領域研究(B), 日本学術振興会, Aug, 2021 - Mar, 2024

小坂田文隆, 雨森賢一, 本田直樹
新自由エネルギー原理の確立

科学研究費助成事業学術変革領域研究(B), 学術変革領域研究(B), 日本学術振興会, Aug, 2021 - Mar, 2024

本田直樹
Analyses of cortical actin dynamics by live-cell imaging and machine-learning

Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Research (Exploratory), Grant-in-Aid for Challenging Research (Exploratory), Japan Society for the Promotion of Science, Jun, 2019 - Mar, 2021

Yoshimura Shigehiro
脳回路構築における軸索配線原理の解読

科学研究費助成事業新学術領域研究(研究領域提案型), 新学術領域研究(研究領域提案型), 日本学術振興会, Apr, 2019 - Mar, 2021

本田直樹
Identification of neural basis of animal behavioral strategy by inverse reinforcement learning

Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B), Grant-in-Aid for Young Scientists (B), Japan Society for the Promotion of Science, Apr, 2016 - Mar, 2020

Honda Naoki
Toward cytoskeleton-based understanding of neuronal morphogenesis

Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B), Grant-in-Aid for Young Scientists (B), Japan Society for the Promotion of Science, Apr, 2013 - Mar, 2016

Honda Naoki
走化性における確率的なシグナル伝達のシステム生物学

科学研究費助成事業特別研究員奨励費, 特別研究員奨励費, 日本学術振興会, 2007 - 2008

本田直樹

Profile Information

Research Interests

Research Areas

Research History

Papers

Misc.

Books and Other Publications

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Professional Memberships

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