Basic Information

Faculty

• 医学部

Professional Memberships

• 日本抗加齢医学会
• 日本基礎老化学会
• 日本人工知能学会
• 日本人類遺伝学会

Academic Degree

• 博士（医科学）(京都大学)
• 修士（医科学）(京都大学)

Academic Resume (Graduate Schools)

• 京都大学, 大学院医学研究科博士後期課程医科学専攻, 修了
• 京都大学, 大学院医学研究科修士課程医科学専攻, 修了

Academic Resume (Undergraduate School/Majors)

• 京都大学, 農学部資源生物科学科, 卒業

Research History

• From Apr. 2025, To Present

  Gifu University, 高等研究院, 特任助教
• From Apr. 2021, To Mar. 2025

  京都大学大学院医学研究科, 附属ゲノム医学センター, 助教
• From Apr. 2019, To Mar. 2021

  日本学術振興会特別研究員DC2

Language of Instruction

• Japanese
• English

ID,URL

• J-Global ID

  202101001861606996

• Researcher number

  10911852

researchmap URL

• https://researchmap.jp/daigo_okada

Research

Research Interests

• 再生医療
• バイオインフォマティクス
• aging

Research Areas

• Informatics, Statistical science
• Life sciences, Genomics
• Informatics, Biological, health, and medical informatics
• Life sciences, Systems genomics

Papers

• The opposite aging effect to single cell transcriptome profile among cell subsets.

  Daigo Okada

  Biogerontology, 11 Sep. 2024, Peer-reviewed, Lead author, Last author, Corresponding author

  
• Identification of epistatic SNP combinations in rheumatoid arthritis using LAMPLINK and Japanese cohorts.

  Mio Shibata; Aika Terada; Takahisa Kawaguchi; Yoichiro Kamatani; Daigo Okada; Kazuhisa Nagashima; Koichiro Ohmura; Fumihiko Matsuda; Shuji Kawaguchi; Jun Sese; Ryo Yamada

  Journal of human genetics, 16 Jul. 2024, Peer-reviewed

  
• Data mining method of single-cell omics data to evaluate a pure tissue environmental effect on gene expression level

  Daigo Okada; Jianshen Zhu; Kan Shota; Yuuki Nishimura; Kazuya Haraguchi

  arXiv, 11 Jun. 2024, Lead author, Corresponding author

  
• Data-driven detection of age-related arbitrary monotonic changes in single-cell gene expression distributions.

  Jian Hao Cheng; Daigo Okada

  PeerJ, 2024, Peer-reviewed, Last author, Corresponding author

  
• Visualization of the landscape of the read alignment shape of ATAC-seq data using Hellinger distance metric.

  Jian Hao Cheng; Cheng Zheng; Ryo Yamada; Daigo Okada

  Genes to cells : devoted to molecular & cellular mechanisms, 21 Nov. 2023, Peer-reviewed, Last author, Corresponding author

  
• Delving into gene-set multiplex networks facilitated by a k-nearest neighbor-based measure of similarity

  Cheng Zheng; Man Wang; Ryo Yamada; Daigo Okada

  Computational and Structural Biotechnology Journal, 11 Oct. 2023, Peer-reviewed, Last author, Corresponding author

  
• Application of a mathematical model to clarify the statistical characteristics of a pan-tissue DNA methylation clock.

  Daigo Okada

  GeroScience, 03 Oct. 2023, Peer-reviewed, Lead author, Last author, Corresponding author

  
• Plasma proteins as potential biomarkers of aging of single tissue and cell type.

  Daigo Okada

  Biogerontology, 14 Sep. 2023, Peer-reviewed, Lead author, Last author, Corresponding author

  
• Bioinformatic Identification of Potential RNA Alterations on the Atrial Fibrillation Remodeling from Human Pulmonary Veins

  Wataru Igarashi; Daichi Takagi; Daigo Okada; Daiki Kobayashi; Miho Oka; Toshiro Io; Kuniaki Ishii; Kyoichi Ono; Hiroshi Yamamoto; Yosuke Okamoto

  International Journal of Molecular Sciences, 22 Jun. 2023, Peer-reviewed

  
• Data-driven identification and classification of nonlinear aging patterns reveals the landscape of associations between DNA methylation and aging.

  Daigo Okada; Jian Hao Cheng; Cheng Zheng; Tatsuro Kumaki; Ryo Yamada

  Human genomics, 11 Feb. 2023, Peer-reviewed, Lead author, Corresponding author

  Access this paper :

  
• Mathematical model for the relationship between single-cell and bulk gene expression to clarify the interpretation of bulk gene expression data.

  Daigo Okada; Cheng Zheng; Jian Hao Cheng

  Computational and structural biotechnology journal, Sep. 2022, Peer-reviewed, Lead author, Corresponding author

  
• Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans.

  Daigo Okada; Yosuke Okamoto; Toshiro Io; Miho Oka; Daiki Kobayashi; Suzuka Ito; Ryo Yamada; Kuniaki Ishii; Kyoichi Ono

  Biomolecules, 20 Jun. 2022, Peer-reviewed, Lead author

  
• Cell population-based framework of genetic epidemiology in the single-cell omics era.

  Daigo Okada; Cheng Zheng; Jian Hao Cheng; Ryo Yamada

  BioEssays : news and reviews in molecular, cellular and developmental biology, 25 Nov. 2021, Peer-reviewed, Lead author, Corresponding author

  
• Data-driven comparison of multiple high-dimensional single-cell expression profiles.

  Daigo Okada; Jian Hao Cheng; Cheng Zheng; Ryo Yamada

  Journal of human genetics, 01 Nov. 2021, Peer-reviewed, Lead author, Corresponding author

  
• Genome-wide association study of individual differences of human lymphocyte profiles using large-scale cytometry data.

  Daigo Okada; Naotoshi Nakamura; Kazuya Setoh; Takahisa Kawaguchi; Koichiro Higasa; Yasuharu Tabara; Fumihiko Matsuda; Ryo Yamada

  Journal of human genetics, 23 Nov. 2020, Peer-reviewed, Lead author

  
• Interpretation of omics data analyses.

  Ryo Yamada; Daigo Okada; Juan Wang; Tapati Basak; Satoshi Koyama

  Journal of human genetics, 08 May 2020, Peer-reviewed

  
• Decomposition of a set of distributions in extended exponential family form for distinguishing multiple oligo-dimensional marker expression profiles of single-cell populations and visualizing their dynamics.

  Daigo Okada; Ryo Yamada

  PloS one, 10 Apr. 2020, Peer-reviewed, Lead author

  Access this paper :

  
• Extension of Sinkhorn Method: Optimal Movement Estimation of Agents Moving at Constant Velocity

  Daigo Okada; Naotoshi Nakamura; Takuya Wada; Ayako Iwasaki; Ryo Yamada

  Transactions of the Japanese Society for Artificial Intelligence, 01 Sep. 2019, Peer-reviewed, Lead author

  
• LAVENDER: latent axes discovery from multiple cytometry samples with non-parametric divergence estimation and multidimensional scaling reconstruction

  Naotoshi Nakamura, Daigo Okada, Kazuya Setoh, Takahisa Kawaguchi, Koichiro Higasa, Yasuharu Tabara, Fumihiko Matsuda, Ryo Yamada

  bioRxiv, 18 Jun. 2019

  
• An intersection network based on combining SNP coassociation and RNA coexpression networks for feed utilization traits in Japanese Black cattle.

  Daigo Okada; Satoko Endo; Hirokazu Matsuda; Shinichiro Ogawa; Yukio Taniguchi; Tomohiro Katsuta; Toshio Watanabe; Hiroaki Iwaisaki

  Journal of animal science, 29 Jun. 2018, Peer-reviewed, Lead author

  

Misc.

• Relationships between total, relative and absolute molecular abundance in aging genomics studies: Simple theoretical consideration.

  Daigo Okada

  Jxiv, Feb. 2024, Lead author, Last author, Corresponding author

  
• 「注目論文：Our Focus on Genetics」大規模サイトメトリーデータを用いた、ヒトリンパ球プロファイルの個人差を対象とするゲノムワイド関連解析

  岡田大瑚

  Dec. 2021

  

Presentations

• 『データの洪水』を乗り越えるすべ ～オミクス解析の観点から～

  岡田大瑚

  日本畜産学会 第132回大会, 17 Sep. 2024, Invited

  
• Comprehensive analysis of age-related changes in transcriptome diversity by single cell RNA-seq data analysis

  Daigo Okada

  第47回日本基礎老化学会大会, 16 Jun. 2024

  
• Delve into inter-gene-set relationships using single-cell transcriptomic data

  Cheng Zheng; Man Wang; Ryo Yamada; Daigo Okada

  日本人類遺伝学会第67回大会, 15 Dec. 2022

  
• ATAC shape information provided biological insight

  Jian Hao Cheng; Cheng Zheng; Ryo Yamada; Daigo Okada

  日本人類遺伝学会第67回大会, 15 Dec. 2022

  
• A mathematical model for the relationship between single cell expression profile and the bulk gene expression analysis

  Daigo Okada; Cheng Zheng; Jian Hao Cheng

  日本人類遺伝学会第67回大会, 15 Dec. 2022

  
• Information geometric approach to embed multiple single cell expression profiles into low dimensional coordinate space

  Daigo Okada; Jian Hao Cheng; Ryo Yamada

  Pacifichem 2021, 18 Dec. 2021

  
• Search and classification of DNA methylation biomarkers of aging focusing on nonlinear age-related changes

  Daigo Okada; Jian hao Cheng; Cheng Zheng; Ryo Yamada

  日本人類遺伝学会第66回大会, 16 Oct. 2021

  
• Combinations of SNPs associated with Rheumatoid Arthritis in Japanese populations by LAMPLINK

  Mio Shibata; Aika Terada; Takahisa Kawaguchi; Yoichiro Kamatani; Izumi Yamaguchi; Daigo Okada; Kazuhisa Nagashima; Koichiro Ohmura; Yasuharu Tabara; Fumihiko Matsuda; Jun Sese; Ryo Yamada

  第2回京都大学医薬系研究交流サロン, Apr. 2021

  
• Kernel DEEF: novel method for representing a single-cell expression data as one point in low dimensional space

  Daigo Okada; Cheng Zheng; Jian Hao Cheng; Ryo Yamada

  第2回京都大学医薬系研究交流サロン, Apr. 2021

  
• Functional data analysis in transcriptomics

  Cheng Zheng; Daigo Okada; Jian Hao Cheng; Ryo Yamada

  第2回京都大学医薬系研究交流サロン, Apr. 2021

  
• Application of functional approaches to sets of epigenomic data

  Jian Hao Cheng; Daigo Okada; Cheng Zheng; Ryo Yamada

  第2回京都大学医薬系研究交流サロン, Apr. 2021

  
• 拡大指数型分布族分解法(DEEF法)によるエピゲノムプロファイルのデータドリブンな異同定量

  岡田大瑚; Cheng Jian Hao; Zheng Cheng; Feng Yi Huan; 山田亮

  日本人類遺伝学会第65回大会, Nov. 2020

  
• 拡大指数型分布族分解法(DEEF法)を用いたエピゲノムプロファイルの異同とその加齢変化の可視化

  岡田大瑚; Cheng Jian Hao; Zheng Cheng; Feng Yi Huan; 山田亮

  酵母遺伝学フォーラム第53回研究報告会, Sep. 2020

  
• 細胞集団プロファイルの軌跡の可視化

  岡田大瑚; 山田亮

  京都大学 医薬系研究交流サロン, Jan. 2020

  
• Epistatic combinations of multiple SNPs commonly confirmed in two different case-control studies of rheumatoid arthritis in Japanese populations.

  M. Shibata; A. Terada; D. Okada; T. Kawaguchi; I. Yamaguchi; Y. Kamatani; F. Matsuda; J. Sese; R. Yamada

  ASHG 2019 Annual Meeting, Oct. 2019

  
• Visualization of comprehensively changes in whole cell subsets after influenza vaccination

  D. Okada; N. Nakamura; K. Setoh; T. Kawaguchi; M. Narahara; K. Higasa; Y. Tabara, F; Matsuda; R. Yamada

  VIZBI 2019, Mar. 2019

  
• 大規模シングルセル発現データを用いた細胞集団プロファイル全体の異同の解析

  岡田大瑚; 中村直俊; 瀬藤和也; 川口喬久; 奈良原舞子; 日笠幸一郎; 田原康玄; 松田文彦; 山田亮

  第 41 回日本分子生物学会年会, Nov. 2018

  
• フローサイトメトリーデータとゲノム / トランスクリプトームデータを組み合わせたヒト免疫表現型の個人差の解析

  岡田大瑚; 中村直俊; 瀬藤和也; 川口喬久; 奈良原舞子; 日笠幸一郎; 田原康玄; 松田文彦; 山田亮

  日本人類遺伝学会第62回大会, Nov. 2017

  
• 季節性インフルエンザワクチンに対する免疫応答から個人差を抽出する

  中村直俊; 岡田大瑚; 瀬藤和也; 川口喬久; 奈良原舞子; 日笠幸一郎; 田原康玄; 松田文彦; 山田亮

  日本人類遺伝学会第62回大会, Nov. 2017

  
• Extension of sinkhorn method: optimal movement estimation of agents under law of inertia

  Daigo Okada; Naotoshi Nakamura; Yosuke Fujii; Takuya Wada; Ayako Iwasaki; Ryo Yamada

  Conference of the International Federation of Classification Societies, Aug. 2017

  
• Bistable individual variability in the immune response to seasonal influenza vaccination

  Naotoshi Nakamura; Daigo Okada; Kazuya Setoh; Takahisa Kawaguchi; Maiko Narahara; Koichiro Higasa; Yasuharu Tabara; Fumihiko Matsuda; Ryo Yamada

  Keystone Symposia, May 2017

  
• 季節性インフルエンザワクチンに対する免疫応答の個人差の解析

  中村直俊; 岡田大瑚; 瀬藤和也; 川口喬久; 奈良原舞子; 日笠幸一郎; 田原康玄; 松田文彦; 山田亮

  第90回日本薬理学会年会, Mar. 2017

  
• ANALYZING INDIVIDUAL HETEROGENEITY IN THE IMMUNE RESPONSE TO SEASONAL INFLUENZA VACCINATION

  N. Nakamura; D. Okada; K. Setoh; T. Kawaguchi; M. Narahara; K. Higasa; Y. Tabara; F. Matsuda; R. Yamada

  Human Genome Meeting, Feb. 2017

  
• EXTRACTING THE FEATURE STATISTICS OF FLOW-CYTOMETRY DATA USING MULTIDIMENSIONAL SCALING AND EVALUATING THEIR CORRESPONDENCE WITH TRANSCRIPTOME DATA

  D. Okada; N. Nakamura; K. Setoh; T. Kawaguchi; M. Narahara; K. Higasa; Y. Tabara; F. Matsuda; R. Yamada

  Human Genome Meeting, Feb. 2017

  
• 多次元フローサイトメトリーデータの分布異同定量に基づくヒト免疫応答の個人差の解析

  中村直俊; 岡田大瑚; 瀬藤和也; 川口喬久; 奈良原舞子; 日笠幸一郎; 田原康玄; 松田文彦; 山田亮

  第39回日本分子生物学会年会, Dec. 2016

  
• 多次元尺度法を用いたフローサイトメトリーデータからの特徴統計量の抽出およびトランスクリプトームデータとの対応関係の評価

  岡田大瑚; 中村直俊; 瀬藤和也; 川口喬久; 奈良原舞子; 日笠幸一郎; 田原康玄; 松田文彦; 山田亮

  第39回日本分子生物学会年会, Dec. 2016

  
• SNP共関連およびRNA共発現の情報を利用した遺伝子ネットワークの推定

  岡田大瑚; 遠藤聡子; 松田洋和; 小川伸一郎; 谷口幸雄; 勝田智博; 渡邊敏夫; 杉本喜憲; 祝前博明

  日本畜産学会第121回大会, Mar. 2016

  

Books and Other Publications

• ポストGWAS時代の遺伝統計学 : オミクス解析と機械学習でヒト疾患を俯瞰する

  岡田, 随象, Contributor, 大規模1細胞データを用いた遺伝統計解析

  羊土社, May 2023

  Find Kyoto University's collection of books :

  

External funds: Kakenhi

• Geometric and functional data analysis for spatiotemporal data mining in medicine and life sciences

  Grant-in-Aid for Research Activity Start-up

  1002:Human informatics, applied informatics and related fields

  Kyoto University

  Daigo Okada

  From 30 Aug. 2021, To 31 Mar. 2023, Project Closed

  幾何学;関数データ解析;老化;オミックス;生命情報学;オミックス解析;画像解析;データマイニング;エピゲノム;バイオインフォマティクス;画像;幾何;眼科学

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21K21316/