Mariko Okada

オカダマリコ | Mariko Okada

Affiliation and department：
Job title： Professor
Homepage URL (1)： http://www.protein.osaka-u.ac.jp/cell_systems/

Research field (2)： Applied biochemistry , Cell biology

Research keywords (10)： BioDX , Bioinformatics , inflammation , immunology , cancer , mathematical modeling , omics , transcriptional regulation , signal transduction , Systems Biology

Research theme for competitive and other funds (13)：

2024 - 2027 Mechanistic analysis of pathogenesis by systems analysis of YAP activation dynamics regulation
2021 - 2026 自然言語処理とシミュレーションによる細胞制御探索法の構築
2021 - 2024 統合解析を用いた網膜神経節細胞別の脆弱性に関わる緑内障障害シグナル伝達経路の探索
2020 - 2023 歯周病進行の細菌・分子間ダイナミクス制御に基づく歯周病重症化予測診断法の開発
2018 - 2023 疾病機序理解のための遺伝子ネットワーク数理モデル基盤の構築

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Papers (174)：

Ken Murakami, Keita Iida, Mariko Okada. An attention-based deep neural network model to detect cis-regulatory elements at the single-cell level from multi-omics data. 2024
Masato Tsutsui, Mariko Okada. DynProfiler: A Python package for comprehensive analysis and interpretation of signaling dynamics leveraged by deep learning techniques. Bioinformatics Advances. 2024. vbae145
Sho Tabata, Keita Matsuda, Shou Soeda, Kenshiro Nagai, Yoshihiro Izumi, Masatomo Takahashi, Yasutaka Motomura, Ayaka Ichikawa Nagasato, Kazuyo Moro, Takeshi Bamba, et al. NFκB dynamics-dependent epigenetic changes modulate inflammatory gene expression and induce cellular senescence. The FEBS Journal. 2024
Keita Iida, Mariko Okada. Identifying Key Regulatory Genes in Drug Resistance Acquisition: Modeling Pseudotime Trajectories of Breast Cancer Single-Cell Transcriptome. Cancers. 2024. 16. 10. 1884-1884
Ayaka Nagasato-Ichikawa, Ken Murakami, Kazuhiro Aoki, Mariko Okada. ErbB2/HER2 expression level determines CDK4-inhibitor sensitivity and cyclin D1 and c-Myc dependency at the G1/S transition. 2024

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MISC (40)：

陳ヨ, 岩淵禎弘, 清野透, 平岡伸介, 飯田渓太, 新井康仁, 横山明彦, 岡田眞里子, 橋本真一, 大木理恵子. PHLDA3 suppresses the malignant progression of non-functional PanNET by regulating cell differentiation and metabolism. 日本癌学会総会記事. 2022. 81回. P-2033
井上カタジナアンナ, 高橋和樹, 須河内昭成, 飯田渓太, 岩淵禎弘, 鯉沼代造, 栗岡恭子, 小西徹, 田中晋, 戒田篤志, et al. がん研究における女性研究者 TGF-βは増殖が低下して運動能が上昇したがん細胞集団を形成することで口腔がんの転移を亢進する(TGF-β enhances metastasis of oral cancer via generation of a population of cancer cells in G1 phase with high motility). 日本癌学会総会記事. 2022. 81回. SS1-5
井上カタジナアンナ, 高橋和樹, 須河内昭成, 飯田渓太, 岩淵禎弘, 鯉沼代造, 栗岡恭子, 小西徹, 田中晋, 戒田篤志, et al. がん研究における女性研究者 TGF-βは増殖が低下して運動能が上昇したがん細胞集団を形成することで口腔がんの転移を亢進する(TGF-β enhances metastasis of oral cancer via generation of a population of cancer cells in G1 phase with high motility). 日本癌学会総会記事. 2022. 81回. SS1-5
Johannes Nicolaus Wibisana, 飯田渓太, 岡田眞里子. 免疫系の1細胞解析による転写制御機構の予測. 医学のあゆみ 1細胞解析・技術と応用(企画菅野純夫). 2021. 276. 10. 983-988
井上正宏, 岡田眞里子, 橋本真一, 木村正, 近藤純平. 子宮頸部神経内分泌腫瘍の腺癌混合腫瘍における分化の可塑性. 日本癌学会総会記事. 2020. 79回. IS3-4

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Books (1)：

Computational Modeling of Signaling Networks
Springer US 2023

Lectures and oral presentations (296)：

Multi-omics data integration revealed that alteration of NFκB dynamics by IκBα reduction links cellular senescence and tissue aging
(The 46th Annual Meeting of Biochemical Society of Japan 2024)
Extracting Knowledge from Literature to Construct Biological Context-Aware Mathematical Models of Signaling Pathways
(1st Asia & Pacific Bioinformatics Joint Conference 2024)
Multi-omics data integration revealed that alteration of NFκB dynamics by IκBα reduction links cellular senescence and tissue aging.
(Cold Spring Harbor Laboratories Meeting, Mechanism of Aging 2024 2024)
ErbB2/HER2 modulates Cyclin D1 and c-Myc dependency at G1/S transition, impacting CDK4 inhibitor sensitivity
(2024)
自然言語処理技術を用いたシグナルダイナミクスの数理モデル構築
(2024年度日本数理生物学会年会 2024)

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Education (1)：

- 1988 Tokyo University of Agriculture and Technology

Work history (10)：

2024/10 - 現在 Imperial College London Department of Bioengineering Provost’s Visiting Professor of Systems Biology (クロアポ)
2016/07 - 現在 Osaka University Institute for Protein Research Professor
2022/12 - 2024/03 Osaka University, WPI Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe) Deputy Director, PI
2022/04 - 2024/03 Osaka University Institute for Protein Research Director
2013 - 2016/06 RIKEN IMS Team leader

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Committee career (11)：

2024/04 - 現在 AMED CREST・PRIME PS
2023/10 - 現在日本学術会議(基礎生物委員会) 会員
2023/08 - 現在国立研究開発法人科学技術振興機構(JST)創発的研究支援事業プログラムオフィサー(PO)
2023/06 - 現在国立研究開発法人科学技術振興機構(JST) 細胞と遊ぶ(CREST)領域アドバイザー
2021 - 現在文部科学省次世代計算基盤に係るシステム検討ワーキンググループ

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Awards (1)：

2018/04 - Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology

Association Membership(s) (7)：

日本生化学会 , 日本免疫学会 , International Society of Systems Biology (ISSB) (Committee Member) , JAPANESE SOCIETY FOR BIOINFORMATICS , THE BIOPHYSICAL SOCIETY OF JAPAN , THE JAPANESE CANCER ASSOCIATION , THE MOLECULAR BIOLOGY SOCIETY OF JAPAN

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