Updated on 2023/12/26

写真a

 
IIDA Midori
 
Scopus Paper Info  
Total Paper Count: 0  Total Citation Count: 0  h-index: 10

Citation count denotes the number of citations in papers published for a particular year.

Affiliation
Faculty of Computer Science and Systems Engineering Department of Physics and Information Technology
Job
Associate Professor
Laboratory
680-4 Kawazu, Iizuka-shi, Fukuoka
Phone
+81-948-29-7729

Research Interests

  • ecotoxicology

  • network science

Research Areas

  • Informatics / Life, health and medical informatics

  • Environmental Science/Agriculture Science / Chemical substance influence on environment

  • Life Science / Aquatic life science

Degree

  • 愛媛大学  -  博士（理学）   2013.03

  • 愛媛大学  -  修士（理学）   2010.03

Biography in Kyutech

  • 2023.04
     

    Kyushu Institute of Technology   Faculty of Computer Science and Systems Engineering   Department of Physics and Information Technology   Associate Professor  

Papers

  • CRISPR-Cas9-Based Functional Analysis in Amphibians: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl Reviewed

    Suzuki M., Iida M., Hayashi T., Suzuki K.I.T.

    Methods in molecular biology (Clifton, N.J.)   2637   341 - 357   2023.01

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    Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1007/978-1-0716-3016-7_26

    Scopus

    Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85147895517&origin=inward

  • Effects of exposure to oxytetracycline on the liver proteome of red seabream (Pagrus major) in a real administration scenario Reviewed International journal

    Iida M., Nguyen H.T., Takahashi F., Bak S.M., Kanda K., Iwata H.

    Comparative Biochemistry and Physiology Part - C: Toxicology and Pharmacology   256   2022.06

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1016/j.cbpc.2022.109325

    Scopus

    Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85126372656&origin=inward

  • Prediction of single-cell mechanisms for disease progression in hypertrophic remodelling by a trans-omics approach Reviewed International journal

    Hamano M., Nomura S., Iida M., Komuro I., Yamanishi Y.

    Scientific Reports   11 ( 1 )   2021.12

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    Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1038/s41598-021-86821-y

    Scopus

    Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85104473302&origin=inward

  • Genome-wide screening reveals a role for subcellular localization of CRBN in the anti-myeloma activity of pomalidomide Reviewed International journal

    Tateno S., Iida M., Fujii S., Suwa T., Katayama M., Tokuyama H., Yamamoto J., Ito T., Sakamoto S., Handa H., Yamaguchi Y.

    Scientific Reports   10 ( 1 )   2020.12

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    Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1038/s41598-020-61027-w

    Scopus

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  • The role of Mediator and Little Elongation Complex in transcription termination Reviewed International journal

    Takahashi H., Ranjan A., Chen S., Suzuki H., Shibata M., Hirose T., Hirose H., Sasaki K., Abe R., Chen K., He Y., Zhang Y., Takigawa I., Tsukiyama T., Watanabe M., Fujii S., Iida M., Yamamoto J., Yamaguchi Y., Suzuki Y., Matsumoto M., Nakayama K.I., Washburn M.P., Saraf A., Florens L., Sato S., Tomomori-Sato C., Conaway R.C., Conaway J.W., Hatakeyama S.

    Nature Communications   11 ( 1 )   2020.12

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    Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1038/s41467-020-14849-1

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  • A simple and practical workflow for genotyping of CRISPR–Cas9-based knockout phenotypes using multiplexed amplicon sequencing Reviewed International journal

    Iida M., Suzuki M., Sakane Y., Nishide H., Uchiyama I., Yamamoto T., Suzuki K.i.T., Fujii S.

    Genes to Cells   25 ( 7 )   498 - 509   2020.07

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1111/gtc.12775

    Scopus

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  • Effects of prenatal bisphenol A exposure on the hepatic transcriptome and proteome in rat offspring Reviewed International journal

    Nguyen H.T., Yamamoto K., Iida M., Agusa T., Ochiai M., Guo J., Karthikraj R., Kannan K., Kim E.Y., Iwata H.

    Science of the Total Environment   720   2020.06

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    Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1016/j.scitotenv.2020.137568

    Scopus

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  • Network-based characterization of disease-disease relationships in terms of drugs and therapeutic targets Reviewed International journal

    Iida M., Iwata M., Yamanishi Y.

    Bioinformatics   36   I516 - I524   2020.01

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    Authorship：Lead author   Language：English   Publishing type：Research paper (international conference proceedings)

    DOI： 10.1093/BIOINFORMATICS/BTAA439

    Scopus

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  • Effects of lithium on developmental toxicity, teratogenicity and transcriptome in medaka embryos Reviewed

    Tominaga Nobuaki, Shino Seiya, Uchida Masaya, Ishibashi Hiroshi, Iida Midori, Okobira Tadashi, Arizono Kayla, Yoshida Noriaki, Arizono Koji

    Fundamental Toxicological Sciences ( The Japanese Society of Toxicology )   6 ( 2 )   31 - 36   2019.02

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    Language：English   Publishing type：Research paper (scientific journal)

    <p>In this study, we assessed embryonic developmental toxicity and teratogenicity of lithium (Li) on medaka (<i>Oryzias latipes</i>) and predict the molecular mechanisms of their effects using a nanosecond pulsed electric field (nsPEF) technique and bioinformatics analysis. The microscopic observation revealed that the 1 mg/L LiCl treatment causes the most severe deformation effects, such as thrombus, heart hypertrophy, deformation of eyes, and growth retardation to embryos. The RNA-seq analysis identified 2,483 up- and down-regulated genes, such as histogenesis and organ growth related genes, in 2 day post-fertilization embryos after treatment with nsPEF and 1 mg/L LiCl. In addition, bioinformatic analyses showed that LiCl affects several aspects of gene ontology, such as molecular functions and cellular components, and some pathways, such as spliceosome, cell cycle, selenocompound metabolism, TGF-β signaling, and RNA degradation. The upregulation of <i>GSK3B</i> (signal transduction and cell growth), <i>BAX </i>(apoptosis), and <i>MAP3K8</i> (cell death, arrest of cell cycle, and inflammation) genes were also observed in embryos exposed to LiCl. Our results suggest that the incorporation of Li compounds into medaka eggs using nsPEF shows adverse effects to the development and teratogenicity, and that these toxic effects may be affected by the alterations of certain gene expression in medaka embryos.</p>

    DOI： 10.2131/fts.6.31

    CiNii Article

    CiNii Research

    Other Link： https://www.jstage.jst.go.jp/article/fts/6/2/6_31/_pdf

  • A network biology-based approach to evaluating the effect of environmental contaminants on human interactome and diseases Reviewed International journal

    Iida M., Takemoto K.

    Ecotoxicology and Environmental Safety   160   316 - 327   2018.09

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1016/j.ecoenv.2018.05.065

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  • Effects of 4-Hydroxy-2,3,3<sup>0</sup>,4<sup>0</sup>,5-Pentachlorobiphenyl (4-OH-CB107) on liver transcriptome in rats: Implication in the disruption of circadian rhythm and fatty acid metabolism Reviewed International journal

    Ochiai M., Iida M., Agusa T., Takaguchi K., Fujii S., Nomiyama K., Iwata H.

    Toxicological Sciences   165 ( 1 )   118 - 130   2018.09

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1093/toxsci/kfy123

    Scopus

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  • Decomposing the effects of ocean environments on predator-prey body-size relationships in food webs Reviewed

    Dobashi T., Iida M., Takemoto K.

    Royal Society Open Science   5 ( 7 )   2018.07

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    Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1098/rsos.180707

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  • Nanosecond pulsed electric field incorporation technique to predict molecular mechanisms of teratogenicity and developmental toxicity of estradiol-17β on medaka embryos Reviewed International journal

    Yamaguchi A., Ishibashi H., Kono S., Iida M., Uchida M., Arizono K., Tominaga N.

    Journal of Applied Toxicology   38 ( 5 )   714 - 723   2018.05

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    Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1002/jat.3579

    Scopus

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  • Functional analysis of thyroid hormone receptor beta in Xenopus tropicalis founders using CRISPR-Cas Reviewed International journal

    Sakane Y., Iida M., Hasebe T., Fujii S., Buchholz D.R., Ishizuya-Oka A., Yamamoto T., Suzuki K.I.T.

    Biology Open   7 ( 1 )   2018.01

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    Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1242/bio.030338

    Scopus

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  • Strain differences in the proteome of dioxin-sensitive and dioxin-resistant mice treated with 2,3,7,8-tetrabromodibenzo-p-dioxin Reviewed International journal

    Nguyen H.T., Tsuchiya M.C.L., Yoo J., Iida M., Agusa T., Hirano M., Kim E.Y., Miyazaki T., Nose M., Iwata H.

    Archives of Toxicology   91 ( 4 )   1763 - 1782   2017.04

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    Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1007/s00204-016-1834-4

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  • Auto-induction mechanism of aryl hydrocarbon receptor 2 (AHR2) gene by TCDD-activated AHR1 and AHR2 in the red seabream (Pagrus major) Reviewed

    Bak S.M., Iida M., Soshilov A.A., Denison M.S., Iwata H., Kim E.Y.

    Archives of Toxicology   91 ( 1 )   301 - 312   2017.01

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    Language：English   Publishing type：Research paper (scientific journal)

    DOI： 10.1007/s00204-016-1732-9

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Publications (Books)

Conference Prsentations (Oral, Poster)

  • ネットワーク生物学による薬剤の組み合わせ予測 Invited

    飯田緑, 山西芳裕

    学術変革B「シナジー創薬学」一般公開シンポジウム  2023.03  山西芳裕

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    Event date： 2023.03.17   Language：Japanese   Country：Japan  

  • 第7回領域会議 Invited

    飯田緑, 山西芳裕

    第7回 シナジー創薬領域会議  2023.02  山西芳裕

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    Event date： 2023.02.23   Language：Japanese   Country：Japan  

  • Artificial intelligence and big data approaches in precision medicine and health science Invited

    Iida Midori

    JSPS/INSERM JOINT SCIENTIFIC SEMINAR  2022.12 

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    Event date： 2022.12.03 - 2022.12.04   Language：English   Country：Japan  

  • Developing a network-based combination therapy approach for complex diseases

    Iida Midori, Yurika Kuniki, Kenta Yagi, Mitsuhiro Goda, Satoko Namba, Jun-ichi Takeshita, Ryusuke Sawada, Michio Iwata, Yoshito Zamami, Keisuke Ishizawa, Yoshihiro Yamanishi

    2022.10 

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    Event date： 2022.10.25 - 2022.10.27   Language：English   Country：Japan  

    Combination therapy, a treatment modality that combines two or more therapeutic drugs, has become the standard treatment for complex diseases—however, the discovery of drug combinations relies on serendipity by clinical experience and intuition [1]. A network-based approach allows us to discover efficient drug combination by quantifying the network-based relationship between drug targets and disease proteins in the human protein–protein interactome [2]. However, conventional methods do not take into account changes in gene expression due to drug administration, resulting in low prediction accuracy. In this study we developed a network-based method to predict synergistic drug effects by integrating interactome and transcriptome data. The proposed method outperformed the previous methods in terms of higher prediction accuracy for several cancers. To validate the prediction results by our proposed method, we carried out in vitro cell surviving assays. The results showed that more than half of the top 20 predicted drug pairs had synergistic effects on the cell survival. Pathway enrichment analysis demonstrated several biological pathways are enriched with the genes used for prediction, suggesting that those pathways contribute to the synergistic effect. This approach allows us to identify drug combinations for complex diseases, offering a powerful methodology to find efficacious combination therapies.

    Other Link： https://cbi-society.org/taikai/taikai22/index.html

  • ネットワーク生物学を用いた化学物質の疾患への影響評価

    飯田緑

    令和4年度日本魚病学会秋季大会  2022.09  酒井　正博

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    Event date： 2022.09.04   Language：Japanese   Country：Japan  

  • Evaluation and prediction of effects of chemicals on humans using network biology Invited

    Iida Midori

    Japanese Society of Txicology  2022.06 

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    Event date： 2022.06.30 - 2022.07.02   Language：Japanese   Country：Japan  

    Other Link： https://doi.org/10.14869/toxpt.49.1.0_S13-2

  • Effects of exposure to oxytetracycline on the liver proteome of red seabream (Pagrus major) in a real administration scenario

    2022.06 

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    Event date： 2022.06.14 - 2022.06.16   Language：Japanese   Country：Japan  

  • ネットワーク生物学を利用した薬物の組み合わせ探索 Invited

    飯田緑

    2021年日本バイオインフォマティクス学会年会 ・第10回生命医薬情報学連合大会 (IIBMP2021)  2021.09  日本バイオインフォマティクス学会(JSBi), 日本オミックス医学会

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    Event date： 2021.09.27 - 2021.09.29   Language：Japanese   Country：Japan  

  • Network-based characterization of disease–disease relationships in terms of drugs and therapeutic targets Invited

    Midori Iida, Michio Iwata and Yoshihiro Yamanishi

    2020.09 

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    Event date： 2020.09.01 - 2020.09.03   Language：Japanese   Country：Japan  

  • Network-based characterization of disease–disease relationships in terms of drugs and therapeutic targets Invited

    Midori Iida, Michio Iwata and Yoshihiro Yamanishi

    ISMB 2020 International Society for Computational Biology  2020.06 

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    Event date： 2020.06.13 - 2020.06.16   Language：English   Country：Canada  

  • ネットワーク生物学で紐解く化学物質と生体の関係性 Invited

    飯田緑

    第23回 環境ホルモン学会研究発表会  2021.09  石塚真由美

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    Event date： 2021.09.12 - 2021.09.13   Language：Japanese   Country：Japan  

  • Atlantic Cod (Gadus morhua) Shrinks in Response to Environmental Pollutants Exposure

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    Event date： 2018.11.04 - 2018.11.08   Language：English   Country：United States  

  • 環境汚染物質とヒト疾患の関連性評価

    飯田緑, 竹本和広

    第24回（2018年）日本環境毒性学会研究発表会  2018.09 

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    Event date： 2018.09.11 - 2018.09.12   Language：English   Country：Japan  

    人間活動に起因する化学的な環境汚染から、環境汚染物質による健康障害が懸念されている。このような健康障害を予測し安全性を判定するには、汚染物質と疾患の関連性を評価することが不可欠である。しかし、疾患の発症メカニズムと化学物質の作用機序はともに複雑であり、疾患と化学物質の関連性を評価することは難しい。ネットワーク生物学１、２）はこのような複雑な関連性の理解に役立つ。そこで、我々はネットワーク生物学の解析手法を用いて、環境化学物質がヒトのインターラクトームや疾患に与える影響を定量的に評価した３）。

    本研究では、環境中に放出されている様々な化学物質のうち、環境への影響が強く懸念されている７つの化学物質カテゴリー（残留性有機汚染物質（POPs）、ダイオキシン類、多環芳香族炭化水素化合物（PAHs）、殺虫剤、フッ素化合物、金属、製薬およびパーソナルケア製品（PPCPs））に着目した。

    まず、化学物質と標的遺伝子の関係を調査するために、データベースに基づきヒト標的遺伝子－化学物質ネットワークを作成した。このネットワークを分析し、TCDDなどの一部の汚染物質は多様な遺伝子を標的としており、エストロゲンレセプターなどのいくつか遺伝子は多くの環境化学物質の標的となっていること見出した。

    次に、汚染物質がヒトインターラクトームに与える影響を評価するため、ヒトのタンパク質－タンパク質相互作用（PPI）ネットワークを作成し、化学物質の標的遺伝子と相互作用する遺伝子の数（次数）を調査した。この結果、化学物質の標的遺伝子の平均次数はPPIに存在する全ての遺伝子の平均次数に比べ有意に高かった。これはPPIに対する汚染物質の影響が大きいことを意味する。また、生存に必須な遺伝子は一般に次数が高い１）ことから、化学物質の標的遺伝子は生存に必須な遺伝子であると予想した。これを検証するため、各化学物質カテゴリーの標的遺伝子に占める生存必須遺伝子の割合を調べた。この結果、PAHsと金属の標的遺伝子にのみ、生存必須遺伝子が有意にエンリッチしていた。これは、PAHsと金属の標的遺伝子は必須遺伝子である傾向にあることを示す。一方で、その他の化学物質は非必須遺伝子を標的にしていた。

    最後に、化学物質と疾患の関係を定量的に評価するため、ヒトPPIネットワーク上で、ヒトの疾患原因遺伝子と化学物質標的遺伝子の距離を調べた。この距離は分子レベルの反応過程数を示し、距離が短いほどふたつの遺伝子の関連性が強いことを意味する２）。結果として、疾患原因遺伝子と化学物質標的遺伝子の距離はランダムに選んだ遺伝子間の平均距離よりも短いことを見出した。これは、その化合物が疾患原因遺伝子（またはこれに関連する遺伝子）と有意に関連することを示す。さらに、特定の疾患に注目し、化合物との関連性を定量的に評価した。疾患原因遺伝子をがん、消化器系疾患、内分泌系疾患等の１４グループに分け、グループごとに化学物質標的遺伝子とそれら疾病関連遺伝子の距離を求めた。この結果、全ての化学物質カテゴリーでがんや消化器系疾患との有意な関連性が認められた。また、POPsやダイオキシン類、殺虫剤、金属、PPCPs標的遺伝子は内分泌系疾患原因遺伝子との距離がランダムに比べ有意に短かった。これは化学物質特異的な疾患があることを意味する。

    本研究では、ネットワーク生物学の技術を応用して、ヒトのインタラクトームに重大な影響を与える化学物質や汚染物質感受性バイオマーカ遺伝子を同定した。さらに、環境汚染物質とヒト疾患との関係を定量化した。得られた知見は疫学的および実験的証拠によって裏付けられた。これらの方法および知見は、環境汚染物質と健康障害の複雑な関係の解明に貢献すると期待できる。

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Works

  • CLiCKAR

    Midori Iida, Miyuki Suzuki, Yuto Sakane, Hiroyo Nishide, Ikuo Uchiyama, Takashi Yamamoto, Ken-ichi T. Suzuki, Satoshi Fujii

    2020.04.23

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    Location：A simple and practical workflow for genotyping of CRISPR-Cas9-based knockout phenotypes using multiplexed amplicon sequencing  

    CLiCKAR provides users with practical reports regarding the positions of insertions/deletions, as well as the frameshift ratio and tables containing mutation sequences, and read counts of each phenotype, with just a few clicks by the implementation of demultiplexing for pooled sample data and calculation of the frameshift ratio.

  • IIBMP2020大会ポスター

    飯田緑

    2020.04

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    2020年日本バイオインフォマティクス学会年会・第9回生命医薬情報学連合大会（IIBMP2020）の大会ポスターを制作しました。

Lectures

  • バイオインフォマティクスへようこそ

    Lamer特別講演  2017.09  岩田久人

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    Event date： 2017.09.02   Language：Japanese   Presentation type：Invited lecture   Venue：愛媛大学