Updated on 2022/04/12

写真a

 
TAKEDA Jun-ichi
 
Organization
Research Institute of Environmental Medicine Division of Stress Adaptation and Protection Designated lecturer
Title
Designated lecturer
Contact information
メールアドレス

Degree 1

  1. Doctor (Life science) ( 2011.3   The University of Tokyo ) 

Research Interests 1

  1. ゲノム科学

Research Areas 1

  1. Life Science / Genome biology

Professional Memberships 1

  1. 日本分子生物学会

 

Papers 19

  1. Regulated splicing of large exons is linked to phase-separation of vertebrate transcription factors

    Kawachi Toshihiko, Masuda Akio, Yamashita Yoshihiro, Takeda Jun-ichi, Ohkawara Bisei, Ito Mikako, Ohno Kinji

    EMBO JOURNAL     page: e107485   2021.10

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  2. IntSplice2: Prediction of the Splicing Effects of Intronic Single-Nucleotide Variants Using LightGBM Modeling

    Takeda Jun-ichi, Fukami Sae, Tamura Akira, Shibata Akihide, Ohno Kinji

    FRONTIERS IN GENETICS   Vol. 12   page: 701076   2021.7

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  3. A set of random forest models for each amino acid substitution to predict pathogenicity of missense variants in the human genome

    Takeda J., Nanatsue K., Yamagishi R., Ito M., Ohno K.

    EUROPEAN JOURNAL OF HUMAN GENETICS   Vol. 28 ( SUPPL 1 ) page: 1003 - 1003   2020.12

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    Language:Japanese  

    Web of Science

  4. Gene Expression Profile at the Motor Endplate of the Neuromuscular Junction of Fast-Twitch Muscle

    Huang Kun, Li Jin, Ito Mikako, Takeda Jun-Ichi, Ohkawara Bisei, Ogi Tomoo, Masuda Akio, Ohno Kinji

    FRONTIERS IN MOLECULAR NEUROSCIENCE   Vol. 13   page: 154   2020.9

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  5. InMeRF: prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution

    Takeda Jun-ichi, Nanatsue Kentaro, Yamagishi Ryosuke, Ito Mikako, Haga Nobuhiko, Hirata Hiromi, Ogi Tomoo, Ohno Kinji

    NAR GENOMICS AND BIOINFORMATICS   Vol. 2 ( 2 ) page: lqaa038   2020.6

  6. InMeRF: prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution Reviewed

    Takeda J, Nanatsue K, Yamagishi R, Ito M, Haga N, Hirata H, Ogi T, Ohno K.

    NAR Genomics and Bioinformatics   Vol. 2 ( 2 )   2020.5

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

    DOI: https://doi.org/10.1093/nargab/lqaa038

  7. tRIP-seq reveals repression of premature polyadenylation by co-transcriptional FUS-U1 snRNP assembly

    Masuda Akio, Kawachi Toshihiko, Takeda Jun-ichi, Ohkawara Bisei, Ito Mikako, Ohno Kinji

    EMBO REPORTS   Vol. 21 ( 5 ) page: e49890   2020.5

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  8. SRSF3 and hnRNP K Antagonistically Regulate Splicing of Large Exons

    Kawachi Toshihiko, Masuda Akio, Takeda Jun-ichi, Ito Mikako, Hamaguchi Tomonari, Ohno Kinji

    FASEB JOURNAL   Vol. 34   2020.4

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  9. Application of Skin Gas GC/MS Analysis for Prediction of the Severity Scale of Parkinson's Disease

    Tsuda Takao, Nonome Tomoaki, Goto Sae, Takeda Jun-ichi, Tsunoda Makoto, Hirayama Masaaki, Ohno Kinji

    CHROMATOGRAPHY   Vol. 40 ( 3 ) page: 149 - 155   2019

  10. Rules and tools to predict the splicing effects of exonic and intronic mutations

    Ohno Kinji, Takeda Jun-ichi, Masuda Akio

    WILEY INTERDISCIPLINARY REVIEWS-RNA   Vol. 9 ( 1 )   2018

  11. SRSF1 suppresses selection of intron-distal 5 ' splice site of DOK7 intron 4 to generate functional full-length Dok-7 protein

    Bin Ahsan Khalid, Masuda Akio, Rahman Mohammad Alinoor, Takeda Jun-ichi, Nazim Mohammad, Ohkawara Bisei, Ito Mikako, Ohno Kinji

    SCIENTIFIC REPORTS   Vol. 7 ( 1 ) page: 10446   2017.9

  12. Splicing regulation and dysregulation of cholinergic expressed at the neuromuscular junction

    Ohno Kinji, Rahman Mohammad Alinoor, Nazim Mohammad, Nasrin Farhana, Lin Yingni, Takeda Jun-ichi, Masuda Akio

    JOURNAL OF NEUROCHEMISTRY   Vol. 142   page: 64 - 72   2017.8

  13. Six GU-rich (6GU(R)) FUS-binding motifs detected by normalization of CLIP-seq by Nascent-seq

    Takeda J, Masuda A, Ohno K.

    GENE   Vol. 618   page: 57 - 64   2017.6

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

    DOI: 10.1016/j.gene.2017.04.008

    Web of Science

    PubMed

  14. Competitive regulation of alternative splicing and alternative polyadenylation by hnRNP H and CstF64 determines acetylcholinesterase isoforms

    Nazim Mohammad, Masuda Akio, Rahman Mohammad Alinoor, Nasrin Farhana, Takeda Jun-Ichi, Ohe Kenji, Ohkawara Bisei, Ito Mikako, Ohno Kinji

    NUCLEIC ACIDS RESEARCH   Vol. 45 ( 3 ) page: 1455 - 1468   2017.2

  15. H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. Reviewed

    Takeda J, Yamasaki C, Murakami K, Nagai Y, Sera M, Hara Y, Obi N, Habara T, Gojobori T, Imanishi T.

    Nucleic Acids Res.     2013.1

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

    DOI: 10.1093/nar/gks1245

    PubMed

  16. H-DBAS: human-transcriptome database for alternative splicing: update 2010. Reviewed

    Takeda J, Suzuki Y, Sakate R, Sato Y, Gojobori T, Imanishi T, Sugano S.

    Nucleic Acids Res.     2010.1

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

    DOI: 10.1093/nar/gkp984

    PubMed

  17. Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs. Reviewed

    Takeda J, Suzuki Y, Sakate R, Sato Y, Seki M, Irie T, Takeuchi N, Ueda T, Nakao M, Sugano S, Gojobori T, Imanishi T.

    Nucleic Acids Res.     2008.11

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

    DOI: 10.1093/nar/gkn677

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  18. H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. Reviewed

    Takeda J, Suzuki Y, Nakao M, Kuroda T, Sugano S, Gojobori T, Imanishi T.

    Nucleic Acids Res.   Vol. 35 ( Database issue ) page: D104-9   2007.1

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

    DOI: https://doi.org/10.1093/nar/gkl854

    PubMed

  19. Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs. Reviewed

    Takeda J, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V, Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T, Imanishi T.

    Nucleic Acids Res.   Vol. 34 ( 14 ) page: 3917-28   2006

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

    DOI: https://doi.org/10.1093/nar/gkl507

    PubMed

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Books 2

  1. 植物ゲノム科学辞典

    駒嶺穆他( Role: Joint author)

    朝倉書店  2009 

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    Language:Japanese

  2. 実験医学増刊「第2章RNA 1. 完全長cDNAデータベース」

    武田淳一、今西規、五條堀孝、鈴木穣、菅野純夫( Role: Joint author)

    羊土社  2008 

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    Language:Japanese

Presentations 3

  1. H-InvDB(ヒト遺伝子統合データベース)と関連データベースの紹介

    武田淳一

    RNAフロンティアミーティング2011 

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    Event date: 2011.8 - 2011.9

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  2. Comparative Analyses of Alternative Splicing Variants between Humans and Mice by Using Full-length cDNAs International conference

    SMBE2011 

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    Event date: 2011.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  3. ヒトとマウスの完全長cDNAを用いた選択的スプライシングの比較ゲノム解析

    武田淳一

    BMB2007 

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    Event date: 2007.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

Research Project for Joint Research, Competitive Funding, etc. 1

  1. 血液系腫瘍を含む各種悪性腫瘍のゲノムリシークエンシングとRNA-seqの同時解析によるスプライシングシス因子の同定

    2014.4 - 2015.3

    名古屋大学大学院医学系研究科北村記念血液疾患研究基金 

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    Grant type:Competitive

    本研究では、血液系腫瘍を含む各種悪性腫瘍の全ゲノム配列を次世代シークエンサーによって決定し(whole genome sequencing, WGS)、同時に包括的なtranscriptomeを次世代シークエンサーによるRNA-seqで求め、ゲノム上の遺伝子変異がスプライシングパターンに与える影響を網羅的に調べる。同一サンプルのWGSとRNA-seqの次世代シークエンサーの生データは、東京大学鈴木穣教授より提供を受けている。RNA-seq解析はTopHat、Cufflinks、MISOを用いて、それぞれGRCh37ヒト配列へのマッピング、転写物構造の決定、スプライシングアイソフォームの同定を行う。WGSはBWAによるGRCh37へのマッピング、SAMtoolsによるフィルタリング、GATKによるSNVコールを行いdbSNP, COSMICを用いたアノテーションを行う。これらのツールを申請者は別プロジェクトで活用している。RNA-seqでスプライシングが有意に変化をするエクソンを同定し、WGS解析結果を用いて、そのエクソンならびに両側イントロン領域のSNVsの有無を網羅的に探索する。これらは、遺伝子変異によって特異的にexonic splicing enhancer(ESE)、exonic splicing silencer(ESS)、intronic splicing enhancer(ISE)、intronic splicing silencer(ISS)が破壊されたと考えられる。これらの解析を行うことにより、未知のスプライシングシス因子の同定が可能になるとともに、腫瘍におけるシス因子の破断を明らかにすることが可能になり、血液系腫瘍を含む各種悪性腫瘍を生じさせるスプライシング異常のメカニズム解明に役立つことが期待される。

KAKENHI (Grants-in-Aid for Scientific Research) 1

  1. Development of integrated pathogenicity prediction system using single nucleotide variants (SNVs)

    Grant number:18K14684  2018.4 - 2021.3

    Grant-in-Aid for Early-Career Scientists

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    Authorship:Principal investigator 

    Grant amount:\2470000 ( Direct Cost: \1900000 、 Indirect Cost:\570000 )