IWAKIRI JUNICHI 岩切淳一

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Iwakiri Junichi 岩切淳一

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Researcher Number	40770160
Other IDs
Affiliation (Current)	2025: 東京大学, 大学院新領域創成科学研究科, 助教
Affiliation (based on the past Project Information) *help	2019 – 2024: 東京大学, 大学院新領域創成科学研究科, 助教 2018: 東京大学, 大学院新領域創成科学研究科, 特任助教 2016 – 2017: 東京大学, 大学院新領域創成科学研究科, 特任研究員
Review Section/Research Field	Principal Investigator Basic Section 62010:Life, health and medical informatics-related / Life / Health / Medical informatics Except Principal Investigator Applied informatics and related fields
Keywords	Principal Investigator RNA-seq / CLIP-seq / 長鎖非コードRNA / lncRNA / アーカイブデータ / 公共データベース / 反復配列 / 細胞内局在 / poly-A化 / 組織特異性 … More / RNA－タンパク質相互作用 / RNAーRNA相互作用 / 難抽出性RNA / リードスルー転写産物 / lncRNAの機能 / 機械学習 / RNA-タンパク質相互作用 / long non-coding RNA / 2次構造 / 核内構造体 / RNA-RNA相互作用 / 長鎖ノンコーディングRNA … More Except Principal Investigator RNA / RNAクロマチン相互作用 / ランダムフォレスト / 相互作用 / トランスポゾン / 長鎖ノンコーディングRNA / クロマチン / オミクスデータ / RNA-DNA相互作用 / リピート要素 / 分子間相互作用 / R-loop / lncRNA / ノンコーディングRNA Less

Exploring repetitive sequence-derived RNAs in public databasesPrincipal Investigator
- Principal Investigator
  
  岩切淳一
- Project Period (FY)
  2023 – 2027
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  The University of Tokyo
Large-scale analysis of archived sequencing data in public database for functional analysis of long non-coding RNAsPrincipal Investigator
- Principal Investigator
  
  Iwakiri Junichi
- Project Period (FY)
  2020 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  The University of Tokyo
RNA-chromatin interaction prediction and application
- Principal Investigator
  
  Hamada Michiaki
- Project Period (FY)
  2017 – 2022
- Research Category
  
  Grant-in-Aid for Challenging Research (Exploratory)
- Research Field
  
  Applied informatics and related fields
- Research Institution
  Waseda University
Prediction of macromolecular interactions involving lncRNAsPrincipal Investigator
- Principal Investigator
  
  Iwakiri Junichi
- Project Period (FY)
  2016 – 2019
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  The University of Tokyo

All 2024 2022 2021 2020 2019 2018 2017 2016

All Journal Article Presentation Book

[Book] Encyclopedia of Bioinformatics and Computational Biology Vol.22018
- Author(s)
  Junichi Iwakiri, Kiyoshi Asai
- Total Pages
  3284
- Publisher
  Elsevier
- Data Source
  KAKENHI-PROJECT-16K16143
[Journal Article] Genomic screening of fish‐specific genes in gnathostomes and their functions in fin development2024
- Author(s)
  Kudoh Hidehiro、Yonei‐Tamura Sayuri、Abe Gembu、Iwakiri Junichi、Uesaka Masahiro、Makino Takashi、Tamura Koji
- Journal Title
  
  Development, Growth & Differentiation
  
  Volume: 66 Issue: 3 Pages: 235-247
- DOI
  10.1111/dgd.12918
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K15133, KAKENHI-PROJECT-22K06232, KAKENHI-PROJECT-21K19202, KAKENHI-PROJECT-22KJ0186, KAKENHI-PUBLICLY-21H05768, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-23K23890, KAKENHI-PROJECT-23K28183
[Journal Article] Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing2022
- Author(s)
  Iwakiri Junichi、Tanaka Kumiko、Chujo Takeshi、Takakuwa Hiro、Yamazaki Tomohiro、Terai Goro、Asai Kiyoshi、Hirose Tetsuro
- Journal Title
  
  RNA
  
  Volume: 29 Issue: 2 Pages: 170-177
- DOI
  10.1261/rna.079469.122
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22K19293, KAKENHI-PLANNED-21H05276, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-20H00448, KAKENHI-PROJECT-20K12041, KAKENHI-PUBLICLY-21H00253, KAKENHI-PROJECT-23K23809
[Journal Article] Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex2022
- Author(s)
  *Shun Sakuraba, Qilin Xie, Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono
- Journal Title
  
  PLoS Computational Biology
  
  Volume: 18 Issue: 1 Pages: 1-21
- DOI
  10.1371/journal.pcbi.1009804
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K12069, KAKENHI-PROJECT-20K12041
[Journal Article] m6A modification of HSATIII lncRNAs regulates temperature‐dependent splicing2021
- Author(s)
  Ninomiya Kensuke、Iwakiri Junichi、Aly Mahmoud Khamis、Sakaguchi Yuriko、Adachi Shungo、Natsume Tohru、Terai Goro、Asai Kiyoshi、Suzuki Tsutomu、Hirose Tetsuro
- Journal Title
  
  The EMBO Journal
  
  Volume: 40 Issue: 15
- DOI
  10.15252/embj.2021107976
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K06478, KAKENHI-PUBLICLY-20H05377, KAKENHI-PLANNED-21H05276, KAKENHI-PROJECT-20H00448, KAKENHI-PROJECT-20K12041, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-18H05272
[Journal Article] Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters2020
- Author(s)
  Sakuraba Shun、Iwakiri Junichi、Hamada Michiaki、Kameda Tomoshi、Tsuji Genichiro、Kimura Yasuaki、Abe Hiroshi、Asai Kiyoshi
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 16 Issue: 9 Pages: 5923-5935
- DOI
  10.1021/acs.jctc.0c00270
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K12041, KAKENHI-PUBLICLY-19H05410, KAKENHI-PROJECT-16H06279
[Journal Article] Finding the Direct Optimal RNA Barrier Energy and Improving Pathways with an Arbitrary Energy Model2020
- Author(s)
  Hiroki Takizawa, Junichi Iwakiri, Goro Terai and Kiyoshi Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 36 Issue: Supplement_1 Pages: i227-i235
- DOI
  10.1093/bioinformatics/btaa469
- Description
  in press
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-20K12041
[Journal Article] MeCP2 Levels Regulate the 3D Structure of Heterochromatic Foci in Mouse Neurons2020
- Author(s)
  Ito-Ishida Aya、Baker Steven A.、Sillitoe Roy V.、Sun Yaling、Zhou Jian、Ono Yukiteru、Iwakiri Junichi、Yuzaki Michisuke、Zoghbi Huda Y.
- Journal Title
  
  The Journal of Neuroscience
  
  Volume: 40 Issue: 45 Pages: 8746-8766
- DOI
  10.1523/jneurosci.1281-19.2020
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20K12041, KAKENHI-PUBLICLY-20H05071, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-20H05628
[Journal Article] RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp2020
- Author(s)
  Hiroki Takizawa, Junichi Iwakiri, Kiyoshi Asai
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 21 Issue: 1 Pages: 210-210
- DOI
  10.1186/s12859-020-3535-5
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H02484, KAKENHI-PROJECT-20K12041, KAKENHI-PROJECT-16H06279
[Journal Article] reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction2019
- Author(s)
  Kawaguchi Risa、Kiryu Hisanori、Iwakiri Junichi、Sese Jun
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 20 Issue: 3 Pages: 130-130
- DOI
  10.1186/s12859-019-2645-4
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K16143, KAKENHI-PROJECT-15H05713, KAKENHI-PROJECT-17J01882, KAKENHI-PUBLICLY-16H01532, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-17K00398
[Journal Article] LncRRIsearch: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data2019
- Author(s)
  Tsukasa Fukunaga, Junichi Iwakiri, Yukiteru Ono and Michiaki Hamada
- Journal Title
  
  Front. Genet.
  
  Volume: - Pages: 462-462
- DOI
  10.3389/fgene.2019.00462
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-17K20032, KAKENHI-PROJECT-16K16143, KAKENHI-PUBLICLY-17H05605, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16H06279
[Journal Article] LncRNA ‐dependent nuclear stress bodies promote intron retention through SR protein phosphorylation2019
- Author(s)
  Ninomiya Kensuke、Adachi Shungo、Natsume Tohru、Iwakiri Junichi、Terai Goro、Asai Kiyoshi、Hirose Tetsuro
- Journal Title
  
  The EMBO Journal
  
  Volume: 39 Issue: 3
- DOI
  10.15252/embj.2019102729
- NAID
  120006876293
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K06478, KAKENHI-PROJECT-19K22374, KAKENHI-PROJECT-17H03630, KAKENHI-PROJECT-16K16143, KAKENHI-PROJECT-16H06279
[Journal Article] Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities2018
- Author(s)
  Hagio Taichi、Sakuraba Shun、Iwakiri Junichi、Mori Ryota、Asai Kiyoshi
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 19 Issue: Suppl 1 Pages: 38-38
- DOI
  10.1186/s12859-018-2018-4
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K16143, KAKENHI-PROJECT-16K17778, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H02484
[Journal Article] Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs2018
- Author(s)
  Chishima Takafumi、Iwakiri Junichi、Hamada Michiaki
- Journal Title
  
  Genes
  
  Volume: 9 Issue: 1 Pages: 23-23
- DOI
  10.3390/genes9010023
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K16143, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H02484, KAKENHI-PROJECT-16H05879
[Journal Article] Computational prediction of lncRNA-mRNA interactions by integrating tissue specificity in human transcriptome2017
- Author(s)
  Iwakiri Junichi、Terai Goro、Hamada Michiaki
- Journal Title
  
  Biology Direct
  
  Volume: 12 Issue: 1 Pages: 15-15
- DOI
  10.1186/s13062-017-0183-4
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K16143, KAKENHI-PROJECT-16H02484, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16H06279
[Journal Article] Computational Approaches for Long Non-coding RNA Research2016
- Author(s)
  岩切淳一、浜田道昭
- Journal Title
  
  Seibutsu Butsuri
  
  Volume: 56 Issue: 4 Pages: 217-220
- DOI
  10.2142/biophys.56.217
- NAID
  130005165637
- ISSN
  0582-4052, 1347-4219
- Language
  Japanese
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] Combinations of repeat sequences in HSATIII lncRNAs dictate nSB subclasses2022
- Author(s)
  Manami Kakuno , Kensuke Ninomiya, Junichi Iwakiri, Kiyoshi Asai, Tetsuro Hirose
- Organizer
  第23回日本RNA学会年会
- Data Source
  KAKENHI-PROJECT-20K12041
[Presentation] 大規模RNA-seqデータ解析とRNA分子間相互作用2022
- Author(s)
  岩切淳一
- Organizer
  RNAインフォマティクス道場2022
- Data Source
  KAKENHI-PROJECT-20K12041
[Presentation] Computational analysis pipeline for recent RNA-seq methods involving induced-substitutions2019
- Author(s)
  Junichi Iwakiri, Martin C. Frith, Michiaki Hamada, Kiyoshi Asai
- Organizer
  FRONTIERS OF GENOME SCIENCE: The International symposium organized by “Platform for Advanced Genome Science”
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] 核内ストレス体による２つのスプライシング制御機構2019
- Author(s)
  二宮賢介， Mahmoud Khamis Aly，坂口裕理子，足達俊吾，夏目徹，岩切淳一，寺井悟朗，浅井潔，鈴木勉，廣瀬哲郎
- Organizer
  第 21 回日本 RNA 学会年会
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] Synthesis of mRNA with site-specific N6-methyladenosine and its translation efficiency2018
- Author(s)
  Akihiro Imaeda, Ryota Oikawa, Kiyoshi Asai, Junichi Iwakiri, Shun Sakuraba, Naoko Abe, Fumiaki Tomoike, Yasuaki Kimura, Hiroshi Abe
- Organizer
  ISNAC2018
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] 先進的RNA-seqのデータ解析を改善するマッピングパラメータ学習2018
- Author(s)
  岩切淳一，Martin C. Frith，浜田道昭，浅井潔
- Organizer
  第20回日本RNA学会年会
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] 核内ストレス体によるストレス回復期のスプライシング制御2018
- Author(s)
  二宮賢介，足達俊吾，夏目徹，岩切淳一，寺井悟朗，浅井潔，廣瀬哲郎
- Organizer
  第20回日本RNA学会年会
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] N6-アルキルアデノシンの導入位置を制御したmRNAの合成とその翻訳能2018
- Author(s)
  今枝昭裕，笈川涼太，浅井潔，岩切淳一，桜庭俊，阿部奈保子，友池史明，木村康明，阿部洋
- Organizer
  第20回日本RNA学会年会
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] Estimation of mapping parameters for PAR-CLIP data using LAST-TRAIN2017
- Author(s)
  Mei Takeda, Junichi Iwakiri, Michiaki Hamada
- Organizer
  第6回生命医薬情報学連合大会(IIBMP)
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] ヒトlncRNA-RNAの網羅的相互作用予測及びデータベースの構築2017
- Author(s)
  福永津嵩，岩切淳一，小野幸輝，浜田道昭
- Organizer
  第五回NGS現場の会
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] lncRNA-mRNAの網羅的相互作用予測へ向けた高速なRNA-RNA相互作用予測ソフトウェアRIblastの開発2017
- Author(s)
  福永津嵩、岩切淳一、小野幸輝、浜田道昭
- Organizer
  第19回日本RNA学会年会
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] lncRNAの組織特異的な発現に関与するTransposable Elementの同定2017
- Author(s)
  千島崇史，岩切淳一，浜田道昭
- Organizer
  第19回日本RNA学会年会
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] Identification of Transposable Elements which contribute to tissue specific expression of lncRNAs2017
- Author(s)
  Takafumi Chishima, Junichi Iwakiri, Michiaki Hamada
- Organizer
  第6回生命医薬情報学連合大会(IIBMP)
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] Computational prediction of lncRNA-mRNA interactions by integrating tissue-specificity of human transcripts2016
- Author(s)
  Junichi Iwakiri, Goro Terai, Michiaki Hamada
- Organizer
  RNA 2016: The 21st Annual Meeting of the RNA Society
- Place of Presentation
  Kyoto International Conference Center
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] Improved accuracy in RNA-protein rigid body docking by incorporating force field for molecular dynamics simulation into the scoring function2016
- Author(s)
  Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, Tomoshi Kameda
- Organizer
  RNA 2016: The 21st Annual Meeting of the RNA Society
- Place of Presentation
  Kyoto International Conference Center
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K16143
[Presentation] Investigation of evolutionarily conserved NEAT1-NEAT1 interactions2016
- Author(s)
  Wataru Okada, Junichi Iwakiri, Michiaki Hamada
- Organizer
  RNA 2016: The 21st Annual Meeting of the RNA Society
- Place of Presentation
  Kyoto International Conference Center
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K16143

1. Hamada Michiaki (00596538)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
2. ASAI Kiyoshi

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
3. 上坂将弘

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
4. 二宮賢介

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
5. 広瀬哲郎

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
6. 笠原浩太

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

IWAKIRI JUNICHI 岩切 淳一

Iwakiri Junichi 岩切 淳一

Research Projects

Research Products

Co-Researchers

Exploring repetitive sequence-derived RNAs in public databasesPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Large-scale analysis of archived sequencing data in public database for functional analysis of long non-coding RNAsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

RNA-chromatin interaction prediction and application

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Prediction of macromolecular interactions involving lncRNAsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

[Book] Encyclopedia of Bioinformatics and Computational Biology Vol.22018

Author(s)

Total Pages

Publisher

Data Source

[Journal Article] Genomic screening of fish‐specific genes in gnathostomes and their functions in fin development2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] m6A modification of HSATIII lncRNAs regulates temperature‐dependent splicing2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Finding the Direct Optimal RNA Barrier Energy and Improving Pathways with an Arbitrary Energy Model2020

Author(s)

Journal Title

DOI

Description

Data Source

[Journal Article] MeCP2 Levels Regulate the 3D Structure of Heterochromatic Foci in Mouse Neurons2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction2019

Author(s)

Journal Title

DOI

Data Source

IWAKIRI JUNICHI 岩切淳一

Iwakiri Junichi 岩切淳一