Google scholar / researchmap

Under submission / Preprint

• 1. Iwakiri, XXX, XXX, XXX, XXX, XXX (in preparation)

  2. XXX, XXX, XXX, Iwakiri, XXX, XXX, XXX (in preparation)

Journal papers (peer-reviewed)

• 1. Kudoh, H., Yonei-Tamura, S., Abe, G., Iwakiri, J., Uesaka, M., Makino, T., & Tamura, K. (2024). Genomic screening of fish-specific genes in gnathostomes and their functions in fin development. Development, Growth & Differentiation, 1–13. https://doi.org/10.1111/dgd.12918

  2. Junichi Iwakiri, Kumiko Tanaka, Takeshi Chujo, Tomohiro Yamazaki, Goro Terai, Kiyoshi Asai,  Tetsuro Hirose, Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing, RNA 29.2 (2023): 170-177.

  3. Satoru Shinriki, Mayumi Hirayama, Akiko Nagamachi et al. DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells, Leukemia 36.11 (2022): 2605-2620.

  4. Shun Sakuraba, Xie Qilin,  Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono, Extended ensemble simulations of a SARS-CoV-2 nsp1–5’-UTR complex. PLOS Computational Biology 18.1 (2022): e1009804.

  5. Kensuke Ninomiya, Junichi Iwakiri, Mahmoud Khamis Aly, Yuriko Sakaguchi, Shungo Adachi, Tohru Natsume, Goro Terai, Kiyoshi Asai, Tsutomu Suzuki, Tetsuro Hirose,  m6A modification of HSATIII lncRNAs regulates temperature-dependent splicing, The EMBO journal (2021)

  6. Aya Ito-Ishida, Steven A. Baker, Roy V. Sillitoe, Yaling Sun, Jian Zhou, Yukiteru Ono, Junichi Iwakiri, Michisuke Yuzaki, Huda Y. Zoghbi, MeCP2 Levels Regulate the 3D Structure of Heterochromatic Foci in Mouse Neurons, Journal of Neuroscience 40.45 (2020): 8746-8766.

  7. Shun Sakuraba, Junichi Iwakiri,  Michiaki Hamada,  Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe,  Kiyoshi Asai, Free-energy calculation of ribonucleic inosines and its application to nearest-neighbor parameters, Journal of Chemical Theory and Computation 16.9 (2020): 5923-5935.

  8. Hiroki Takizawa, Junichi Iwakiri, Goro Terai, Kiyoshi Asai, Finding the Direct Optimal RNA Barrier Energy and Improving Pathways with an Arbitrary Energy Model, Bioinformatics, 36(Supplement_1), i227-i235 (2020) 

  9. Hiroki Takizawa, Junichi Iwakiri, Kiyoshi Asai, RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp, BMC Bioinformatics 21, 210 (2020)

  10. Kensuke Ninomiya, Shungo Adachi, Tohru Natsume, Junichi Iwakiri, Goro Terai, Kiyoshi Asai, Tetsuro Hirose, LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation, The EMBO journal (2019).

  11. Tsukasa Fukunaga#, Junichi Iwakiri#, Yukiteru Ono, Michiaki Hamada,  LncRRIsearch: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data, Frontiers in Genetics, 10, 2019

  12. Risa Kawaguchi, Hisanori Kiryu, Junichi Iwakiri, Jun Sese, reactIDR: Evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction, BMC Bioinformatics, 20 (3), 130, 2019

  13. Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori and Kiyoshi Asai, Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities, BMC Bioinformatics, 19 (1), 38, 2018

  14. Takashi Chishima, Junichi Iwakiri, Michiaki Hamada, Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs, Genes 9.1 (2018): 23. 

  15. Junichi Iwakiri, Goro Terai, Michiaki Hamada, Computational prediction of lncRNA-mRNA interactions by integrating tissue specificity in human transcriptome, Biology Direct, 12:15, 2017

  16. Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, Tomoshi Kameda, Improved accuracy in RNA-protein rigid body docking by incorporating force field for molecular dynamics simulation into the scoring function, Journal of chemical theory and computation 12.9 (2016): 4688-4697

  17. Goro Terai#, Junichi Iwakiri#, Tomoshi Kameda, Michiaki Hamada, Kiyoshi Asai. Comprehensive prediction of lncRNA–RNA interactions in human transcriptome, BMC Genomics, 17 Suppl 1, 12, 2016 (#joint first authors)

  18. Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada. Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions, Bioinformatics, 29(20), 2524-2528, 2013

  19. 山森一人，薛晨，岩切淳一，剣持直哉，吉原郁夫．構造モデルに基づく塩基配列からのboxC/D型snoRNA遺伝子検出法，情報処理学会論文誌 数理モデル化と応用（TOM），6(1)，79 – 89，2013

  20. Kunihito Yamamori, Takuro Matsuo, Junichi Iwakiri, Naoya Kenmochi, Ikuo Yoshihara. A detection method for intronic snoRNA genes using extended-weight-updating SOM with appearance probability of bases, Artificial Life and Robotics, 17(3), 405–411, 2013

  21. Junichi Iwakiri, Hiroki Tateishi, Anirban Chakraborty, Prakash Patil and Naoya Kenmochi. Dissecting the protein–RNA interface: the role of protein surface shapes and RNA secondary structures in protein–RNA recognition, Nucleic Acids Research, 40(8), 3299–3306, 2012

Review papers (peer-reviewed)

• 1. Tsukasa Fukunaga, Junichi Iwakiri, Michiaki Hamada, Web Services for RNA-RNA Interaction Prediction, Methods in Molecular Biology, 2586, 175-195, 2023

  2. 岩切 淳一 ．大規模配列データにより加速するノンコーディングRNA研究，JSBi Bioinformatics Review, 3(1) , 1-10, 2022

  3. 岩切淳一，浜田道昭．長鎖ノンコーディングRNAのためのバイオインフォマティクス，生物物理，56(4)，217-220，2016

  4. Junichi Iwakiri#, Michiaki Hamada#, and Kiyoshi Asai. Bioinformatics tools for lncRNA research. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1859(1), 23-30, 2016 (#joint first authors)

Books

• 1. Risa Karakida Kawaguchi and Junichi Iwakiri (Editors), RNA Structure Prediction, Springer Nature, 2023/01

  2. 福永 津嵩，岩切 淳一．バイオインフォマティクスのための生命科学入門，コロナ社，2022/07/13

  3. Junichi Iwakiri and Kiyoshi Asai, RNA Structure Prediction, Chapter in Encyclopedia of Bioinformatics and Computational Biology, Vol.2, 575-584, 2018