LncRNA‐dependent nuclear stress bodies promote intron retention through SR protein phosphorylation K Ninomiya, S Adachi, T Natsume, J Iwakiri, G Terai, K Asai, T Hirose The EMBO journal, 2019 | 116 | 2019 |
LncRRIsearch: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data T Fukunaga, J Iwakiri, Y Ono, M Hamada Frontiers in Genetics 10, 462, 2019 | 114 | 2019 |
Bioinformatics tools for lncRNA research J Iwakiri, M Hamada, K Asai Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1859 (1), 23-30, 2016 | 65 | 2016 |
Comprehensive prediction of lncRNA–RNA interactions in human transcriptome G Terai, J Iwakiri, T Kameda, M Hamada, K Asai BMC genomics 17 (1), 12, 2016 | 63 | 2016 |
Dissecting the protein–RNA interface: the role of protein surface shapes and RNA secondary structures in protein–RNA recognition J Iwakiri, H Tateishi, A Chakraborty, P Patil, N Kenmochi Nucleic acids research 40 (8), 3299-3306, 2012 | 58 | 2012 |
Computational prediction of lncRNA-mRNA interactions by integrating tissue specificity in human transcriptome J Iwakiri, G Terai, M Hamada Biology direct 12 (1), 15, 2017 | 51 | 2017 |
Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs T Chishima, J Iwakiri, M Hamada Genes 9 (1), 23, 2018 | 50 | 2018 |
m6A modification of HSATIII lncRNAs regulates temperature‐dependent splicing K Ninomiya, J Iwakiri, MK Aly, Y Sakaguchi, S Adachi, T Natsume, G Terai, ... The EMBO Journal 40 (15), e107976, 2021 | 46 | 2021 |
Improved Accuracy in RNA–Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function J Iwakiri, M Hamada, K Asai, T Kameda Journal of chemical theory and computation 12 (9), 4688-4697, 2016 | 28 | 2016 |
MeCP2 Levels Regulate the 3D Structure of Heterochromatic Foci in Mouse Neurons A Ito-Ishida, SA Baker, RV Sillitoe, Y Sun, J Zhou, Y Ono, J Iwakiri, ... Journal of Neuroscience 40 (45), 8746-8766, 2020 | 19 | 2020 |
DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells S Shinriki, M Hirayama, A Nagamachi, A Yokoyama, T Kawamura, ... Leukemia 36 (11), 2605-2620, 2022 | 14 | 2022 |
Analysis of base-pairing probabilities of RNA molecules involved in protein–RNA interactions J Iwakiri, T Kameda, K Asai, M Hamada Bioinformatics 29 (20), 2524-2528, 2013 | 14 | 2013 |
Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities T Hagio, S Sakuraba, J Iwakiri, R Mori, K Asai BMC bioinformatics 19 (1), 38, 2018 | 9 | 2018 |
Extended ensemble simulations of a SARS-CoV-2 nsp1–5’-UTR complex S Sakuraba, Q Xie, K Kasahara, J Iwakiri, H Kono PLOS Computational Biology 18 (1), e1009804, 2022 | 6 | 2022 |
Modeling SARS-CoV-2 nsp1–5’-UTR complex via the extended ensemble simulations S Sakuraba, X Qilin, K Kasahara, J Iwakiri, H Kono bioRxiv, 2021.02. 24.432807, 2021 | 6 | 2021 |
Free-energy calculation of ribonucleic inosines and its application to nearest-neighbor parameters S Sakuraba, J Iwakiri, M Hamada, T Kameda, G Tsuji, Y Kimura, H Abe, ... Journal of Chemical Theory and Computation 16 (9), 5923-5935, 2020 | 5 | 2020 |
Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing J Iwakiri, K Tanaka, T Chujo, H Takakuwa, T Yamazaki, G Terai, K Asai, ... RNA 29 (2), 170-177, 2023 | 3 | 2023 |
reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction R Kawaguchi, H Kiryu, J Iwakiri, J Sese BMC bioinformatics 20 (3), 15-24, 2019 | 3 | 2019 |
Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model H Takizawa, J Iwakiri, G Terai, K Asai Bioinformatics 36 (Supplement_1), i227-i235, 2020 | 2 | 2020 |
RNA Structure Prediction RK Kawaguchi, J Iwakiri Springer Nature, 2023 | 1 | 2023 |