Junichi Iwakiri
Junichi Iwakiri
Department of Computational Biology and Medical Sciences, the University of Tokyo
Verified email at - Homepage
Cited by
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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
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
Bioinformatics tools for lncRNA research
J Iwakiri, M Hamada, K Asai
Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1859 (1), 23-30, 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
RNA Structure Prediction
RK Kawaguchi, J Iwakiri
Springer Nature, 2023
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