J. Iwakiri

发表

Dissecting the protein–RNA interface: the role of protein surface shapes and RNA secondary structures in protein–RNA recognition

J. Iwakiri, Hiroki Tateishi, A. Chakraborty, 2011, Nucleic acids research.

RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp

Kiyoshi Asai, Junichi Iwakiri, Hiroki Takizawa, 2020, BMC Bioinformatics.

Bioinformatics tools for lncRNA research.

J. Iwakiri, K. Asai, Michiaki Hamada, 2016, Biochimica et biophysica acta.

LncRNA‐dependent nuclear stress bodies promote intron retention through SR protein phosphorylation

J. Iwakiri, K. Asai, G. Terai, 2019, The EMBO journal.

LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation

J. Iwakiri, K. Asai, G. Terai, 2019, bioRxiv.

Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach

J. Iwakiri, K. Asai, Michiaki Hamada, 2018, bioRxiv.

Molecular Epidemiological Analysis of an Outbreak Case with Sporadic Cases of Diarrhea Caused by Heat-labile Enterotoxin and Heat-stable Enterotoxin-producing Enterotoxigenic Escherichia coli 06: H16 by Using Pulsed-field Gel Electrophoresis Method

J. Iwakiri, Kazutoshi Nakamura, K. Kawano, 2003 .

Computational Approaches for Long Non-coding RNA Research

J. Iwakiri, Michiaki Hamada, 2016 .

DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells

J. Iwakiri, K. Asai, H. Kawai, 2022, Leukemia.

Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing

J. Iwakiri, K. Asai, G. Terai, 2022, bioRxiv.

Extended ensemble simulations of a SARS-CoV-2 nsp1–5’-UTR complex

J. Iwakiri, H. Kono, S. Sakuraba, 2022, PLoS Comput. Biol..

Modeling SARS-CoV-2 nsp1–5’-UTR complex via the extended ensemble simulations

J. Iwakiri, H. Kono, S. Sakuraba, 2021, bioRxiv.

Free-energy calculation of ribonucleic inosines and its application to nearest-neighbor parameters.

J. Iwakiri, K. Asai, Michiaki Hamada, 2020, Journal of chemical theory and computation.

Computational prediction of lncRNA-mRNA interactions by integrating tissue specificity in human transcriptome

Michiaki Hamada, Junichi Iwakiri, Goro Terai, 2017, Biology Direct.

m6A modification of HSATIII lncRNAs regulates temperature‐dependent splicing

J. Iwakiri, K. Asai, Tsutomu Suzuki, 2021, The EMBO journal.

MeCP2 Levels Regulate the 3D Structure of Heterochromatic Foci in Mouse Neurons

H. Zoghbi, J. Iwakiri, M. Yuzaki, 2020, The Journal of Neuroscience.

RNA Structure Prediction

Junichi Iwakiri, Kiyoshi Asai, J. Iwakiri, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities

Kiyoshi Asai, Ryota Mori, Junichi Iwakiri, 2018, BMC Bioinformatics.

Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function.

Kiyoshi Asai, Michiaki Hamada, Junichi Iwakiri, 2016, Journal of chemical theory and computation.

Comprehensive prediction of lncRNA–RNA interactions in human transcriptome

Kiyoshi Asai, Michiaki Hamada, Junichi Iwakiri, 2016, BMC Genomics.

reactIDR: Evaluation of the statistical reproducibility of high-throughput structural analyses for a robust RNA reactivity classification

Risa Kawaguchi, Hisanori Kiryu, Junichi Iwakiri, 2018, bioRxiv.

Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs

J. Iwakiri, Michiaki Hamada, Takafumi Chishima, 2018, Genes.

Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions

Kiyoshi Asai, Michiaki Hamada, Junichi Iwakiri, 2013, Bioinform..

LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data

Tsukasa Fukunaga, Michiaki Hamada, Junichi Iwakiri, 2019, Front. Genet..

Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model

Kiyoshi Asai, Junichi Iwakiri, Hiroki Takizawa, 2020, Bioinform..

Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities

J. Iwakiri, K. Asai, S. Sakuraba, 2018, BMC Bioinformatics.

Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome

J. Iwakiri, G. Terai, Michiaki Hamada, 2017, Biology Direct.

reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction

Risa Kawaguchi, Hisanori Kiryu, Junichi Iwakiri, 2019, BMC Bioinformatics.