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  • 2020
  • 2019
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  • Michiaki Hamada
2020

Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with tretinoin increases the sunitinib sensitivity to better suppress the RCC progression

Shi, H., Sun, Y., He, M., Yang, X., Hamada, M., Fukunaga, T., Zhang, X. & Chang, C., 2020 Jan 16, In : Oncogene. 39, 3, p. 530-545 16 p.

Research output: Contribution to journalArticle

Open Access
2019

Lncrrisearch: A web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data

Fukunaga, T., Iwakiri, J., Ono, Y. & Hamada, M., 2019 Jan 1, In : Frontiers in Genetics. 10, MAY, 462.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Stromal fibroblasts induce metastatic tumor cell clusters via epithelial–mesenchymal plasticity

Matsumura, Y., Ito, Y., Mezawa, Y., Sulidan, K., Daigo, Y., Hiraga, T., Mogushi, K., Wali, N., Suzuki, H., Itoh, T., Miyagi, Y., Yokose, T., Shimizu, S., Takano, A., Terao, Y., Saeki, H., Ozawa, M., Abe, M., Takeda, S., Okumura, K. & 5 others, Habu, S., Hino, O., Takeda, K., Hamada, M. & Orimo, A., 2019 Jan 1, In : Life Science Alliance. 2, 4, e201900425.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)
2018

A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs

Fukunaga, T. & Hamada, M., 2018 Sep 1, In : Journal of Computational Biology. 25, 9, p. 976-986 11 p.

Research output: Contribution to journalArticle

Beyond similarity assessment: Selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm

Takeda, T. & Hamada, M., 2018 Feb 15, In : Bioinformatics. 34, 4, p. 576-584 9 p.

Research output: Contribution to journalArticle

Computational approaches for alternative and transient secondary structures of ribonucleic acids

Fukunaga, T. & Hamada, M., 2018 Jan 1, In : Briefings in Functional Genomics. 18, 3, p. 182-191 10 p.

Research output: Contribution to journalArticle

DeepM6ASeq: Prediction and characterization of m6A-containing sequences using deep learning

Zhang, Y. & Hamada, M., 2018 Dec 31, In : BMC Bioinformatics. 19, 524.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data

Nishida, S., Sakuraba, S., Asai, K. & Hamada, M., 2018 Mar 9, (Accepted/In press) In : IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Research output: Contribution to journalArticle

Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

Zeng, C., Fukunaga, T. & Hamada, M., 2018 May 29, In : BMC Genomics. 19, 1, 414.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Identification of RNA biomarkers for chemical safety screening in neural cells derived from mouse embryonic stem cells using RNA deep sequencing analysis

Tani, H., Matsutani, T., Aoki, H., Nakamura, K., Hamaguchi, Y., Nakazato, T. & Hamada, M., 2018 Jan 1, (Accepted/In press) In : Biochemical and Biophysical Research Communications.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs

Chishima, T., Iwakiri, J. & Hamada, M., 2018 Jan 1, In : Genes. 9, 1, 23.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Identifying sequence features that drive ribosomal association for lncRNA 06 Biological Sciences 0604 Genetics

Zeng, C. & Hamada, M., 2018 Dec 31, In : BMC Genomics. 19, 906.

Research output: Contribution to journalArticle

2017

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

Iwakiri, J., Terai, G. & Hamada, M., 2017 Jun 8, In : Biology Direct. 12, 1, 15.

Research output: Contribution to journalComment/debate

14 Citations (Scopus)

In silico approaches to RNA aptamer design

Hamada, M., 2017, (Accepted/In press) In : Biochimie.

Research output: Contribution to journalArticle

6 Citations (Scopus)

RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach

Fukunaga, T. & Hamada, M., 2017 Sep 1, In : Bioinformatics (Oxford, England). 33, 17, p. 2666-2674 9 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)

Training alignment parameters for arbitrary sequencers with LAST-TRAIN

Hamada, M., Ono, Y., Asai, K., Frith, M. C. & Hancock, J., 2017, In : Bioinformatics. 33, 6, p. 926-928 3 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)
2016

AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana

Ishii, K., Kazama, Y., Hirano, T., Hamada, M., Ono, Y., Yamada, M. & Abe, T., 2016, In : Genes and Genetic Systems. 91, 4, p. 229-233 5 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Bioinformatics tools for lncRNA research

Iwakiri, J., Hamada, M. & Asai, K., 2016 Jan 1, In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1859, 1, p. 23-30 8 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

Comprehensive prediction of lncRNA-RNA interactions in human transcriptome

Terai, G., Iwakiri, J., Kameda, T., Hamada, M. & Asai, K., 2016 Jan 11, In : BMC Genomics. 17, 1, 12.

Research output: Contribution to journalArticle

31 Citations (Scopus)

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

Iwakiri, J., Hamada, M., Asai, K. & Kameda, T., 2016 Sep 13, In : Journal of Chemical Theory and Computation. 12, 9, p. 4688-4697 10 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Rtools: a web server for various secondary structural analyses on single RNA sequences

Hamada, M., Ono, Y., Kiryu, H., Sato, K., Kato, Y., Fukunaga, T., Mori, R. & Asai, K., 2016 Jul 8, In : Nucleic Acids Research. 44, W1, p. W302-W307

Research output: Contribution to journalArticle

10 Citations (Scopus)