研究業績

Under reveiw

Meta-analysis and multi-omics to elucidate pathogenic mechanisms of age-related knee osteoarthritis
Hirotaka Iijima, Gabrielle Gilmer, Kai Wang, Sruthi Sivakumar, Christopher Evans, Yusuke Matsui, Fabrisia Ambrosio
bioRxiv 2021.05.06.442993; doi:https://doi.org/10.1101/2021.05.06.442993

2022

Meta-analysis integrated with multi-omics data analysis to elucidate pathogenic mechanisms of age-related knee osteoarthritis in mice.
Iijima H, Gilmer G, Wang K, Sivakumar S, Evans C, Matsui Y, Ambrosio F.
The Journals of Gerontology: Series A, 2022; glab386, https://doi.org/10.1093/gerona/glab386

2021

Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin.
Shimizu, D., Taniue, K., Matsui, Y. et al. 
 Cancer Gene Ther (2021). https://doi.org/10.1038/s41417-021-00401-w
RoDiCE: robust differential protein co-expression analysis for cancer complexome.
Matsui Y, Abe Y, Uno K, Miyano S.
Bioinformatics. 2021 Sep 16:btab612. doi: 10.1093/bioinformatics/btab612. Epub ahead of print. PMID: 34529752.
Pre-stimulus alpha oscillation and post-stimulus cortical activity differ in localization between consciously perceived and missed near-threshold somatosensory stimuli.
Uemura, J., Hoshino, A., Igarashi, G., Matsui, Y., Chishima, M., & Hoshiyama, M.
European Journal of Neuroscience 2021. 1– 13. https://doi.org/10.1111/ejn.15388

2020

原著論文

An in vitro coculture system of human peripheral blood mononuclear cells with hepatocellular carcinoma-derived cells for predicting drug-induced liver injury.
Oda, S., Uchida, Y., Aleo, M.D. Petra H. Koza-Taylor, Yusuke Matsui, Masanori Hizue, Lisa D. Marroquin, Jessica Whritenour, Eri Uchida & Tsuyoshi Yokoi.
Arch Toxicol (2020). https://doi.org/10.1007/s00204-020-02882-4
EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells.
Yoshino, S#., Matsui, Y#., Fukui, Y. et al.  # These authors equally contributed to this study.
Sci Rep 10, 9275 (2020). https://doi.org/10.1038/s41598-020-66455-2
Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells. 
Higashijima Y, Matsui Y, Shimamura T, Nakaki R, Nagai N, Tsutsumi S, Abe Y, Link VM, Osaka M, Yoshida M, Watanabe R, Tanaka T, Taguchi A, Miura M, Ruan X, Li G, Inoue T, Nangaku M, Kimura H, Furukawa T, Aburatani H, Wada Y, Ruan Y, Glass CK, Kanki Y.
EMBO J. 2020 Mar 3:e103949. doi: 10.15252/embj.2019103949.

2019

原著論文

Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-wild-type Diffuse Astrocytic Gliomas.
Fumiharu Ohka, Keiko Shinjo, Shoichi Deguchi, Yusuke Matsui, Yusuke Okuno, Keisuke Katsushima, Miho Suzuki, Akira Kato, Noboru Ogiso, Akane Yamamichi, Kosuke Aoki, Hiromichi Suzuki, Shinya Sato, Nirmala Arul Rayan, Shyam Prabhakar, Jonathan Göke, Teppei Shimamura, Reo Maruyama, Satoru Takahashi, Akio Suzumura, Hiroshi Kimura, Toshihiko Wakabayashi, Hui Zong, Atsushi Natsume and Yutaka Kondo.
​Cancer Research (2019). DOI: 10.1158/0008-5472.CAN-19-1272
A Network of Networks Approach for Modeling Interconnected Brain Tissue-Specific Networks
Hideko Kawakubo, Yusuke Matsui, Itaru Kushima, Norio Ozaki, Teppei Shimamura​. (2019)
Bioinformatics. btz032
Tumor subclonal progression model for cancer hallmark acquisition.
Matsui Y, Miyano S, Shimamura T. (2019)
​Lecture Notes in Bioinformatics (In press)
​GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics.
Shimamura T, Matsui Y, Kajino T, Ito S, Takahashi T and Miyano S. (2019)
​Lecture Note in Bioinformatics (In press)

2018

原著論文

A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer. 
Tomoko Saito, Atsushi Niida, Ryutaro Uchi, Hidenari Hirata, Hisateru Komatsu, Shotaro Sakimura, Shuto Hayashi, Sho Nambara, Yosuke Kuroda, Shuhei Ito, Hidetoshi Eguchi, Takaaki Masuda, Keishi Sugimachi, Taro Tobo, Haruto Nishida, Tsutomu Daa, Kenichi Chiba, Yuichi Shiraishi, Tetsuichi Yoshizato, Masaaki Kodama, Tadayoshi Okimoto, Kazuhiro Mizukami, Ryo Ogawa, Kazuhisa Okamoto, Mitsutaka Shuto, Kensuke Fukuda, Yusuke Matsui, Teppei Shimamura, Takanori Hasegawa, Yuichiro Doki, Satoshi Nagayama, Kazutaka Yamada, Mamoru Kato, Tatsuhiro Shibata, Masaki Mori, Hiroyuki Aburatani, Kazunari Murakami, Yutaka Suzuki, Seishi Ogawa, Satoru Miyano & Koshi Mimori, 
​Nature Communications. 2018;9:2884. doi:10.1038/s41467-018-05226-0.
Identification of Cardiomyocyte-Fated Progenitors from Human-Induced Pluripotent Stem Cells Marked with CD82.
Takeda M, Kanki Y, Masumoto H, Funakoshi S, Hatani T, Fukushima H, Izumi-Taguchi A, Matsui Y, Shimamura T, Yoshida Y, Yamashita JK. (2018)  
​Cell Reports ;22(2):546-556. doi: 10.1016/j.celrep.2017.12.057.

2017

原著論文

ER stress signaling promotes the survival of cancer 'persister cells' tolerant to EGFR tyrosine kinase inhibitors. Cancer Res.
Terai H, Kitajima S, Potter DS, Matsui Y, Gutierrez Quiceno L, Chen T, Kim TJ, Rusan M, Thai TC, Piccioni F, Donovan KA, Kwiatkowski N, Hinohara K, Wei G, Gray NS, Fischer ES, Wong KK, Shimamura T, Letai A, Hammerman PS, Barbie DA. (2017)
​Cancer Res; pii: canres.1904.2017. doi: 10.1158/0008-5472.CAN-17-1904.
phyC: Clustering cancer evolutionary trees.
Matsui Y, Niida A, Uchi R, Mimori K, Miyano S, Shimamura T (2017)
​PLoS Comput Biol 13(5): e1005509

国際会議プロシーディングス

Tumor subclonal progression model for cancer hallmark acquisition.
Matsui Y, Miyano S, Shimamura T. (2017)
Proceedings of CIBB2017
GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics.
Shimamura T, Matsui Y, Kajino T, Ito S, Takahashi T and Miyano S. (2017)
Proceedings of CIBB2017

2016

原著論文

NECAB3 Promotes Activation of Hypoxia-inducible factor-1 during Normoxia and Enhances Tumourigenicity of Cancer Cells.
Nakaoka H.J, Hara T, Yoshino S, Kanamori A, Matsui Y, Shimamura T, Sato H, Murakami Y, Seiki M, Sakamoto T. (2016)  Sci Rep. 7;622784
D3M：Detection of differential distributions of methylation levels.
Matsui Y, Mizuta M, Ito S, Miyano S, and Shimamura T. (2016)  Bioinformatics. Btw138: 1-8.