原著論文
Preprints
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mmVelo: A deep generative model for estimating cell state-dependent dynamics across multiple modalities.
Nomura S, Kojima Y, Minoura K, Hayashi S, Abe K, Hirose H, Shimamura T. bioRxiv 2024.12.11.628059; doi: https://doi.org/10.1101/2024.12.11.628059. Preprint. |
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scSurv: a deep generative model for single-cell survival analysis.
Mizukoshi C, Kojima Y, Hayashi S, Abe K, Kasugai D, Shimamura T. bioRxiv 2024.12.10.627659; doi: https://doi.org/10.1101/2024.12.10.627659. Preprint. |
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Unsupervised deep learning enables blur-free super-resolution in two-photon microscopy.
Morita H, Hayashi S, Tsuji T, Kato D, Wake H, Shimamura T. bioRxiv. 2024.04.30.591870; doi: https://doi.org/10.1101/2024.04.30.591870. Preprint. |
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Inferring extrinsic factor-dependent single-cell transcriptome dynamics using a deep generative model.
Kojima Y, Arioka Y, Hirose H, Hayashi S, Mizuno Y, Nagaharu K, Ishikawa M, Ohishi K, Suzuki Y, Ozaki N, Shimamura T. bioRxiv. 2024.04.01.587302; doi: https://doi.org/10.1101/2024.04.01.587302. Preprint. |
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A deep generative model integrating single-cell time-frequency characteristics transformed from electrophysiological data with transcriptomic features.
Furumichi K, Kojima Y, Nomura S, Shimamura T. bioRxiv. 2024.03.29.587341; doi: https://doi.org/10.1101/2024.03.29.587341. Preprint. |
2024
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Survivability and life support in sealed mini-ecosystems with simulated planetary soils.
Sato T, Abe K, Koseki J, Seto M, Yokoyama J, Akashi T, Terada M, Kadowaki K, Yoshida S, Yamashiki YA, Shimamura T. Sci Rep. 2024 Nov 1;14(1):26322. doi: 10.1038/s41598-024-75328-x. PMID: 39487149 |
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DeepKINET: a deep generative model for estimating single-cell RNA splicing and degradation rates.
Mizukoshi C, Kojima Y, Nomura S, Hayashi S, Abe K, Shimamura T. Genome Biol. 2024 Sep 6;25(1):229. doi: 10.1186/s13059-024-03367-8. PMID: 39237934 |
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LineageVAE: Reconstructing Historical Cell States and Transcriptomes toward Unobserved Progenitors.
Majima K, Kojima Y, Minoura K, Abe K, Hirose H, Shimamura T. Bioinformatics. 2024 Aug 22:btae520. doi: 10.1093/bioinformatics/btae520. Online ahead of print. PMID: 39172488 |
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Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis.
Hashimoto M, Kojima Y, Sakamoto T, Ozato Y, Nakano Y, Abe T, Hosoda K, Saito H, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Hata T, Nagayama S, Kagawa K, Goto Y, Utou M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Takahashi K, Niida A, Hirose H, Hayashi S, Koseki J, Fukuchi S, Murakami K, Yoshizumi T, Kadomatsu K, Tobo T, Oda Y, Uemura M, Eguchi H, Doki Y, Mori M, Oshima M, Shibata T, Suzuki Y, Shimamura T*, Mimori K*. * Corresponding author EBioMedicine. 2024 Apr 9:105102. doi: 10.1016/j.ebiom.2024.105102. Online ahead of print. |
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Single-cell colocalization analysis using a deep generative model.
Kojima Y, Mii S, Hayashi S, Hirose H, Ishikawa M, Akiyama M, Enomoto A, Shimamura T. Cell Syst. 2024 Feb 21;15(2):180-192.e7. doi: 10.1016/j.cels.2024.01.007. |
2023
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Metastases and treatment-resistant lineages in patient-derived cancer cells of colorectal cancer.
Fujino S, Miyoshi N, Ito A, Hayashi R, Yasui M, Matsuda C, Ohue M, Horie M, Yachida S, Koseki J, Shimamura T, Hata T, Ogino T, Takahashi H, Uemura M, Mizushima T, Doki Y, Eguchi H. Commun Biol. 2023 Nov 24;6(1):1191. doi: 10.1038/s42003-023-05562-y. |
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FXYD3 functionally demarcates an ancestral breast cancer stem cell subpopulation with features of drug-tolerant persisters.
Li M, Nishimura T, Takeuchi Y, Hongu T, Wang Y, Shiokawa D, Wang K, Hirose H, Sasahara A, Yano M, Ishikawa S, Inokuchi M, Ota T, Tanabe M, Tada KI, Akiyama T, Cheng X, Liu CC, Yamashita T, Sugano S, Uchida Y, Chiba T, Asahara H, Nakagawa M, Sato S, Miyagi Y, Shimamura T, Nagai LAE, Kanai A, Katoh M, Nomura S, Nakato R, Suzuki Y, Tojo A, Voon DC, Ogawa S, Okamoto K, Foukakis T, Gotoh N. J Clin Invest. 2023 Nov 15;133(22):e166666. doi: 10.1172/JCI166666. |
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Acidic extracellular pH drives accumulation of N1-acetylspermidine and recruitment of protumor neutrophils.
Kato M, Maeda K, Nakahara R, Hirose H, Kondo A, Aki S, Sugaya M, Hibino S, Nishida M, Hasegawa M, Morita H, Ando R, Tsuchida R, Yoshida M, Kodama T, Yanai H, Shimamura T, Osawa T. PNAS Nexus. 2023 Oct 10;2(10):pgad306. doi: 10.1093/pnasnexus/pgad306. eCollection 2023 Oct. |
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Hypoxia activates SREBP2 through Golgi disassembly in bone marrow-derived monocytes for enhanced tumor growth.
Nakahara R, Aki S, Sugaya M, Hirose H, Kato M, Maeda K, Sakamoto DM, Kojima Y, Nishida M, Ando R, Muramatsu M, Pan M, Tsuchida R, Matsumura Y, Yanai H, Takano H, Yao R, Sando S, Shibuya M, Sakai J, Kodama T, Kidoya H, Shimamura T, Osawa T. EMBO J. 2023 Nov 15;42(22):e114032. doi: 10.15252/embj.2023114032. Epub 2023 Oct 2. |
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UNMF: a unified nonnegative matrix factorization for multi-dimensional omics data.
Abe K, Shimamura T. Brief Bioinform. 2023 Jul 21:bbad253. doi: 10.1093/bib/bbad253. Online ahead of print. |
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Plucked scalp hair follicle samples are useful RNA sources for mRNA analysis of most genodermatosis-associated genes
Takeuchi S, Takeichi T, Muro Y, Shimamura T, Akiyama M. J Dermatol Sci. 2023 Jun 15:S0923-1811(23)00144-5. doi: 10.1016/j.jdermsci.2023.06.004. Online ahead of print. |
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Topological data analysis of protein structure and inter/intra- molecular interaction changes attributable to amino acid mutations
Koseki J, Hayashi S, Kojima Y, Hirose H, Shimamura T. Comput Struct Biotechnol J. in press. doi: doi.org/10.1016/j.csbj.2023.05.009. |
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Convergent genomic diversity and novel BCAA metabolism in intrahepatic cholangiocarcinoma.
Kitagawa A, Osawa T, Noda M, Kobayashi Y, Aki S, Nakano Y, Saito T, Shimizu D, Komatsu H, Sugaya M, Takahashi J, Kosai K, Takao S, Motomura Y, Sato K, Hu Q, Fujii A, Wakiyama H, Tobo T, Uchida H, Sugimachi K, Shibata K, Utsunomiya T, Kobayashi S, Ishii H, Hasegawa T, Masuda T, Matsui Y, Niida A, Soga T, Suzuki Y, Miyano S, Aburatani H, Doki Y, Eguchi H, Mori M, Nakayama KI, Shimamura T, Shibata T, Mimori K. Br J Cancer. 2023 Apr 19. doi: 10.1038/s41416-023-02256-4. Online ahead of print. |
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Increased flexibility of the SARS-CoV-2 RNA-binding site causes resistance to remdesivir.
Torii S, Kim KS, Koseki J, Suzuki R, Iwanami S, Fujita Y, Jeong YD, Ito J, Asakura H, Nagashima M, Sadamasu K, Yoshimura K; Genotype to Phenotype Japan (G2P-Japan) Consortium; Sato K, Matsuura Y, Shimamura T, Iwami S, Fukuhara T. PLoS Pathog. 2023 Mar 27;19(3):e1011231. doi: 10.1371/journal.ppat.1011231. |
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Spatial and single-cell transcriptomics to decipher the cellular society containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer
Ozato Y, Kojima Y, Kobayashi Y, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Kagawa K, Goto Y, Utou M, Fukunaga M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Niida A, Sakamoto T, Hirose H, Hayashi S, Koseki J, Oki E, Fukuchi S, Murakami K, Oshima M, Tobo T, Nagayama S, Uemura M, Doki Y, Eguchi H, Mori M, Iwasaki T, Oda Y, Shibata T, Suzuki Y, Shimamura T*, Mimori K*. *: corresponding author. Cell Rep 2023 42:111929. doi: doi.org/10.1016/j.celrep.2022.111929 |
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Smoking enhances the expression of angiotensin-converting enzyme 2 involved in the efficiency of severe acute respiratory syndrome coronavirus 2 infection.
Suzuki R, Ono Y, Noshita K, Kim KS, Ito H, Morioka Y, Tamura T, Okuzaki D, Tagawa T, Takenaka T, Yoshizumi T, Shimamura T, Iwami S, Fukuhara T. Microbiol Immunol. 2023 Jan;67(1):22-31. doi: 10.1111/1348-0421.13034. Epub 2022 Nov 2. |
2022
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Bayesian statistical method for detecting structural and topological diversity in polymorphic proteins.
Hayashi S, Koseki S, Shimamura T. Comput Struct Biotechnol J. in press. doi: doi.org/10.1016/j.csbj.2022.11.038. |
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Metabolic remodeling of pyrimidine synthesis pathway and serine synthesis pathway in human glioblastoma.
Nakamizo A, Miyamatsu Y, Hirose H, Amano T, Matsuo S, Fujiwara M, Shimamura T, Yoshimoto K. Sci Rep. 2022 Sep 29;12(1):16277. doi: 10.1038/s41598-022-20613-w. PMID: 36175487 |
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Detecting time-evolving phenotypic components of adverse reactions against BNT162b2 mRNA SARS-CoV-2 vaccine via non-negative tensor factorization.
Ikeda K, Nakada TA, Kageyama T, Tanaka S, Yoshida N, Ishikawa T, Goshima Y, Otaki N, Iwami S, Shimamura T, Taniguchi T, Igari H, Hanaoka H, Yokote K, Tsuyuzaki K, Nakajima H, Kawakami E. iScience. 2022 Sep 28:105237. doi: 10.1016/j.isci.2022.105237. Online ahead of print. |
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Metabolome and transcriptome analysis on muscle of sporadic inclusion body myositis.
Murakami A, Noda S, Kazuta T, Hirano S, Kimura S, Nakanishi H, Matsuo K, Tsujikawa K, Iida M, Koike H, Sakamoto K, Hara Y, Kuru S, Kadomatsu K, Shimamura T, Ogi T, Katsuno M. Ann Clin Transl Neurol. 2022 Sep 15. doi: 10.1002/acn3.51657. Online ahead of print. PMID: 36107781 |
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An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis
Takahashi K, Abe K*, Kubota SI*, Fukatsu N*, Morishita Y, Yoshimatsu Y, Hirakawa S, Kubota Y, Watabe T, Ehata S, Ueda HR, Shimamura T#, Miyazono K# (#corresponding autor、*equally contributed), Nat Commun, 13: 5239 (2022). doi: 10.1038/s41467-022-32848-2 |
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A bifurcation concept for B-lymphoid/plasmacytoid dendritic cells with largely fluctuating transcriptome dynamics.
Nagaharu K*, Kojima Y*, Hirose H, Minoura K, Hinohara K, Minami H, Kageyama Y, Sugimoto Y, Masuya M, Nii S, Seki M, Suzuki Y, Tawara I, Shimamura T, Katayama N, Nishikawa H, Ohishi K. (* Equally contributed) Cell Rep. 2022 Aug 30;40(9):111260. doi: 10.1016/j.celrep.2022.111260. |
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UVB-Induced Skin Autoinflammation Due to Nlrp1b Mutation and Its Inhibition by Anti-IL-1β Antibody.
Murase Y, Takeichi T, Koseki J, Miyasaka Y, Muro Y, Ohno T, Shimamura T, Akiyama M. Front. Immunol. 2022 June 17;13:876390. doi: 10.3389/fimmu.2022.876390 |
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Exome sequencing of Japanese schizophrenia multiplex families supports the involvement of calcium ion channels.
Toyama M, Takasaki Y, Branko A, Kimura H, Kato H, Nawa Y, Kushima I, Ishizuka K, Shimamura T, Ogi T, Ozaki N. PLoS One. 2022 May 10;17(5):e0268321. doi: 10.1371/journal.pone.0268321. eCollection 2022. |
2021
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Depletion of central memory CD8+ T cells might impede the antitumor therapeutic effect of Mogamulizumab.
Maeda Y, Wada H, Sugiyama D, Saito T, Irie T, Itahashi K, Minoura K, Suzuki S, Kojima T, Kakimi K, Nakajima J, Funakoshi T, Iida S, Oka M, Shimamura T, Doi T, Doki Y, Nakayama E, Ueda R, Nishikawa H. Nat Commun. 2021 Dec 14;12(1):7280. doi: 10.1038/s41467-021-27574-0. |
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A mixture-of-experts multimodal deep generative model for single-cell multiomics data analysis
Minoura K, Abe K, Nam H, Nishikawa H, Shimamura T. Cell Reports Methods. 2021 Sep 27;1(5):100071. doi: 10.1016/j.crmeth.2021.100071. |
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Hierarchical non-negative matrix factorization using clinical information for microbial communities
Abe K, Hirayama M, Ohno K, Shimamura T. BMC Genomics. 2021 Feb 4;22(1):104. doi: 10.1186/s12864-021-07401-y. |
2020
原著論文
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Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson's Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder.
Nishiwaki H, Hamaguchi T, Ito M, Ishida T, Maeda T, Kashihara K, Tsuboi Y, Ueyama J, Shimamura T, Mori H, Kurokawa K, Katsuno M, Hirayama M, Ohno K. mSystems. 2020 Dec 8;5(6):e00797-20. doi: 10.1128/mSystems.00797-20. |
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CYBERTRACK2.0: zero-inflated model-based cell clustering and population tracking method for longitudinal mass cytometry data
Minoura K, Abe K, Maeda Y, Nishikawa H, Shimamura T. Bioinformatics. 2020 Oct 14:btaa873. doi: 10.1093/bioinformatics/btaa873 |
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Model-based clustering for flow and mass cytometry data with clinical information
Abe K, Minoura K, Maeda Y, Nishikawa H, Shimamura T. BMC Bioinformatics. 2020 Sep 17;21(Suppl 13):393. doi: 10.1186/s12859-020-03671-7 |
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ARHGAP10, which encodes Rho GTPase-activating protein 10, is a novel gene for schizophrenia risk
Mori D, Sekiguchi M, Sobue A, Kushima I, Chenyao W, Arioka Y, Kato H, Kodama A, Kubo H, Ito N, Sawahata M, Hada K, Ikeda R, Shinno M, Mizukoshi C, Tsujimura K, Yoshimi A, Ishizuka K, Takasaki Y, Kimura H, Xing J, Yu Y, Yamamoto M, Okada T, Shishido E, Inada T, Nakatochi M, Takano T, Kuroda K, Amano M, Aleksic B, Yamamoto T, Sakuma T, Aida T, Tanaka K, Hashimoto R, Arai M, Ikeda M, Iwata N, Shimamura T, Nagai T, Nabeshima T, Kaibuchi K, Yamada K, Ozaki N. Translational Psychiatry, in press. |
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Integrated multiomics analysis of hepatoblastoma unravels its heterogeneity and provides novel druggable targets.
Sekiguchi M, Seki M, Kawai T, Yoshida K, Yoshida M, Isobe T, Hoshino N, Shirai R, Tanaka M, Souzaki R, Watanabe K, Arakawa Y, Nannya Y, Suzuki H, Fujii Y, Kataoka K, Shiraishi Y, Chiba K, Tanaka H, Shimamura T, Sato Y, Sato-Otsubo A, Kimura S, Kubota Y, Hiwatari M, Koh K, Hayashi Y, Kanamori Y, Kasahara M, Kohashi K, Kato M, Yoshioka T, Matsumoto K, Oka A, Taguchi T, Sanada M, Tanaka Y, Miyano S, Hata K, Ogawa S, Takita J. NPJ Precis Oncol. 2020 Jul 7;4:20. doi: 10.1038/s41698-020-0125-y. eCollection 2020. |
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Meta‐Analysis of Gut Dysbiosis in Parkinson's Disease
Nishiwaki H, Ito M, Ishida T, Hamaguchi T, Maeda T, Kashihara K, Tsuboi Y, Ueyama J, Shimamura T, Mori H, Kurokawa K, Katsuno M, Hirayama M, Ohno K. Mov Disord. 2020 Jun 18. doi: 10.1002/mds.28119. Online ahead of print. PMID: 32557853 |
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EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells.
Yoshino S, Matsui Y, Fukui Y, Seki M, Yamaguchi K, Kanamori A, Saitoh Y, Shimamura T, Suzuki Y, Furukawa Y, Kaneko S, Seiki M, Murakami Y, Inoue JI, Sakamoto T. Sci Rep. 2020 Jun 9;10(1):9275. doi: 10.1038/s41598-020-66455-2. |
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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
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Model-based cell clustering and population tracking for time-series flow cytometry data
Minoura K, Abe K, Maeda Y, Nishikawa H, Shimamura T. BMC Bioinformatics. 2019 Dec 27;20(Suppl 23):633. doi: 10.1186/s12859-019-3294-3. |
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Phosphoethanolamine Accumulation Protects Cancer Cells under Glutamine Starvation through Downregulation of PCYT2
Osawa T, Shimamura T, Saito K, Hasegawa Y, Ishii N, Nishida M, Ando R, Kondo A, Anwar M, Tsuchida R, Hino S, Sakamoto A, Igarashi K, Saito K, Kato K, Endo K, Yamano S, Kanki Y, Matsumura Y, Minami T, Tanaka T, Anai M, Wada Y, Wanibuchi H, Hayashi M, Hamada A, Yoshida M, Yachida S, Nakao M, Sakai J, Aburatani H, Shibuya M, Hanada K, Miyano S, Soga T, Kodama T. Cell Rep. 2019 Oct 1;29(1):89-103. doi: 10.1016/j.celrep.2019.08.087 |
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Replication stress triggers microsatellite destabilization and hypermutation leading to clonal expansion in vitro
Matsuno Y, Atsumi Y, Shimizu A, Katayama K, Fujimori H, Hyodo M, Minakawa Y, Nakatsu Y, Kaneko S, Hamamoto R, Shimamura T, Miyano S, Tsuzuki T, Hanaoka F, Yoshioka K Nat Commun. 2019 Sep 2; 10(1):3925. doi: 10.1038/s41467-019-11760-2. |
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Distinct methylation levels of mature microRNAs in gastrointestinal cancers.
Konno M, Koseki J, Asai A, Yamagata A, Shimamura T, Motooka D, Okuzaki D, Kawamoto K, Mizushima T, Eguchi H, Takiguchi S, Satoh T, Mimori K, Ochiya T, Doki Y, Ofusa K, Mori M, Ishii H. Nat Commun. 2019 Aug 29;10(1):3888. doi: 10.1038/s41467-019-11826-1. |
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Meflin-positive cancer-associated fibroblasts inhibit pancreatic carcinogenesis.
Mizutani Y, Kobayashi H, Iida T, Asai N, Masamune A, Hara A, Esaki N, Ushida K, Mii S, Shiraki Y, Ando K, Weng L, Ishihara S, Ponik SM, Conklin MW, Haga H, Nagasaka A, Miyata T, Matsuyama M, Kobayashi T, Fujii T, Yamada S, Yamaguchi J, Wang T, Woods SL, Worthley D, Shimamura T, Fujishiro M, Hirooka Y, Takahashi M, Enomoto A. Cancer Res. 2019 Aug 22. pii: canres.0454.2019. doi: 10.1158/0008-5472.CAN-19-0454 |
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Pathogenic epigenetic consequences of genetic alterations in IDH-wild-type diffuse astrocytic gliomas.
Ohka F, Shinjo K, Deguchi S, Matsui Y, Okuno Y, Katsushima K, Suzuki M, Kato A, Ogiso N, Yamamichi A, Aoki K, Suzuki H, Sato S, Rayan NA, Prabhakar S, Göke J, Shimamura T, Maruyama R, Takahashi S, Suzumura A, Kimura H, Wakabayashi T, Zong H, Natsume A, Kondo Y. Cancer Research. in press. doi: 10.1158/0008-5472.CAN-19-1272. |
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Divergent lncRNA MYMLR regulates MYC by eliciting DNA looping and promoter-enhancer interaction.
Kajino T, Shimamura T, Gong S, Yanagisawa K, Ida L, Nakatochi M, Griesing S, Shimada Y, Kano K, Suzuki M, Miyano S, Takahashi T. EMBO J. 2019 Jul 30:e98441. doi: 10.15252/embj.201798441. |
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ENIGMA: An Enterotype-Like Unigram Mixture Model for Microbial Association Analysis.
Abe K, Hirayama H, Ohno K, Shimamura T. BMC Genomics. 2019 Apr 4;20(Suppl 2):191. doi: 10.1186/s12864-019-5476-9. |
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Regnase-1-mediated post-transcriptional regulation is essential for hematopoietic stem and progenitor cell homeostasis.
Kidoya H, Muramatsu F, Shimamura T, Jia W, Satoh T, Hayashi Y, Naito H, Kunisaki Y, Arai F, Seki M, Suzuki Y, Osawa T, Akira S, Takakura N. Nat Commun. 2019 Mar 6;10(1):1072. |
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A Network of Networks Approach for Modeling Interconnected Brain Tissue-Specific Networks.
Kawakubo H, Matsui Y, Kushima I, Ozaki N, Shimamura T. Bioinformatics. 2019 Sep 1;35(17):3092-3101. doi: 10.1093/bioinformatics/btz032. |
2018
原著論文
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GIMLET: Identifying biological modulators in context-specific gene regulation using local energy statistics.
Shimamura T, Matsui Y, Kajino T, Ito S, Takahashi T, Miyano S. Lecture Notes in Bioinformatics, Volume 10834, Computational Intelligence Methods for Bioinformatics and Biostatistics, 115-123. |
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Tumor subclonal progression model for cancer hallmark acquisition.
Matsui Y, Miyano S, Shimamura T. Lecture Notes in Bioinformatics, Volume 10834, Computational Intelligence Methods for Bioinformatics and Biostatistics, 124-137. |
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Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights.
Kushima I, Aleksic B, Nakatochi M, Shimamura T, Okada T, Uno Y, Morikawa M, Ishizuka K, Shiino T, Kimura H, Arioka Y, Yoshimi A, Takasaki Y, Yu Y, Nakamura Y, Yamamoto M, Iidaka T, Iritani S, Inada T, Ogawa N, Shishido E, Torii Y, Kawano N, Omura Y, Yoshikawa T, Uchiyama T, Yamamoto T, Ikeda M, Hashimoto R, Yamamori H, Yasuda Y, Someya T, Watanabe Y, Egawa J, Nunokawa A, Itokawa M, Arai M, Miyashita M, Kobori A, Suzuki M, Takahashi T, Usami M, Kodaira M, Watanabe K, Sasaki T, Kuwabara H, Tochigi M, Nishimura F, Yamasue H, Eriguchi Y, Benner S, Kojima M, Yassin W, Munesue T, Yokoyama S, Kimura R, Funabiki Y, Kosaka H, Ishitobi M, Ohmori T, Numata S, Yoshikawa T, Toyota T, Yamakawa K, Suzuki T, Inoue Y, Nakaoka K, Goto YI, Inagaki M, Hashimoto N, Kusumi I, Son S, Murai T, Ikegame T, Okada N, Kasai K, Kunimoto S, Mori D, Iwata N, Ozaki N. Cell Rep. 2018 Sep 11;24(11):2838-2856. doi: 10.1016/j.celrep.2018.08.022. |
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A latent allocation model for the analysis of microbial composition and disease.
Abe K, Hirayama H, Ohno K, Shimamura T. BMC Bioinformatics. 2018 Dec 31;19(Suppl 19):519. doi: 10.1186/s12859-018-2530-6. |
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A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer.
Saito T, Niida A, Uchi R, Hirata H, Komatsu H, Sakimura S, Hayashi S, Nambara S, Kuroda Y, Ito S, Eguchi H, Masuda T, Sugimachi K, Tobo T, Nishida H, Daa T, Chiba K, Shiraishi Y, Yoshizato T, Kodama M, Okimoto T, Mizukami K, Ogawa R, Okamoto K, Shuto M, Fukuda K, Matsui Y, Shimamura T, Hasegawa T, Doki Y, Nagayama S, Yamada K, Kato M, Shibata T, Mori M, Aburatani H, Murakami K, Suzuki Y, Ogawa S, Miyano S, Mimori K. Nat Commun. 2018 Jul 23;9(1):2884. doi: 10.1038/s41467-018-05226-0. |
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ATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D.
Komura K, Yoshikawa Y, Shimamura T, Chakraborty G, Gerke TA, Hinohara K, Chadalavada K, Jeong SH, Armenia J, Du SY, Mazzu YZ, Taniguchi K, Ibuki N, Meyer CA, Nanjangud GJ, Inamoto T, Lee GM, Mucci LA, Azuma H, Sweeney CJ, Kantoff PW. J Clin Invest. 2018 Jun 4. pii: 96769. doi: 10.1172/JCI96769. |
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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. Cell Rep. 2018 Jan 9;22(2):546-556. doi: 10.1016/j.celrep.2017.12.057. |
2017
国際会議 Proceedings
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GIMLET: Identifying biological modulators in context-specific gene regulation using local energy statistics.
Shimamura T, Matsui Y, Kajino T, Ito S, Takahashi T, Miyano S. To be appeared in Proceedings of CIBB2017. The extended version will be published in Lecture Notes in Bioinformatics. |
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Tumor subclonal progression model for cancer hallmark acquisition.
Matsui Y, Miyano S, Shimamura T. To be appeared in Proceedings of CIBB2017. The extended version will be published in Lecture Notes in Bioinformatics. |
原著論文
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ER stress signaling promotes the survival of cancer 'persister cells' tolerant to EGFR tyrosine kinase inhibitors.
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. Cancer Res. 2017 Dec 19. pii: canres.1904.2017. doi: 10.1158/0008-5472.CAN-17-1904. [Epub ahead of print] |
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Integrated molecular characterization of the lethal pediatric cancer pancreatoblastoma.
Isobe T, Seki M, Yoshida K, Sekiguchi M, Shiozawa Y, Shiraishi Y, Kimura S, Yoshida M, Inoue Y, Yokoyama A, Kakiuchi N, Suzuki H, Kataoka K, Sato Y, Kawai T, Chiba K, Tanaka H, Shimamura T, Kato M, Iguchi A, Hama A, Taguchi T, Akiyama M, Fujimura J, Inoue A, Ito T, Deguchi T, Kiyotani C, Iehara T, Hosoi H, Oka A, Sanada M, Tanaka Y, Hata K, Miyano S, Ogawa S, Takita J. Cancer Res. 2017 Dec 12. pii: canres.2581.2017. doi: 10.1158/0008-5472.CAN-17-2581. |
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Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks.
Park H, Shimamura T, Imoto S, Miyano S. J Comput Biol. 2017 Oct 20. doi: 10.1089/cmb.2017.0120. [Epub ahead of print] |
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Comprehensive genetic analysis of donor cell derived leukemia with KMT2A rearrangement.
Taniguchi R, Muramatsu H, Okuno Y, Suzuki K, Obu S, Nakatochi M, Shimamura T, Takahashi Y, Horikoshi Y, Watanabe K, Kojima S. Pediatr Blood Cancer. 2017 Sep 19. doi: 10.1002/pbc.26823. |
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Japanese genome-wide association study identifies a significant colorectal cancer susceptibility locus at chromosome 10p14.
Takahashi Y, Sugimachi K, Yamamoto K, Niida A, Shimamura T, Sato T, Watanabe M, Tanaka J, Kudo S, Sugihara K, Hase K, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Suzuki Y, Miyano S, Mori M, Mimori K. Cancer Sci. 2017 Sep 4. doi: 10.1111/cas.13391. |
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PRC2-mediated transcriptomic alterations at the embryonic stage govern tumorigenesis and clinical outcome in MYCN-driven neuroblastoma.
Tsubota S, Kishida S, Shimamura T, Ohira M, Yamashita S, Cao D, Kiyonari S, Ushijima T, Kadomatsu K. Cancer Res. 2017 Aug 14. pii: canres.3144.2016. doi: 10.1158/0008-5472.CAN-16-3144. |
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Prognostic relevance of genetic alterations in diffuse lower-grade gliomas.
Aoki K, Nakamura H, Suzuki H, Matsuo K, Kataoka K, Shimamura T, Motomura K, Ohka F, Shiina S, Yamamoto T, Nagata Y, Yoshizato Y, Mizoguchi M, Abe T, Momii Y, Muragaki Y, Watanabe R, Ito I, Sanada M, Yajima H, Morita N, Takeuchi I, Miyano S, Wakabayashi T, Oagwa S, Natsume A. Neuro-Oncology, nox132. https://doi.org/10.1093/neuonc/nox132. |
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Recurrent SPI1 (PU.1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia.
Seki M, Kimura S, Isobe T, Yoshida K, Ueno H, Nakajima-Takagi Y, Wang C, Lin L, Kon A, Suzuki H, Shiozawa Y, Kataoka K, Fujii Y, Shiraishi Y, Chiba K, Tanaka H, Shimamura T, Masuda K, Kawamoto H, Ohki K, Kato M, Arakawa Y, Koh K, Hanada R, Moritake H, Akiyama M, Kobayashi R, Deguchi T, Hashii Y, Imamura T, Sato A, Kiyokawa N, Oka A, Hayashi Y, Takagi M, Manabe A, Ohara A, Horibe K, Sanada M, Iwama A, Mano H, Miyano S, Ogawa S, Takita J. Nat Genet. 2017 Jul 3. doi: 10.1038/ng.3900. |
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Long non-coding RNA JHDM1D-AS1 promotes tumor growth by regulating angiogenesis in response to nutrient starvation.
Kondo A, Nonaka A, Shimamura T, Yamamoto S, Yoshida T, Kodama T, Aburatani H, Osawa T. Mol Cell Biol. 2017 Jun 26. pii: MCB.00125-17. doi: 10.1128/MCB.00125-17. |
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phyC: Clustering cancer evolutionary trees.
Matsui Y, Niida A, Uchi R, Mimori K, Miyano S, Shimamura T. PLoS Comput Biol. 2017 May 1;13(5):e1005509. doi: 10.1371/journal.pcbi.1005509. |
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Dynamically and epigenetically coordinated GATA/ETS/SOX transcription factor expression is indispensable for endothelial cell differentiation.
Kanki Y†, Nakaki R†, Shimamura T†, Matsunaga T, Yamamizu K, Katayama S, Suehiro JI, Osawa T, Aburatani H, Kodama T, Wada Y, Yamashita JK, Minami T. †These authors contributed equally to the paper as first authors Nucleic Acids Res. 2017 Mar 17. doi: 10.1093/nar/gkx159. |
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Addiction to the IGF2-ID1-IGF2 circuit for maintenance of the breast cancer stem-like cells.
Tominaga K, Shimamura T, Kimura N, Murayama T, Matsubara D, Kanauchi H, Niida A, Shimizu S, Nishioka K, Tsuji EI, Yano M, Sugano S, Shimono Y, Ishii H, Saya H, Mori M, Akashi K, Tada KI, Ogawa T, Tojo A, Miyano S, Gotoh N. Oncogene. 2017 Mar 2;36(9):1276-1286. |
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Extracellular Acidic pH Activates the Sterol Regulatory Element-Binding Protein 2 to Promote Tumor Progression.
Kondo A, Yamamoto S, Nakaki R, Shimamura T, Hamakubo T, Sakai J, Kodama T, Yoshida T, Aburatani H, Osawa T. Cell Rep. 2017 Feb 28;18(9):2228-2242. doi: 10.1016/j.celrep.2017.02.006. |
2016
原著論文
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Aberrant Methylation of FOXE1 Contributes to a Poor Prognosis for Patients with Colorectal Cancer.
Sugimachi K, Matsumura T, Shimamura T, Hirata H, Uchi R, Ueda M, Sakimura S, Iguchi T, Eguchi H, Masuda T, Morita K, Takenaka K, Maehara Y, Mori M, Mimori K. Ann Surg Oncol. 2016 Jun 6. |
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High-resolution copy number variation analysis of schizophrenia in Japan.
Kushima I, Aleksic B, Nakatochi M, Shimamura T, Shiino T, Yoshimi A, Kimura H, Takasaki Y, Wang C, Xing J, Ishizuka K, Oya-Ito T, Nakamura Y, Arioka Y, Maeda T, Yamamoto M, Yoshida M, Noma H, Hamada S, Morikawa M, Uno Y, Okada T, Iidaka T, Iritani S, Yamamoto T, Miyashita M, Kobori A, Arai M, Itokawa M, Cheng MC, Chuang YA, Chen CH, Suzuki M, Takahashi T, Hashimoto R, Yamamori H, Yasuda Y, Watanabe Y, Nunokawa A, Someya T, Ikeda M, Toyota T, Yoshikawa T, Numata S, Ohmori T, Kunimoto S, Mori D, Iwata N, Ozaki N. Mol Psychiatry. 2016 May 31. doi: 10.1038/mp.2016.88. |
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D3M: Detection of differential distributions of methylation levels.
Matsui Y, Mizuta M, Miyano S, Shimamura T. Bioinformatics. 2016 (in press). |
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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. Sci Rep. 2016 Mar 7;622784. doi:10.1038/srep22784. |
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Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution
Uchi R, Takahashi Y, Niida A, Shimamura T, Hirata H, Sugimachi K, Sawada G, Iwaya T, Kurashige J, Shinden Y, Iguchi T, Eguchi H, Chiba K, Shiraishi Y, Nagae G, Yoshida K, Nagata Y, Haeno H, Yamamoto H, Ishii H, Doki Y, Iinuma H, Sasaki S, Nagayama S, Yamada K, Yachida S, Kato M, Shibata T, Oki E, Saeki H, Shirabe K, Oda Y, Maehara Y, Komune S, Mori M, Suzuki Y, Yamamoto K, Aburatani H, Ogawa S, Miyano S, Mimori K. PLoS Genet. 2016 Feb 18;12(2):e1005778. doi: 10.1371/journal.pgen.1005778. |
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Genomic Landscape of Esophageal Squamous Cell Carcinoma in a Japanese Population
Sawada G, Niida A, Uchi R, Hirata H, Shimamura T, Suzuki Y, Shiraishi Y, Chiba K, Imoto S, Takahashi Y, Iwaya T, Sudo T, Hayashi T, Takai H, Kawasaki Y, Matsukawa T, Eguchi H, Sugimachi K, Tanaka F, Suzuki H, Yamamoto K, Ishii H, Shimizu M, Yamazaki H, Yamazaki M, Tachimori Y, Kajiyama Y, Natsugoe S, Fujita H, Mafune K, Tanaka Y, Kelsell DP, Scott CA, Tsuji S, Yachida S, Shibata T, Sugano S, Doki Y, Akiyama T, Aburatani H, Ogawa S, Miyano S, Mori M, Mimori K. Gastroenterology. 2016 Feb 9. pii: S0016-5085(16)00134-7. doi: 10.1053/j.gastro.2016.01.035. |
2015
原著論文
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An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma
Sawada G, Niida A, Hirata H, Komatsu H, Uchi R, Shimamura T, Takahashi Y, Kurashige J, Matsumura T, Ueo H, Takano Y, Ueda M, Sakimura S, Shinden Y, Eguchi H, Sudo T, Sugimachi K, Yamasaki M, Tanaka F, Tachimori Y, Kajiyama Y, Natsugoe S, Fujita H, Tanaka Y, Calin G, Miyano S, Doki Y, Mori M, Mimori K. PLoS One. 2015 Oct 14;10(10):e0139808. doi: 10.1371/journal.pone.0139808. eCollection 2015. |
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Integrated molecular analysis of adult T cell leukemia/lymphoma
Kataoka K, Nagata Y, Kitanaka A, Shiraishi Y, Shimamura T, Yasunaga J, Totoki Y, Chiba K, Sato-Otsubo A, Nagae G, Ishii R, Muto S, Kotani S, Watatani Y, Takeda J, Sanada M, Tanaka H, Suzuki H, Sato Y, Shiozawa Y, Yoshizato T, Yoshida K, Makishima H, Iwanaga M, Ma G, Nosaka K, Hishizawa M, Itonaga H, Imaizumi Y, Munakata W, Ogasawara H, Sato T, Sasai K, Muramoto K, Penova M, Kawaguchi T, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Nakamaki T, Ishiyama K, Miyawaki S, Yoon SS, Tobinai K, Miyazaki Y, Takaori-Kondo A, Matsuda F, Takeuchi K, Nureki O, Aburatani H, Watanabe T, Shibata T, Matsuoka M, Miyano S, Shimoda K, Ogawa S. Nat Genet. 2015 Nov;47(11):1304-15. doi: 10.1038/ng.3415. Epub 2015 Oct 5. |
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A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models
Hasegawa T, Niida A, Mori T, Shimamura T, Yamaguchi R, Miyano S, Akutsu T, Imoto S. Computational Statistics & Data Analysis 02/2016; 94:63-74. DOI:10.1016/j.csda.2015.08.003 |
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Elevated β-catenin pathway as a novel target for patients with resistance to EGF receptor targeting drugs
Nakata A, Yoshida R, Yamaguchi R, Yamauchi M, Tamada Y, Fujita A, Shimamura T, Imoto S, Higuchi T, Nomura M, Kimura T, Nokihara H, Higashiyama M, Kondoh K, Nishihara H, Tojo A, Yano S, Miyano S, Gotoh N. Sci Rep. 2015 Aug 13;5:13076. doi: 10.1038/srep13076. |
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Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma
Seki M, Nishimura R, Yoshida K, Shimamura T, Shiraishi Y, Sato Y, Kato M, Chiba K, Tanaka H, Hoshino N, Nagae G, Shiozawa Y, Okuno Y, Hosoi H, Tanaka Y, Okita H, Miyachi M, Souzaki R, Taguchi T, Koh K, Hanada R, Kato K, Nomura Y, Akiyama M, Oka A, Igarashi T, Miyano S, Aburatani H, Hayashi Y, Ogawa S, Takita J. Nat Commun. 2015 Jul 3;6:7557. doi: 10.1038/ncomms8557. |
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Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks
Hasegawa T, Mori T, Yamaguchi R, Shimamura T, Miyano S, Imoto S, Akutsu T. BMC Syst Biol. 2015 Mar 13;9:14. doi: 10.1186/s12918-015-0154-2. |
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Mutational landscape and clonal architecture in grade II and III gliomas
Suzuki H, Aoki K, Chiba K, Sato Y, Shiozawa Y, Shiraishi Y, Shimamura T, Niida A, Motomura K, Ohka F, Yamamoto T, Tanahashi K, Ranjit M, Wakabayashi T, Yoshizato T, Kataoka K, Yoshida K, Nagata Y, Sato-Otsubo A, Tanaka H, Sanada M, Kondo Y, Nakamura H, Mizoguchi M, Abe T, Muragaki Y, Watanabe R, Ito I, Miyano S, Natsume A, Ogawa S. Nat Genet. 2015 May;47(5):458-68. doi: 10.1038/ng.3273. Epub 2015 Apr 13. |
2014
原著論文
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Robust prediction of anti-cancer drug sensitivity and sensitivity-specific biomarker
Park H, Shimamura T, Miyano S, Imoto S. PLoS One. 2014 Oct 17;9(10):e108990. doi: 10.1371/journal.pone.0108990. eCollection 2014. |
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Loss of CDCP1 expression promotes invasiveness and poor prognosis in esophageal squamous cell carcinoma
Sawada G, Takahashi Y, Niida A, Shimamura T, Kurashige J, Matsumura T, Ueo H, Uchi R, Takano Y, Ueda M, Hirata H, Sakimura S, Shinden Y, Eguchi H, Sudo T, Sugimachi K, Miyano S, Doki Y, Mori M, Mimori K. Ann Surg Oncol. 2014 Dec;21 Suppl 4:S640-7. doi: 10.1245/s10434-014-3740-4. Epub 2014 May 22. |
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Biallelic DICER1 mutations in sporadic pleuropulmonary blastoma
Seki M, Yoshida K, Shiraishi Y, Shimamura T, Sato Y, Nishimura R, Okuno Y, Chiba K, Tanaka H, Kato K, Kato M, Hanada R, Nomura Y, Park MJ, Ishida T, Oka A, Igarashi T, Miyano S, Hayashi Y, Ogawa S, Takita J. Cancer Res. 2014 May 15;74(10):2742-9. doi: 10.1158/0008-5472.CAN-13-2470. Epub 2014 Mar 27. |
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Allelic imbalance at an 8q24 oncogenic SNP is involved in activating MYC in human colorectal cancer
Sugimachi K, Niida A, Yamamoto K, Shimamura T, Imoto S, Iinuma H, Shinden Y, Eguchi H, Sudo T, Watanabe M, Tanaka J, Kudo S, Hase K, Kusunoki M, Yamada K, Shimada Y, Sugihara K, Maehara Y, Miyano S, Mori M, Mimori K. Ann Surg Oncol. 2014 Dec;21 Suppl 4:S515-21. doi: 10.1245/s10434-013-3468-6. Epub 2014 Jan 6. |
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Systems biology analysis of Drosophila in vivo screen data elucidates core networks for DNA damage repair in SCA1
Barclay SS, Tamura T, Ito H, Fujita K, Tagawa K, Shimamura T, Katsuta A, Shiwaku H, Sone M, Imoto S, Miyano S, Okazawa H. Hum Mol Genet. 2014 Mar 1;23(5):1345-64. doi: 10.1093/hmg/ddt524. Epub 2013 Oct 31. |
