Personnel Information

写真a

SHIMAMURA TEPPEI


Job title

Professor
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Campus Career 【 display / non-display 】

  • 2023.01
    -
    Now
    Tokyo Medical and Dental University， Medical Research Institute， Division of Biological Data Science， Department of Computational and Systems Biology， Professor
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External Career 【 display / non-display 】

  • 2019.06
    -
    2023.03
    Nagoya University, Graduate School of Medicine, Professor
  • 2021.01
    -
    2023.03
    Nagoya University, Professor
  • 2023.01
    -
    2024.09
    Tokyo Medical and Dental University, Medical Research Institute, Professor
  • 2023.04
    -
    Now
    Nagoya University, Graduate School of Medicine, Designated Professor
  • 2024.10
    -
    Now
    Institute of Science Tokyo, Department of Computational and Systems Biology, Medical Research Laboratory, Institute of Integrated Research, Professor
  • 2024.10
    -
    Now
    Institute of Science Tokyo, Department of Computational and Systems Biology, Medical Research Laboratory, Professor

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Academic Society Affiliations 【 display / non-display 】

  • JAPANESE SOCIETY OF COMPUTATIONAL STATISTICS

  • THE JAPANESE CANCER ASSOCIATION

  • THE MOLECULAR BIOLOGY SOCIETY OF JAPAN

  • JAPANESE SOCIETY FOR BIOINFORMATICS

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Research Areas 【 display / non-display 】

  • Life, health and medical informatics

  • System genome science

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Research Theme 【 display / non-display 】

  • Platform for Advanced Genome Science, 2022.04 - 2028.03

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Published Papers & Misc 【 display / non-display 】

  1. DeepKINET: a deep generative model for estimating single-cell RNA splicing and degradation rates. 2024.09; 25 (1): 229. ( PubMed, DOI )

  2. [Koichiro Majima,Yasuhiro Kojima,Kodai Minoura,Ko Abe,Haruka Hirose,Teppei Shimamura]. LineageVAE: Reconstructing Historical Cell States and Transcriptomes toward Unobserved Progenitors. 2024.08; ( PubMed, DOI )

  3. [Yasuhiro Kojima,Yuko Arioka,Haruka Hirose,Shuto Hayashi,Yusuke Mizuno,Keiki Nagaharu,Hiroki Okumura,Masato Ishikawa,Kohshi Ohishi,Yutaka Suzuki,Norio Ozaki,Teppei Shimamura]. Inferring extrinsic factor-dependent single-cell transcriptome dynamics using a deep generative model 2024.04; ( DOI )

  4. [Masahiro Hashimoto,Yasuhiro Kojima,Takeharu Sakamoto,Yuki Ozato,Yusuke Nakano,Tadashi Abe,Kiyotaka Hosoda,Hideyuki Saito,Satoshi Higuchi,Yuichi Hisamatsu,Takeo Toshima,Yusuke Yonemura,Takaaki Masuda,Tsuyoshi Hata,Satoshi Nagayama,Koichi Kagawa,Yasuhiro Goto,Mitsuaki Utou,Ayako Gamachi,Kiyomi Imamura,Yuta Kuze,Junko Zenkoh,Ayako Suzuki,Kazuki Takahashi,Atsushi Niida,Haruka Hirose,Shuto Hayashi,Jun Koseki,Satoshi Fukuchi,Kazunari Murakami,Tomoharu Yoshizumi,Kenji Kadomatsu,Taro Tobo,Yoshinao Oda,Mamoru Uemura,Hidetoshi Eguchi,Yuichiro Doki,Masaki Mori,Masanobu Oshima,Tatsuhiro Shibata,Yutaka Suzuki,Teppei Shimamura,Koshi Mimori]. Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis 2024.04; 103 105102. ( PubMed, DOI )

  5. [Yasuhiro Kojima,Shinji Mii,Shuto Hayashi,Haruka Hirose,Masato Ishikawa,Masashi Akiyama,Atsushi Enomoto,Teppei Shimamura]. Single-cell colocalization analysis using a deep generative model 2024.02; 15 (2): 180-192.e7. ( PubMed, DOI )

  6. [Mengjiao Li,Tatsunori Nishimura,Yasuto Takeuchi,Tsunaki Hongu,Yuming Wang,Daisuke Shiokawa,Kang Wang,Haruka Hirose,Asako Sasahara,Masao Yano,Satoko Ishikawa,Masafumi Inokuchi,Tetsuo Ota,Masahiko Tanabe,Kei-Ichiro Tada,Tetsu Akiyama,Xi Cheng,Chia-Chi Liu,Toshinari Yamashita,Sumio Sugano,Yutaro Uchida,Tomoki Chiba,Hiroshi Asahara,Masahiro Nakagawa,Shinya Sato,Yohei Miyagi,Teppei Shimamura,Luis Augusto E Nagai,Akinori Kanai,Manami Katoh,Seitaro Nomura,Ryuichiro Nakato,Yutaka Suzuki,Arinobu Tojo,Dominic C Voon,Seishi Ogawa,Koji Okamoto,Theodoros Foukakis,Noriko Gotoh]. FXYD3 functionally demarcates an ancestral breast cancer stem cell subpopulation with features of drug-tolerant persisters 2023.11; 133 (22): ( PubMed, DOI )

  7. [Shiki Fujino,Norikatsu Miyoshi,Aya Ito,Rie Hayashi,Masayoshi Yasui,Chu Matsuda,Masayuki Ohue,Masafumi Horie,Shinichi Yachida,Jun Koseki,Teppei Shimamura,Tsuyoshi Hata,Takayuki Ogino,Hidekazu Takahashi,Mamoru Uemura,Tsunekazu Mizushima,Yuichiro Doki,Hidetoshi Eguchi]. Metastases and treatment-resistant lineages in patient-derived cancer cells of colorectal cancer 2023.11; 6 (1): 1191. ( PubMed, DOI )

  8. [Ryuichi Nakahara,Sho Aki,Maki Sugaya,Haruka Hirose,Miki Kato,Keisuke Maeda,Daichi M Sakamoto,Yasuhiro Kojima,Miyuki Nishida,Ritsuko Ando,Masashi Muramatsu,Melvin Pan,Rika Tsuchida,Yoshihiro Matsumura,Hideyuki Yanai,Hiroshi Takano,Ryoji Yao,Shinsuke Sando,Masabumi Shibuya,Juro Sakai,Tatsuhiko Kodama,Hiroyasu Kidoya,Teppei Shimamura,Tsuyoshi Osawa]. Hypoxia activates SREBP2 through Golgi disassembly in bone marrow-derived monocytes for enhanced tumor growth 2023.10; 42 (22): e114032. ( PubMed, DOI )

  9. [Miki Kato,Keisuke Maeda,Ryuichi Nakahara,Haruka Hirose,Ayano Kondo,Sho Aki,Maki Sugaya,Sana Hibino,Miyuki Nishida,Manami Hasegawa,Hinano Morita,Ritsuko Ando,Rika Tsuchida,Minoru Yoshida,Tatsuhiko Kodama,Hideyuki Yanai,Teppei Shimamura,Tsuyoshi Osawa]. Acidic extracellular pH drives accumulation of N1-acetylspermidine and recruitment of protumor neutrophils PNAS nexus. 2023.10; 2 (10): pgad306. ( PubMed, DOI )

  10. [Ko Abe,Teppei Shimamura]. UNMF: a unified nonnegative matrix factorization for multi-dimensional omics data 2023.07; 24 (5): ( PubMed, DOI )

  11. [So Takeuchi,Takuya Takeichi,Yoshinao Muro,Teppei Shimamura,Masashi Akiyama]. Plucked scalp hair follicle samples are useful RNA sources for mRNA analysis of most genodermatosis-associated genes 2023.07; 111 (2): 68-70. ( PubMed, DOI )

  12. [Jun Koseki,Shuto Hayashi,Yasuhiro Kojima,Haruka Hirose,Teppei Shimamura]. Topological data analysis of protein structure and inter/intra- molecular interaction changes attributable to amino acid mutations 2023.05; 21 2950-2959. ( PubMed, DOI )

  13. [Akihiro Kitagawa,Tsuyoshi Osawa,Miwa Noda,Yuta Kobayashi,Sho Aki,Yusuke Nakano,Tomoko Saito,Dai Shimizu,Hisateru Komatsu,Maki Sugaya,Junichi Takahashi,Keisuke Kosai,Seiichiro Takao,Yushi Motomura,Kuniaki Sato,Qingjiang Hu,Atsushi Fujii,Hiroaki Wakiyama,Taro Tobo,Hiroki Uchida,Keishi Sugimachi,Kohei Shibata,Tohru Utsunomiya,Shogo Kobayashi,Hideshi Ishii,Takanori Hasegawa,Takaaki Masuda,Yusuke Matsui,Atsushi Niida,Tomoyoshi Soga,Yutaka Suzuki,Satoru Miyano,Hiroyuki Aburatani,Yuichiro Doki,Hidetoshi Eguchi,Masaki Mori,Keiichi I Nakayama,Teppei Shimamura,Tatsuhiro Shibata,Koshi Mimori]. Convergent genomic diversity and novel BCAA metabolism in intrahepatic cholangiocarcinoma 2023.04; 128 (12): 2206-2217. ( PubMed, DOI )

  14. [Shiho Torii,Kwang Su Kim,Jun Koseki,Rigel Suzuki,Shoya Iwanami,Yasuhisa Fujita,Yong Dam Jeong,Jumpei Ito,Hiroyuki Asakura,Mami Nagashima,Kenji Sadamasu,Kazuhisa Yoshimura,Kei Sato,Yoshiharu Matsuura,Teppei Shimamura,Shingo Iwami,Takasuke Fukuhara]. Increased flexibility of the SARS-CoV-2 RNA-binding site causes resistance to remdesivir 2023.03; 19 (3): e1011231. ( PubMed, DOI )

  15. [Yuki Ozato,Yasuhiro Kojima,Yuta Kobayashi,Yuuichi Hisamatsu,Takeo Toshima,Yusuke Yonemura,Takaaki Masuda,Kouichi Kagawa,Yasuhiro Goto,Mitsuaki Utou,Mituko Fukunaga,Ayako Gamachi,Kiyomi Imamura,Yuta Kuze,Junko Zenkoh,Ayako Suzuki,Atsushi Niida,Haruka Hirose,Shuto Hayashi,Jun Koseki,Eiji Oki,Satoshi Fukuchi,Kazunari Murakami,Taro Tobo,Satoshi Nagayama,Mamoru Uemura,Takeharu Sakamoto,Masanobu Oshima,Yuichiro Doki,Hidetoshi Eguchi,Masaki Mori,Takeshi Iwasaki,Yoshinao Oda,Tatsuhiro Shibata,Yutaka Suzuki,Teppei Shimamura,Koshi Mimori]. Spatial and single-cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer 2023.01; 42 (1): 111929. ( PubMed, DOI )

  16. [Jun Koseki,Haruka Hirose,Masamitsu Konno,Teppei Shimamura]. Theoretical Computational Analysis Predicts Interaction Changes Due to Differences of a Single Molecule in DNA 2023.01; 13 (1): 510. ( DOI )

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