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Identification of the differences in molecular networks between idiopathic pulmonary fibrosis and lung squamous cell carcinoma using machine learning
Yosui Nojima, Kenji Mizuguchi
Computational Biology and Chemistry Vol. 119 p. 108560-108560 2025/06/27 Research paper (scientific journal)
Publisher: Elsevier BV
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Single-cell RNA sequencing and machine learning provide candidate drugs against drug-tolerant persister cells in colorectal cancer
Yosui Nojima, Ryoji Yao, Takashi Suzuki
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease Vol. 1871 No. 3 p. 167693-167693 2025/01/30 Research paper (scientific journal)
Publisher: Elsevier BV
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Identification of the differences in molecular networks between idiopathic pulmonary fibrosis and lung squamous cell carcinoma using machine learning
Yosui Nojima, Kenji Mizuguchi
bioRxiv 2024/11/26
Publisher: Cold Spring Harbor Laboratory
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Phosphoproteomic subtyping of gastric cancer reveals dynamic transformation with chemotherapy and guides targeted cancer treatment
Hirokazu Shoji, Hidekazu Hirano, Yosui Nojima, Daigo Gunji, Akina Shinkura, Satoshi Muraoka, Yuichi Abe, Ryohei Narumi, Chioko Nagao, Masahiko Aoki, Kazutaka Obama, Kazufumi Honda, Kenji Mizuguchi, Takeshi Tomonaga, Yutaka Saito, Takaki Yoshikawa, Ken Kato, Narikazu Boku, Jun Adachi
Cell Reports p. 114774-114774 2024/10 Research paper (scientific journal)
Publisher: Elsevier BV
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Integration of pharmacoproteomic and computational approaches reveals the cellular signal transduction pathways affected by apatinib in gastric cancer cell lines
Yosui Nojima, Masahiko Aoki, Suyong Re, Hidekazu Hirano, Yuichi Abe, Ryohei Narumi, Satoshi Muraoka, Hirokazu Shoji, Kazufumi Honda, Takeshi Tomonaga, Kenji Mizuguchi, Narikazu Boku, Jun Adachi
Computational and Structural Biotechnology Journal Vol. 21 p. 2172-2187 2023/03 Research paper (scientific journal)
Publisher: Elsevier BV
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Identification of CD14 and lipopolysaccharide-binding protein as novel biomarkers for sarcoidosis using proteomics of serum extracellular vesicles
Yu Futami, Yoshito Takeda, Taro Koba, Ryohei Narumi, Yosui Nojima, Mari Ito, Mana Nakayama, Mimiko Ishida, Hanako Yoshimura, Yujiro Naito, Kiyoharu Fukushima, Takayuki Takimoto, Ryuya Edahiro, Takanori Matsuki, Satoshi Nojima, Haruhiko Hirata, Shohei Koyama, Kota Iwahori, Izumi Nagatomo, Yuya Shirai, Yasuhiko Suga, Shingo Satoh, Shinji Futami, Kotaro Miyake, Takayuki Shiroyama, Yoshikazu Inoue, Jun Adachi, Takeshi Tomonaga, Koji Ueda, Atsushi Kumanogoh
International Immunology Vol. 34 No. 6 p. 327-340 2022/06/04 Research paper (scientific journal)
Publisher: Oxford University Press (OUP)
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Data-driven patient stratification and drug target discovery by using medical information and serum proteome data of idiopathic pulmonary fibrosis patients
Yayoi Natsume-Kitatani, Mari N Itoh, Yoshito Takeda, Masataka Kuroda, Haruhiko Hirata, Kohtaro Miyake, Takayuki Shiroyama, Yuya Shirai, Yoshimi Noda, Yuichi Adachi, Takatoshi Enomoto, Saori Amiya, Jun Adachi, Ryohei Narumi, Satoshi Muraoka, Takeshi Tomonaga, Sadao Kurohashi, Fei Cheng, Ribeka Tanaka, Shuntaro Yada, Eiji Aramaki, Shoko Wakamiya, Yi-An Chen, Chihiro Higuchi, Yosui Nojima, Takeshi Fujiwara, Chioko Nagao, Yasushi Matsumura, Kenji Mizuguchi, Atsushi Kumanogoh, Naonori Ueda
Research Square 2022/03/29
Publisher: Research Square Platform LLC
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Temporal dynamics from phosphoproteomics using endoscopic biopsy specimens provides new therapeutic targets in stage IV gastric cancer
Hidekazu Hirano, Yuichi Abe, Yosui Nojima, Masahiko Aoki, Hirokazu Shoji, Junko Isoyama, Kazufumi Honda, Narikazu Boku, Kenji Mizuguchi, Takeshi Tomonaga, Jun Adachi
Scientific Reports Vol. 12 No. 1 p. 4419-4419 2022/03/25 Research paper (scientific journal)
Publisher: Springer Science and Business Media LLC
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Characterization of Heat Shock Protein 60 as an Interacting Partner of Superoxide Dismutase 2 in the Silkworm, Bombyx mori, and Its Response to the Molting Hormone, 20-Hydroxyecdysone
Yosui Nojima
Antioxidants Vol. 10 No. 9 p. 1385-1385 2021/08/30 Research paper (scientific journal)
Publisher: MDPI AG
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CD14 and LBP as Novel Biomarkers for Sarcoidosis by Proteomics of Extracellular Vesicles
Yu Futami, Yoshito Takeda, Taro Koba, Ryohei Narumi, Yosui Nojima, Mari Ito, Mana Nakayama, Mimiko Ishida, Hanako Yoshimura, Yujiro Naito, Kiyoharu Fukushima, Takayuki Takimoto, Ryuya Edahiro, Tomonori Matsuki, Satoshi Nojima, Haruhiko Hirata, Shohei Koyama, Kota Iwahori, Izumi Nagatomo, Yuya Shirai, Yasuhiko Suga, Shingo Satoh, Shinji Futami, Kotaro Miyake, Takayuki Shiroyama, Yoshikazu Inoue, Jun Adachi, Takeshi Tomonaga, Koji Ueda, Atsushi Kumanogoh
Research Square 2021/08/19
Publisher: Research Square Platform LLC
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Expression of Cancer Stem Cell Markers EpCAM and CD90 Is Correlated with Anti- and Pro-Oncogenic EphA2 Signaling in Hepatocellular Carcinoma
Nobuhiko Asakura, Naotoshi Nakamura, Atsushi Muroi, Yosui Nojima, Taro Yamashita, Shuichi Kaneko, Kazuki Ikeda, Naohiko Koshikawa, Takashi Suzuki
International Journal of Molecular Sciences Vol. 22 No. 16 p. 8652-8652 2021/08/11 Research paper (scientific journal)
Publisher: MDPI AG
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Omics Data Analysis Tools for Biomarker Discovery and the Tutorial
Yosui Nojima, Yoshito Takeda
Springer Proceedings in Mathematics & Statistics p. 266-273 2021 Part of collection (book)
Publisher: Springer Singapore
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Proteomics of serum extracellular vesicles identifies a novel COPD biomarker, fibulin-3 from elastic fibres
Taro Koba, Yoshito Takeda, Ryohei Narumi, Takashi Shiromizu, Yosui Nojima, Mari Ito, Muneyoshi Kuroyama, Yu Futami, Takayuki Takimoto, Takanori Matsuki, Ryuya Edahiro, Satoshi Nojima, Yoshitomo Hayama, Kiyoharu Fukushima, Haruhiko Hirata, Shohei Koyama, Kota Iwahori, Izumi Nagatomo, Mayumi Suzuki, Yuya Shirai, Teruaki Murakami, Kaori Nakanishi, Takeshi Nakatani, Yasuhiko Suga, Kotaro Miyake, Takayuki Shiroyama, Hiroshi Kida, Takako Sasaki, Koji Ueda, Kenji Mizuguchi, Jun Adachi, Takeshi Tomonaga, Atsushi Kumanogoh
ERJ Open Research Vol. 7 No. 1 p. 00658-2020 2021/01 Research paper (scientific journal)
Publisher: European Respiratory Society (ERS)
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Metabolomic analysis of fibrotic mice combined with public RNA‐Seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis
Yosui Nojima, Yoshito Takeda, Yohei Maeda, Takeshi Bamba, Eiichiro Fukusaki, Mari N. Itoh, Kenji Mizuguchi, Atsushi Kumanogoh
FEBS Open Bio Vol. 10 No. 11 p. 2427-2436 2020/10/05 Research paper (scientific journal)
Publisher: Wiley
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Estimation of relationships between chemical substructures and antibiotic resistance-related gene expression in bacteria: Adapting a canonical correlation analysis for small sample data of gathered features using consensus clustering
Tsuyoshi Esaki, Takaaki Horinouchi, Yayoi Natsume-Kitatani, Yosui Nojima, Iwao Sakane, Hidetoshi Matsui
Chem-Bio Informatics Journal Vol. 20 No. 0 p. 58-61 2020/09/30 Research paper (scientific journal)
Publisher: Chem-Bio Informatics Society
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Panomicon: A web-based environment for interactive, visual analysis of multi-omics data
Rodolfo S. Allendes Osorio, Johan T. Nyström-Persson, Yosui Nojima, Yuji Kosugi, Kenji Mizuguchi, Yayoi Natsume-Kitatani
Heliyon Vol. 6 No. 8 p. e04618-e04618 2020/08 Research paper (scientific journal)
Publisher: Elsevier BV
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Superoxide dismutase down-regulation and the oxidative stress is required to initiate pupation in Bombyx mori
Yosui Nojima, Hidemasa Bono, Takeshi Yokoyama, Kikuo Iwabuchi, Ryoichi Sato, Katsuhiko Arai, Hiroko Tabunoki
Scientific Reports Vol. 9 No. 1 2019/10
Publisher: Springer Science and Business Media {LLC}
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The role of glycogen in development and adult fitness in Drosophila
Takayuki Yamada, Okiko Habara, Yuka Yoshii, Ryota Matsushita, Hitomi Kubo, Yosui Nojima, Takashi Nishimura
Development Vol. 146 No. 8 p. dev176149-dev176149 2019/04/15 Research paper (scientific journal)
Publisher: The Company of Biologists
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The development of artificial intelligence for drug target discovery
Yosui Nojima, Kenji Mizuguchi
Journal of Clinical and Experimental Medicine Vol. 268 No. 12 p. 988-991 2019/03
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Comparative analysis of seven types of superoxide dismutases for their ability to respond to oxidative stress in Bombyx mori.
Yuta Kobayashi, Yosui Nojima, Takuma Sakamoto, Kikuo Iwabuchi, Takeru Nakazato, Hidemasa Bono, Atsushi Toyoda, Asao Fujiyama, Michael R. Kanost, Hiroko Tabunoki
Scientific reports Vol. 9 No. 1 p. 2170-2170 2019/02 Research paper (scientific journal)
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Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processes
Akira Kikuchi, Takeru Nakazato, Katsuhiko Ito, Yosui Nojima, Takeshi Yokoyama, Kikuo Iwabuchi, Hidemasa Bono, Atsushi Toyoda, Asao Fujiyama, Ryoichi Sato, Hiroko Tabunoki
BMC GENOMICS Vol. 18 2017/01 Research paper (scientific journal)
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Superoxide dismutases, SOD1 and SOD2, play a distinct role in the fat body during pupation in silkworm Bombyx mori.
Nojima Y, Ito K, Ono H, Nakazato T, Bono H, Yokoyama T, Sato R, Suetsugu Y, Nakamura Y, Yamamoto K, Satoh J, Tabunoki H, Fugo H
PloS one 2015 Research paper (scientific journal)
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Production of wild-type and mutant-type human DAP12 proteins by Bombyx mori nucleopolyhedrovirus vector
Nozomi Uemura, Hiroko Tabunoki, Taiki Suzuki, Kazuhiro Ishikawa, Yosui Nojima, Susumu Katsuma, Ryoichi Sato, Jun-ichi Satoh
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY Vol. 78 No. 1 p. 71-74 2014/01 Research paper (scientific journal)
