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An adjuvant database for preclinical evaluation of vaccines and immunotherapeutics
Yayoi Natsume-Kitatani, Kouji Kobiyama, Yoshinobu Igarashi, Taiki Aoshi, Noriyuki Nakatsu, Lokesh P. Tripathi, Junichi Ito, Johan Nyström-Persson, Yuji Kosugi, Rodolfo S. Allendes Osorio, Chioko Nagao, Burcu Temizoz, Etsushi Kuroda, Daron M. Standley, Hiroshi Kiyono, Kenji Nakanishi, Satoshi Uematsu, Isao Hamaguchi, Yasuhiro Yasutomi, Jun Kunisawa, Sho Yamasaki, Cevayir Coban, Hiroshi Yamada, Kenji Mizuguchi, Ken J. Ishii
Cell Chemical Biology 2025年8月 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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Unveiling unique expression patterns of D20S16 satellite DNA in human embryonic development
Yajie Hu, Kenji Mizuguchi, Kosuke Hashimoto
Scientific Reports Vol. 15 No. 1 2025年7月23日 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media LLC
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Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis
Eiichi Yoshimura, Yuka Hamada, Yoichi Hatamoto, Takashi Nakagata, Hinako Nanri, Yui Nakayama, Chiharu Iwasaka, Takanori Hayashi, Ippei Suzuki, Takafumi Ando, Kazuko Ishikawa-Takata, Shigeho Tanaka, Rei Ono, Michihiro Araki, Hitoshi Kawashima, Yi-An Chen, Jonguk Park, Koji Hosomi, Kenji Mizuguchi, Jun Kunisawa, Motohiko Miyachi
Gut Microbes Vol. 17 No. 1 2025年6月9日 研究論文（学術雑誌）
出版者・発行元：Informa UK Limited
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NIBN Japan Microbiome Database, a database for exploring the correlations between human microbiome and health
Yi-An Chen, Hitoshi Kawashima, Jonguk Park, Attayeb Mohsen, Koji Hosomi, Takashi Nakagata, Haruka Murakami, Hinako Nanri, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi
Scientific Reports Vol. 15 No. 1 2025年6月4日 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media LLC
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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 2025年6月 研究論文（学術雑誌）
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A Novel Method for Endometrial Cancer Patient Stratification Considering ARID1A Protein Expression and Activity with Effective Use of Multi-omics Data
Junsoo Song, Ayako Ui, Kenji Mizuguchi, Reiko Watanabe
Computational and Structural Biotechnology Journal 2025年6月 研究論文（学術雑誌）
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Dual antioxidant and cytotoxic activities of novel 1,2,3-triazole-decorated unsymmetrical monocarbonyl curcumin analogs
Bayu Ardiansah, Ahmad Farhan, Novita Sari Nurhasanah, Mochammad Arfin Fardiansyah Nasution, Noordini M. Salleh, Kenji Mizuguchi, Antonius Herry Cahyana, Lina Mardiana
Case Studies in Chemical and Environmental Engineering Vol. 11 p. 101031-101031 2025年6月 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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Improving the accuracy of prediction models for small datasets of Cytochrome P450 inhibition with deep learning
Elpri Eka Permadi, Reiko Watanabe, Kenji Mizuguchi
Journal of Cheminformatics Vol. 17 No. 1 2025年4月30日 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media LLC
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Biological age prediction using a DNN model based on pathways of steroidogenesis
Qiuyi Wang, Zi Wang, Kenji Mizuguchi, Toshifumi Takao
Science Advances Vol. 11 No. 11 2025年3月14日 研究論文（学術雑誌）
出版者・発行元：American Association for the Advancement of Science (AAAS)
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Effects of Malted Rice Amazake Consumption on Nutritional Status and Gut Microbiome in Older Patients and Residents of an Integrated Facility for Medical and Long-Term Care
Miki Doi, Rikako Inoue, Koji Hosomi, Jonguk Park, Hitomi Yumioka, A. Yasmin Syauki, Suzumi Kageyama, Haruka Sakaue, Kozo Tanabe, Kenji Mizuguchi, Jun Kunisawa, Yasuyuki Irie
Journal of Nutrition in Gerontology and Geriatrics p. 1-23 2025年1月16日 研究論文（学術雑誌）
出版者・発行元：Informa UK Limited
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Clinical Phenotypes Associated with the Gut Microbiome in Older Japanese People with Care Needs in a Nursing Home
Rikako Inoue, Koji Hosomi, Jonguk Park, Haruka Sakaue, Hitomi Yumioka, Hiroko Kamitani, Yoshiharu Kinugasa, Kaori Harano, A. Yasmin Syauki, Miki Doi, Suzumi Kageyama, Kazuhiro Yamamoto, Kenji Mizuguchi, Jun Kunisawa, Yasuyuki Irie
Nutrients Vol. 16 No. 22 p. 3839-3839 2024年11月8日 研究論文（学術雑誌）
出版者・発行元：MDPI AG
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High barley intake in non-obese individuals is associated with high natto consumption and abundance of butyrate-producing bacteria in the gut: a cross-sectional study
Satoko Maruyama, Tsubasa Matsuoka, Koji Hosomi, Jonguk Park, Haruka Murakami, Motohiko Miyachi, Hitoshi Kawashima, Kenji Mizuguchi, Toshiki Kobayashi, Tadao Ooka, Zentaro Yamagata, Jun Kunisawa
Frontiers in Nutrition Vol. 11 2024年10月31日 研究論文（学術雑誌）
出版者・発行元：Frontiers Media SA
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Association Between Gut Microbiome Composition and Physical Characteristics in Patients with Severe Motor and Intellectual Disabilities: Perspectives from Microbial Diversity
Suzumi Kageyama, Rikako Inoue, Koji Hosomi, Jonguk Park, Hitomi Yumioka, Miki Doi, Miyuu Miyake, Yuka Nagashio, Yoshiko Shibuya, Nobue Oka, Hirofumi Akazawa, Susumu Kanzaki, Kenji Mizuguchi, Jun Kunisawa, Yasuyuki Irie
Nutrients Vol. 16 No. 20 p. 3546-3546 2024年10月19日 研究論文（学術雑誌）
出版者・発行元：MDPI AG
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A modern multi-omics data exploration experience with Panomicon
Rodolfo S Allendes Osorio, Yuji Kosugi, Johan T Nyström-Persson, Kenji Mizuguchi, Yayoi Natsume-Kitatani
Bioinformatics Advances 2024年10月3日 研究論文（学術雑誌）
出版者・発行元：Oxford University Press (OUP)
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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年10月 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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Group X phospholipase A2 links colonic lipid homeostasis to systemic metabolism via host-microbiota interaction
Hiroyasu Sato, Yoshitaka Taketomi, Remi Murase, Jonguk Park, Koji Hosomi, Takayuki Jujo Sanada, Kenji Mizuguchi, Makoto Arita, Jun Kunisawa, Makoto Murakami
Cell Reports Vol. 43 No. 10 p. 114752-114752 2024年10月 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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Construction of a Tm-Value Prediction Model and Molecular Dynamics Study of AmNA-Containing Gapmer Antisense Oligonucleotide
Masataka Kuroda, Yuuya Kasahara, Masako Hirose, Harumi Yamaguma, Masayuki Oda, Chioko Nagao, Kenji Mizuguchi
Molecular Therapy - Nucleic Acids p. 102272-102272 2024年7月16日 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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Effect of resistance training and chicken meat on muscle strength and mass and the gut microbiome of older women: A randomized controlled trial
Masataka Uchida, Jonguk Park, Shumpei Fujie, Koji Hosomi, Naoki Horii, Kohei Watanabe, Kiyoshi Sanada, Yasushi Shinohara, Kenji Mizuguchi, Jun Kunisawa, Motoyuki Iemitsu, Motohiko Miyachi
Physiological Reports Vol. 12 No. 12 2024年6月18日 研究論文（学術雑誌）
出版者・発行元：Wiley
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SFTPB in serum extracellular vesicles as a biomarker of progressive pulmonary fibrosis
Takatoshi Enomoto, Yuya Shirai, Yoshito Takeda, Ryuya Edahiro, Shigeyuki Shichino, Mana Nakayama, Miho Takahashi-Itoh, Yoshimi Noda, Yuichi Adachi, Takahiro Kawasaki, Taro Koba, Yu Futami, Moto Yaga, Yuki Hosono, Hanako Yoshimura, Saori Amiya, Reina Hara, Makoto Yamamoto, Daisuke Nakatsubo, Yasuhiko Suga, Maiko Naito, Kentaro Masuhiro, Haruhiko Hirata, Kota Iwahori, Izumi Nagatomo, Kotaro Miyake, Shohei Koyama, Kiyoharu Fukushima, Takayuki Shiroyama, Yujiro Naito, Shinji Futami, Yayoi Natsume-Kitatani, Satoshi Nojima, Masahiro Yanagawa, Yasushi Shintani, Mari Nogami-Itoh, Kenji Mizuguchi, Jun Adachi, Takeshi Tomonaga, Yoshikazu Inoue, Atsushi Kumanogoh
JCI Insight Vol. 9 No. 11 2024年6月10日 研究論文（学術雑誌）
出版者・発行元：American Society for Clinical Investigation
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Galectin-10 in serum extracellular vesicles reflects asthma pathophysiology
Hanako Yoshimura, Yoshito Takeda, Yuya Shirai, Makoto Yamamoto, Daisuke Nakatsubo, Saori Amiya, Takatoshi Enomoto, Reina Hara, Yuichi Adachi, Ryuya Edahiro, Moto Yaga, Kentaro Masuhiro, Taro Koba, Miho Itoh-Takahashi, Mana Nakayama, So Takata, Yuki Hosono, Sho Obata, Masayuki Nishide, Akinori Hata, Masahiro Yanagawa, Satoko Namba, Michio Iwata, Momoko Hamano, Haruhiko Hirata, Shohei Koyama, Kota Iwahori, Izumi Nagatomo, Yasuhiko Suga, Kotaro Miyake, Takayuki Shiroyama, Kiyoharu Fukushima, Shinji Futami, Yujiro Naito, Takahiro Kawasaki, Kenji Mizuguchi, Yusuke Kawashima, Yoshihiro Yamanishi, Jun Adachi, Mari Nogami-Itoh, Shigeharu Ueki, Atsushi Kumanogoh
Journal of Allergy and Clinical Immunology 2024年3月 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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Structural and accessibility studies highlight the differential binding of clemizole to TRPC5 and TRPC6
Uzma Saqib, Isaac S. Demaree, Alexander G. Obukhov, Mirza S. Baig, Mohd Shahnawaz Khan, Nojood Altwaijry, Mochammad Arfin Fardiansyah Nasution, Kenji Mizuguchi, Krishnan Hajela
Journal of Biomolecular Structure and Dynamics 2024年1月27日 研究論文（学術雑誌）
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Idiopathic pulmonary fibrosis-specific Bayesian network integrating extracellular vesicle proteome and clinical information
Mei Tomoto, Yohei Mineharu, Noriaki Sato, Yoshinori Tamada, Mari Nogami-Itoh, Masataka Kuroda, Jun Adachi, Yoshito Takeda, Kenji Mizuguchi, Atsushi Kumanogoh, Yayoi Natsume-Kitatani, Yasushi Okuno
Scientific Reports Vol. 14 No. 1 2024年1月15日 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media LLC
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Impact of Hydrogen Bonding on P-Glycoprotein Efflux Transport as Revealed by Evaluation of a De Novo Prediction Model
Yulong Gou, Suyong Re, Kenji Mizuguchi, Chioko Nagao
ACS Medicinal Chemistry Letters 2023年12月21日 研究論文（学術雑誌）
出版者・発行元：American Chemical Society (ACS)
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Attention network for predicting T-cell receptor–peptide binding can associate attention with interpretable protein structural properties
Kyohei Koyama, Kosuke Hashimoto, Chioko Nagao, Kenji Mizuguchi
Frontiers in Bioinformatics Vol. 3 2023年12月18日 研究論文（学術雑誌）
出版者・発行元：Frontiers Media SA
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Association of skeletal muscle function, quantity, and quality with gut microbiota in Japanese adults: A cross-sectional study.
Chiharu Iwasaka, Hinako Nanri, Takashi Nakagata, Harumi Ohno, Kumpei Tanisawa, Kana Konishi, Haruka Murakami, Koji Hosomi, Jonguk Park, Yosuke Yamada, Rei Ono, Kenji Mizuguchi, Jun Kunisawa, Motohiko Miyachi
Geriatrics & gerontology international 2023年12月14日 研究論文（学術雑誌）
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Effects of energy loads on energy and nutrient absorption rates and gut microbiome in humans: A randomized crossover trial
Eiichi Yoshimura, Yuka Hamada, Yoichi Hatamoto, Takashi Nakagata, Hinako Nanri, Yui Nakayama, Takanori Hayashi, Ippei Suzuki, Takafumi Ando, Kazuko Ishikawa‐Takata, Shigeho Tanaka, Rei Ono, Jonguk Park, Koji Hosomi, Kenji Mizuguchi, Jun Kunisawa, Motohiko Miyachi
Obesity 2023年11月5日 研究論文（学術雑誌）
出版者・発行元：Wiley
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Changes in Fecal Gut Microbiome of Home Healthcare Patients with Disabilities through Consumption of Malted Rice Amazake
Suzumi Kageyama, Rikako Inoue, Jonguk Park, Koji Hosomi, Hitomi Yumioka, Tomo Suka, Kazuaki Teramoto, A. Yasmin Syauki, Miki Doi, Haruka Sakaue, Miyuu Miyake, Kenji Mizuguchi, Jun Kunisawa, Yasuyuki Irie
Physiological Genomics 2023年9月11日 研究論文（学術雑誌）
出版者・発行元：American Physiological Society
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Ramen Consumption and Gut Microbiota Diversity in Japanese Women: Cross-Sectional Data from the NEXIS Cohort Study
Jonguk Park, Hiroto Bushita, Ayatake Nakano, Ai Hara, Hiroshi M. Ueno, Naoki Ozato, Koji Hosomi, Hitoshi Kawashima, Yi-An Chen, Attayeb Mohsen, Harumi Ohno, Kana Konishi, Kumpei Tanisawa, Hinako Nanri, Haruka Murakami, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi, Michihiro Araki
Microorganisms Vol. 11 No. 8 p. 1892-1892 2023年7月26日 研究論文（学術雑誌）
出版者・発行元：MDPI AG
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Gut microbiota alternation with training periodization and physical fitness in Japanese elite athletes
Nobuhiko Akazawa, Mariko Nakamura, Nobuhiko Eda, Haruka Murakami, Takashi Nakagata, Hinako Nanri, Jonguk Park, Koji Hosomi, Kenji Mizuguchi, Jun Kunisawa, Motohiko Miyachi, Masako Hoshikawa
Frontiers in Sports and Active Living Vol. 5 2023年7月14日 研究論文（学術雑誌）
出版者・発行元：Frontiers Media SA
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DruMAP: A Novel Drug Metabolism and Pharmacokinetics Analysis Platform
Hitoshi Kawashima, Reiko Watanabe, Tsuyoshi Esaki, Masataka Kuroda, Chioko Nagao, Yayoi Natsume-Kitatani, Rikiya Ohashi, Hiroshi Komura, Kenji Mizuguchi
Journal of Medicinal Chemistry 2023年7月14日 研究論文（学術雑誌）
出版者・発行元：American Chemical Society (ACS)
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Predicting thrombotic cardiovascular outcomes induced by waterpipe-associated chemicals using comparative toxicogenomic database: Genes, phenotypes, and pathways
Ahmed B. Alarabi, Attayab Mohsen, Ziyad Ben Taleb, Kenji Mizuguchi, Fatima Z. Alshbool, Fadi T. Khasawneh
Life Sciences Vol. 323 p. 121694-121694 2023年6月 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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Evidence-Based Prediction of Cellular Toxicity for Amorphous Silica Nanoparticles
Martin, Reiko Watanabe, Kosuke Hashimoto, Kazuma Higashisaka, Yuya Haga, Yasuo Tsutsumi, Kenji Mizuguchi
ACS Nano 2023年5月30日 研究論文（学術雑誌）
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Characteristic Gut Bacteria in High Barley Consuming Japanese Individuals without Hypertension
Satoko Maruyama, Tsubasa Matsuoka, Koji Hosomi, Jonguk Park, Mao Nishimura, Haruka Murakami, Kana Konishi, Motohiko Miyachi, Hitoshi Kawashima, Kenji Mizuguchi, Toshiki Kobayashi, Tadao Ooka, Zentaro Yamagata, Jun Kunisawa
Microorganisms Vol. 11 No. 5 2023年5月9日 研究論文（学術雑誌）
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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 2023年3月 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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医薬品関連文書の利活用に向けたインタビューフォームの構造化の提案
長尾 知生子, 鎌田 真由美, 中津井 雅彦, 深川 明子, 片山 俊明, 川島 秀一, 水口 賢司, 安倍 理加
医薬品情報学 Vol. 24 No. 4 p. 187-195 2023年2月28日 研究論文（学術雑誌）
出版者・発行元：一般社団法人 日本医薬品情報学会
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DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein–protein interactions
Kazuyoshi Ikeda, Yuta Maezawa, Tomoki Yonezawa, Yugo Shimizu, Toshiyuki Tashiro, Satoru Kanai, Nobuyoshi Sugaya, Yoshiaki Masuda, Naoko Inoue, Tatsuya Niimi, Keiichi Masuya, Kenji Mizuguchi, Toshio Furuya, Masanori Osawa
Frontiers in Chemistry Vol. 10 2023年1月9日 研究論文（学術雑誌）
出版者・発行元：Frontiers Media SA
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Prediction of the Contribution Ratio of a Target Metabolic Enzyme to Clearance from Chemical Structure Information
Reiko Watanabe, Toshio Kawata, Shinya Ueda, Takumi Shinbo, Mitsuo Higashimori, Yayoi Natsume-Kitatani, Kenji Mizuguchi
Molecular Pharmaceutics 2022年12月20日 研究論文（学術雑誌）
出版者・発行元：American Chemical Society (ACS)
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Identification of Human Gut Microbiome Associated with Enterolignan Production
Kento Sawane, Koji Hosomi, Jonguk Park, Kouta Ookoshi, Hinako Nanri, Takashi Nakagata, Yi-An Chen, Attayeb Mohsen, Hitoshi Kawashima, Kenji Mizuguchi, Motohiko Miyachi, Jun Kunisawa
Microorganisms Vol. 10 No. 11 p. 2169-2169 2022年10月31日 研究論文（学術雑誌）
出版者・発行元：MDPI AG
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Structural dynamics of the N‐terminal SH2 domain of PI3K in its free and CD28‐bound states
Yuhi Hosoe, Yohei Miyanoiri, Suyong Re, Saki Ochi, Yuya Asahina, Toru Kawakami, Masataka Kuroda, Kenji Mizuguchi, Masayuki Oda
The FEBS Journal Vol. 290 No. 9 p. 2366-2378 2022年10月25日 研究論文（学術雑誌）
出版者・発行元：Wiley
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Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota
Koji Hosomi, Mayu Saito, Jonguk Park, Haruka Murakami, Naoko Shibata, Masahiro Ando, Takahiro Nagatake, Kana Konishi, Harumi Ohno, Kumpei Tanisawa, Attayeb Mohsen, Yi-An Chen, Hitoshi Kawashima, Yayoi Natsume-Kitatani, Yoshimasa Oka, Hidenori Shimizu, Mari Furuta, Yoko Tojima, Kento Sawane, Azusa Saika, Saki Kondo, Yasunori Yonejima, Haruko Takeyama, Akira Matsutani, Kenji Mizuguchi, Motohiko Miyachi, Jun Kunisawa
Nature Communications Vol. 13 No. 1 p. 4477-4477 2022年8月18日 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media LLC
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TargetMine 2022: A new vision into drug target analysis.
Yi-An Chen, Rodolfo S Allendes Osorio, Kenji Mizuguchi
Bioinformatics (Oxford, England) 2022年7月27日 研究論文（学術雑誌）
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Integrative Network Modeling Highlights the Crucial Roles of Rho-GDI Signaling Pathway in the Progression of Non-Small Cell Lung Cancer.
Saransh Gupta, Haswanth Vundavilli, Rodolfo S Allendes Osorio, Mari N Itoh, Attayeb Mohsen, Aniruddha Datta, Kenji Mizuguchi, Lokesh P Tripathi
IEEE journal of biomedical and health informatics Vol. PP 2022年7月12日 研究論文（学術雑誌）
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Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2
Attayeb Mohsen, Yi-An Chen, Rodolfo S. Allendes Osorio, Chihiro Higuchi, Kenji Mizuguchi
Frontiers in Bioinformatics Vol. 2 p. 893933-893933 2022年7月1日 研究論文（学術雑誌）
出版者・発行元：Frontiers Media SA
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Dietary Vitamin B1 Intake Influences Gut Microbial Community and the Consequent Production of Short-Chain Fatty Acids.
Jonguk Park, Koji Hosomi, Hitoshi Kawashima, Yi-An Chen, Attayeb Mohsen, Harumi Ohno, Kana Konishi, Kumpei Tanisawa, Masako Kifushi, Masato Kogawa, Haruko Takeyama, Haruka Murakami, Tetsuya Kubota, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi
Nutrients Vol. 14 No. 10 2022年5月16日 研究論文（学術雑誌）
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Co-expression analysis to identify key modules and hub genes associated with COVID-19 in platelets
Ahmed B. Alarabi, Attayeb Mohsen, Kenji Mizuguchi, Fatima Z. Alshbool, Fadi T. Khasawneh
BMC Medical Genomics Vol. 15 No. 1 2022年4月 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media {LLC}
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Altered gut microbiota and its association with inflammation in patients with chronic thromboembolic pulmonary hypertension: a single-center observational study in Japan
Yumiko Ikubo, Takayuki Jujo Sanada, Koji Hosomi, Jonguk Park, Akira Naito, Hiroki Shoji, Tomoko Misawa, Rika Suda, Ayumi Sekine, Toshihiko Sugiura, Ayako Shigeta, Hinako Nanri, Seiichiro Sakao, Nobuhiro Tanabe, Kenji Mizuguchi, Jun Kunisawa, Takuji Suzuki, Koichiro Tatsumi
BMC Pulmonary Medicine Vol. 22 No. 1 2022年4月 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media LLC
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Classification of the Occurrence of Dyslipidemia Based on Gut Bacteria Related to Barley Intake
Satoko Maruyama, Tsubasa Matsuoka, Koji Hosomi, Jonguk Park, Mao Nishimura, Haruka Murakami, Kana Konishi, Motohiko Miyachi, Hitoshi Kawashima, Kenji Mizuguchi, Toshiki Kobayashi, Tadao Ooka, Zentaro Yamagata, Jun Kunisawa
Frontiers in Nutrition Vol. 9 2022年3月24日 研究論文（学術雑誌）
出版者・発行元：Frontiers Media SA
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α-Amino acid and peptide synthesis using catalytic cross-dehydrogenative coupling
Taro Tsuji, Kayoko Hashiguchi, Mana Yoshida, Tetsu Ikeda, Yunosuke Koga, Yusaku Honda, Tsukushi Tanaka, Suyong Re, Kenji Mizuguchi, Daisuke Takahashi, Ryo Yazaki, Takashi Ohshima
Nature Synthesis Vol. 1 No. 4 p. 304-312 2022年3月14日 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media 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 2022年3月 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media LLC
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Relationships between barley consumption and gut microbiome characteristics in a healthy Japanese population: a cross-sectional study
Tsubasa Matsuoka, Koji Hosomi, Jonguk Park, Yuka Goto, Mao Nishimura, Satoko Maruyama, Haruka Murakami, Kana Konishi, Motohiko Miyachi, Hitoshi Kawashima, Kenji Mizuguchi, Toshiki Kobayashi, Hiroshi Yokomichi, Jun Kunisawa, Zentaro Yamagata
BMC Nutrition Vol. 8 No. 1 p. 23-23 2022年3月 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media LLC
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The Gut Microbiome as a Biomarker of Cancer Progression Among Female Never-smokers With Lung Adenocarcinoma
TAKEHIRO OTOSHI, TATSUYA NAGANO, JONGUK PARK, KOJI HOSOMI, TOMOYA YAMASHITA, MOTOKO TACHIHARA, TOKIKO TABATA, REINA SEKIYA, YUGO TANAKA, KAZUYUKI KOBAYASHI, KENJI MIZUGUCHI, TOMOO ITOH, YOSHIMASA MANIWA, JUN KUNISAWA, YOSHIHIRO NISHIMURA
Anticancer Research Vol. 42 No. 3 p. 1589-1598 2022年3月 研究論文（学術雑誌）
出版者・発行元：Anticancer Research USA Inc.
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Group IIA secreted phospholipase A2 controls skin carcinogenesis and psoriasis by shaping the gut microbiota
Yoshimi Miki, Yoshitaka Taketomi, Yuh Kidoguchi, Kei Yamamoto, Kazuaki Muramatsu, Yasumasa Nishito, Jonguk Park, Koji Hosomi, Kenji Mizuguchi, Jun Kunisawa, Tomoyoshi Soga, Eric Boilard, Siddabasave Gowda B. Gowda, Kazutaka Ikeda, Makoto Arita, Makoto Murakami
JCI Insight Vol. 7 No. 2 2022年1月25日 研究論文（学術雑誌）
出版者・発行元：American Society for Clinical Investigation
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Selective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide
Daiki Yamane, Satsuki Onitsuka, Suyong Re, Hikaru Isogai, Rui Hamada, Tadanari Hiramoto, Eiji Kawanishi, Kenji Mizuguchi, Naoya Shindo, Akio Ojida
Chemical Science Vol. 13 No. 10 p. 3027-3034 2022年 研究論文（学術雑誌）
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Flavivirus recruits the valosin-containing protein (VCP)/NPL4 complex to induce stress granule disassembly for efficient viral genome replication
Masashi Arakawa, Keisuke Tabata, Kotaro Ishida, Makiko Kobayashi, Arisa Arai, Tomohiro Ishikawa, Ryosuke Suzuki, Hiroaki Takeuchi, Lokesh P. Tripathi, Kenji Mizuguchi, Eiji Morita
Journal of Biological Chemistry p. 101597-101597 2022年1月 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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Effects of Malted Rice Amazake on Constipation Symptoms and Gut Microbiota in Children and Adults with Severe Motor and Intellectual Disabilities: A Pilot Study
Suzumi Kageyama, Rikako Inoue, Koji Hosomi, Jonguk Park, Hitomi Yumioka, Tomo Suka, Yoshihiro Kurohashi, Kazuaki Teramoto, A. Yasmin Syauki, Miki Doi, Haruka Sakaue, Kenji Mizuguchi, Jun Kunisawa, Yasuyuki Irie
Nutrients Vol. 13 No. 12 p. 4466-4466 2021年12月14日 研究論文（学術雑誌）
出版者・発行元：MDPI AG
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Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts
Jonguk Park, Kumiko Kato, Haruka Murakami, Koji Hosomi, Kumpei Tanisawa, Takashi Nakagata, Harumi Ohno, Kana Konishi, Hitoshi Kawashima, Yi-An Chen, Attayeb Mohsen, Jin-zhong Xiao, Toshitaka Odamaki, Jun Kunisawa, Kenji Mizuguchi, Motohiko Miyachi
BMC Microbiology Vol. 21 No. 1 p. 151-151 2021年12月 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media LLC
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Categorization of the Ocular Microbiome in Japanese Stevens–Johnson Syndrome Patients With Severe Ocular Complications
Mayumi Ueta, Koji Hosomi, Jonguk Park, Kenji Mizuguchi, Chie Sotozono, Shigeru Kinoshita, Jun Kunisawa
Frontiers in Cellular and Infection Microbiology Vol. 11 p. 741654-741654 2021年11月19日 研究論文（学術雑誌）
出版者・発行元：Frontiers Media SA
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Deep Learning Prediction of Adverse Drug Reactions in Drug Discovery Using Open TG–GATEs and FAERS Databases
Attayeb Mohsen, Lokesh P. Tripathi, Kenji Mizuguchi
Frontiers in Drug Discovery Vol. 1 2021年10月27日 研究論文（学術雑誌）
出版者・発行元：Frontiers Media SA
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Relationship between Human Gut Microbiota and Nutrition Intake in Hypertensive Discordant Monozygotic Twins
Rie Tomizawa, Jonguk Park, Natsuko Matsumoto, Koji Hosomi, Hitoshi Kawashima, Kenji Mizuguchi, Jun Kunisawa, Chika Honda
Journal of Hypertension: Open Access Vol. 10 No. 8 2021年8月 研究論文（学術雑誌）
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Distinct Age-Specific miRegulome Profiling of Isolated Small and Large Intestinal Epithelial Cells in Mice
Juneyoung Lee, Attayeb Mohsen, Anik Banerjee, Louise D. McCullough, Kenji Mizuguchi, Motomu Shimaoka, Hiroshi Kiyono, Eun Jeong Park
International Journal of Molecular Sciences Vol. 22 No. 7 p. 3544-3544 2021年3月29日 研究論文（学術雑誌）
出版者・発行元：MDPI AG
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Relationship between Nutrient Intake and Human Gut Microbiota in Monozygotic Twins
Natsuko Matsumoto, Jonguk Park, Rie Tomizawa, Hitoshi Kawashima, Koji Hosomi, Kenji Mizuguchi, Chika Honda, Ritsuko Ozaki, Yoshinori Iwatani, Mikio Watanabe, Jun Kunisawa
Medicina Vol. 57 No. 3 p. 275-275 2021年3月16日 研究論文（学術雑誌）
出版者・発行元：MDPI AG
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Network Modeling and Inference of Peroxisome Proliferator-Activated Receptor Pathway in High fat diet-linked Obesity.
Haswanth Vundavilli, Lokesh P.Tripathi, Aniruddha Datta, Kenji Mizuguchi
Journal of theoretical biology p. 110647-110647 2021年2月25日 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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Development of an In Silico Prediction Model for P-glycoprotein Efflux Potential in Brain Capillary Endothelial Cells toward the Prediction of Brain Penetration
Reiko Watanabe, Tsuyoshi Esaki, Rikiya Ohashi, Masataka Kuroda, Hitoshi Kawashima, Hiroshi Komura, Yayoi Natsume-Kitatani, Kenji Mizuguchi
Journal of Medicinal Chemistry 2021年2月23日 研究論文（学術雑誌）
出版者・発行元：American Chemical Society (ACS)
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Glycan Cluster Shielding and Antibody Epitopes on Lassa Virus Envelop Protein
Suyong Re, Kenji Mizuguchi
The Journal of Physical Chemistry B Vol. 125 No. 8 p. 2089-2097 2021年2月19日 研究論文（学術雑誌）
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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年1月 研究論文（学術雑誌）
出版者・発行元：European Respiratory Society (ERS)
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Integrative Analysis Reveals Common and Unique Roles of Tetraspanins in Fibrosis and Emphysema
Lokesh P. Tripathi, Mari N. Itoh, Yoshito Takeda, Kazuyuki Tsujino, Yasushi Kondo, Atsushi Kumanogoh, Kenji Mizuguchi
Frontiers in Genetics Vol. 11 p. 585998-585998 2020年12月10日 研究論文（学術雑誌）
出版者・発行元：Frontiers Media SA
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MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data
Yi-An Chen, Jonguk Park, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Attayeb Mohsen, Koji Hosomi, Kumpei Tanisawa, Harumi Ohno, Kana Konishi, Haruka Murakami, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi
PLOS ONE Vol. 15 No. 12 p. e0243609-e0243609 2020年12月4日 研究論文（学術雑誌）
出版者・発行元：Public Library of Science (PLoS)
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Developing a Kinase-Specific Target Selection Method Using a Structure-Based Machine Learning Approach
Arina Afanasyeva, Chioko Nagao, Kenji Mizuguchi
Advances and Applications in Bioinformatics and Chemistry Vol. Volume 13 p. 27-40 2020年12月 研究論文（学術雑誌）
出版者・発行元：Informa UK Limited
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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年9月22日 研究論文（学術雑誌）
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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年8月 研究論文（学術雑誌）
出版者・発行元：Elsevier BV
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Update of the GRIP web service.
Akira Saito, Daiki Tsuchiya, Seiji Sato, Atsushi Okamoto, Yoichi Murakami, Kenji Mizuguchi, Hiroyuki Toh, Wataru Nemoto
Journal of receptor and signal transduction research Vol. 40 No. 4 p. 348-356 2020年8月 研究論文（学術雑誌）
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Gut microbial composition in patients with atrial fibrillation: effects of diet and drugs.
Tokiko Tabata, Tomoya Yamashita, Koji Hosomi, Jonguk Park, Tomohiro Hayashi, Naofumi Yoshida, Yoshihiro Saito, Koji Fukuzawa, Kana Konishi, Haruka Murakami, Hitoshi Kawashima, Kenji Mizuguchi, Motohiko Miyachi, Jun Kunisawa, Ken-Ichi Hirata
Heart and vessels Vol. 36 No. 1 p. 105-114 2020年7月18日 研究論文（学術雑誌）
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Gut microbiota modification suppresses the development of pulmonary arterial hypertension in an SU5416/hypoxia rat model
Takayuki J. Sanada, Koji Hosomi, Hiroki Shoji, Jonguk Park, Akira Naito, Yumiko Ikubo, Asako Yanagisawa, Takayuki Kobayashi, Hideki Miwa, Rika Suda, Seiichiro Sakao, Kenji Mizuguchi, Jun Kunisawa, Nobuhiro Tanabe, Koichiro Tatsumi
Pulmonary Circulation Vol. 10 No. 3 p. 204589402092914-204589402092914 2020年7月 研究論文（学術雑誌）
出版者・発行元：SAGE Publications
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Novel anti-flavivirus drugs targeting the nucleolar distribution of core protein.
Makoto Tokunaga, Yoichi Miyamoto, Tatsuya Suzuki, Mayumi Otani, Shinsuke Inuki, Tsuyoshi Esaki, Chioko Nagao, Kenji Mizuguchi, Hiroaki Ohno, Yoshihiro Yoneda, Toru Okamoto, Masahiro Oka, Yoshiharu Matsuura
Virology Vol. 541 p. 41-51 2020年2月 研究論文（学術雑誌）
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Actin Cytoskeletal Reorganization Function of JRAB/MICAL-L2 Is Fine-tuned by Intramolecular Interaction between First LIM Zinc Finger and C-terminal Coiled-coil Domains
Miyake K, Sakane A, Tsuchiya Y, Sagawa I, Tomida Y, Kasahara J, Imoto I, Watanabe S, Higo D, Mizuguchi K, Sasaki T
Scientific Reports Vol. 9 No. 1 p. 12794-12794 2019年12月 研究論文（学術雑誌）
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A prospective compound screening contest identified broader inhibitors for Sirtuin 1
Shuntaro Chiba, Masahito Ohue, Anastasiia Gryniukova, Petro Borysko, Sergey Zozulya, Nobuaki Yasuo, Ryunosuke Yoshino, Kazuyoshi Ikeda, Woong-Hee Shin, Daisuke Kihara, Mitsuo Iwadate, Hideaki Umeyama, Takaaki Ichikawa, Reiji Teramoto, Kun-Yi Hsin, Vipul Gupta, Hiroaki Kitano, Mika Sakamoto, Akiko Higuchi, Nobuaki Miura, Kei Yura, Masahiro Mochizuki, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Itsuo Nakane, Nanako Uchida, Hayase Hakariya, Modong Tan, Hironori K. Nakamura, Shogo D. Suzuki, Tomoki Ito, Masahiro Kawatani, Kentaroh Kudoh, Sakurako Takashina, Kazuki Z. Yamamoto, Yoshitaka Moriwaki, Keita Oda, Daisuke Kobayashi, Tatsuya Okuno, Shintaro Minami, George Chikenji, Philip Prathipati, Chioko Nagao, Attayeb Mohsen, Mari Ito, Kenji Mizuguchi, Teruki Honma, Takashi Ishida, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima
Scientific Reports Vol. 9 No. 1 2019年12月 研究論文（学術雑誌）
出版者・発行元：Springer Science and Business Media LLC
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Development of an in silico prediction system of human renal excretion and clearance from chemical structure information incorporating fraction unbound in plasma as a descriptor
Watanabe R, Ohashi R, Esaki T, Kawashima H, Natsume-Kitatani Y, Nagao C, Mizuguchi K
Scientific Reports Vol. 9 No. 1 p. 18782-18782 2019年12月 研究論文（学術雑誌）
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Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks
Mohsen A, Park J, Chen YA, Kawashima H, Mizuguchi K
BMC Bioinformatics Vol. 20 No. 1 2019年12月 研究論文（学術雑誌）
出版者・発行元：
-
CLINE: a web-tool for the comparison of biological dendrogram structures
Allendes Osorio RS, Tripathi LP, Mizuguchi K
BMC Bioinformatics Vol. 20 No. 1 2019年12月 研究論文（学術雑誌）
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The TargetMine Data Warehouse: Enhancement and Updates
Chen YA, Tripathi LP, Fujiwara T, Kameyama T, Itoh MN, Mizuguchi K
Frontiers in Genetics Vol. 10 2019年10月 研究論文（学術雑誌）
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B cell-intrinsic MyD88 signaling controls IFN-γ-mediated early IgG2c class switching in mice in response to a particulate adjuvant
Michelle Sue Jann Lee, Yayoi Natsume-Kitatani, Burcu Temizoz, Yukiko Fujita, Aki Konishi, Kyoko Matsuda, Yoshikatsu Igari, Toshihiro Tsukui, Kouji Kobiyama, Etsushi Kuroda, Motoyasu Onishi, Thomas Marichal, Wataru Ise, Takeshi Inoue, Tomohiro Kurosaki, Kenji Mizuguchi, Shizuo Akira, Ken J. Ishii, Cevayir Coban
European Journal of Immunology Vol. 49 No. 9 p. 1433-1440 2019年9月1日 研究論文（学術雑誌）
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Constructing an in silico three-class predictor of human intestinal absorption with Caco-2 permeability and dried-DMSO solubility
Esaki T, Ohashi R, Watanabe R, Natsume-Kitatani Y, Kawashima H, Nagao C, Komura H, Mizuguchi K
Journal of Pharmaceutical Sciences Vol. 108 No. 11 p. 3630-3639 2019年7月 研究論文（学術雑誌）
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Computational Model To Predict the Fraction of Unbound Drug in the Brain
Tsuyoshi Esaki, Rikiya Ohashi, Reiko Watanabe, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Chioko Nagao, Kenji Mizuguchi
Journal of Chemical Information and Modeling Vol. 59 No. 7 p. 3251-3261 2019年7月 研究論文（学術雑誌）
出版者・発行元：American Chemical Society ({ACS})
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Development of Simplified in Vitro P-Glycoprotein Substrate Assay and in Silico Prediction Models To Evaluate Transport Potential of P-Glycoprotein
Rikiya Ohashi, Reiko Watanabe, Tsuyoshi Esaki, Tomomi Taniguchi, Nao Torimoto-Katori, Tomoko Watanabe, Yuko Ogasawara, Tsuyoshi Takahashi, Mikiko Tsukimoto, Kenji Mizuguchi
Molecular Pharmaceutics Vol. 16 No. 5 p. 1851-1863 2019年4月 研究論文（学術雑誌）
出版者・発行元：American Chemical Society ({ACS})
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High-Contrast Facile Imaging with Target-Directing Fluorescent Molecular Rotors, the N3-Modified Thioflavin T Derivatives
Yuka Kataoka, Hiroto Fujita, Arina Afanaseva, Chioko Nagao, Kenji Mizuguchi, Yuuya Kasahara, Satoshi Obika, Masayasu Kuwahara
Biochemistry Vol. 58 No. 6 p. 493-498 2019年2月 研究論文（学術雑誌）
出版者・発行元：American Chemical Society ({ACS})
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Assessing drug target suitability using TargetMine
Yi-An Chen, Erika Yogo, Naoko Kurihara, Tomoshige Ohno, Chihiro Higuchi, Masatomo Rokushima, Kenji Mizuguchi
F1000Research Vol. 8 p. 233-233 2019年2月 研究論文（学術雑誌）
出版者・発行元：F1000 ( Faculty of 1000 Ltd)
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Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing
Yasuharu Takahashi, Jonguk Park, Koji Hosomi, Tomonori Yamada, Ayaka Kobayashi, Yuji Yamaguchi, Susumu Iketani, Jun Kunisawa, Kenji Mizuguchi, Nobuko Maeda, Tomoko Ohshima
Journal of Oral Biosciences Vol. 61 No. 2 p. 120-128 2019年1月1日 研究論文（学術雑誌）
出版者・発行元：
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Prediction of the secondary structure of short DNA aptamers
Arina Afanasyeva, Chioko Nagao, Kenji Mizuguchi
Biophysics and Physicobiology Vol. 16 No. 0 p. 287-294 2019年 研究論文（学術雑誌）
出版者・発行元：Biophysical Society of Japan
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Data Curation can Improve the Prediction Accuracy of Metabolic Intrinsic Clearance.
Esaki T, Watanabe R, Kawashima H, Ohashi R, Natsume-Kitatani Y, Nagao C, Mizuguchi K
Molecular informatics Vol. 38 No. 1-2 2018年9月 研究論文（学術雑誌）
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Predicting Fraction Unbound in Human Plasma from Chemical Structure: Improved Accuracy in the Low Value Ranges.
Watanabe R, Esaki T, Kawashima H, Natsume-Kitatani Y, Nagao C, Ohashi R, Mizuguchi K
Molecular pharmaceutics Vol. 15 No. 11 p. 5302-5311 2018年9月 研究論文（学術雑誌）
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Double deletion of tetraspanins CD9 and CD81 in mice leads to a syndrome resembling accelerated aging.
Yingji Jin, Yoshito Takeda, Yasushi Kondo, Lokesh P Tripathi, Sujin Kang, Hikari Takeshita, Hanako Kuhara, Yohei Maeda, Masayoshi Higashiguchi, Kotaro Miyake, Osamu Morimura, Taro Koba, Yoshitomo Hayama, Shohei Koyama, Kaori Nakanishi, Takeo Iwasaki, Satoshi Tetsumoto, Kazuyuki Tsujino, Muneyoshi Kuroyama, Kota Iwahori, Haruhiko Hirata, Takayuki Takimoto, Mayumi Suzuki, Izumi Nagatomo, Ken Sugimoto, Yuta Fujii, Hiroshi Kida, Kenji Mizuguchi, Mari Ito, Takashi Kijima, Hiromi Rakugi, Eisuke Mekada, Isao Tachibana, Atsushi Kumanogoh
Scientific reports Vol. 8 No. 1 p. 5145-5145 2018年3月23日 研究論文（学術雑誌）
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An Antigen-Free, Plasmacytoid Dendritic Cell-Targeting Immunotherapy To Bolster Memory CD8+ T Cells in Nonhuman Primates.
Yuji Masuta, Takuya Yamamoto, Yayoi Natsume-Kitatani, Tomohiro Kanuma, Eiko Moriishi, Kouji Kobiyama, Kenji Mizuguchi, Yasuhiro Yasutomi, Ken J Ishii
Journal of immunology (Baltimore, Md. : 1950) Vol. 200 No. 6 p. 2067-2075 2018年3月15日 研究論文（学術雑誌）
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PSOPIA: Toward more reliable protein-protein interaction prediction from sequence information
Yoichi Murakami, Kenji Mizuguchi
ICIIBMS 2017 - 2nd International Conference on Intelligent Informatics and Biomedical Sciences Vol. 2018- p. 255-261 2018年2月2日 研究論文（国際会議プロシーディングス）
出版者・発行元：Institute of Electrical and Electronics Engineers Inc.
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Essential role of CARD14 in murine experimental psoriasis
Mayuri Tanaka, Kouji Kobiyama, Tetsuya Honda, Kozue Uchio-Yamada, Yayoi Natsume-Kitatani, Kenji Mizuguchi, Kenji Kabashima, Ken J. Ishii
Journal of Immunology Vol. 200 No. 1 p. 71-81 2018年1月1日 研究論文（学術雑誌）
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Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism
Shandar Ahmad, Philip Prathipati, Lokesh P. Tripathi, Yi-An Chen, Ajay Arya, Yoichi Murakami, Kenji Mizuguchi
Nucleic Acids Research Vol. 46 No. 1 p. 54-70 2018年 研究論文（学術雑誌）
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Quantifying the relative immune cell activation from whole tissue/organ-derived differentially expressed gene data
Edward Wijaya, Yoshinobu Igarashi, Noriyuki Nakatsu, Yasunari Haseda, Joel Billaud, Yi-An Chen, Kenji Mizuguchi, Hiroshi Yamada, Ken Ishii, Taiki Aoshi
SCIENTIFIC REPORTS Vol. 7 No. 1 2017年10月 研究論文（学術雑誌）
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Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity.
Koji Hosomi, Harumi Ohno, Haruka Murakami, Yayoi Natsume-Kitatani, Kumpei Tanisawa, Soichiro Hirata, Hidehiko Suzuki, Takahiro Nagatake, Tomomi Nishino, Kenji Mizuguchi, Motohiko Miyachi, Jun Kunisawa
Scientific reports Vol. 7 No. 1 p. 4339-4339 2017年6月28日 研究論文（学術雑誌）
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Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences
Munazah Andrabi, Andrew Paul Hutchins, Diego Miranda-Saavedra, Hidetoshi Kono, Ruth Nussinov, Kenji Mizuguchi, Shandar Ahmad
SCIENTIFIC REPORTS Vol. 7 No. 1 2017年6月 研究論文（学術雑誌）
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Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates
Johan Nystroem-Persson, Yayoi Natsume-Kitatani, Yoshinobu Igarashi, Daisuke Satoh, Kenji Mizuguchi
SCIENTIFIC REPORTS Vol. 7 No. 1 2017年5月 研究論文（学術雑誌）
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A-kinase anchoring protein BIG3 coordinates oestrogen signalling in breast cancer cells
Tetsuro Yoshimaru, Masaya Ono, Yoshimi Bando, Yi-An Chen, Kenji Mizuguchi, Hiroshi Shima, Masato Komatsu, Issei Imoto, Keisuke Izumi, Junko Honda, Yasuo Miyoshi, Mitsunori Sasa, Toyomasa Katagiri
NATURE COMMUNICATIONS Vol. 8 2017年5月 研究論文（学術雑誌）
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Classification of idiopathic interstitial pneumonias using anti-myxovirus resistance-protein 1 autoantibody
Yoshimasa Hamano, Hiroshi Kida, Shoichi Ihara, Akihiro Murakami, Masahiro Yanagawa, Ken Ueda, Osamu Honda, Lokesh P. Tripathi, Toru Arai, Masaki Hirose, Toshimitsu Hamasaki, Yukihiro Yano, Tetsuya Kimura, Yasuhiro Kato, Hyota Takamatsu, Tomoyuki Otsuka, Toshiyuki Minami, Haruhiko Hirata, Koji Inoue, Izumi Nagatomo, Yoshito Takeda, Masahide Mori, Hiroyoshi Nishikawa, Kenji Mizuguchi, Takashi Kijima, Masanori Kitaichi, Noriyuki Tomiyama, Yoshikazu Inoue, Atsushi Kumanogoh
SCIENTIFIC REPORTS Vol. 7 2017年2月 研究論文（学術雑誌）
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Syndecan-4 as a biomarker to predict clinical outcome for glioblastoma multiforme treated with WT1 peptide vaccine.
Satoshi Takashima, Yoshihiro Oka, Fumihiro Fujiki, Soyoko Morimoto, Hiroko Nakajima, Yoshiki Nakae, Jun Nakata, Sumiyuki Nishida, Naoki Hosen, Naoya Tatsumi, Kenji Mizuguchi, Naoya Hashimoto, Yusuke Oji, Akihiro Tsuboi, Atsushi Kumanogoh, Haruo Sugiyama
Future science OA Vol. 2 No. 4 2016年12月 研究論文（学術雑誌）
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Conformational plasticity of JRAB/MICAL-L2 provides "law and order" in collective cell migration
Ayuko Sakane, Shin Yoshizawa, Masaomi Nishimura, Yuko Tsuchiya, Natsuki Matsushita, Kazuhisa Miyake, Kazuki Horikawa, Issei Imoto, Chiharu Mizuguchi, Hiroyuki Saito, Takato Ueno, Sachi Matsushita, Hisashi Haga, Shinji Deguchi, Kenji Mizuguchi, Hideo Yokota, Takuya Sasaki
MOLECULAR BIOLOGY OF THE CELL Vol. 27 No. 20 p. 3095-3108 2016年10月 研究論文（学術雑誌）
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Improved pose and affinity predictions using different protocols tailored on the basis of data availability
Philip Prathipati, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN Vol. 30 No. 9 p. 817-828 2016年9月 研究論文（学術雑誌）
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Ligand-induced Ordering of the C-terminal Tail Primes STING for Phosphorylation by TBK1
Yuko Tsuchiya, Nao Jounai, Fumihiko Takeshita, Ken J. Ishii, Kenji Mizuguchi
EBIOMEDICINE Vol. 9 p. 87-96 2016年7月 研究論文（学術雑誌）
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Integration of Ligand and Structure Based Approaches for CSAR-2014
Philip Prathipati, Kenji Mizuguchi
JOURNAL OF CHEMICAL INFORMATION AND MODELING Vol. 56 No. 6 p. 974-987 2016年6月 研究論文（学術雑誌）
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The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops
Yuko Tsuchiya, Kenji Mizuguchi
PROTEIN SCIENCE Vol. 25 No. 4 p. 815-825 2016年4月 研究論文（学術雑誌）
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An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework
Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION Vol. 2016 2016年3月 研究論文（学術雑誌）
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Retinoblastoma-binding Protein 4-regulated Classical Nuclear Transport Is Involved in Cellular Senescence
Akira Tsujii, Yoichi Miyamoto, Tetsuji Moriyama, Yuko Tsuchiya, Chikashi Obuse, Kenji Mizuguchi, Masahiro Oka, Yoshihiro Yoneda
JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 290 No. 49 p. 29375-29388 2015年12月 研究論文（学術雑誌）
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Profiles of microRNA networks in intestinal epithelial cells in a mouse model of colitis
Juneyoung Lee, Eun Jeong Park, Yoshikazu Yuki, Shandar Ahmad, Kenji Mizuguchi, Ken J. Ishii, Motomu Shimaoka, Hiroshi Kiyono
SCIENTIFIC REPORTS Vol. 5 2015年12月 研究論文（学術雑誌）
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Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target
Shuntaro Chiba, Kazuyoshi Ikeda, Takashi Ishida, M. Michael Gromiha, Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama, Kun-Yi Hsin, Hiroaki Kitano, Kazuki Yamamoto, Nobuyoshi Sugaya, Koya Kato, Tatsuya Okuno, George Chikenji, Masahiro Mochizuki, Nobuaki Yasuo, Ryunosuke Yoshino, Keisuke Yanagisawa, Tomohiro Ban, Reiji Teramoto, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, Philip Prathipati, Junichi Ito, Yuko Tsuchiya, Kenji Mizuguchi, Teruki Honma, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima
SCIENTIFIC REPORTS Vol. 5 2015年11月 研究論文（学術雑誌）
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Two distinct effector memory cell populations of WT1 (Wilms' tumor gene 1)-specific cytotoxic T lymphocytes in acute myeloid leukemia patients
Yoshiki Nakae, Yoshihiro Oka, Fumihiro Fujiki, Soyoko Morimoto, Toshio Kamiya, Satoshi Takashima, Jun Nakata, Sumiyuki Nishida, Hiroko Nakajima, Naoki Hosen, Akihiro Tsuboi, Taiichi Kyo, Yusuke Oji, Kenji Mizuguchi, Atsushi Kumanogoh, Haruo Sugiyama
CANCER IMMUNOLOGY IMMUNOTHERAPY Vol. 64 No. 7 p. 791-804 2015年7月 研究論文（学術雑誌）
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BIG3 Inhibits the Estrogen-Dependent Nuclear Translocation of PHB2 via Multiple Karyopherin-Alpha Proteins in Breast Cancer Cells
Nam-Hee Kim, Tetsuro Yoshimaru, Yi-An Chen, Taisuke Matsuo, Masato Komatsu, Yasuo Miyoshi, Eiji Tanaka, Mitsunori Sasa, Kenji Mizuguchi, Toyomasa Katagiri
PLOS ONE Vol. 10 No. 6 2015年6月 研究論文（学術雑誌）
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Pathway-Based Analysis of Genome-Wide siRNA Screens Reveals the Regulatory Landscape of App Processing (10, e0115369, 2015)
Luiz Miguel Camargo, Xiaohua Douglas Zhang, Patrick Loerch, Ramon Miguel Caceres, Shane D. Marine, Paolo Uva, Marc Ferrer, Emanuele de Rinaldis, David J. Stone, John Majercak, William J. Ray, Chen Yi-An, Mark S. Shearman, Kenji Mizuguchi
PLOS ONE Vol. 10 No. 6 2015年6月
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Pathway-Based Analysis of Genome-Wide siRNA Screens Reveals the Regulatory Landscape of App Processing
Luiz Miguel Camargo, Xiaohua Douglas Zhang, Patrick Loerch, Ramon Miguel Caceres, Shane D. Marine, Paolo Uva, Marc Ferrer, Emanuele de Rinaldis, David J. Stone, John Majercak, William J. Ray, Chen Yi-An, Mark S. Shearman, Kenji Mizuguchi
PLOS ONE Vol. 10 No. 2 2015年2月 研究論文（学術雑誌）
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PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs
Jun-ichi Ito, Kazuyoshi Ikeda, Kazunori Yamada, Kenji Mizuguchi, Kentaro Tomii
NUCLEIC ACIDS RESEARCH Vol. 43 No. D1 p. D392-D398 2015年1月 研究論文（学術雑誌）
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Altered Actions of Memantine and NMDA-Induced Currents in a New Grid2-Deleted Mouse Line
Ayako Kumagai, Akira Fujita, Tomoki Yokoyama, Yuki Nonobe, Yasuhiro Hasaba, Tsutomu Sasaki, Yumi Itoh, Minako Koura, Osamu Suzuki, Shigeki Adachi, Haruko Ryo, Arihiro Kohara, Lokesh P. Tripathi, Masato Sanosaka, Toshiki Fukushima, Hiroyuki Takahashi, Kazuo Kitagawa, Yasuo Nagaoka, Hidehisa Kawahara, Kenji Mizuguchi, Taisei Nomura, Junichiro Matsuda, Toshihide Tabata, Hiroshi Takemori
Genes Vol. 5 No. 4 p. 1095-1114 2014年12月 研究論文（学術雑誌）
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Dextran sulfate-resistant A/Puerto Rico/8/34 influenza virus is associated with the emergence of specific mutations in the neuraminidase glycoprotein
Hiroshi Yamada, Chioko Nagao, Ahmad M. Haredy, Yasuko Mori, Kenji Mizuguchi, Koichi Yamanishi, Shigefumi Okamoto
ANTIVIRAL RESEARCH Vol. 111 p. 69-77 2014年11月 研究論文（学術雑誌）
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High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations
Hiroki Shirai, Kazuyoshi Ikeda, Kazuo Yamashita, Yuko Tsuchiya, Jamica Sarmiento, Shide Liang, Tatsuaki Morokata, Kenji Mizuguchi, Junichi Higo, Daron M. Standley, Haruki Nakamura
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Vol. 82 No. 8 p. 1624-1635 2014年8月 研究論文（学術雑誌）
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Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type -helical structure
Yi-An Chen, Yoichi Murakami, Shandar Ahmad, Tetsuro Yoshimaru, Toyomasa Katagiri, Kenji Mizuguchi
BMC Research Notes Vol. 7 No. 1 2014年7月6日 研究論文（学術雑誌）
出版者・発行元：BioMed Central Ltd.
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Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators
Yoichi Murakami, Kenji Mizuguchi
BMC BIOINFORMATICS Vol. 15 No. 1 2014年6月 研究論文（学術雑誌）
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Integrated Pathway Clusters with Coherent Biological Themes for Target Prioritisation
Yi-An Chen, Lokesh P. Tripathi, Benoit H. Dessailly, Johan Nystroem-Persson, Shandar Ahmad, Kenji Mizuguchi
PLOS ONE Vol. 9 No. 6 2014年6月 研究論文（学術雑誌）
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Crystal structure of FtsA from Staphylococcus aureus
Junso Fujita, Yoko Maeda, Chioko Nagao, Yuko Tsuchiya, Yuma Miyazaki, Mika Hirose, Eiichi Mizohata, Yoshimi Matsumoto, Tsuyoshi Inoue, Kenji Mizuguchi, Hiroyoshi Matsumura
FEBS LETTERS Vol. 588 No. 10 p. 1879-1885 2014年5月 研究論文（学術雑誌）
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Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability
Munazah Andrabi, Kenji Mizuguchi, Shandar Ahmad
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Vol. 82 No. 5 p. 841-857 2014年5月 研究論文（学術雑誌）
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Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome
Naoki Takemura, Takumi Kawasaki, Jun Kunisawa, Shintaro Sato, Aayam Lamichhane, Kouji Kobiyama, Taiki Aoshi, Junichi Ito, Kenji Mizuguchi, Thangaraj Karuppuchamy, Kouta Matsunaga, Shoichiro Miyatake, Nobuko Mori, Tohru Tsujimura, Takashi Satoh, Yutaro Kumagai, Taro Kawai, Daron M. Standley, Ken J. Ishii, Hiroshi Kiyono, Shizuo Akira, Satoshi Uematsu
NATURE COMMUNICATIONS Vol. 5 2014年3月 研究論文（学術雑誌）
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Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests
Chioko Nagao, Nozomi Nagano, Kenji Mizuguchi
PLOS ONE Vol. 9 No. 1 2014年1月 研究論文（学術雑誌）
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Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform
Johan Nystroem-Persson, Yoshinobu Igarashi, Maori Ito, Mizuki Morita, Noriyuki Nakatsu, Hiroshi Yamada, Kenji Mizuguchi
BIOINFORMATICS Vol. 29 No. 23 p. 3080-3086 2013年12月 研究論文（学術雑誌）
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Expression, purification, crystallization and preliminary crystallographic study of FtsA from methicillin-resistant Staphylococcus aureus
Junso Fujita, Yuma Miyazaki, Mika Hirose, Chioko Nagao, Eiichi Mizohata, Yoshimi Matsumoto, Kenji Mizuguchi, Tsuyoshi Inoue, Hiroyoshi Matsumura
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS Vol. 69 No. 8 p. 895-898 2013年8月 研究論文（学術雑誌）
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Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter
Prabha Tiwari, Lokesh P. Tripathi, Teppei Nishikawa-Matsumura, Shandar Ahmad, Soken-Nakazawa J. Song, Tomoyasu Isobe, Kenji Mizuguchi, Kazuyuki Yoshizaki
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS Vol. 1830 No. 6 p. 3650-3655 2013年6月 研究論文（学術雑誌）
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Understanding the Biological Context of NS5A-Host Interactions in HCV Infection: A Network-Based Approach
Lokesh P. Tripathi, Hiroto Kambara, Yi-An Chen, Yorihiro Nishimura, Kohji Moriishi, Toru Okamoto, Eiji Morita, Takayuki Abe, Yoshio Mori, Yoshiharu Matsuura, Kenji Mizuguchi
JOURNAL OF PROTEOME RESEARCH Vol. 12 No. 6 p. 2537-2551 2013年6月 研究論文（学術雑誌）
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Functional site plasticity in domain superfamilies
Benoit H. Dessailly, Natalie L. Dawson, Kenji Mizuguchi, Christine A. Orengo
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS Vol. 1834 No. 5 p. 874-889 2013年5月 研究論文（学術雑誌）
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The Chemotherapeutic Agent DMXAA as a Unique IRF3-Dependent Type-2 Vaccine Adjuvant
Choon Kit Tang, Taiki Aoshi, Nao Jounai, Junichi Ito, Keiichi Ohata, Kouji Kobiyama, Benoit H. Dessailly, Etsushi Kuroda, Shizuo Akira, Kenji Mizuguchi, Cevayir Coban, Ken J. Ishii
PLOS ONE Vol. 8 No. 3 2013年3月 研究論文（学術雑誌）
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Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells.
Tetsuro Yoshimaru, Masato Komatsu, Taisuke Matsuo, Yi-An Chen, Yoichi Murakami, Kenji Mizuguchi, Eiichi Mizohata, Tsuyoshi Inoue, Miki Akiyama, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Yasuo Miyoshi, Mitsunori Sasa, Yusuke Nakamura, Toyomasa Katagiri
Nature communications Vol. 4 p. 2443-2443 2013年 研究論文（学術雑誌）
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Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions
Chioko Nagao, Nozomi Izako, Shinji Soga, Samia Haseeb Khan, Shigeki Kawabata, Hiroki Shirai, Kenji Mizuguchi
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Vol. 80 No. 10 p. 2426-2436 2012年10月 研究論文（学術雑誌）
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Proteomic Analysis of Hepatitis C Virus (HCV) Core Protein Transfection and Host Regulator PA28 gamma Knockout in HCV Pathogenesis: A Network-Based Study
Lokesh P. Tripathi, Hiroto Kambara, Kohji Moriishi, Eiji Morita, Takayuki Abe, Yoshio Mori, Yi-An Chen, Yoshiharu Matsuura, Kenji Mizuguchi
JOURNAL OF PROTEOME RESEARCH Vol. 11 No. 7 p. 3664-3679 2012年7月 研究論文（学術雑誌）
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Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes
Tim R. Blower, Francesca L. Short, Feng Rao, Kenji Mizuguchi, Xue Y. Pei, Peter C. Fineran, Ben F. Luisi, George P. C. Salmond
NUCLEIC ACIDS RESEARCH Vol. 40 No. 13 p. 6158-6173 2012年7月 研究論文（学術雑誌）
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Inhibitory Roles of Signal Transducer and Activator of Transcription 3 in Antitumor Immunity during Carcinogen-Induced Lung Tumorigenesis
Shoichi Ihara, Hiroshi Kida, Hisashi Arase, Lokesh P. Tripathi, Yi-An Chen, Tetsuya Kimura, Mitsuhiro Yoshida, Yozo Kashiwa, Haruhiko Hirata, Reiko Fukamizu, Ruriko Inoue, Kana Hasegawa, Sho Goya, Ryo Takahashi, Toshiyuki Minami, Kazuyuki Tsujino, Mayumi Suzuki, Satoshi Kohmo, Koji Inoue, Izumi Nagatomo, Yoshito Takeda, Takashi Kijima, Kenji Mizuguchi, Isao Tachibana, Atsushi Kumanogoh
CANCER RESEARCH Vol. 72 No. 12 p. 2990-2999 2012年6月 研究論文（学術雑誌）
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Sagace: A web-based search engine for biomedical databases in Japan
Mizuki Morita, Yoshinobu Igarashi, Maori Ito, Yi-An Chen, Chioko Nagao, Yuki Sakaguchi, Ryuichi Sakate, Tohru Masui, Kenji Mizuguchi
BMC Research Notes Vol. 5 2012年 研究論文（学術雑誌）
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Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data
Mizuki Morita, AVSK M. Katta, Shandar Ahmad, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi
BMC Biophysics Vol. 4 No. 1 2011年12月14日 研究論文（学術雑誌）
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Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data
Shandar Ahmad, Kenji Mizuguchi
PLOS ONE Vol. 6 No. 12 2011年12月 研究論文（学術雑誌）
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Prediction of dinucleotide-specific RNA-binding sites in proteins
Michael Fernandez, Yutaro Kumagai, Daron M. Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad
BMC BIOINFORMATICS Vol. 12 No. S-13 2011年11月 研究論文（学術雑誌）
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Using Knowledge of Protein Structural Constraints to Predict the Evolution of HIV-1
Simon G. Williams, Rachit Madan, Matthew G. S. Norris, John Archer, Kenji Mizuguchi, David L. Robertson, Simon C. Lovell
JOURNAL OF MOLECULAR BIOLOGY Vol. 410 No. 5 p. 1023-1034 2011年7月 研究論文（学術雑誌）
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Identification of novel functional organic anion-transporting polypeptide 1B3 polymorphisms and assessment of substrate specificity
Ute I. Schwarz, Henriette E. Meyer Zu Schwabedissen, Rommel G. Tirona, Atsuko Suzuki, Brenda F. Leake, Younes Mokrab, Kenji Mizuguchi, Richard H. Ho, Richard B. Kim
PHARMACOGENETICS AND GENOMICS Vol. 21 No. 3 p. 103-114 2011年3月 研究論文（学術雑誌）
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TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery
Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi
PLOS ONE Vol. 6 No. 3 2011年3月 研究論文（学術雑誌）
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A structural dissection of amino acid substitutions in helical transmembrane proteins
Younes Mokrab, Tim J. Stevens, Kenji Mizuguchi
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Vol. 78 No. 14 p. 2895-2907 2010年11月 研究論文（学術雑誌）
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Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores
Sukanta Mondal, Chioko Nagao, Kenji Mizuguchi
PROTEIN ENGINEERING DESIGN & SELECTION Vol. 23 No. 11 p. 859-869 2010年11月 研究論文（学術雑誌）
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Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins
Shandar Ahmad, Yumlembam Hemajit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi
BMC BIOINFORMATICS Vol. 11 2010年10月 研究論文（学術雑誌）
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On nucleotide solvent accessibility in RNA structure
Yumlembam H. Singh, Munazah Andrabi, Bratati Kahali, Tapash Chandra Ghosh, Kenji Mizuguchi, Alex V. Kochetov, Shandar Ahmad
GENE Vol. 463 No. 1-2 p. 41-48 2010年9月 研究論文（学術雑誌）
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Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies
Chioko Nagao, Nozomi Nagano, Kenji Mizuguchi
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Vol. 78 No. 10 p. 2369-2384 2010年8月 研究論文（学術雑誌）
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CCRXP: exploring clusters of conserved residues in protein structures
Shandar Ahmad, Ozlem Keskin, Kenji Mizuguchi, Akinori Sarai, Ruth Nussinov
NUCLEIC ACIDS RESEARCH Vol. 38 No. SUPPL. 2 p. W398-W401 2010年7月 研究論文（学術雑誌）
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Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites.
Yoichi Murakami, Kenji Mizuguchi
Bioinformatics Vol. 26 No. 15 p. 1841-1848 2010年6月6日 研究論文（学術雑誌）
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Creation of lysine-deficient mutant lymphotoxin-alpha with receptor selectivity by using a phage display system
Yasuo Yoshioka, Hikaru Watanabe, Tomohiro Morishige, Xinglei Yao, Shinji Ikemizu, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi, Shin-ichi Tsunoda, Yasuo Tsutsumi, Yohei Mukai, Naoki Okada, Shinsaku Nakagawa
BIOMATERIALS Vol. 31 No. 7 p. 1935-1943 2010年3月 研究論文（学術雑誌）
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Network based analysis of hepatitis C virus Core and NS4B protein interactions
Lokesh P. Tripathi, Chikako Kataoka, Shuhei Taguwa, Kohji Moriishi, Yoshio Mori, Yoshiharu Matsuura, Kenji Mizuguchi
MOLECULAR BIOSYSTEMS Vol. 6 No. 12 p. 2539-2553 2010年 研究論文（学術雑誌）
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Structural insights into the enzyme mechanism of a new family of d-2-hydroxyacid dehydrogenases, a close homolog of 2-ketopantoate reductase.
Mondal S, Mizuguchi K
Genome informatics. International Conference on Genome Informatics Vol. 23 No. 1 p. 98-105 2009年10月1日 研究論文（学術雑誌）
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Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks
Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai, Shandar Ahmad
BMC STRUCTURAL BIOLOGY Vol. 9 2009年5月 研究論文（学術雑誌）
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Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks
Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai, Shandar Ahmad
BMC Structural Biology Vol. 9 2009年 研究論文（学術雑誌）
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Molecular Basis for SUMOylation-dependent Regulation of DNA Binding Activity of Heat Shock Factor 2
Yukihiro Tateishi, Mariko Ariyoshi, Ryuji Igarashi, Hideyuki Hara, Kenji Mizuguchi, Azusa Seto, Akira Nakai, Tetsuro Kokubo, Hidehito Tochio, Masahiro Shirakawa
JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 284 No. 4 p. 2435-2447 2009年1月 研究論文（学術雑誌）
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Lipophobicity and the residue environments of the transmembrane alpha-helical bundle
Younes Mokrab, Thn J. Stevens, Kenji Mizuguchi
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Vol. 74 No. 1 p. 32-49 2009年1月 研究論文（学術雑誌）
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Docking of cytochrome c(6) and plastocyanin to the aa(3)-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum
Sarah E. Hart, Christopher J. Howe, Kenji Mizuguchi, Juan Fernandez-Recio
PROTEIN ENGINEERING DESIGN & SELECTION Vol. 21 No. 12 p. 689-698 2008年12月 研究論文（学術雑誌）
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Drosophila Neurotrophins Reveal a Common Mechanism for Nervous System Formation
Bangfu Zhu, Jenny A. Pennack, Peter McQuilton, Manuel G. Forero, Kenji Mizuguchi, Ben Sutcliffe, Chun-Jing Gu, Janine C. Fenton, Alicia Hidalgo
PLOS BIOLOGY Vol. 6 No. 11 p. 2476-2495 2008年11月 研究論文（学術雑誌）
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A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins
Xavier Bailly, Stefano Vanin, Christine Chabasse, Kenji Mizuguchi, Serge N. Vinogradov
BMC EVOLUTIONARY BIOLOGY Vol. 8 No. 1 2008年9月
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Exploring ligand recognition and ion flow in comparative models of the human GABA type A receptor
Younes Mokrab, Vassiliy N. Bavro, Kenji Mizuguchi, N. P. Todorov, Ian L. Martin, Susan M. J. Dunn, S. L. Chan, P. -L. Chau
JOURNAL OF MOLECULAR GRAPHICS & MODELLING Vol. 26 No. 4 p. 760-774 2007年11月 研究論文（学術雑誌）
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A model of globin evolution
Serge N. Vinogradov, David Hoogewijs, Xavier Bailly, Kenji Mizuguchi, Sylvia Dewilde, Luc Moens, Jacques R. Vanfleteren
GENE Vol. 398 No. 1-2 p. 132-142 2007年8月 研究論文（学術雑誌）
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Environment specific substitution tables for thermophilic proteins
K. Mizuguchi, M. Sele, M. V. Cubellis
BMC BIOINFORMATICS Vol. 8 2007年 研究論文（学術雑誌）
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Disrupted in schizophrenia 1 interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia
L. M. Camargo, V. Collura, J-C Rain, K. Mizuguchi, H. Hermjakob, S. Kerrien, T. P. Bonnert, P. J. Whiting, N. J. Brandon
MOLECULAR PSYCHIATRY Vol. 12 No. 1 p. 74-86 2007年1月 研究論文（学術雑誌）
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FlyMine: an integrated database for Drosophila and Anopheles genomics
Rachel Lyne, Richard Smith, Kim Rutherford, Matthew Wakeling, Andrew Varley, Francois Guillier, Hilde Janssens, Wenyan Ji, Peter Mclaren, Philip North, Debashis Rana, Tom Riley, Julie Sullivan, Xavier Watkins, Mark Woodbridge, Kathryn Lilley, Steve Russell, Michael Ashburner, Kenji Mizuguchi, Gos Micklem
GENOME BIOLOGY Vol. 8 No. 7 2007年 研究論文（学術雑誌）
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The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97
Kumiko Shiozawa, Natsuko Goda, Toshiyuki Shimizu, Kenji Mizuguchi, Naomi Kondo, Nobuyuki Shimozawa, Masahiro Shirakawa, Hidekazu Hiroaki
FEBS JOURNAL Vol. 273 No. 21 p. 4959-4971 2006年11月 研究論文（学術雑誌）
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The guanidino-group modifying enzymes: Structural basis for their diversity and commonality
Hiroki Shirai, Younes Mokrab, Kenji Mizuguchi
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Vol. 64 No. 4 p. 1010-1023 2006年9月 研究論文（学術雑誌）
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A novel mechanism of allosteric regulation of archaeal phosphoenolpyruvate carboxylase: a combined approach to structure-based alignment and model assessment
Hiroyoshi Matsumura, Katsura Izui, Kenji Mizuguchi
PROTEIN ENGINEERING DESIGN & SELECTION Vol. 19 No. 9 p. 409-419 2006年9月 研究論文（学術雑誌）
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Organic anion transporting polypeptides of the OATP/SLCO superfamily: Identification of new members in nonmammalian species, comparative modeling and a potential transport mode
F Meier-Abt, Y Mokrab, K Mizuguchi
JOURNAL OF MEMBRANE BIOLOGY Vol. 208 No. 3 p. 213-227 2006年4月20日 研究論文（学術雑誌）
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Functional restraints on the patterns of amino acid substitutions: Application to sequence-structure homology recognition
Chelliah, V, T Blundell, K Mizuguchi
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Vol. 61 No. 4 p. 722-731 2005年12月 研究論文（学術雑誌）
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Amino-acid substitutions in membrane proteins: Applications to homology recognition and comparative modelling
Younes Mokrab, Kenji Mizuguchi
BMC BIOINFORMATICS Vol. 6 No. S-3 2005年9月
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A model of a transmembrane drug-efflux pump from Gram-negative bacteria
J Fernandez-Recio, F Walas, L Federici, JV Pratap, VN Bavro, RN Miguel, K Mizuguchi, B Luisi
FEBS LETTERS Vol. 578 No. 1-2 p. 5-9 2004年12月 研究論文（学術雑誌）
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Distinct protein interfaces in transmembrane domains suggest an in vivo folding model
TJ Stevens, K Mizuguchi, IT Arkin
PROTEIN SCIENCE Vol. 13 No. 11 p. 3028-3037 2004年11月 研究論文（学術雑誌）
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HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database
LA Stebbings, K Mizuguchi
NUCLEIC ACIDS RESEARCH Vol. 32 No. Database-Issue p. D203-D207 2004年1月 研究論文（学術雑誌）
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Prediction of the structure and function of AstA and AstB, the first two enzymes of the arginine succinyltransferase pathway of arginine catabolism
H Shirai, K Mizuguchi
FEBS LETTERS Vol. 555 No. 3 p. 505-510 2003年12月 研究論文（学術雑誌）
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The export of coat protein from enteroaggregative Escherichia coli by a specific ATP-binding cassette transporter system
J Nishi, J Sheikh, K Mizuguchi, B Luisi, Burland, V, A Boutin, DJ Rose, FR Blattner, JP Nataro
JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 278 No. 46 p. 45680-45689 2003年11月 研究論文（学術雑誌）
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Structure of the periplasmic domain of Pseudomonas aeruginosa TolA: evidence for an evolutionary relationship with the TonB transporter protein
M Witty, C Sanz, A Shah, JG Grossmann, K Mizuguchi, RN Perham, B Luisi
EMBO JOURNAL Vol. 21 No. 16 p. 4207-4218 2002年8月 研究論文（学術雑誌）
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The SWIB and the MDM2 domains are homologous and share a common fold
R Bennett-Lovsey, SE Hart, H Shirai, K Mizuguchi
BIOINFORMATICS Vol. 18 No. 4 p. 626-630 2002年4月 研究論文（学術雑誌）
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A family of proteins related to Spätzle, the Toll receptor ligand, are encoded in the Drosophila genome
James S. Parker, Kenji Mizuguchi, Nicholas J. Gay, Nicholas J. Gay
Proteins: Structure, Function and Genetics Vol. 45 No. 1 p. 71-80 2001年10月 研究論文（学術雑誌）
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HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families
PIW de Bakker, A Bateman, DF Burke, RN Miguel, K Mizuguchi, J Shi, H Shirai, TL Blundell
BIOINFORMATICS Vol. 17 No. 8 p. 748-749 2001年8月 研究論文（学術雑誌）
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A novel superfamily of enzymes that catalyze the modification of guanidino groups
H Shirai, TL Blundell, K Mizuguchi
TRENDS IN BIOCHEMICAL SCIENCES Vol. 26 No. 8 p. 465-468 2001年8月 研究論文（学術雑誌）
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FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
JY Shi, TL Blundell, K Mizuguchi
JOURNAL OF MOLECULAR BIOLOGY Vol. 310 No. 1 p. 243-257 2001年6月 研究論文（学術雑誌）
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Sequence-structure homology recognition by iterative alignment refinement and comparative modeling
MG Williams, H Shirai, J Shi, HG Nagendra, J Mueller, K Mizuguchi, RN Miguel, SC Lovell, CA Innis, CM Deane, L Chen, N Campillo, DF Burke, TL Blundell, PIW de Bakker
PROTEINS-STRUCTURE FUNCTION AND GENETICS Vol. 45 No. SUPPL. 5 p. 92-97 2001年 研究論文（学術雑誌）
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Analysis of conservation and substitutions of secondary structure elements within protein superfamilies
K Mizuguchi, TL Blundell
BIOINFORMATICS Vol. 16 No. 12 p. 1111-1119 2000年12月 研究論文（学術雑誌）
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β3: An additional auxiliary subunit of the voltage-sensitive sodium channel that modulates channel gating with distinct kinetics
Kevin Morgan, Edward B. Stevens, Bhaval Shah, Peter J. Cox, Alistair K. Dixon, Kevin Lee, Robert D. Pinnock, John Hughes, Peter J. Richardson, Kenji Mizuguchi, Antony P. Jackson
Proceedings of the National Academy of Sciences of the United States of America Vol. 97 No. 5 p. 2308-2313 2000年2月 研究論文（学術雑誌）
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Characterisation of the gene for Drosophila amphiphysin
A Razzaq, Y Su, JE Mehren, K Mizuguchi, AP Jackson, NJ Gay, CJ O'Kane
GENE Vol. 241 No. 1 p. 167-174 2000年1月 研究論文（学術雑誌）
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A six-stranded double-psi β barrel is shared by several protein superfamilies
Richard M. Castillo, Kenji Mizuguchi, Venugopal Dhanaraj, Armando Albert, Tom L. Blundell, Alexey G. Murzin
Structure Vol. 7 No. 2 p. 227-236 1999年2月 研究論文（学術雑誌）
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An iterative structure-assisted approach to sequence alignment and comparative modeling
DF Burke, CM Deane, HA Nagarajaram, N Campillo, M Martin-Martinez, J Mendes, F Molina, J Perry, BVB Reddy, CM Soares, RE Steward, M Williams, MA Carrondo, TL Blundell, K Mizuguchi
PROTEINS-STRUCTURE FUNCTION AND GENETICS Vol. 37 p. 55-60 1999年 研究論文（学術雑誌）
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A third fibronectin type III domain in the extracellular region of the insulin receptor family
C Marino-Buslje, K Mizuguchi, K Siddle, TL Blundell
FEBS LETTERS Vol. 441 No. 2 p. 331-336 1998年12月 研究論文（学術雑誌）
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Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies
R Sowdhamini, DF Burke, C Deane, JF Huang, K Mizuguchi, HA Nagarajaram, JP Overington, N Srinivasan, RE Steward, TL Blundell
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY Vol. 54 p. 1168-1177 1998年11月 研究論文（学術雑誌）
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CAMPASS: a database of structurally aligned protein superfamilies
R Sowdhamini, DF Burke, JF Huang, K Mizuguchi, HA Nagarajaram, N Srinivasan, RE Steward, TL Blundell
STRUCTURE WITH FOLDING & DESIGN Vol. 6 No. 9 p. 1087-1094 1998年9月 研究論文（学術雑誌）
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Getting knotted: a model for the structure and activation of Spatzle
K Mizuguchi, JS Parker, TL Blundell, NJ Gay
TRENDS IN BIOCHEMICAL SCIENCES Vol. 23 No. 7 p. 239-242 1998年7月 研究論文（学術雑誌）
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HOMSTRAD: A database of protein structure alignments for homologous families
Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, John, P. Overington
Protein Science Vol. 7 p. 2469-2471 1998年1月1日 研究論文（学術雑誌）
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Erratum: Getting knotted: A model for the structure and activation of Spatzle (TIBS 23 (239-242))
K. Mizuguchi
Trends in Biochemical Sciences Vol. 23 No. 9 p. 361-361 1998年1月1日 研究論文（学術雑誌）
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JOY: protein sequence-structure representation and analysis
K Mizuguchi, CM Deane, TL Blundell, MS Johnson, JP Overingon
BIOINFORMATICS Vol. 14 No. 7 p. 617-623 1998年 研究論文（学術雑誌）
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Crystal structure of glutathione synthetase at optimal pH: Domain architecture and structural similarity with other proteins
K Matsuda, K Mizuguchi, T Nishioka, H Kato, N Go, J Oda
PROTEIN ENGINEERING Vol. 9 No. 12 p. 1083-1092 1996年12月 研究論文（学術雑誌）
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Comparison of spatial arrangements of secondary structural elements in proteins
K. Mizuguchi, N. Go
Protein Engineering Vol. 8 No. 4 p. 353-362 1995年 研究論文（学術雑誌）
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Collective motions in proteins investigated by X‐ray diffuse scattering
Proteins: Structure, Function, and Bioinformatics Vol. 18 No. 1 p. 34-48 1994年1月 研究論文（学術雑誌）
