山本博之,
"質量分析インフォマティクスとケモインフォマティクスによる代謝物構造推定"
ケモインフォマティクスにおけるデータ収集の最適化と解析手法,技術情報協会, 2023.
[ link ]
山本博之,
"メタボロミクスにおける「質量分析インフォマティクス」"
バイオインフォマティクスの世界（別冊医学のあゆみ）,医歯薬出版, 2023.
[ link ]
山本博之,
"多変量解析，エンリッチメント解析，代謝マップ描画"
メタボロミクス実践ガイド, 羊土社, 2021.
[ link ]
山本博之,
"メタボロームデータベースの構築の現状と創薬応用"
in silico創薬におけるスクリーニングの高速化・高精度化技術, 技術情報協会, 2018.
[ link ]
Hiroyuki Yamamoto,
"The Principal Component Analysis of Omics Data"
Principal Component Analysis: Methods, Applications and Technology, Nova Science Publishers, 2017.
[ link ]
プレプリント
Misaki Kurata, Hiroyuki Yamamoto, Hiroshi Tsugawa
"OAC-PCA: orthogonal adjustment of confounding effects in principal component analysis for metabolomics data mining", bioRxiv, (2026).
[ link ]
Hiroyuki Yamamoto
"MSplusR: An R Package for Visualization of MS/MS Spectral Data Using UMAP", Jxiv, (2025).
[ link ]
Hiroyuki Yamamoto
"Over-Representation Analysis with Undetected Metabolites", Jxiv, (2024).
[ link ]
Hiroyuki Yamamoto
"Single sample enrichment analysis for mass spectrometry-based omics data", Jxiv, (2023).
[ link ]
Hiroyuki Yamamoto
"One-sided Kernel Principal Component Analysis", Jxiv, (2023).
[ link ]
Hiroyuki Yamamoto
"Multiset partial least squares with rank order of groups for integrating multi-omics data", bioRxiv, (2022).
[ link ]
論文
Tomoaki Nitta, Hiroyuki Yamamoto, Hajime Tomatsu, Rira Matsuta, Kenjiro Kami, Kazunori Sasaki
"Peptidomics and Beyond: Development of a Novel Platform Based on Capillary Electrophoresis–Mass Spectrometry for Metabolomics of Medium-Molecular-Weight Compounds",
Journal of Proteome Research 25, 2669–2676 (2026)
[ link
(Pubmed) ]
Rira Matsuta, Hiroyuki Yamamoto*, Atsushi Fukushima, Sho Tabata, Hideki Makinoshima, Tomoyoshi Soga, Rintaro Saito, Eisuke Hayakawa
"An enrichment-based approach to interpreting metabolomic data using differential metabolomic profiles within the iDMET framework",
BMC Bioinformatics 27, 131 (2026)
[ link
(Pubmed) ] (* corresponding author)
Saki Kiuchi, Mi Hwa Chung, Hina Sakai, Taiki Nakaya, Katsuya Ohbuchi, Kazuya Tsumagari, Koshi Imami, Yasuhiro Otoguro, Tomoaki Nitta, Hiroyuki Yamamoto, Kazunori Sasaki, Hiroshi Tsugawa
"Unraveling anti-inflammatory metabolic signatures of Glycyrrhiza uralensis and isoliquiritigenin through multiomics", npj Systems Biology and Applications 11, 145 (2025)
[ link (Pubmed)]
Yota Tatara+, Hiroyuki Yamamoto+, Kozue Terai, Rira Matsuta, Shuya Kasai, Yoshinori Tamada, Tatsuya Mikami, Koichi Murashita, Ken Itoh
"Multi-marker discovery for mild cognitive impairment in metabolomics using machine learning with a global surrogate model via partial least squares", Metabolomics 21, 164 (2025)
[ link (Pubmed)](+ equally contributed)
Katsutaka Oishi, Yuta Yoshida, Kosuke Kaida, Kozue Terai, Hiroyuki Yamamoto, Atsushi Toyoda
"Potential non-invasive biomarkers of chronic sleep disorders identified by salivary metabolomic profiling among middle-aged Japanese men", Scientific Reports 15, 10980 (2025)
[ link (Pubmed)]
Ryo Uchimido, Kenjiro Kami, Hiroyuki Yamamoto, Ryo Yokoe, Issei Tsuchiya, Yoko Nukui, Yuki Goto, Mariko Hanafusa, Takeo Fujiwara, Kenji Wakabayashi
"Longitudinal Metabolomics Reveals Metabolic Dysregulation Dynamics in Patients with Severe COVID-19", Metabolites 14(12): 656 (2024)
[ link (Pubmed)]
Saki Kiuchi, Yasuhiro Otoguro, Tomoaki Nitta, Mi Hwa Chung, Taiki Nakaya, Yuki Matsuzawa, Katsuya Ohbuchi, Kazunori Sasaki, Hiroyuki Yamamoto*, Hiroshi Tsugawa*
"Using Variable Data-Independent Acquisition for Capillary Electrophoresis-Based Untargeted Metabolomics", Journal of the American Society for Mass Spectrometry, 35(9) (2024) 2118-2127.
[ link (Pubmed)] (* corresponding author)
Tetsuo Sugishita, Masanori Tokunaga, Kenjiro Kami, Kozue Terai, Hiroyuki Yamamoto, Hajime Shinohara, and Yusuke Kinugasa
"Determination of the Minimum Sample Amount for Capillary Electrophoresis-Fourier Transform Mass Spectrometry (CE-FTMS)-Based Metabolomics of Colorectal Cancer Biopsies", Biomedicines, 11(6) (2023) 1706.
[ link ]
Rira Matsuta, Hiroyuki Yamamoto*, Masaru Tomita, Rintaro Saito
"iDMET: network-based approach for integrating differential analysis of cancer metabolomics.", BMC Bioinformatics, 23, 508 (2022).
[ link (Pubmed)] (* corresponding author)
Eiji Sasaki, Hiroyuki Yamamoto, Toru Asari, Rira Matsuta, Seiya Ota, Yuka Kimura, Shizuka Sasaki, Kyota Ishibashi, Yuji Yamamoto, Kenjiro Kami, Masataka Ando, Eiichi Tsuda, Yasuyuki Ishibashi
"Metabolomics with severity of radiographic knee osteoarthritis and early phase synovitis in middle-aged women from the Iwaki Health Promotion Project: a cross-sectional study", Arthritis Research & Therapy, 24 (2022) 145.
[ link (Pubmed)]
Hiroyuki Yamamoto*, Makoto Suzuki, Rira Matsuta, Kazunori Sasaki, Moon-Il Kang, Kenjiro Kami, Yota Tatara, Ken Itoh* and Shigeyuki Nakaji
"Capillary Electrophoresis Mass Spectrometry-Based Metabolomics of Plasma Samples from Healthy Subjects in a Cross-Sectional Japanese Population Study ", Metabolites, 11(5) (2021) 314.
[ link (Pubmed)] (* corresponding author)
Hiroyuki Yamamoto*, Yasumune Nakayama, Hiroshi Tsugawa
"OS-PCA: Orthogonal Smoothed Principal Component Analysis Applied to Metabolome Data", Metabolites, 11(3) (2021) 149.
[ link (Pubmed)] (* corresponding author)
Yuichiro Nishida, Kazutoshi Nishijima, Yosuke Yamada, Hiroaki Tanaka, Akiko Matsumoto, Jianglin Fan, Yoichi Uda, Hajime Tomatsu, Hiroyuki Yamamoto, Kenjiro Kami, Shuji Kitajima and Keitaro Tanaka
"Whole-body insulin resistance and energy expenditure indices, serum lipids, and skeletal muscle metabolome in a state of lipoprotein lipase overexpression.", Metabolomics, 17, (2021) 26.
[ link (Pubmed)]
Hiroshi Tsugawa, Ryo Nakabayashi, Tetsuya Mori, Yutaka Yamada, Mikiko Takahashi, Amit Rai, Ryosuke Sugiyama, Hiroyuki Yamamoto, Taiki Nakaya, Mami Yamazaki, Rik Kooke, Johanna Bac-Molenaar, Nihal Oztolan-Erol, Joost Keurentjes, Masnaori Arita, and Kazuki Saito
"A cheminformatics approach to characterize metabolomes in stable isotope-labeled organisms", Nature Methods, 16 (2019) 295-298.
[ link (Pubmed)]
Kazunori Sasaki, Hitoshi Sagawa, Makoto Suzuki, Hiroyuki Yamamoto, Masaru Tomita, Tomoyoshi Soga, and Yoshiaki Ohashi
"Metabolomics platform with capillary electrophoresis coupled with high-resolution mass spectrometry for plasma analysis", Analytical Chemistry, 91(2) (2019) 1295-1301.
[ link (Pubmed)]
Yoshihisa Wakita, Yumi Shimomura, Yusuke Kitada, Hiroyuki Yamamoto, Yoshiaki Ohashi, Mitsuharu Matsumoto,
"Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut", BMC microbiology, 18:188 (2018)
[ link (Pubmed)]
Noriyuki Kawamura, Kosaku Shinoda, Hajime Sato, Kazunori Sasaki, Makoto Suzuki, Kumi Yamaki, Tamaki Fujimori, Hiroyuki Yamamoto, Douglas Osei-Hyiaman, Yoshiaki Ohashi,
"Plasma metabolome analysis of patients with major depressive disorder.", Psychiatry and Clinical Neurosciences, 72(5) (2018) 349-361.
[ link (Pubmed)]
Hiroyuki Yamamoto,
"PLS-ROG: Partial least squares with rank order of groups.", Journal of Chemometrics, 31(3) (2017) e2883.
[ link / preprint (older version) ]
Hiroyuki Yamamoto+*, Kazunori Sasaki+,
"Metabolomics-based approach for ranking the candidate structures of unidentified peaks in capillary electrophoresis time-of-flight mass spectrometry", Electrophoresis, 38(7) (2017) 1053-1059.
[ link (Pubmed) / cover picture ] (+ equally contributed, * corresponding author)
Hiroyuki Yamamoto+, Kazuhiro Kondo+, Takayuki Tanaka, Takahiko Muramatsu, Hiroo Yoshida, Akira Imaizumi, Kenji Nagao, Yasushi Noguchi, Hiroshi Miyano,
"Reference intervals for plasma-free amino acid in a Japanese population" Annals of Clinical Biochemistry, 53 (2016) 357-364.
[ link (Pubmed)] (+ equally contributed)
Hiroo Yoshida, Kazuhiro Kondo, Hiroyuki Yamamoto, Naoko Kageyama, Shin-ichi Ozawa, Kazutaka Shimbo, Takahiko Muramatsu, Akira Imaizumi, Toshimi Mizukoshi, Junichi Masuda, Daisuke Nakayama, Yoshihiro Hayakawa, Kyoko Watanabe, Kazuo Mukaibatake, Hiroshi Miyano,
"Validation of an analytical method for human plasma free amino acids by high-performance liquid chromatography ionization mass spectrometry using automated precolumn derivatization",
Journal of Chromatography B, 998-999 (2015) 88-96.
[ link ]
Hiroyuki Yamamoto*, Tamaki Fujimori, Hajime Sato, Gen Ishikawa, Kenjiro Kami, Yoshiaki Ohashi,
"Statistical hypothesis testing of factor loading in principal component analysis and its application to metabolite set enrichment analysis"
BMC Bioinformatics, (2014) 15(1):51.
[ link (Pubmed) / errata / preprint (older version) / R package / sample code ] (* corresponding author)
