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vClean: assessing virus sequence contamination in viral genomes. NAR Genom Bioinform. 2025 Jan 7;7(1):lqae185. doi: 10.1093/nargab/lqae185. PMID: 39781513; PMCID: PMC11704788.
2. Nishimura M, Takahashi K, Hosokawa M.
Recent advances in single-cell RNA sequencing of bacteria: Techniques, challenges, and applications. J Biosci Bioeng. 2025;139(5):341–346. doi:10.1016/j.jbiosc.2025.01.008.
3. Suwa S, Ando M, Kashiwagi K, Kyotani T, Hasegawa K, Safiullah H, Kifushi M, Nishikawa Y, Anai T, Ohkama-Ohtsu N, Takeyama H.
Single-cell Raman spectroscopic analysis of bacteroids in soybean nodules to observe the relationship between biomolecular constituents and symbiotic nitrogen fixation activity. Plant Biotechnol (Tokyo). 2025;42(3):335-343. doi:10.5511/plantbiotechnology.25.0414a.
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Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria. ISME Commun. 2025 Jan 1;5(1):ycaf086. doi:10.1093/ismeco/ycaf086.
5. Miyake R, Ando M, Kobayashi K, Nagai K, Ohshiro T, Tomoda H, Takeyama H.
Raman Imaging of an Amphotericin B Potentiator in Single-Cell Saccharomyces cerevisiae. J Phys Chem B. 2025;129(23):5720–5727. doi:10.1021/acs.jpcb.5c02477.
6. Kakiuchi R, Fukaya T, Tamakoshi S, Tsuji S, Fujimori H, Shimazawa M, Tamura T, Hamachi I, Ochi T, Matsunaga H, Takeyama H, Nagasawa H, Hirayama T.
N-Oxide-Driven Heme-Activatable Biomolecule Labeling for Visualization of Labile Heme in Living Cells and Mouse Brain. J Am Chem Soc. 2025;147(31):27484–27493. doi:10.1021/jacs.5c04990.
7. Yoshimoto D, Iuchi H, Taguchi A, Sone K, Tamai K, Mori A, Kitamura S, Duong AQ, Ishizaka A, Kusakabe M, Yamamoto Y, Takase A, Ikemura M, Matsunaga H, Iriyama T, Kukimoto I, Kawazu M, Hamada M, Ushiku T, Oda K, Takeyama H, Hirota Y, Osuga Y.
Downregulation of HLA Class I Expression Through HLA-A DNA Methylation Is Associated with Reduced CD8+ T Cell Infiltration in Cervical Cancer. Cancer Immunol Res. 2025 Oct 27. doi: 10.1158/2326-6066.CIR-25-0594.
8. Ueda S, Kakita M, Hosokawa M, Arikawa K, Takahashi K, Shiota R, Kakeyama M, Matsunaga H, Takeyama H, Takemoto-Kimura S.
Divergent and subnucleus-specific gene expression responses to chronic stress hormone exposure in the amygdala. Front Mol Neurosci. 2025;18:1659846. doi:10.3389/fnmol.2025.1659846.
9. Kifushi M, Nishikawa Y, Hosokawa M, Ide K, Kogawa M, Anai T, Takeyama H.
Strain‐level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics. DNA Res. 2025 Nov 6;dsaf032. doi:10.1093/dnares/dsaf032.
10. Arai H, Nishikawa Y, Konagaya T, Kogawa M, Kifushi M, Takeyama H, Anbutsu H, Kageyama D. Single-cell genome analysis of a feminizing Wolbachia in Eurema butterflies reveals a shared origin with male-killing Wolbachia. Microb Genom. 2025;11(11):001578. doi:10.1099/mgen.0.001578.
11. Dell M, Kogawa M, Streiff AB, Shiraishi T, Lotti A, Meier CM, Schorn MA, Field C, Cahn JKB, Yokoyama H, Yamada Y, Peters E, Egami Y, Nakashima Y, Co Tan K, Rückert C, Alanjary M, Kalinowski J, Kuzuyama T, Cardenas P, Pomponi S, Sipkema D, Wright A, Takada K, Abe I, Wakimoto T, Takeyama H, Piel J.
Chemical richness and diversity of uncultivated ‘Entotheonella’ symbionts in marine sponges. Nat Chem Biol. 2025 Nov 13. doi:10.1038/s41589-025-02066-0.
12. Sen A, Ishihara S, Ando M, Kaneko H, Mishima R, Nishimura T, Hishida Y, Tanaka M, Takeyama H, Odamaki T. Role of 70 °C heating on immunostimulatory effects of probiotic Bifidobacteria in infant formula. Food Res Int. 2025;223:117846. doi:10.1016/j.foodres.2025.117846.