• Novel Escherichia coli Phages Representing a Distinct Genus within Stephanstirmvirinae: Genome and Host Range Characteristics
  • T. Kaneko, J. Uchiyama, T. Osaka, S. Tsuneda
  • bioRxiv, 2025/02

• A Phage Collection Propagated in Escherichia coli K-12 Shows Broad Lytic Activity Against a Diverse Panel of Multidrug-Resistant Isolates
  • T. Kaneko, Y. Aiba, K. Miyanaga, L. Cui, S. Tsuneda
  • PHAGE : Therapy, Applications, and Research. 4:3. 2025/02

• Multilocus sequence typing, antimicrobial susceptibility, and phage discovery of motile Aeromonas species from the pond-cultured goldfish Carassius auratus on two farms in Japan
  • K. Fudeshima, K. Kitaoka, T. Kaneko, S. Yamamura, Y. Yamasaki, H. Mizutani, K. Miyanaga, Y. Tanji, N. Mano, S. Tsuneda
  • Fisheries Science, 2024/12

• From phenotype to receptor: validating physiological clustering of Escherichia coli phages through comprehensive receptor analysis
  • T. Kaneko, T. Osaka, M. Inagaki, S. Tsuneda
  • bioRxiv, 2024/11

• Harnessing a T1 Phage-Derived Spanin for Developing Phage-Based Antimicrobial Development
  • W. Yamashita, S. Ojima, A. Tamura, A. H. Azam, K. Kondo, Z. Yuancheng, L. Cui, M. Shintani, M. Suzuki, Y. Takahashi, K. Watashi, S. Tsuneda, K. Kiga
  • BioDesign Research, 6, 0028. 2024/3

• Variation in growth rates between cultures hinders the cultiv a tion of ammonia-oxidizing bacteria
  • R. Isshiki, H. Fujitani, S. Tsuneda
  • FEMS Microbiology Letters 371 (2024): fnae013 2024/3

• Arg-73 of the RNA endonuclease MazF in Salmonella enterica subsp. arizonae contributes to guanine and uracil recognition in the cleavage sequence
  • T. Okabe, R. Aoi, A. Yokota, H. Tamiya-Ishitsuka, Y. Jiang, A. Sasaki, S. Tsuneda, N. Noda
  • Journal of Biological Chemistry 300.2 (2024). 2024/2

• Effects of Co-existing Heterotrophs on Physiology of and Nitrogen Metabolism in Autotrophic Nitrite-oxidizing Candidatus Nitrotoga
  • H. Ide, K. Ishii, Y. Takahashi, H. Fujitani, S. Tsuneda
  • Microbes and environments 38.4 (2023): ME23076. 2023/12

• Water-in-oil droplet-mediated method for detecting and isolating infectious bacteriophage particles via fluorescent staining
  • M. Hoshino, Y. Ota, T. Suyama, Y. Morishita, S. Tsuneda, N. Noda
  • Frontiers in Microbiology 14 (2023): 1282372. 2023/12

• Tailoring effective phage cocktails for long-term lysis of Escherichia coli based on physiological properties of constituent phages
  • T. Kaneko, T. Osaka, S. Tsuneda
  • PHAGE : Therapy, Applications, and Research. 4:3. 2023/09

• Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer
  • S. Kikuchi, H. Fujitani, K. Ishii, R. Isshiki, Y. Sekiguchi, S. Tsuneda
  • Environmental Microbiology Reports. 15. 2023/08

• Establishment of isogenic induced pluripotent stem cells with or without pathogenic mutation for understanding the pathogenesis of myeloproliferative neoplasms
  • C. Liu, M. Imai, Y. Edahiro, S. Mano, H. Takei, M. Nudejima, A. Kurose, S. Morishita, M. Ando, S. Tsuneda, M. Araki, N. Komatsu
  • Experimental Hematology. 118. 2023/02

• Relationship between Phage Lytic Spectra and Sequence Types in Extended-Spectrum β-lactamase-Producing Escherichia coli isolated in Japan
  • S. Yamamura, K. Kitaoka, Y. Yamasaki, K. Fudeshima, K. Miyanaga, Y. Tanji, S. Tuneda
  • Japanese Journal of Infectious Diseases. 75(6) . 2022/11

• Nitrite Production by Nitrifying Bacteria in Urban Groundwater Used in a Chlorinated Public Bath System in Japan
  • Y. Takahashi, K. Ishii, Y. Kikkawa, K. Horikiri, S. Tsuneda
  • Microbes and Environments. 37(1) . 2022/10

• ldhA-induced persister in Escherichia coli is formed through accidental SOS response via intracellular metabolic perturbation
  • N. Yamamoto, Y. Ohno, S. Tsuneda
  • Medical Microbiology and Immunology. 66(225) . 2022/05

• Long-term limitation effects of Se(VI), Zn(II), and Ni(II) on start-up of the anammox process using gel carrier
  • K. Isaka, S. Nitta, D. Sugawara, H. Yamazaki, Y. Kimura, T. Osaka, S. Tsuneda
  • Frontiers in Bioengineering and Biotechnology. 10(1) . 2022/03

• Effect of inorganic carbon limitation on the nitrogen removal performance of the single-stage reactor containing anammox and nitritation gel carriers
  • K. Isaka, S. Nitta, T. Osaka, S. Tsuneda
  • Journal of Bioscience and Bioengineering. 133(70) . 2022/01

• Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq
  • K. Chihara, L. Barquist, K. Takasugi, N. Noda, S. Tsuneda
  • bioRxiv. . 2020/08

• 高温条件がアナモックスプロセスにおよぼす影響
  • 井坂和一，豊田透花，大前周平，高橋悠，大坂利文，常田聡
  • 化学工学論文集. 47(217) . 2021/12

• Microdroplet-based system for culturing of environmental microorganisms using FNAP-sort
  • K. Saito, Y. Ota, D. M. Tourlousse, S. Matsukura, H. Fujitani, M. Morita, S. Tsuneda & N. Noda
  • Scientific Reports. 11(1) . 2021/05

• Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq
  • K. Chihara, L. Barquist, K. Takasugi, N. Noda, S. Tsuneda
  • RNA Biology. 2021/04

• EB3L1 overexpression as a potential diagnostic marker of Philadelphia chromosome–negative myeloproliferative neoplasms
  • S. Morishita,H. Yasuda,S. Yamawaki,H. Kawaji,M. Itoh,Y. Edahiro,M. Imai,Y. Kogo,S. Tsuneda,A. Ohsaka,Y. Hayashizaki,M. Ito,M. Araki,N. Komatsu
  • Cancer Science. 112(2). 2021/02

• Methanol tolerance and acclimation in the anammox process using a gel carrier
  • K. Isaka, T. Osaka, Y. Kimura, N. Iwasaki, S. Tsuneda
  • Biochemical Engineering Journal. 165 . 2021/01

• Nitrogen and Oxygen Isotope Signatures of Nitrogen Compounds during Anammox in the Laboratory and a Wastewater Treatment Plant
  • S. Kotajima, K. Koba, D. Ikeda, A. Terada, K. Isaka, K. Nishina, Y. Kimura, A. Makabe, M. Yano, H. Fujitani, N. Ushiki, S. Tsuneda, M. Yoh
  • Microbes and Environments. 35(4) . 2020/11

• Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated from a Drinking Water Treatment Plant
  • H. Fujitani, K. Momiuchi, K. Ishii, M. Nomachi, S. Kikuchi, N. Ushiki, Y. Sekiguchi ,S. Tsuneda
  • Frontiers in Microbiology. 11(545190) . 2020/9

• Enrichment of Comammox and Nitrite-Oxidizing Nitrospira From Acidic Soils
  • Y. Takahashi, H. Fujitani, Y. Hirono, K. Tago, Y. Wang, M. Hayatsu, S. Tsuneda
  • Frontiers in Microbiology. 11(1737). 2020/7

• Physiological and genomic characterization of a new ‘Candidatus Nitrotoga’ isolate
  • K. Ishii, H. Fujitani, Y. Sekiguchi, S. Tsuneda
  • Environmental Microbiology 22(6) 2365 - 2382 2020/6

• Transcriptome Analysis of the Ammonia-Oxidizing Bacterium Nitrosomonas mobilis Ms1 Reveals Division of Labor between Aggregates and Free-living Cells
  • R. Isshiki, H. Fujitani, S. Tsuneda
  • Microbes and Environments 35(2) 1 - 9 2020/6

• Quantification of native mRNA dynamics in living neurons using fluorescence correlation spectroscopy and reduction-triggered fluorescent probes
  • H. Fujita, R. Oikawa, M. Hayakawa, F. Tomoike, Y. Kimura, H. Okuno, Y. Hatashita, C. Oliveros, H. Bito, T. Ohshima, S. Tsuneda, H. Abe, T. Inoue.
  • Journal of Biological Chemistry 295(23). 2020/4

• MazF Endoribonucleolytic Toxin Conserved in Nitrospira Specifically Cleaves the AACU, AACG, and AAUU Motifs
  • R. Aoi, T. Miyamoto, A. Yokota, Y. Ota, H. Fujitani, S. Tsuneda, N. Noda
  • Toxins 12(5) 2020/4

• Successful enrichment of low-abundant comammox Nitrospira from nitrifying granules under ammonia-limited conditions
  • H. Fujitani, M. Nomachi, Y. Takahashi, Y. Hasebe, M. Eguchi, S. Tsuneda
  • FEMS Microbiology Letters. 367(1),fnaa025. 2020/3

• Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing
  • K. Chihara, T. Bischler, L. Barquist, V. Monzon, N. Noda, J. Vogel, S. Tsuneda
  • mSystems 2019/12

• Draft Genome Sequence of Acidovorax sp. Strain NB1, Isolated from a Nitrite-Oxidizing Enrichment Culture
  • H. Ide, K. Ishii, H. Fujitani, S. Tsuneda
  • Microbiology Resource Announcements. 8(33),e0054719-19. 2019/8

• Fluorescent Nucleic Acid Probe in Droplets for Bacterial Sorting (FNAP-Sort) as a High-Throughput Screening Method for Environmental Bacteria with Various Growth Rates
  • Y. Ota, K. Saito, T. Takagi, S. Matsukura, M. Morita, S. Tsuneda, N. Noda
  • PLoS ONE. 14(4),e0214533. 2019/4

• End-Sealed High Aspect Ratio Hollow Nanotubes Encapsulating an Anticancer Drug: Torpedo-Shaped Peptidic Nanocapsules
  • M. Ueda, S. Seo, B. G. Nair, S. Müller, E. Takahashi, T. Arai, T. Iyoda, S. Fujii, S. Tsuneda, Y. Ito
  • ACS Nano. 13(1). 305-312. 2019/1

• Nitrosomonas europaea MazF Specifically Recognises the UGG Motif and Promotes Selective RNA Degradation
  • T. Miyamoto, A. Yokota, Y. Ota, M. Tsuruga, R. Aoi, S. Tsuneda, N. Noda
  • Frontiers in Microbiology. 9(2386). 1-10. 2018/10

• Stochastic expression of lactate dehydrogenase A induces Escherichia coli persister formation
  • N. Yamamoto, R. Isshiki, Y. Kawai, D. Tanaka, T. Sekiguchi, S. Matsumoto, S. Tsuneda
  • J. Biosci. Bioeng. 126(1). 30-37. 2018/7

• Skewed megakaryopoiesis in human induced pluripotent stem cell-derived haematopoietic progenitor cells harbouring calreticulin mutations
  • H. Takei, Y. Edahiro, S. Mano, N. Masubuchi, Y. Mizukami, M. Imai, S. Morishita, S. Tsuneda, H. Endo, S. Nakamura, K. Eto, A. Ohsaka, M. Araki, N. Komatsu
  • British Journal of Haematology 181(6). 791-802. 2018/6

• "Low-temperature Culturing Improves Survival Rate of Tissue-engineered Cardiac Cell Sheets"
  • K. Sakaguchi, Y. Hinata, Y.Kagawa, K. Iwasaki, S. Tsuneda, T. Shimizu, M. Umezu
  • Biochem. Biophys. Rep. 14. 89-97. 2018/7

• AldB controls persister formation in Escherichia coli depending on environmental stress
  • Y. Kawai, S. Matsumoto, Y. Ling, S. Okuda, S. Tsuneda
  • Microbiol. Immunol. 62(5). 299-304. 2018/5

• “All-in-one” in vitro selection of collagen-binding vascular endothelial growth factor
  • S.-H. Park, T. Uzawa, F. Hattori, S. Ogino, N. Morimoto, S. Tsuneda, Y. Ito
  • Biomaterials 161. 270-278. 2018/2

• Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity
  • N. Ushiki, H. Fujitani, Y. Shimada, T. Morohoshi, Y. Sekiguchi, S. Tsuneda
  • Frontiers in Microbiology 8(2637). 1-12. 2018/1

• Unique Transcriptional Profile of Native Persisters in Escherichia coli
  • S. Matsumoto, Y. Kawai, S. Miyagawa, Y. Iwamoto, S. Okuda, A. Sanchez-Gorostiaga, M. Vicente, S. Tsuneda
  • J. Biosci. Bioeng. 125(1). 15-22. 2018/1

• High-Rate Nitrification of Electronic Industry Wastewater by Using Nitrifying Granules
  • Y. Hasebe, H. Meguro, Y. Kanai, M. Eguchi, T. Osaka, S. Tsuneda
  • Water Sci. Technol. 76(11). 3171-3180. 2017/12

• Characterization of a Deinococcus radiodurans MazF: A UACA-specific RNA endoribonuclease
  • Tatsuki Miyamoto, Yuri Ota, Akiko Yokota, Tetsushi Suyama, Satoshi Tsuneda, Naohiro Noda
  • MicrobiologyOpen e501. 2017/12

• Meta-analysis of Fecal Microbiota and Metabolites in Experimental Colitic Mice during the Inflammatory and Healing Phases
  • T. Osaka, E. Moriyama, S. Arai, Y. Date, J. Yagi, J. Kikuchi, S. Tsuneda
  • Nutrients 9(12). 1329. 2017/12

• Enrichment and Physiological Characterization of a Cold-Adapted Nitrite Oxidizer Nitrotoga sp. from Eelgrass Sediment
  • K. Ishii, H. Fujitani, K. Soh, T. Nakagawa, R. Takahashi, S. Tsuneda
  • Appl. Environ. Microbiol. 83(14). e00549-17. 2017/7

• First Full-Scale Nitritation-Anammox Plant Using Gel Entrapment Technology for Ammonia Plant Effluent
  • K. Isaka, Y. Kimura, M. Matsuura, T. Osaka, S. Tsuneda
  • Biochem. Eng. J. 122.115-122. 2017/6

• Real-Time Quantitation of Internal Metabolic Activity of Three-Dimensional Engineered Tissues Using an Oxygen Microelectrode and Optical Coherence Tomography
  • Y. Kagawa, Y. Haraguchi, S. Tsuneda, T. Shimizu
  • Journal of Biomedical Materials Research: Part B 105(4).855-864. 2017/5

• Nitrite Oxidation Kinetics of Two Nitrospira Strains: the Quest for Competition and Ecological Niche Differentiation
  • N. Ushiki, M. Jinno, H. Fujitani, T. Suenaga, A. Terada, S. Tsuneda
  • J. Biosci. Bioeng. 123(5).581-589. 2017/5

• Four Aromatic Sulfates with an Inhibitory Effect against HCV NS3 Helicase from the Crinoid Alloeocomatella polycladia
  • I. Hermawan, A. Furuta, M. Higashi, Y. Fujita, N. Akimitsu, A. Yamashita, K. Moriishi, S. Tsuneda, H. Tani, M. Nakakoshi, M. Tsubuki, Y. Sekiguchi, N. Noda, J. Tanaka
  • Marine Drugs 15 (117). 1-10. 2017/4

• pH-Gradient Ion-exchange Microbial Cell Chromatography as a Simple Method for Microbial Separation
  • Y. Aoi, Y. Kaneko, S. Tsuneda
  • J. Biosci. Bioeng. 123(4).431-436. 2017/4

• A Rapid Collection of Yet Unknown Ammonia Oxidizers in Pure Culture from Activated Sludge
  • T. Abe, N. Ushiki, H. Fujitani, S. Tsuneda
  • Water Res. 108(1).169-178. 2016/12

• Ecophysiology and Comparative Genomics of Nitrosomonas mobilis Ms1 Isolated from Autotrophic Nitrifying Granules of Wastewater Treatment Bioreactor
  • S. M. Thandar, N. Ushiki, H. Fujitani, Y. Sekiguchi, S. Tsuneda
  • Frontiers in Microbiology. 7(1869).1-14. 2016/11

• Physical Enrichment of Uncultured Accumulibacter and Nitrospira from Activated Sludge by Unlabeled Cell Sorting Technique
  • K. Irie, H. Fujitani, S. Tsuneda
  • J. Biosci. Bioeng. 122(4).475-481. 2016/10

• AAU-specific RNA cleavage mediated by MazF toxin endoribonuclease conserved in Nitrosomonas europaea
  • T. Miyamoto, Y. Kato, Y. Sekiguchi, S. Tsuneda, N. Noda
  • Toxins. 8(6). n° 174. 2016/6

• Characterization of MazF-mediated Sequence-specific RNA Cleavage in Pseudomonas putida using Massive Parallel Sequencing
  • T. Miyamoto, Y. Kato, Y. Sekiguchi, S. Tsuneda, N. Noda
  • PLoS ONE. 11(2). e0149494. 2016/2

• System for Measuring Oxygen Consumption Rates of Mammalian Cells in Static Culture Under Hypoxic Conditions
  • Y. Kagawa, H. Miyahara, Y. Ota, S. Tsuneda
  • Biotechnol Prog. 32(1). 189-197. 2016/2

• Effect of Lipopolysaccharide on the Progression of Non-Alcoholic Fatty Liver Disease in High Caloric Diet-Fed Mice
  • N. Matsushita, T. Osaka, I. Haruta, H. Ueshiba, N. Yanagisawa, M. Omori-Miyake, E. Hashimoto, N. Shibata, K. Tokushige, K. Saito, S. Tsuneda, J. Yagi
  • Scand. J. Immunol. 83. 109-118. 2016/1

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