Publications

  • Kamei,K.F., Okura,R., Kobayashi-Kirschvink,K.J., Katayama,Y., Wakamoto,Y. Raman spectra identify heterogeneous vancomycin resistance and transcriptomes of Staphylococcus aureus. (2024)bioRxiv. https://www.biorxiv.org/content/10.1101/2024.05.12.593718v1 (link)
  • Pollack,D., Nozoe,T., Kussell,E. Proteolytic stability and aggregation in a key metabolic enzyme of bacteria. (2024). PNAS, 121 (19) e2301458121. https://www.pnas.org/doi/10.1073/pnas.2301458121 (link)
  • Kamei,K.F., Kobayashi-Kirschvink,K.J., Nozoe,T., Nakaoka,H., Umetani,M., Wakamoto,Y. Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns. (2024)bioRxiv. https://www.biorxiv.org/content/10.1101/2023.05.09.539921v2 (link)
  • Umetani, M., Fujisawa, M., Okura, R., Nozoe, T., Suenaga, S., Nakaoka, H., Kussell, E., Wakamoto, Y. Observation of non-dormant persister cells reveals diverse modes of survival in antibiotic persistence. (2022)  bioRxiv. https://doi.org/10.1101/2021.10.28.466227 (link)
  • Genthon, A., Nozoe, T., Peliti, L., Lacoste, D. Cell Lineage Statistics with Incomplete Population Trees. (2023) . PRX Life 1, 013014 . https://journals.aps.org/prxlife/abstract/10.1103/PRXLife.1.013014  (link)
  • Koganezawa, Y., Wakamoto, Y., Sato, M., Umetani, M. Detecting Photoactivatable Cre-mediated Gene Deletion Efficiency in Escherichia coli. (2023)  . Bio-protocol 13(11): e4685. https://doi.org/10.21769/BioProtoc.4685 (link)
  • Yamauchi, S., Nozoe, T., Okura, R., Kussell, E., Wakamoto, Y. A unified framework for measuring selection on cellular lineages and traits. (2022) eLife. 11, e72299. doi: https://doi.org/10.7554/eLife.72299 (link)
  • Koganezawa, Y., Umetani, M., Sato, M., Wakamoto, Y. History-Dependent Physiological Adaptation to Lethal Genetic Modification under Antibiotic Exposure. (2022)  eLife. 11:e74486. https://elifesciences.org/articles/74486 (link)
  • Koga, R., Moriyama, M., Onodera-Tanifuji, N., Ishii, Y., Takai, H., Mizutani, M., Oguchi, K., Okura, R., Suzuki, S., Goto, Y., Hayashi, T., Seki, M., Suzuki, Y., Nishide, Y., Hosokawa, T., Wakamoto, Y., Furusawa, C., Fukatsu, T. Single mutation makes Escherichia coli an insect mutualist. (2022) Nat Microbiol 7, 1141–1150. https://doi.org/10.1038/s41564-022-01179-9 (link)
  • Shimaya, T., Okura, R., Wakamoto, Y., Takeuchi, K. A. Scale invariance of cell size fluctuations in starving bacteria. (2021)  Communications Physics, 4:238. doi.org/10.1038/s42005-021-00739-5 (link).
  • Seita, A., Nakaoka, H., Okura, R., Wakamoto, Y. Intrinsic growth heterogeneity of mouse leukemia cells underlies differential susceptibility to a growth-inhibiting anticancer drug. (2021) PLoS ONE. 16(2): e0236534. doi:https://doi.org/10.1371/journal.pone.0236534 (link).
  • Kobayashi-Kirschvink, K. J., Nakaoka, H., Oda, A., Kamei, K. F., Nosho, K., Fukushima, H., Kanesaki, Y., Yajima, S., Masaki, H., Ohta, K., Wakamoto, Y.  Linear Regression Links Transcriptomic Data and Cellular Raman Spectra. (2018) Cell Systems 7(1): 104-117.E4. doi: https://doi.org/10.1016/j.cels.2018.05.015 (link).
  • Nakaoka, H. Live fast, die fast principle in a single cell of fission yeast. (2017) Microbial Cell, 4(9): 308-310. doi: 10.15698/mic2017.09.591, PMID: 28913346 (link).
  • Nakaoka, H., Wakamoto, Y. Aging, mortality, and the fast growth trade-off of Schizosaccharomyses pombe. (2017) PLoS Biology 15(6): e2001109. doi: https://doi.org/10.1371/journal.pbio.2001109, PMID: 28632741 (link).
  • Nozoe, T., Kussell, E., Wakamoto, Y. Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data. (2017) PLoS Genetics. 13(3): e1006653, doi: 10.1371/journal.pgen.1006653, PMID: 28267748 (link).
  • Nakajima, A., Ishida, M., Fujimori, T., Wakamoto, Y., Sawai, S. The Microfluidic lighthouse: an omnidirectional gradient generator. (2016) Lab Chip. 16: 4382-4394. doi: 10.1039/c6lc00898d, PMID: 27735954 (link).
  • Hashimoto, M., Nozoe, T., Nakaoka, H., Okura, R., Akiyoshi, K., Kaneko, K., Kussell, E., Wakamoto, Y. Noise-driven growth rate gain in clonal cellular populations. (2016) Proc Natl Acad Sci USA. 113: 3251-3256. doi:10.1073/pnas.1519412113, PMID: 26951676 (link)
  • Pleška, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E., Guet, C. C. Bacterial autoimmunity due to a restriction-modification system. (2016) Curr Biol. 26(3): 404-409., doi:10.1016/j.cub.2015.12.041, PMID: 26804559 (link)
  • Santi, I., Dhar, N., Bousbaine, D., Wakamoto, Y., McKinney, J. D. Single-cell dynamics of the chromosome replication and cell division cycles in mycobacteria. (2013) Nature Communications. 4: 2470, doi:10.1038/ncomms3470, PMID: 24036848 (link)
  • Wakamoto, Y., Dhar, N., Chait, R., Schneider, K., Signorino-Gelo, F., Leibler, S., McKinney, J. D. Dynamic Persistence of Antibiotic-Stressed Mycobacteria. (2013) Science. 339(6115): 91-95. PMID: 23288538 (link)
  • Toyota, T., Wakamoto, Y., Hayashi, K., Ohnuma, K. (2012) Controlling Cell Migration with Micropatterns, Innovations in Biotechnology, Dr. Eddy C. Agbo (Ed.), ISBN: 978-953-51-0096-6, InTech, (link)
  • Wakamoto, Y., Grosberg, A. Y., Kussell, E. Optimal lineage principle for age-structured populations. (2012) Evolution. 66(1): 115-134. PMID: 22220869 (link)
  • Tomita, T., Sugawara, T., Wakamoto, Y. Multitude of morphological dynamics of giant multilamellar vesicles in regulated nonequilibrium environments. (2011) Langmuir. 27(16): 10106-12. PMID:21702436 (link)
  • Umehara, S., Inoue, I., Wakamoto, Y., Yasuda, K. Origin of individuality of two daughter cells during the division process examined by the simultaneous measurement of growth and swimming property using an on-chip single-cell cultivation system. (2007) Biophys J. 93(3): 1061-7. PMID: 17496044 (link)
  • Ayano, S., Wakamoto, Y., Yamashita, S., Yasuda, K. Quantitative measurement of damage caused by 1064-nm wavelength optical trapping of Escherichia coli cells using on-chip single cell cultivation system. (2006) Biochem Biophys Res Commun. 350(3): 678-84. PMID: 17027921 (link)
  • Wakamoto, Y., Yasuda, K. Quantitative evaluation of cell-to-cell communication effects in cell group class using on-chip individual-cell-based cultivation system. (2006) Biochem Biophys Res Commun. 349(3): 1030-8. PMID: 16970916 (link)
  • Wakamoto, Y., Yasuda, K. Epigenetic inheritance of elongated phenotypes between generations revealed by individual-cell-based direct observation (2006) Meas Sci Technol. 17(12): 3171-7. (link)
  • Matsumura, K., Orita, K., Wakamoto, Y., Yasuda, K. Phagocytic response to fully controlled plural stimulation of antigens on macrophage using on-chip microcultivation system. (2006) J Nanobiotechnology. 4:7. PMID: 16914039 (link)
  • Wakamoto, Y., Ramsden, J., Yasuda, K. Single-cell growth and division dynamics showing epigenetic correlations. (2005) Analyst. 130(3): 311-7. PMID: 15724159 (link)
  • Umehara, S., Hattori, A., Wakamoto, Y., Yasuda, K. Simultaneous measurement of growth and movement of cells exploiting on-chip single-cell cultivation assay. (2004) Jpn J Appl Phys. 43(3): 1214-1217. (link)
  • Moriguchi, H., Takahashi, K., Sugio, Y., Wakamoto, Y., Inoue, I., Jimbo, Y., Yasuda, K. On-chip neural cell cultivation using agarose-microchamber array constructed by a photothermal etching method. (2004) Electr Eng Jpn. 146(2): 37-42 (link)
  • Hattori, A., Umehara, S., Wakamoto, Y., Yasuda, K. Measurement of incident angle dependence of swimming bacterium reflection using on-chip single-cell cultivation assay. (2003) Jpn J Appl Phys. 42 Part 2 No. 7B: L873-5. (link)
  • Umehara, S., Wakamoto, Y., Inoue, I., Yasuda, K. On-chip single-cell microcultivation assay for monitoring environmental effects on isolated cells. (2003) Biochem Biophys Res Commun. 305(3): 534-40. PMID: 12763026 (link)
  • Wakamoto, Y., Umehara, S., Matsumura, K., Inoue, I., Yasuda, K. Development of non-destructive, non-contact single-cell based differential cell assay using on-chip microcultivation and optical tweezers. (2003) Sens and Actuat, B. 96(3): 693-700. (link)
  • Moriguchi, H., Wakamoto, Y., Sugio, Y., Takahashi, K., Inoue, I., Yasuda, K. An agar-microchamber cell-cultivation system: flexible change of microchamber shapes during cultivation by photo-thermal etching. (2002) Lab Chip. 2(2): 125-32. PMID: 15100846 (link)
  • Wakamoto, Y., Inoue, I., Moriguchi, H., Yasuda, K. On-chip single-cell cultivation system. (2001) Seikagaku. 73(12): 1439-43. PMID: 11831037. In Japanese.
  • Inoue, I., Wakamoto, Y., Moriguchi, H., Okano, K., Yasuda, K. On-chip culture system for observation of isolated individual cells. (2001) Lab Chip. 1(1): 50-5. PMID: 15100889 (link)
  • Inoue, I., Wakamoto, Y., Yasuda, K. Non-genetic variability of division cycle and growth of isolated individual cells in on-chip culture system. (2001) Proc Japan Acad. 77, Ser.B: 145-50. (link)
  • Wakamoto, Y., Inoue, I., Moriguchi, H., Yasuda, K. Analysis of single-cell differences by use of an on-chip microculture system and optical trapping. (2001) Fresenius J Anal Chem. 371(2): 276-81. PMID: 11678202 (link)