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)
若本祐一. ラマン分光を用いた細胞内の遺伝子発現の推定. (2020) 実験医学増刊「機械学習を生命科学に使う!」（小林徹也, 杉村薫, 舟橋啓編）. 38(20): 3376-3383. (link)
小林鉱石, 亀井健一郎, 中岡秀憲, 若本祐一. ラマンスペクトルから細胞の遺伝子発現を推定する. (2020) 生物物理. 60(2): 108-110. doi: 10.2142/biophys.60.108 (link).
亀井健一郎, 小林鉱石, 中岡秀憲, 若本祐一. 細胞のラマンスペクトルから遺伝子発現プロファイルを推定する新手法. (2019) バイオサイエンスとインダストリー, 77(1): 17-21.
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).
若本祐一. 細胞成長・増殖の定量生物学. 定量生物学– 生命現象を定量的に理解するために– (小林徹也編). 70-92. 化学同人(京都). 2018.
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).
中岡秀憲, 梅谷実樹, 若本祐一. 1細胞レベルの環境応答と選択の計測. (2017) 化学と生物. 55(4): 263-268, doi: 10.1271/kagakutoseibutsu.55.263 (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)
若本祐一. 細胞表現型ゆらぎの適応的意義と1細胞統計. (2015) 顕微鏡 50: 86-91.
野添嵩,若本祐一. 細胞集団の適応ダイナミクスと細胞状態の揺らぎ. (2014) 生体の科学 65(5) : 464-465.
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)
若本祐一. 「細胞の成長」が回路に組み込まれた幹細胞分化の転写制御. (2013) 実験医学. 31(16): 2597-2598.
野添嵩, 橋本幹弘, 若本祐一. 1細胞計測で明らかになる集団の増殖と適応. (2013) 実験医学. 31(8): 1209-1216.
若本祐一. ネガティブフィードバックのトレードオフを回避するウイルスの発現制御回路. (2013) 実験医学. 31(6): 893-4.
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)
若本祐一. 生細胞１個の質量変化を測る. (2012) 実験医学. 30(18): 2950-1.
若本祐一. 抗生物質に対する耐性菌進化の予測は可能か？. (2012) 実験医学. 30(8): 1294-5.
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)
若本祐一. 確率的表現型変化によるがん細胞構成比の安定性. (2011) 実験医学. 29(18): 2980-1.
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)
L.P.カダノフ若本祐一訳. ネットワークの理解のしかた. (2009) パリティ. 24(12): 44-6.
J.ミラー若本祐一訳. 非生物系で探る生物同期現象. (2009) パリティ. 24(10): 46-9.
若本祐一. 細胞システムのもつゆらぎとその役割. (2008) パリティ. 23(1): 68-70.
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)
森口裕之, 高橋一憲, 杉尾嘉宏, 若本祐一, 井之上一平, 神保泰彦, 安田賢二. 集束光加熱エッチング法によって加工したアガロースマイクロチャンバーアレイを用いた神経細胞の培養. (2002) 電気学会論文誌. C, 電子・情報・システム部門誌 122(9): 1453-8.
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)
井之上一平, 若本祐一, 安田賢二. マイクロチップを利用した1細胞長期培養装置. (2001) 生物物理. 41: 111-3. (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)

若本研究室

Publications