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[28] Rodolfo Sebastian Allendes Osorio, Toshiya Nishimura, Yuichi Shigihara, Takanori Takebe, Takahiro Nemoto, "OddSNP: a predictive framework for optimizing multiplexed single-cell RNA-seq experiments", bioRxiv 2025.12.08.692882 (2025).
[27] Tommaso Ocari, Emilia A Zin, Muge Tekinsoy, Timothé Van Meter, Chiara Cammarota, Deniz Dalkara, Takahiro Nemoto, Ulisse Ferrari, "Optimal sequencing depth for measuring the concentrations of molecular barcodes", Nucleic Acids Research 53 (16), gkaf793 (2025). (open access).
[26] Rei Kamuro, Masahito Yoshihara, Susumu Hara, Takahiro Nemoto, Laura Howard, Ai Honda, Ayano Yamamoto, Toru Takigawa, Susumu Sakimoto, Koichi Baba, Andrew J Quantock, Kohji Nishida, Communications Biology 8, 1220 (2025) (open access).
[25] T. Nemoto, T. Ocari, A. Planul, M. Tekinsoy, E. A. Zin, D. Dalkara, U. Ferrari, "ACIDES: on-line monitoring of forward genetic screens for protein engineering", Nature Communications 14, 8504 (2023) (open access).
[24] T. Nemoto, M. Aubry, Y. Teissier, R. Paul, V.-M. Cao-Lormeau, H. Salje, S. Cauchemez, "Reconstructing long-term dengue virus immunity in French Polynesia", PLOS Neglected Tropical Diseases 16(10): e0010367 (2022) (open access).
[23] H. Horii, R. Lefevere, M. Itami, T. Nemoto, “Anomalous fluctuations of renewal-reward processes with heavy-tailed distributions”, Phys. Rev. E 106, 034130 (2022) / arXiv:2203.08584 (preprint) (2022)
[22] H. Horii, R. Lefevere, T. Nemoto, “Large time asymptotic of heavy tailed renewal processes”, Journal of Statistical Physics 186.1 (2022) / arXiv:2106.03182 (preprint)
[21] M. Ukita, N. Hozé, T. Nemoto, S. Cauchemez, S. Asakura, G. Makingi, R. Kazwala, K. Makita, “Quantitative evaluation of the infection dynamics of bovine brucellosis in Tanzania”, Preventive Veterinary Medicine 194 (2021): 105425 (open access)
[20] T. Nemoto and A. Alexakis, “Do extreme events trigger turbulence decay? – a numerical study of turbulence decay time in pipe flows”, Journal of Fluid Mechanics, 912, A38 (2021) / arXiv:2005.03530 (preprint)
[19] A. Lagarde, N. Dagès, T. Nemoto, V. Démery, D. Bartolo, T. Gibaud, “Colloidal transport in bacteria suspensions: from bacteria scattering to anomalous and enhanced diffusion”, Soft Matter 16 (32), 7503-7512 (2020) / arXiv:2002.10144 (preprint)
[18] R. L. Jack, T. Nemoto, V. Lecomte, “Dynamical phase coexistence in the Fredrickson-Andersen model”, Journal of Statistical Mechanics: Theory and Experiment 2020 (5), 053204 (2020) / arXiv:1912.02465 (preprint)
[17] E. Fodor, T. Nemoto, S. Vaikuntanathan, “Dissipation controls transport and phase transitions in active fluids: Mobility, diffusion and biased ensembles”, New Journal of Physics 22.1 (2020): 013052 (open access).
[16] L. Tociu, E. Fodor, T. Nemoto, S. Vaikuntanathan, “How Dissipation Constrains Fluctuations in Nonequilibrium Liquids: Diffusion, Structure, and Biased Interactions”, Phys. Rev. X 9, 041026 (2019) (open access).
[15] A. van Kan, T. Nemoto, A. Alexakis, “Rare transitions to thin-layer turbulent condensates”, J. Fluid Mech. 822, 364 (2019) / arXiv:1903.05578 (preprint)
[14] O. Shpielberg and T. Nemoto, “Imitating non-equilibrium steady states using time-varying equilibrium force in many-body diffusive systems”, Phys. Rev. E 100, 032104 (2019) / arXiv:1904.11787 (preprint)
[13] I. Hanasaki, T. Nemoto, Y. Y. Tanaka, “Soft trapping lasts longer: Dwell time of a Brownian particle varied by potential shape”, Phys. Rev. E 99, 022119 (2019).
[12] T. Nemoto, E. Fodor, M. Cates, R. Jack, J. Tailleur, “Optimizing active work: dynamical phase transitions, collective motion and jamming”, Phys. Rev. E 99, 022605 (2019) / arXiv:1805.02887 (preprint)
[11] O. Shpielberg, T. Nemoto, J. Caetano, “Universality in dynamical phase transitions of diffusive systems”, Phys. Rev. E 98, 052116 (2018) [Editors' Suggestion] / arXiv:1807.01099 (preprint)
[10] T. Nemoto and A. Alexakis, “Method to measure efficiently rare fluctuations of turbulence intensity for turbulent-laminar transitions in pipe flows”, Phys. Rev. E 97, 022207 (2018) / arXiv:1707.04819 (preprint)
[9] E. G. Hidalgo, T. Nemoto, V. Lecomte, “Finite-time and finite-size scalings in the evaluation of large-deviation functions : Numerical approach in continuous time”, Phys. Rev. E 95 062134, (2017) / arXiv:1607.08804 (preprint)
[8] T. Nemoto, V. Lecomte, R. L. Jack, “Finite-size scaling of a first-order dynamical phase transition: Adaptive population dynamics and an effective model”, Phys. Rev. Lett. 118 115702, (2017) / arXiv:1611.08239 (preprint)
[7] T. Nemoto, E. G. Hidalgo, V. Lecomte, “Finite-time and finite-size scalings in the evaluation of large-deviation functions : Analytical study using a birth-death process”, Phys. Rev. E 95 012102, (2017) / arXiv:1607.04752 (preprint)
[6] T. Nemoto, F. Bouchet, R. L. Jack, V. Lecomte, “Population dynamics method with a multi-canonical feedback control”, Phys. Rev. E 93, 062123 (2016) / arXiv:1601.06648 (preprint)
[5] T. Nemoto, V. Lecomte, S. Sasa, F. van Wijland, “Finite size effects in a mean-field kinetically constrained model: dynamical glassiness and quantum criticality”, J. Stat. Mech. (2014) P10001 / arXiv:1405.1658 (preprint)
[4] T. Nemoto, S. Sasa, “Computation of Large Deviation Statistics via Iterative Measurement-and-Feedback Procedure”, Phys. Rev. Lett. 112, 090602 (2014) / arXiv:1309.7200 (preprint)
[3] T. Nemoto, “Zon-Cohen singularity and negative inverse temperature in a trapped particle limit”, Phys. Rev. E 85, 061124 (2012) / arXiv:1205.1903 (preprint)
[2] T. Nemoto, S. Sasa, “Thermodynamic formula for the cumulant generating function of time-averaged current”, Phys. Rev. E 84, 061113 (2011) / arXiv:1109.0797 (preprint)
[1] T. Nemoto, S. Sasa, “Variational formula for experimental determination of high-order correlations of current fluctuations in driven systems”, Phys. Rev. E 83, 030105(R) (2011) / arXiv:1009.3379 (preprint)
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