1. Oveisi, M., Shukla, M., Seymen, N., Ohno, M., Taniguchi, Y., Nahata, S., Loos, R., Mufti, G. J., Allshire, R. C., Dimitrov, S., Karimi, M. M. “iNucs: inter-nucleosome interactions”, Bioinformatics, btab698 (2021)
  2. Ohno, M., Ando, T., Priest, D. G., Taniguchi, Y. “Hi-CO: 3D genome structure analysis with nucleosome resolution”, Nature Protocols  16, 3439–3469 (2021) 
  3. Shinkai, S., Nakagawa, M., Sugawara, T., Togashi, Y., Ochiai, H., Nakato, R., Taniguchi, Y., Onami, S. “PHi-C: deciphering Hi-C data into polymer dynamics“, NAR Genomics and Bioinformatics, 2, lqaa020 (2020) 
  4. Kumar, V., Leclerc, S., Taniguchi, Y. “BHi-Cect: A top-down algorithm for identifying the multi-scale hierarchical structure of chromosomes”, Nucleic Acids Research, 48, e26 (2020)
  5. Leclerc, S., Arntz, Y., Taniguchi, Y. “Proteome-wide quantification of labeling homogeneity at the single molecule level”, Journal of Visualized Experiments  146, e59199 (2019)
  6. Yoshida, Y., Taniguchi, Y. “Simultaneous single-cell measurements demonstrate a positive correlation between RNA copy number for mitochondrial division and fusion genes and mitochondrial fragmentation”, Cytologia  84, 15-23 (2019)

    *Illustration selected as a cover image

  7. Yoshida, Y., Taniguchi, Y. “Simultaneous measurements of RNA molecules transcribed from mitochondrial division or fusion genes in single cells”, Cytologia  84, 1-2 (2019)
  8. Ohno, M., Ando, T., Priest, D. G., Kumar, V., Yoshida, Y., Taniguchi, Y. “Sub-nucleosomal genome structure reveals distinct nucleosome folding motifs”, Cell  176, 520-534 (2019)

    *Illustration selected as a cover image

    Risca, Viviana, I. “Nucleosome orientation map finds two new chromatin folding motifs”, Cell (2019)

  9. Leclerc, S., Arntz, Y., Taniguchi, Y. “Extending single molecule imaging to proteome analysis by quantitation of fluorescent labeling homogeneity in complex protein samples”, Bioconjugate Chemistry  29, 2541-2549 (2018)
  10. Ohno, M., Priest, D.G., Taniguchi, Y. “Nucleosome-level 3D organization of the genome”, Biochemical Society Transactions  46, 491-501 (2018)

    *Illustration selected as a cover image

  11. Priest, D.G., Tanaka, N., Tanaka, Y., Taniguchi, Y. “Micro-patterned agarose gel devices for single-cell high-throughput microscopy of E. coli cells”, Scientific Reports 7 17750 (2017)
  12. Taniguchi, Y. “Autofluorescence imaging of tissue samples using super-high sensitivity fluorescence microscopy”, Global Imaging Insights 2, 1-2 (2017)
  13. Taniguchi, Y. “Genome-wide analysis of protein and mRNA copy numbers in single Escherichia coli cells with single-molecule sensitivity”, Methods in Mol. Biol.  1346, 55-67 (2015)
  14. Ohno, M., Karagiannis, P., Taniguchi, Y. “Protein expression analyses at the single cell level”, Molecules  19, 13932-13947 (2014)
  15. Taniguchi, Y., Choi, P. J., Li, G., Chen, H., Babu, M., Hearn, J., Emili, A., Xie, X. S. “Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells”, Science 329, 533-538 (2010)

    Tyagi, Sanjay “E. coli, What a noisy bugScience  329, 518-519 (2010)

    Evanko, Daniel “Single molecules meet systems biology”, Nature Methods  7, 672 (2010)

    Peng, Wayne “Trends in biotech literature 2011”, Nature Biotechnology  30, 910 (2012)

    Dickey, Gwyneth “Noisy bacteria” ScienceNews (2010)

    Day, Charles “The noisy expression of genes into proteins” Physics Today (2010)

    Scudellari, Megan “’Identical’ cells? Not so much” The (2010)

    Anderson, Andrea “Study: Lack of correlation between messenger RNA, protein

    product levels in single E. coli cells” GenomeWeb News (2010)

    Arnaud, Celia Henry “Proteomics: Single-molecule methods quantify bacterium’s proteome” Chemical & Engineering News 88, 15 (2010)

  16. Taniguchi, Y., Yanagida, T. “The forward and backward stepping processes of kinesin are gated by ATP binding”, Biophysics  4, 11-18 (2008)
  17. Ishii, Y., Taniguchi, Y., Iwaki, M., Yanagida, T. “Thermal fluctuations biased for directional motion in molecular motors”, Biosystems  93, 34-38 (2008)
  18. Taniguchi, Y., Karagiannis, P., Nishiyama, M., Ishii, Y., Yanagida, T. “Single molecule thermodynamics in biological motors”, Biosystems  88, 283-292 (2007)
  19. Taniguchi, Y. “Entropy rectifies the Brownian steps of kinesin”, Annual Report of Osaka University  7, 47 (2006)
  20. Taniguchi, Y., Nishiyama, M., Ishii, Y., Yanagida, T. “Entropy rectifies the Brownian steps of kinesin”, Nature Chemical Biology  1, 342-347 (2005)

    Amos, Linda A. “Molecular motors: rocking and rolling.Nature Chemical Biology  1, 319 (2005).

  21. Nishiyama, M., Higuchi, H., Ishii, Y., Taniguchi, Y., Yanagida, T. “Single molecule processes on the stepwise movement of ATP-driven molecular motors”, Biosystems  71, 145-156 (2003)
  22. Ishii, Y., Komori, Y., Okada, T., Iwaki, M., Taniguchi, Y., Yanagida, T. “Detection of thermal processes of protein function”, Single molecules  3, 149-153 (2002)


  1. Kumar, V., Leclerc, S., Taniguchi, Y. 「Single molecule detection in the study of gene expression」, Single-Molecule Science (eds. Appasani, K. and Appasani, R. K.), Cambridge University Press, p127-141,May 2022
  2. Taniguchi, Y.「Thinking small numbers: When, where, and how many molecules there are in the cell」Minotiries and small numbers from molecules to organisms in biology (eds. Nagai, T., Togashi, Y.)、Springer、p93-98、November 2018


  1. Taniguchi, Y., Johmura, M. Spectroscopic analysis device, spectroscopic analysis method, program, recording medium and microscope, PCT/JP2018/048329
  2. Taniguchi, Y., Leclerc, S. Data analyzer, program and recording medium and data analysis method, JP2017177070A
  3. Taniguchi, Y., Nishimura, K. Microscope, focusing unit, fluid holding unit, and optical unit, JP6086366, US9880378, US1222601, US0712547, DE202014011312, DE02014011332, EP2983029, EP3657229
  4. Xie, X. S., Sims, P. A., Greenleaf, W. J., Taniguchi, Y., Shiroguchi, K., Kim, S. Methods and systems for single-molecule RNA expression profiling, WO/2010/138960