Laboratory for Cell Systems Control | RIKEN BDR

Laboratory for Cell Systems Control

Team Leader

Yuichi TaniguchiPh.D.

Photo of principal investigator

  • Location:Osaka / Quantitative Biology Buildings
  • E-mail:taniguchi[at]riken.jpPlease replace [at] with @.
  • Lab Website

Elucidating the rules and logic of single cell systems dynamics

Research Summary

We are working to reveal rules and logic of single cell systems dynamics by developing innovative technologies. We aim to explore comprehensive and exhaustive properties of single cells based on cutting-edge technologies including single molecule imaging, high-throughput analysis, 3D genome structure analysis, molecular dynamics simulation, machine learning, MEMS and bioinformatics. We also intend to create new concepts for describing and understanding complex behaviors of single cells regulated by vast numbers of genes and bio-molecules. Ultimately, we aim to provide key principles for forecasting and controlling complex cell behaviors.

Research Theme

  • Establishment of single-molecule imaging methods for detecting biomolecules in single cells.
  • Development of methods for comprehensive and exhaustive characterization of the cell.
  • Exploring regulatory mechanisms of the cell based on genome structure and epigenome analyses.
  • Modeling rules and logic for complex single cell systems dynamics.
  • Development of methods for controlling cellular states and medical applications.

Main Publications List

  • Ohno M, Ando T, Priest DG, Taniguchi Y.
    Hi-CO: 3D genome structure analysis with nucleosome resolution.
    Nature Protocols (2021) doi: 10.1038/s41596-021-00543-z
  • Shinkai S, Nakagawa M, Sugawara T, et al.
    PHi-C: deciphering Hi-C data into polymer dynamics.
    NAR Genomics and Bioinformatics 2, lqaa020 (2020) doi: 10.1093/nargab/lqaa020
  • 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) doi: 10.1093/nar/gkaa004
  • Leclerc S, Arntz Y, Taniguchi Y.
    Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level.
    Journal of visualized experiments : JoVE (146). e59199 (2019) doi: 10.3791/59199
  • 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(1). 15-23 (2019) doi: 10.1508/cytologia.84.15
  • Ohno M, Ando T, Priest D.G.,
    Sub-nucleosomal genome structure reveals distinct nucleosome folding motifs.
    Cell 176(3). 520-534.e25 (2019) doi: 10.1016/j.cell.2018.12.014
  • 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 (2018) doi: 10.1021/acs.bioconjchem.8b00226
  • Ohno M, Priest DG, Taniguchi Y.
    Nucleosome-level 3D organization of the genome.
    Biochemical Society Transactions (2018) doi: 10.1042/BST20170388
  • Priest D, 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) doi: 10.1038/s41598-017-17544-2
  • Taniguchi Y.
    Autofluorescence imaging of tissue samples using super-high sensitivity fluorescence microscopy.
    Global Imaging Insights 2. 1-2 (2017) doi: 10.15761/GII.1000135
  • Taniguchi Y.
    Genome-Wide Analysis of Protein and mRNA Copy Numbers in Single Escherichia coli Cells with Single-Molecule Sensitivity.
    Methods in Molecular Biology 1346. 55-67 (2015) doi: 10.1007/978-1-4939-2987-0_5
  • Ohno M, Karagiannis P, Taniguchi Y.
    Protein Expression Analyses at the Single Cell Level.
    Molecules 19(9). 13932-13947 (2014) doi: 10.3390/molecules190913932
  • 谷口雄一、西村和哉
  • Taniguchi Y, Choi PJ, Li GW, et al.
    Quantifying E-coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells.
    Science 329(5991). 533-538 (2010) doi: 10.1126/science.1188308
  • Taniguchi Y, Nishiyama M, Ishii Y, Yanagida T.
    Entropy rectifies the Brownian steps of kinesin.
    Nature Chem. Biol. 1. 342-347 (2005)
  • ature Chem. Biol. 1. 342-347 (2005)