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Research

Research

BDR researchers coming from diverse research fields are working together to achieve higher goals.

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Seminars & Symposia

BDR hosts annual symposium and regular seminars inviting international scientists in life science.

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Careers & Study

BDR embraces people from diverse backgrounds, and strives to create an open and supportive setting for research.

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Outreach

BDR communicates the appeal and significance of our research to society through the use of various media and activities.

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About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Team leder, Yuichi Taniguch

Team Leader
Yuichi Taniguchi Ph.D.

Laboratory for Cell Systems Control

LocationOsaka / Quantitative Biology Buildings

E-mailtaniguchi[at]riken.jp

Please replace [at] with @.

Elucidating the rules and logic of single cell systems dynamics

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.

Selected Publications

Ohno M, Ando T, Priest DG, Taniguchi Y.
Hi-CO: 3D genome structure analysis with nucleosome resolution.
Nature Protocols 16(7), 3439-3469 (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: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa004/5713458

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, et al.
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.
Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level.
Journal of visualized experiments : JoVE (2019) doi: 10.3791/59199

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(8), 2541-2549 (2018) doi: 10.1021/acs.bioconjchem.8b00226

Ohno M, Priest DG, Taniguchi Y.
Nucleosome-level 3D organization of the genome.
Biochemical Society transactions 46(3), 491-501 (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

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)

Members

Yuichi Taniguchi

Team Leader

Masae Ohno Johmura

Visiting Scientist

Soo Yeon Kim

Special Postdoctoral Researcher

Mayumi Ishida

Technical Staff I

Kaori Tsujimura

Technical Staff I

Binti Kamarulzaman Latiefa

Student Trainee

Shouko Ohara

Administrative Part-time Worker II

Yuriko Okuda

Assistant

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