[Single Cell Analysis] Innovative technology platforms for integrated single cell analysis

※ Affiliations and titles are as of the end of the research activity.

Strategic Objects

Creation of Integrated Single Cell Analysis Fundamental Technology contribute to the elucidation of biological functions

Research Supervisor

Itaru Hamachi(Professor, Graduate School of Engineering, Kyoto University)


This Research Area will bring together individual researchers with technological challenges, thereby navigating their challenges towards the establishment of core technologies in next-generation single-cell analysis toolkits.
We would like aim to construct a platform made of fundamental analytical technologies that streamlines data-based single cell phenotyping. This platform is anticipated to realize quantitative, multiplexed analyses of a variety of biomolecules including nucleic acids, proteins, saccharides, lipids etc and the complex interactions at the intracellular and intercellular levels. Obviously, it requires diverse interdisciplinary approaches in nanotechnology, engineering, chemistry, optics, materials science, chemical biology, information science, which should be mixed with the steady progress in traditional biotechnology, on the basis of the deep understanding of real needs in life science communities. Therefore this Research Area welcomes ambitious young individuals to form a multidisciplinary virtual-network institute and nurtures them with its diversity to help them found their own unique technologies.
Open innovation is an integral part of this Research Area. Marketing might be considered even at the early phase in some cases, although too short-sighted project is not supported. Rather, all the PRESTO researchers are required to recognize that matured technologies must be accepted by intended users, and that the long-running development process must involve active, collaborative, and open efforts with both academic and industrial stakeholders at all times. Thus synergistically, this Research Area as a whole is committed to world-leading single cell analysis community with its potential to drive science and technology innovation.

Research Area Advisors

・Kazunari Akiyoshi
Professor, Kyoto University

・Hiroyuki Aburatani
Professor, The University of Tokyo

・Takehiko Itoh
Professor, Tokyo Institute of Technology

・Mitsuyoshi Ueda
Professor, Kyoto University

・Takeaki Ozawa
Professor, The University of Tokyo

・Hideki Kambara
Fellow Emeritus, Hitachi, Ltd.

・Yukiko Gotoh
Professor, The University of Tokyo

・Keiko Shimamoto
Manager and Exective Researcher,
Suntory Foundation for Life Sciences Bioorganic Research Institute

・Kouhei Tsumoto
Professor, The University of Tokyo

・Hiroyuki Noji
Professor, The University of Tokyo

・Yoshinobu Baba
Professor, Nagoya University

・Michiyuki Matsuda
Professor, Kyoto University

Year Started : 2014

Development of nanodiamond bioimaging for three-dimensional structural dynamics

Research Director:
Ryuji Igarashi(PRESTO Researcher, Japan Science and Technology Agency)

Development of deep imaging techniques for analyzing single cells in tissues

Research Director:
Keisuke Isobe(Research Scientist, Center for Advanced Photonics, RIKEN)

Single-cell manipulation of gene expression dynamics in three dimensional tissues

Research Director:
Itaru Imayoshi(Associate Professor, Graduate School of Biostudies, Kyoto University)

Single cell analysis for circadian clock regulated cell fate decidion

Research Director:
Motomu Endo(Associate Professor, Graduate school of biostudies, Kyoto University)

Ultrafast fluorescence imaging for image-activated flow cytometry

Research Director:
Sadao Ota(PRESTO Researcher, Japan Science and Technology Agency)

Elucidating how fine-scale subnetworks that have a reciprocal connection and share common inputs process information

Research Director:
Fumitaka Osakada(Associate Professor, Graduate School of Pharmaceutical Sciences, Nagoya University)

RNA imaging in living cells by using novel artificial nucleic acid, SNA

Research Director:
Hiromu Kashida(Associate Professor, Graduate School of Engineering, Nagoya University)

Single cell analysis by using multifunctional fluorescence probes

Research Director:
Mako Kamiya(Lecturer, Graduate School of Medicine, The University of Tokyo)

Ultra-sensitive CE-MS Analytical System for Trace-level Proteomics Abstract

Research Director:
Takayuki Kawai(Special Postdoctoral Researcher, Quantitative Biology Center (QBiC), RIKEN)

Development of Nano ElectroChemical Microscopy for Chemical Mapping

Research Director:
Yasufumi Takahashi(Associate Professor, College of Science and Engineering, Kanazawa University)

Creation of spatial cell dissection technology for disassembling single cells

Research Director:
Kyohei Terao(Associate Professor, Faculty of Engineering, Kagawa University)

Cryogenic fluorescence microscope designed for localization of individual proteins in a cell

Research Director:
Satoru Fujiyoshi(Assitant Professor, Department of Physics, School of Science, Tokto Institute of Technology)

Live imaging of hierarchical chromatin structures

Research Director:
Yusuke Miyanari(Associated professor, Okazaki Institute for Integrative Bioscience, National Institute for Natural Science)

DNA Barclock Technology to track cellular lineages at the single cell resolution

Research Director:
Nozomu Yachie(Associate Professor, Research Center for Advanced Science and Technology, The University of Tokyo)

Year Started : 2015

Application of fluid to analysis of developmental system

Research Director:
Hidehiko Inomata(Team Leader, Center for Developmental Biology (CDB), RIKEN)

Development of comprehensive analysis technology for intercellular phenotypic heterogeneity

Research Director:
Hiroshi Ochiai(PRESTO Researcher, Japan Science and Technology Agency)

Development of a single-cell nucleic acid analytical technique for understanding biological systems and its applications for medical sciences

Research Director:
Katsuyuki Shiroguchi(Unit Leader, Center for Biosystems Dynamics Research, RIKEN)

Comprehensive cell analysis by 3D histopathology

Research Director:
Etsuo Susaki(Lecturer, Graduate school of medicine, The University of Tokyo)

Single-cell energy perturbation and quantification in a living organism

Research Director:
Madoka Suzuki(Lecturer, Institute for Protein Research, Osaka University)

Functional and molecular characterization of neuronal microcircuits located in deep brain structures to elucidate emotion regulation

Research Director:
Sayaka Takemoto-Kimura(Professor, Research Institute of Environmental Medicine, Nagoya University)

Linking dynamics of genome, transcriptome and proteome in single cells

Research Director:
Yuichi Taniguchi(Unit Leader, Quantitative Biology Center (QBiC), RIKEN)

Deciphering the individuality of a cell by single molecule analysis of membrane molecule dynamics

Research Director:
Hiroko Bannai(PRESTO Researcher, Japan Science and Technology Agency)

Analysis of secretion from single cells by using droplet-based analytical system

Research Director:
Mao Fukuyama(Associate Professor, Institute of Multidisciplinary Research for Advanced Material, Tohoku Univesity)

Massively parallel single-cell genomics for elucidation of intra-tissue genetic heterogeneity

Research Director:
Masahito Hosokawa(PRESTO Researcher, Japan Science and Technology Agency)

Development of Single Cell Analytical Technology to Elucidate Biological Functions of Cancer Stem Cells

Research Director:
Michiya Matsusaki(Associate Professor, Department of Applied Chemistry, Graduate School of Engineering, Osaka University)

Simultaneous acquisition of methylome and transcriptome data from a single cell

Research Director:
Fumihito Miura(Lecturer, Graduate School of Medical Sciences, Kyushu University)

Development of ultimate spatiotemporal resolution AFM for visualizing membrane molecular dynamics in single living cell

Research Director:
Hayato Yamashita(Assistant Professor, Center for Science and Technology under Extreme Conditions, Graduate School of Engineering Science, Osaka University)

Unlocking the mysteries of cellular heterogeneity by single cell proteome profiling

Research Director:
Masaki Wakabayashi(Laboratory Chief, Omics Research Center, National Cerebral and Cardiovascular Center)

Year Started : 2016

Reverse optogenetics for hypothesis-free neural network analysis at single-cell resolution

Research Director:
Wataru Aoki(Assistant Professor, Graduate School of Agriculture, Kyoto University)

Development of polymer-based photonic crystal nanoresonator array with intracellular functions and its application for label-free detection of single cell metabolites

Research Director:
Tatsuro Endo(Associate Professor, Graduate School of Engineering, Osaka Prefecture University)

Predictive control of three-dimensional tissue morphogenesis based on complete modeling of single cell dynamics

Research Director:
Satoru Okuda(Associate Professor, Research Promotion Affairs Division, Kanazawa University)

Development of a microfluidic palpation device for single-cell analysis

Research Director:
Noritada Kaji(Professor, Graduate School of Engineering, Kyushu University)

Creation of precise analytical techniques for the investigation of intracellular lipid dynamics

Research Director:
Masayasu Taki(Designated Associate Professor, Institute of Transformative Bio-Molecules, Nagoya University)

Development of an ultrasensitive and nondestructive method to analyze single cell glycome

Research Director:
Hiroaki Tateno(Chief Senior Researcher, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology)

Ultrastructural examination of single neurons in mammalian brains

Research Director:
Yusuke Hirabayashi(Postdoctoral Fellow, Department of Neuroscience, Columbia University)

Analysis of somatic mutations in brain cells using a cell nuclei separation technique

Research Director:
Miki Bundo(Associate professor, Faculty of Life Sciences, Kumamoto University)

Comprehensive, single-cell analysis of the localization and dynamics of endogenous proteins in brain tissue

Research Director:
Takayasu Mikuni(Research Scientist, Neuronal Signal Transduction Group, Max Planck Florida Institute for Neuroscience)

Photo-responsive cell-immobilization surfaces for single-cell manipulation

Research Director:
Satoshi Yamaguchi(Lecturer, Research Center for Advanced Science and Technology, The University of Tokyo)

DNA aptamer scaffolds for mesenchymal cells regulation

Research Director:
Keitaro Yoshimoto(Associate Professor, Graduate School of Arts and Sciences, The University of Tokyo)

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