Dr. Kobayashi leads an interdisciplinary research group that integrates physics, machine learning, and genomics to investigate dynamic biological processes at single-cell resolution. The lab develops new optical and molecular tools to reveal how cells self-organize into complex multicellular structures—such as embryos and tissues—and to elucidate immune-cell function within the tumor microenvironment. The group is particularly focused on a “live-cell omics” approach that measures genome-wide expression in living single cells, which is nearly impossible with conventional omics methods. These methods enable longitudinal tracking of genomic changes in individual cells, illuminating the molecular mechanisms of cell-fate determination and disease progression. The lab also builds next-generation, label-free microscopes that reduce the long acquisition times of conventional instruments, opening new possibilities for large-scale studies of molecular dynamics in vitro and in vivo.
Broad Institute of MIT and Harvard
Boston
Postdoc - Biophysics
2025
University of Tokyo
Tokyo
PhD - Biophysics
2018
University of Tokyo
Tokyo
B.E. - Applied Physics
2013
Capture, Confine, Characterize: High-Throughput Dielectrophoresis-Based Single-Cell Microfluidics Platform to Analyze Mammalian and Yeast Cells Using Raman Spectroscopy.
Capture, Confine, Characterize: High-Throughput Dielectrophoresis-Based Single-Cell Microfluidics Platform to Analyze Mammalian and Yeast Cells Using Raman Spectroscopy. bioRxiv. 2025 Sep 03.
PMID: 40950121
A Multimodal Imaging Framework to Advance Phenotyping of Living Label-free Breast Cancer Cells.
A Multimodal Imaging Framework to Advance Phenotyping of Living Label-free Breast Cancer Cells. J Vis Exp. 2025 Aug 22; (222).
PMID: 40920637
Inference of single cell profiles from histology stains with the Single Cell omics from Histology Analysis Framework (SCHAF).
Inference of single cell profiles from histology stains with the Single Cell omics from Histology Analysis Framework (SCHAF). bioRxiv. 2025 Jun 13.
PMID: 36993643
Label-Free Detection of Biochemical Changes during Cortical Organoid Maturation via Raman Spectroscopy and Machine Learning.
Label-Free Detection of Biochemical Changes during Cortical Organoid Maturation via Raman Spectroscopy and Machine Learning. Anal Chem. 2025 Mar 11; 97(9):5029-5037.
PMID: 39993137
Spatial multiomic landscape of the human placenta at molecular resolution.
Spatial multiomic landscape of the human placenta at molecular resolution. Nat Med. 2024 Dec; 30(12):3495-3508.
PMID: 39567716
High-Throughput Raman Spectroscopy by Horizontally Shifted Collection Fibers.
High-Throughput Raman Spectroscopy by Horizontally Shifted Collection Fibers. Anal Chem. 2024 Aug 06; 96(31):12598-12601.
PMID: 39038806
Label-free morpho-molecular phenotyping of living cancer cells by combined Raman spectroscopy and phase tomography.
Label-free morpho-molecular phenotyping of living cancer cells by combined Raman spectroscopy and phase tomography. Commun Biol. 2024 06 29; 7(1):785.
PMID: 38951178
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA.
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. Nat Biotechnol. 2024 Nov; 42(11):1726-1734.
PMID: 38200118
Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria.
Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria. ISME J. 2024 Jan 08; 18(1).
PMID: 38366018
Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells.
Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells. Biosensors (Basel). 2023 Nov 07; 13(11).
PMID: 37998148