Dr. Kobayashi leads an interdisciplinary research group that integrates expertise from physics, machine learning, and genomics to investigate dynamical biological processes at single-cell resolution. The lab specializes in developing novel optical and genomic technologies aimed at uncovering fundamental principles underlying cellular self-organization into complex multicellular systems, such as embryos and organoids, and elucidating mechanisms of tumor development from otherwise healthy tissues.
A central approach of Dr. Kobayashi's research is combining label-free microscopy techniques, notably Raman microscopy, with genomic profiling methods, including single-cell RNA sequencing, leveraging machine learning methodologies. This integration led to the creation of Raman2RNA, a method demonstrating the capability to predict genomic profiles in live single cells through deep neural networks. Raman2RNA realizes a ‘live-cell omics’, enabling one to monitor genomic changes in individual cells over extended periods.
Additionally, Dr. Kobayashi's lab develops advanced high-speed Raman microscopes designed to overcome the typically long measurement times associated with conventional Raman imaging. Reducing these measurement times is essential as it facilitates new research applications, particularly in studying gene expression dynamics on large scales, both in vitro and in vivo.
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
Episymbiotic bacterium induces intracellular lipid droplet production in its host bacteria.
Episymbiotic bacterium induces intracellular lipid droplet production in its host bacteria. bioRxiv. 2023 Sep 06.
PMID: 37732248
Linear Regression Links Transcriptomic Data and Cellular Raman Spectra.
Linear Regression Links Transcriptomic Data and Cellular Raman Spectra. Cell Syst. 2018 07 25; 7(1):104-117.e4.
PMID: 29936183
cAMP-CRP acts as a key regulator for the viable but non-culturable state in Escherichia coli.
cAMP-CRP acts as a key regulator for the viable but non-culturable state in Escherichia coli. Microbiology (Reading). 2018 03; 164(3):410-419.
PMID: 29458560