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.
Nosho K, Fukushima H, Asai T, Nishio M, Takamaru R, Kobayashi-Kirschvink KJ, Ogawa T, Hidaka M, Masaki H
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.
cAMP-CRP acts as a key regulator for the viable but non-culturable state in Escherichia coli.
Kobayashi-Kirschvink KJ, Nakaoka H, Oda A, Kamei KF, Nosho K, Fukushima H, Kanesaki Y, Yajima S, Masaki H, Ohta K, Wakamoto Y
Linear Regression Links Transcriptomic Data and Cellular Raman Spectra. Cell Syst. 2018 07 25; 7(1):104-117.e4.
Linear Regression Links Transcriptomic Data and Cellular Raman Spectra.
Dong PT, Tian J, Kobayashi-Kirschvink KJ, Cen L, McLean JS, Bor B, Shi W, He X
bioRxiv : the preprint server for biology
Episymbiotic bacterium induces intracellular lipid droplet production in its host bacteria. bioRxiv. 2023 Sep 06.
Episymbiotic bacterium induces intracellular lipid droplet production in its host bacteria.
Bruno G, Lipinski M, Kobayashi-Kirschvink KJ, Tentellino C, So PTC, Kang JW, De Angelis F
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.
Label-Free Detection of Biochemical Changes during Cortical Organoid Maturation via Raman Spectroscopy and Machine Learning.
Kobayashi-Kirschvink KJ, Comiter CS, Gaddam S, Joren T, Grody EI, Ounadjela JR, Zhang K, Ge B, Kang JW, Xavier RJ, So PTC, Biancalani T, Shu J, Regev A
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. Nat Biotechnol. 2024 Nov; 42(11):1726-1734.
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA.
Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria. ISME J. 2024 Jan 08; 18(1).
Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria.
Ghislanzoni S, Kang JW, Bresci A, Masella A, Kobayashi-Kirschvink KJ, Polli D, Bongarzone I, So PTC
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).
Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells.
Ounadjela JR, Zhang K, Kobayashi-Kirschvink KJ, Jin K, J C Russell A, Lackner AI, Callahan C, Viggiani F, Dey KK, Jagadeesh K, Maxian T, Prandstetter AM, Nadaf N, Gong Q, Raichur R, Zvezdov ML, Hui M, Simpson M, Liu X, Min W, Knöfler M, Chen F, Haider S, Shu J
Spatial multiomic landscape of the human placenta at molecular resolution. Nat Med. 2024 Dec; 30(12):3495-3508.
Spatial multiomic landscape of the human placenta at molecular resolution.
Bresci A, Kobayashi-Kirschvink KJ, Cerullo G, Vanna R, So PTC, Polli D, Kang JW
Label-free morpho-molecular phenotyping of living cancer cells by combined Raman spectroscopy and phase tomography. Commun Biol. 2024 06 29; 7(1):785.
Label-free morpho-molecular phenotyping of living cancer cells by combined Raman spectroscopy and phase tomography.
Kobayashi-Kirschvink KJ, Matlock A, So PTC, Kang JW
High-Throughput Raman Spectroscopy by Horizontally Shifted Collection Fibers. Anal Chem. 2024 Aug 06; 96(31):12598-12601.
High-Throughput Raman Spectroscopy by Horizontally Shifted Collection Fibers.