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research areas: Spectrum Analysis, Raman
research areas: Single-Cell Analysis
research areas: Transcriptome
research areas: Gene Expression Profiling
research areas: Microscopy
mailing address: https://profiles.uchicago.edu/profiles/profile/59710921
middle name or initial: J
overview: 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.
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Authorship 180355
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linked author: Kobayashi-Kirschvink, Koseki
linked information resource: Label-free morpho-molecular phenotyping of living cancer cells by combined Raman spectroscopy and phase tomography.

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linked information resource: Episymbiotic bacterium induces intracellular lipid droplet production in its host bacteria.

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linked information resource: Label-Free Detection of Biochemical Changes during Cortical Organoid Maturation via Raman Spectroscopy and Machine Learning.

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linked information resource: Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells.

Authorship 180359
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linked information resource: Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA.

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linked information resource: Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria.

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linked information resource: Linear Regression Links Transcriptomic Data and Cellular Raman Spectra.

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linked information resource: cAMP-CRP acts as a key regulator for the viable but non-culturable state in Escherichia coli.

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linked information resource: High-Throughput Raman Spectroscopy by Horizontally Shifted Collection Fibers.

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linked information resource: Spatial multiomic landscape of the human placenta at molecular resolution.

cAMP-CRP acts as a key regulator for the viable but non-culturable state in Escherichia coli.
PubMed Identifier: 29458560
author list: Nosho K, Fukushima H, Asai T, Nishio M, Takamaru R, Kobayashi-Kirschvink KJ, Ogawa T, Hidaka M, Masaki H
published in: Microbiology (Reading, England)
information resource reference: 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.
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Linear Regression Links Transcriptomic Data and Cellular Raman Spectra.
PubMed Identifier: 29936183
author list: Kobayashi-Kirschvink KJ, Nakaoka H, Oda A, Kamei KF, Nosho K, Fukushima H, Kanesaki Y, Yajima S, Masaki H, Ohta K, Wakamoto Y
published in: Cell systems
information resource reference: Linear Regression Links Transcriptomic Data and Cellular Raman Spectra. Cell Syst. 2018 07 25; 7(1):104-117.e4.
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Episymbiotic bacterium induces intracellular lipid droplet production in its host bacteria.
PubMed Identifier: 37732248
author list: Dong PT, Tian J, Kobayashi-Kirschvink KJ, Cen L, McLean JS, Bor B, Shi W, He X
published in: bioRxiv : the preprint server for biology
information resource reference: Episymbiotic bacterium induces intracellular lipid droplet production in its host bacteria. bioRxiv. 2023 Sep 06.
journal title abbreviation: bioRxiv
publication date: 2023-09-06T00:00:00
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Label-Free Detection of Biochemical Changes during Cortical Organoid Maturation via Raman Spectroscopy and Machine Learning.
PubMed Identifier: 39993137
author list: Bruno G, Lipinski M, Kobayashi-Kirschvink KJ, Tentellino C, So PTC, Kang JW, De Angelis F
published in: Analytical chemistry
information resource reference: 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.
journal title abbreviation: Anal Chem
publication date: 2025-02-24T00:00:00
year: 2025
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Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA.
PubMed Identifier: 38200118
author list: 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
published in: Nature biotechnology
information resource reference: Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. Nat Biotechnol. 2024 Nov; 42(11):1726-1734.
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publication date: 2024-01-10T00:00:00
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Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria.
PubMed Identifier: 38366018
author list: Dong PT, Tian J, Kobayashi-Kirschvink KJ, Cen L, McLean JS, Bor B, Shi W, He X
published in: The ISME journal
information resource reference: Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria. ISME J. 2024 Jan 08; 18(1).
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Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells.
PubMed Identifier: 37998148
author list: Ghislanzoni S, Kang JW, Bresci A, Masella A, Kobayashi-Kirschvink KJ, Polli D, Bongarzone I, So PTC
published in: Biosensors
information resource reference: 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).
journal title abbreviation: Biosensors (Basel)
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Spatial multiomic landscape of the human placenta at molecular resolution.
PubMed Identifier: 39567716
author list: 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
published in: Nature medicine
information resource reference: Spatial multiomic landscape of the human placenta at molecular resolution. Nat Med. 2024 Dec; 30(12):3495-3508.
journal title abbreviation: Nat Med
publication date: 2024-11-20T00:00:00
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type: Academic Article
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Label-free morpho-molecular phenotyping of living cancer cells by combined Raman spectroscopy and phase tomography.
PubMed Identifier: 38951178
author list: Bresci A, Kobayashi-Kirschvink KJ, Cerullo G, Vanna R, So PTC, Polli D, Kang JW
published in: Communications biology
information resource reference: Label-free morpho-molecular phenotyping of living cancer cells by combined Raman spectroscopy and phase tomography. Commun Biol. 2024 06 29; 7(1):785.
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High-Throughput Raman Spectroscopy by Horizontally Shifted Collection Fibers.
PubMed Identifier: 39038806
author list: Kobayashi-Kirschvink KJ, Matlock A, So PTC, Kang JW
published in: Analytical chemistry
information resource reference: High-Throughput Raman Spectroscopy by Horizontally Shifted Collection Fibers. Anal Chem. 2024 Aug 06; 96(31):12598-12601.
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publication date: 2024-07-22T00:00:00
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