Koseki Kobayashi-Kirschvink
| Title | Assistant Professor |
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| Institution | University of Chicago |
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| Department | Medicine-Genetic Medicine |
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| Address | Chicago IL 60637
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| vCard | Download vCard |
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Overview
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.
Biography
| University of Tokyo, Tokyo | PhD | 09/2018 | Biophysics |
| University of Tokyo, Tokyo | B.E. | 03/2013 | Applied Physics |
| Broad Institute of MIT and Harvard, Boston | Postdoc | 05/2025 | Biophysics |
Bibliographic
PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media.
(Note that publications are often cited in additional ways that are not shown here.)
Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication.
Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication.
Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.)
Click a Field or Translation tag to filter the publications.
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Jung BJ, Hohreiter A, Cook D, Hansen L, Taylor S, Kobayashi-Kirschvink KJ, Chaiken J, Guha S, Basu A. 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; PMCID: PMC12424688.
Citations:
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Bianchi L, Bresci A, Kobayashi-Kirschvink KJ, Paroni G, Saccomandi P, So PTC, Kang JW. A Multimodal Imaging Framework to Advance Phenotyping of Living Label-free Breast Cancer Cells. J Vis Exp. 2025 Aug 22; (222).
PMID: 40920637.
Citations: Fields:
Translation:
HumansCells
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Comiter C, Chen X, Vaishnav ED, Kobayashi-Kirschvink KJ, Ciampricotti M, Zhang K, Murray J, Monticolo F, Qi J, Tanaka R, Brodowska SE, Li B, Yang Y, Rodig SJ, Karatza A, Villalonga AQ, Turner M, Pfaff KL, Jané-Valbuena J, Slyper M, Waldman J, Vigneau S, Wu J, Blosser TR, Segerstolpe Å, Abravanel DL, Wagle N, Demehri S, Zhuang X, Rudin CM, Klughammer J, Rozenblatt-Rosen O, Stultz CM, Shu J, Regev A. Inference of single cell profiles from histology stains with the Single Cell omics from Histology Analysis Framework (SCHAF). bioRxiv. 2025 Jun 13.
PMID: 36993643; PMCID: PMC10055250.
Citations:
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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.
PMID: 39993137; PMCID: PMC11912127.
Citations:
3 Fields:
Translation:
HumansCells
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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.
PMID: 39567716; PMCID: PMC12660148.
Citations:
9 Fields:
Translation:
HumansCells
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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.
PMID: 39038806; PMCID: PMC11307246.
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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.
PMID: 38951178; PMCID: PMC11217291.
Citations:
1 Translation:
HumansCells
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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.
PMID: 38200118; PMCID: PMC11233426.
Citations:
33 Fields:
Translation:
AnimalsCells
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Dong PT, Tian J, Kobayashi-Kirschvink KJ, Cen L, McLean JS, Bor B, Shi W, He X. Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria. ISME J. 2024 Jan 08; 18(1).
PMID: 38366018; PMCID: PMC10939385.
Citations:
10 Fields:
Translation:
HumansCells
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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).
PMID: 37998148; PMCID: PMC10669708.
Citations:
3 Fields:
Translation:
HumansCells
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Dong PT, Tian J, Kobayashi-Kirschvink KJ, Cen L, McLean JS, Bor B, Shi W, He X. Episymbiotic bacterium induces intracellular lipid droplet production in its host bacteria. bioRxiv. 2023 Sep 06.
PMID: 37732248; PMCID: PMC10508740.
Citations:
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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.
PMID: 29936183.
Citations:
23 Fields:
Translation:
AnimalsCells
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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.
PMID: 29458560.
Citations:
12 Fields:
Translation:
Cells
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| Year | Publications |
|---|
| 2018 | 2 |
| 2023 | 2 |
| 2024 | 5 |
| 2025 | 4 |
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This graph shows the number and percent of publications by field.
Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications.
Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
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