A photo of Matthew Kofron.

J. Matthew Kofron, PhD

  • Director, Confocal Imaging Core
  • Professor, UC Department of Pediatrics



I chose to become a researcher because of my passion for discovery and innovation. My research interests include developmental biology, germ layer formation, cell signaling, microscopy, immunology, lung biology and digestive disease. I began my work at Cincinnati Children’s in 2000 and have more than 30 years of research experience. I received the Senior Faculty Service award in 2020 from Cincinnati Children’s.

In my early career, I focused on embryonic development and cell-cell signaling. I now facilitate the use of microscopy and advanced imaging for other researchers in the Cincinnati Children’s Research Foundation in the Confocal Imaging Core (CIC). This type of advanced imaging provides a high resolution that allows microscopic visualization down to the subcellular level. In addition to imaging, we have developed tools for analysis and methodologies for image interpretation for quantitative analysis.

My work has been published in various publications, including Nature, Cell Stem Cell, Developmental Cell, Nature Cell Biology, Clinical Cytometry, Genes and Brain Behavior and Hepatology.


In situ mapping identifies distinct vascular niches for myelopoiesis. Zhang, J; Wu, Q; Johnson, CB; Pham, G; Kinder, JM; Olsson, A; Slaughter, A; May, M; Weinhaus, B; D’Alessandro, A; et al. Nature. 2021; 590:457-462.

Patient-Derived Organotypic Epithelial Rafts Model Phenotypes in Juvenile-Onset Recurrent Respiratory Papillomatosis. Bedard, MC; Brusadelli, MG; Carlile, A; Ruiz-Torres, S; Lodin, H; Lee, D; Kofron, M; Lambert, PF; Lane, A; Ameziane, N; et al. Viruses. 2021; 13.

Single-Cell Profiling of AKI in a Murine Model Reveals Novel Transcriptional Signatures, Profibrotic Phenotype, and Epithelial-to-Stromal Crosstalk. Rudman-Melnick, V; Adam, M; Potter, A; Chokshi, SM; Ma, Q; Drake, KA; Schuh, MP; Matthew Kofron, J; Devarajan, P; Steven Potter, S. Journal of the American Society of Nephrology : JASN. 2020; 31:2793-2814.

Lipopolysaccharide Reverses Hepatic Stellate Cell Activation Through Modulation of cMyb, Small Mothers Against Decapentaplegic, and CCAAT/Enhancer-Binding Protein C/EBP Transcription Factors. Sharma, A; Verma, AK; Kofron, M; Kudira, R; Miethke, A; Wu, T; Wang, J; Gandhi, CR. Hepatology. 2020; 72:1800-1818.

Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition. Hinge, A; He, J; Bartram, J; Javier, J; Xu, J; Fjellman, E; Sesaki, H; Li, T; Yu, J; Wunderlich, M; et al. Cell Stem Cell. 2020; 26:420-430.e6.

Endosome-Mediated Epithelial Remodeling Downstream of Hedgehog-Gli Is Required for Tracheoesophageal Separation. Nasr, T; Mancini, P; Rankin, SA; Edwards, NA; Agricola, ZN; Kenny, AP; Kinney, JL; Daniels, K; Vardanyan, J; Han, L; et al. Developmental Cell. 2019; 51:665-674.e6.

Human stomach-on-a-chip with luminal flow and peristaltic-like motility. Lee, KK; McCauley, HA; Broda, TR; Kofron, MJ; Wells, JM; Hong, CI. Lab on a Chip - Miniaturisation for Chemistry and Biology. 2018; 18:3079-3085.

AMP kinase promotes glioblastoma bioenergetics and tumour growth. Chhipa, RR; Fan, Q; Anderson, J; Muraleedharan, R; Huang, Y; Ciraolo, G; Chen, X; Waclaw, R; Chow, LM; Khuchua, Z; et al. Nature Cell Biology. 2018; 20:823-835.

A guide to choosing fluorescent protein combinations for flow cytometric analysis based on spectral overlap. Kleeman, B; Olsson, A; Newkold, T; Kofron, M; DeLay, M; Hildeman, D; Grimes, HL. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2018; 93:556-562.

From the Blog

Of Mice and Molecules: Our Confocal Imaging Core
Imaging Sciences

Of Mice and Molecules: Our Confocal Imaging Core

J. Matthew Kofron, PhD6/30/2019