J. Matthew Kofron, PhD

Director, Bio-Imaging and Analysis Facility
Professor, UC Department of Pediatrics

About

Biography

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 Bio-Imaging and Analysis Facility. 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.

Interests

Early vertebrate patterning; germ layer formation

Research Areas

Publications

Differential regulation of fetal bone marrow and liver hematopoiesis by yolk-sac-derived myeloid cells. Weinhaus, B; Homan, S; Kincaid, M; Tadwalkar, A; Gu, X; Kumar, S; Slaughter, A; Zhang, J; Wu, Q; Kofron, JM; Troutman, TD; DeFalco, T; Lucas, D. Nature Communications. 2025; 16:4427.

Metabolic adaptation of regenerative hematopoiesis depends on docking-independent mitochondrial connexin 43. Singh, AK; D'Alessandro, A; Wellendorf, AM; Gonzalez-Nieto, D; Kofron, M; Dzieciatkowska, M; Mejia, L; Barrio, LC; Filippi, M; Cancelas, JA. Blood. 2025; 146:2306-2321.

Foxi2 and Sox3 are master transcription regulators that control ectoderm germ layer specification in Xenopus. Hendrickson, CL; Blitz, IL; Hussein, A; Paraiso, KD; Cho, JS; Klymkowsky, MW; Kofron, MJ; Cho, KW Y. PLoS Biology. 2025; 23:e3003476.

Early Life Injury Alters Spinal Astrocyte Development. Yoo, JJ; Serafin, EK; Kofron, JM; Baccei, ML. The Journal of neuroscience : the official journal of the Society for Neuroscience. 2025; 45:e1197252025.

Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in Xenopus trachea-esophageal morphogenesis. Edwards, NA; Rankin, SA; Kashyap, A; Warren, A; Agricola, ZN; Kenny, AP; Kofron, M; Shen, Y; Chung, WK; Zorn, AM. Developmental Cell. 2025; 60:2487-2502.e4.

Gucy1α1 specifically marks kidney, heart, lung and liver fibroblasts. Rudman-Melnick, V; Vanhoutte, D; Stowers, K; Sargent, M; Adam, M; Ma, Q; Perl, AK T; Miethke, AG; Burg, A; Shi, T; Hildeman, DA; Woodle, ES S; Kofron, JM; Devarajan, P. Scientific Reports. 2024; 14:29307.

Single-cell sequencing dissects the transcriptional identity of activated fibroblasts and identifies novel persistent distal tubular injury patterns in kidney fibrosis. Rudman-Melnick, V; Adam, M; Stowers, K; Potter, A; Ma, Q; Chokshi, SM; Vanhoutte, D; Valiente-Alandi, I; Lindquist, DM; Nieman, ML; Kofron, JM; Chung, E; Park, JS; Potter, SS; Devarajan, P. Scientific Reports. 2024; 14:439.

Trade-Offs in Deep Learning Model Loss and Configuration for Sparse Histological Segmentation: A Case Study in Pediatric Ileal Histology. Heekin, S; Lopez-Nunez, O; Smith, J; Denson, N; Denson, L; Miethke, A; Dillman, J; Miraldi, E; Kofron, JM; Dhaliwal, J; Erdman, L. (2024) Institute of Electrical and Electronics Engineers (IEEE). 00:1-8.

Heterogeneity of the Erythromyeloblastic Island (EMBI) Niche during Baseline and Stress Erythropoiesis. Seu, K; Romano, L; Ntoumaziou, A; Stewart, M; Gardner, JC; Paulson, R; Zheng, Y; Kofron, M; Blanc, L; Salomonis, N; Kalfa, TA. Blood. 2024; 144:163.

From the Blog

Imaging Sciences

Of Mice and Molecules: Our Confocal Imaging Core

J. Matthew Kofron, PhD6/30/2019