Darren Cusanovich, PhD

Assistant Professor, Cellular and Molecular Medicine

Our lab is interested in understanding how the human genome regulates itself to bring about all of the cellular diversity present in our bodies. In addition, we are interested in how genetic variation and environmental exposures in human populations impact that regulation and sometimes leads to complex disease. The particular disease model that we focus on is asthma, a complex disease affecting ~10-20% of the population that involves many cell types of the lung and immune system and offers exquisitely detailed examples of gene-environment interactions that influence disease outcomes. To study these phenomena, we use single-cell genomics technologies so that we can evaluate the impact of genetic and environmental variability from the perspective of whole tissues rather than having to isolate individual cell types or use simplistic cellular models. Working at the nexus of functional genomics, computational biology, and cellular biology, our group is both experimental and computational and often has to develop novel technologies or methods to address our research questions.

Molecular Medicine Grad Program: 



Adelus, M. L., J. Ding, B. T. Tran, A. C. Conklin, A. K. Golebiewski, L. K. Stolze, M. B. Whalen, D. A. Cusanovich, and C. E. Romanoski, "Single cell 'omic profiles of human aortic endothelial cells and human atherosclerotic lesions reveals heterogeneity of endothelial subtype and response to activating perturbations.", bioRxiv, 2024 Jan 17. PMCID: PMC10104082  PMID: 37066416


Kang, HJ., S. Allison, A. Spangenberg, T. Carr, R. Sprissler, M. Halonen, and D. A. Cusanovich, "Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 infection.", Sci Rep, vol. 12, issue 1, pp. 3047, 23 FEB 2022. PMCID: PMC8866503  PMID: 35197492


Watson, A. W., A. D. Grant, S. S. Parker, S. Hill, M. B. Whalen, J. Chakrabarti, M. W. Harman, M. R. Roman, B. L. Forte, C. C. Gowan, et al., "Breast tumor stiffness instructs bone metastasis via maintenance of mechanical conditioning.", Cell Rep, vol. 35, issue 13, pp. 109293, 2021 Jun 29. PMID: 34192535


Rai, V., D. X. Quang, M. R. Erdos, D. A. Cusanovich, R. M. Daza, N. Narisu, L. S. Zou, J. P. Didion, Y. Guan, J. Shendure, et al., "Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures.", Mol Metab, vol. 32, pp. 109-121, 2020 02 01. PMCID: PMC6961712  PMID: 32029221
Chang, E. H., A. L. Willis, C. E. Romanoski, D. A. Cusanovich, N. Pouladi, J. Li, Y. A. Lussier, and F. D. Martinez, "RV Infections in Asthmatics Increase ACE2 Expression and Cytokine Pathways Implicated in COVID-19.", Am J Respir Crit Care Med, 2020 Jul 10. PMID: 32649217
Domcke, S., A. J. Hill, R. M. Daza, J. Cao, D. R. O'Day, H. A. Pliner, K. A. Aldinger, D. Pokholok, F. Zhang, J. H. Milbank, et al., "A human cell atlas of fetal chromatin accessibility.", Science, vol. 370, issue 6518, 2020 11 13. PMCID: PMC7785298  PMID: 33184180


Allan, C. M., P. J. Heizer, Y. Tu, N. P. Sandoval, R. S. Jung, J. E. Morales, E. Sajti, T. D. Troutman, T. L. Saunders, D. A. Cusanovich, et al., "An upstream enhancer regulates expression in a tissue-specific manner.", J Lipid Res, vol. 60, issue 4, pp. 869-879, 2019 04 01. PMCID: PMC6446700  PMID: 30598475


Cusanovich, D. A., A. J. Hill, D. Aghamirzaie, R. M. Daza, H. A. Pliner, J. B. Berletch, G. N. Filippova, X. Huang, L. Christiansen, W. S. DeWitt, et al., "A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.", Cell, 2018 Jul 18. PMID: 30078704
Pliner, H. A., J. S. Packer, J. L. McFaline-Figueroa, D. A. Cusanovich, R. M. Daza, D. Aghamirzaie, S. Srivatsan, X. Qiu, D. Jackson, A. Minkina, et al., "Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.", Mol Cell, 2018 Jul 23. PMID: 30078726