Thomas Hagan.

Thomas Hagan, PhD

  • Assistant Professor, UC Department of Pediatrics



Vaccines are incredibly effective tools for improving public health, as demonstrated by the recent COVID-19 pandemic. However, there is significant variability across vaccines in their capability to induce broad, potent and long-lasting immune responses. The mechanisms by which some vaccines promote more potent or durable responses than others are not well understood. Gaining insight into these mechanisms will improve future vaccine development.

My research aims to harness computational approaches for integrating diverse high-throughput datasets to understand how the immune system's various components coordinate during response to infection or stimulation. I am particularly interested in using these approaches to understand how novel adjuvants or vaccine formulations can improve the magnitude, breadth and durability of immune responses to vaccination.

Another area of interest in my lab is examining how changes in the gut microbiome shape immune homeostasis and responsiveness. During my postdoctoral training, I demonstrated that antibiotics-induced gut microbiome perturbation could impair antibody responses to influenza vaccination in humans (Hagan et al., Cell 2019).

Furthermore, multi-omic data integration in this study identified strong associations between perturbations in bile acid metabolism due to loss of key bacterial species in the gut and systemic inflammatory responses detected in blood following antibiotics treatment, demonstrating the potential for the gut microbiome to regulate immunity through its impact on host metabolism. These findings have prompted further work in my lab to understand microbiome-immune system interactions and the relationship between the microbiome and chronic inflammation during aging, which is a central component of the pathogenesis of many age-related diseases.

I began my work at Cincinnati Children's in 2021.

BS: Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN.

PhD: Bioengineering, University of California, San Diego, La Jolla, CA.

Postdoctoral Fellowship: Stanford University, Stanford, CA.


Systems immunology; vaccinology; microbiome-immune system interaction

Research Areas

Infectious Diseases



Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses. Hagan, T; Gerritsen, B; Tomalin, LE; Fourati, S; Mulè, MP; Chawla, DG; Rychkov, D; Henrich, E; Miller, HE R; Diray-Arce, J; et al. Nature Immunology. 2022; 23:1788-1798.


Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Arunachalam, PS; Scott, MK D; Hagan, T; Li, C; Feng, Y; Wimmers, F; Grigoryan, L; Trisal, M; Edara, VV; Lai, L; et al. Nature. 2021; 596:410-416.


Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans. Hagan, T; Cortese, M; Rouphael, N; Boudreau, C; Linde, C; Maddur, MS; Das, J; Wang, H; Guthmiller, J; Zheng, NY; et al. Cell. 2019; 178:1313-1328.e13.

Multi-omics analysis of mucosal and systemic immunity to SARS-CoV-2 after birth. Wimmers, F; Burrell, AR; Feng, Y; Zheng, H; Arunachalam, PS; Hu, M; Spranger, S; Nyhoff, LE; Joshi, D; Trisal, M; et al. Cell. 2023; 186:4632-4651.e23.

SREBP signaling is essential for effective B cell responses. Luo, W; Adamska, JZ; Li, C; Verma, R; Liu, Q; Hagan, T; Wimmers, F; Gupta, S; Feng, Y; Jiang, W; et al. Nature Immunology. 2023; 24:337-348.

Ablation of Adar1 in myeloid cells imprints a global antiviral state in the lung and heightens early immunity against SARS-CoV-2. Adamska, JZ; Verma, R; Gupta, S; Hagan, T; Wimmers, F; Floyd, K; Li, Q; Valore, EV; Wang, Y; Trisal, M; et al. Cell Reports. 2023; 42:112038.

The Immune Signatures data resource, a compendium of systems vaccinology datasets. Diray-Arce, J; Miller, HE R; Henrich, E; Gerritsen, B; Mulè, MP; Fourati, S; Gygi, J; Hagan, T; Tomalin, L; Rychkov, D; et al. Scientific Data. 2022; 9:635.

Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination. Fourati, S; Tomalin, LE; Mulè, MP; Chawla, DG; Gerritsen, B; Rychkov, D; Henrich, E; Miller, HE R; Hagan, T; Diray-Arce, J; et al. Nature Immunology. 2022; 23:1777-1787.

Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. Ozonoff, A; Schaenman, J; Jayavelu, ND; Milliren, CE; Calfee, CS; Cairns, CB; Kraft, M; Baden, LR; Shaw, AC; Krammer, F; et al. EBioMedicine. 2022; 83:104208.

Candida albicans oscillating UME6 expression during intestinal colonization primes systemic Th17 protective immunity. Shao, TY; Kakade, P; Witchley, JN; Frazer, C; Murray, KL; Ene, IV; Haslam, DB; Hagan, T; Noble, SM; Bennett, RJ; et al. Cell Reports. 2022; 39:110837.