Hagan Lab

Publications

Doni Jayavelu, N; Samaha, H; Wimalasena, ST; Hoch, A; Gygi, JP; Gabernet, G; Ozonoff, A; Liu, S; Milliren, CE; Levy, O; Diray-Arce, J; Becker, PM; Rouphael, N; Altman, MC. Machine learning models predict long COVID outcomes based on baseline clinical and immunologic factors. Communications Medicine. 2026; 6(1):1.

Jayavelu, ND; Qi, J; Milliren, CE; Ozonoff, A; Liu, S; Levy, O; Baden, LR; Melamed, E; Mccomsey, GA; Cairns, CB; Montgomery, RR; Becker, PM; Altman, MC; Fourati, S. Type 2 immune responses are associated with less severe COVID-19 in a hospitalized cohort. Journal of Allergy and Clinical Immunology: Global. 2025; 4(4):100515.

Rowley, CA; Oliveira, A; Siddiqa, A; Otto, W; Danziger-Isakov, L; Hagan, T. Systems analysis of influenza vaccine response in chronic dialysis patients reveals altered immunometabolism 9399. Journal of Immunology. 2025; 214(Supplement_1).

Costa Monteiro, AC; Pickering, H; Sarma, A; Taylor, CS; Jenkins, MM; Hsu, F-M; Nadel, B; Levy, O; Baden, LR; Melamed, E; Salehi-Rad, R; Matthay, MA; Reed, EF; Sapru, A. Circulating endothelial signatures correlate with worse outcomes in COVID-19, respiratory failure and ARDS. Critical Care. 2025; 29(1):432.

Feng, Y; De Jong, SE; Oliveira, APBN; Samaha, H; Yang, F; Hu, M; Wang, Y; Beydoun, N; Xie, X; Zhang, H; Boyd, SD; Hagan, T; Rouphael, N; Pulendran, B. Antibiotic-induced gut microbiome perturbation alters the immune responses to the rabies vaccine. Cell Host and Microbe. 2025; 33(5):705-718.e5.

Hu, M; Oliveira, APBN; Fang, Z; Feng, Y; Miranda, M; Kowli, S; Arunachalam, PS; Vasudevan, G; Hui, HS-Y; Grifoni, A; Hagan, T; Dhillon, G; Nicolls, MR; Pulendran, B. Altered baseline immunological state and impaired immune response to SARS-CoV-2 mRNA vaccination in lung transplant recipients. Cell Reports Medicine. 2025; 6(4):102050.

Pickering, H; Schaenman, J; Phan, HV; Maguire, C; Tsitsiklis, A; Rouphael, N; Higuita, NIA; Atkinson, MA; Brakenridge, S; Fung, M; Baden, L; Levy, O; Reed, EF; Langelier, CR. Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients. Nature Communications. 2025; 16(1):586.

Cortese, M; Hagan, T; Rouphael, N; Wu, S-Y; Xie, X; Kazmin, D; Wimmers, F; Gupta, S; Van Der Most, R; Coccia, M; Mulligan, MJ; Khurana, S; Golding, H; Pulendran, B. System vaccinology analysis of predictors and mechanisms of antibody response durability to multiple vaccines in humans. Nature Immunology. 2025; 26(1):116-130.

Prates-Syed, WA; Lima, AA; Cortes, N; Carvalho, E; Queiroz Silva, JD; Hamaguchi, B; Durães-Carvalho, R; Cabral-Marques, O; Hagan, T; Krieger, JE; Cabral-Miranda, G. VaxGO: an interactive web tool for systems vaccinology data analysis. Bioinformatics Advances. 2025; 5(1):vbaf101.

Apps, R; Biancotto, A; Candia, J; Kotliarov, Y; Perl, S; Cheung, F; Farmer, R; Mulè, MP; Rachmaninoff, N; Chen, J; Dickler, HB; Germain, RN; Schwartzberg, PL; Tsang, JS. Acute and persistent responses after H5N1 vaccination in humans. Cell reports. 2024; 43(9):114706.

Saha, I; Chawla, AS; Oliveira, APBN; Elfers, EE; Warrick, K; Meibers, HE; Jain, VG; Hagan, T; Katz, JD; Pasare, C. Alloreactive memory CD4 T cells promote transplant rejection by engaging DCs to induce innate inflammation and CD8 T cell priming. Proceedings of the National Academy of Sciences of the United States of America. 2024; 121(34):e2401658121.

Haslund-Gourley, BS; Woloszczuk, K; Hou, J; Connors, J; Cusimano, G; Bell, M; Taramangalam, B; Fourati, S; Mege, N; Bernui, M; Kutzler, MA; Cairns, CB; Haddad, EK; Comunale, MA. IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. Nature Communications. 2024; 15(1):404.

Ozonoff, A; Jayavelu, ND; Liu, S; Melamed, E; Milliren, CE; Qi, J; Geng, LN; Mccomsey, GA; Cairns, CB; Baden, LR; Altman, MC; Montgomery, RR; Becker, PM; Rouphael, N. Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. Nature Communications. 2024; 15(1):216.

Rosenberg-Hasson, Y; Holmes, TH; Diray-Arce, J; Chen, J; Kellogg, R; Snyder, M; Becker, PM; Ozonoff, A; Rouphael, N; Reed, EF; Maecker, HT. Relationship of Heterologous Virus Responses and Outcomes in Hospitalized COVID-19 Patients. Journal of Immunology. 2023; 211(8):1224-1231.

Wimmers, F; Burrell, AR; Feng, Y; Zheng, H; Arunachalam, PS; Hu, M; Spranger, S; Nyhoff, LE; Joshi, D; Trisal, M; Khurana, S; Khatri, P; Staat, MA; Pulendran, B. Multi-omics analysis of mucosal and systemic immunity to SARS-CoV-2 after birth. Cell. 2023; 186(21):4632-4651.e23.

Luo, W; Adamska, JZ; Li, C; Verma, R; Liu, Q; Hagan, T; Wimmers, F; Gupta, S; Feng, Y; Jiang, W; Trisal, M; Subramaniam, S; Osborne, TF; Pulendran, B. SREBP signaling is essential for effective B cell responses. Nature Immunology. 2023; 24(2):337-348.

Adamska, JZ; Verma, R; Gupta, S; Hagan, T; Wimmers, F; Floyd, K; Li, Q; Valore, EV; Wang, Y; Trisal, M; Walkley, CR; Suthar, MS; Li, JB; Pulendran, B. Ablation of Adar1 in myeloid cells imprints a global antiviral state in the lung and heightens early immunity against SARS-CoV-2. Cell reports. 2023; 42(1):112038.

Fourati, S; Tomalin, LE; Mulè, MP; Chawla, DG; Gerritsen, B; Rychkov, D; Henrich, E; Miller, HER; Hagan, T; Diray-Arce, J; Suárez-Fariñas, M; Pulendran, B; Kleinstein, SH; Sékaly, R-P. Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination. Nature Immunology. 2022; 23(12):1777-1787.

Hagan, T; Gerritsen, B; Tomalin, LE; Fourati, S; Mulè, MP; Chawla, DG; Rychkov, D; Henrich, E; Miller, HER; Diray-Arce, J; Suárez-Fariñas, M; Sékaly, R-P; Kleinstein, SH; Pulendran, B. Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses. Nature Immunology. 2022; 23(12):1788-1798.

Diray-Arce, J; Miller, HER; Henrich, E; Gerritsen, B; Mulè, MP; Fourati, S; Gygi, J; Hagan, T; Tomalin, L; Rychkov, D; Floratos, A; Gottardo, R; Kleinstein, SH; Suárez-Fariñas, M. The Immune Signatures data resource, a compendium of systems vaccinology datasets. Scientific Data. 2022; 9(1):635.

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

Shao, T-Y; Kakade, P; Witchley, JN; Frazer, C; Murray, KL; Ene, IV; Haslam, DB; Hagan, T; Noble, SM; Bennett, RJ; Way, SS. Candida albicans oscillating UME6 expression during intestinal colonization primes systemic Th17 protective immunity. Cell reports. 2022; 39(7):110837.