Publications

Chan, C., Loh, J. X., Sin, W.-X., Teo, D. B., Tan, N. K., Nagarajan, C., Chen, Y., Lim, F. L., Birnbaum, M. E., Williams, R. B. H., & Springs, S. L. (2025). Extracellular viral microRNAs as biomarkers of virus infection in human cells. Molecular Therapy Nucleic Acids, 36(1), 102444.

Lagattuta, K. A., Kohlgruber, A. C., Abdelfattah, N. S., Nathan, A., Rumker, L., Birnbaum, M. E., Elledge, S. J., & Raychaudhuri, S. (2025). The T cell receptor sequence influences the likelihood of T cell memory formation. Cell Reports, 44(1), 115098.

Cheung, K.-W., Kairi, F., Lin Teo, D. B., Sin, W.-X., Lee, Y. H., & Birnbaum, M. E. (2025). Use of cellular FAD autofluorescence as a label-free cellular attribute for the production of Chimeric Antigen Receptor-T Cells. bioRxiv.

Xu, E. J. K., Smith, B. E., Conce Alberto, W. D., Walsh, M. J., Lim, B., Hoffman, M. T., Qiang, L., Dong, J., Garmilla, A., Zhao, Q. H., Perez, C. R., Gaglione, S. A., Dobson, C. S., Dougan, M., Dougan, S. K., & Birnbaum, M. E. (2024). Peptide-MHC-targeted retroviruses enable in vivo expansion and gene delivery to tumor-specific T cells. bioRxiv.

Gaglione, S. A., Rosales, T. J., Schmidt-Hong, L., Baker, B. M., & Birnbaum, M. E. (2024). SARS-COV-2 spike does not interact with the T cell receptor or directly activate T cells. Proceedings of the National Academy of Sciences, 121(31).

Jeon, H., Perez, C. R., Kyung, T., Birnbaum, M. E., & Han, J. (2024). Separation of activated T cells using multidimensional double spiral (MDDS) inertial microfluidics for high-efficiency CAR T cell manufacturing. Analytical Chemistry, 96(26), 10780–10790.

Sin, W.-X., Jagannathan, N. S., Teo, D. B., Kairi, F., Fong, S. Y., Tan, J. H., Sandikin, D., Cheung, K.-W., Luah, Y. H., Wu, X., Raymond, J. J., Lim, F. L., Lee, Y. H., Seng, M. S.-F., Soh, S. Y., Chen, Q., Ram, R. J., Tucker-Kellogg, L., & Birnbaum, M. E. (2024). A high-density microfluidic bioreactor for the automated manufacturing of CAR T cells. Nature Biomedical Engineering, 8(12), 1571–1591.

Tano-Menka, R., Singh, N. K., Muzhingi, I., Li, X., Mandanas, M. V., Kaseke, C., Crain, C. R., Zhang, A., Ogunshola, F. J., Vecchiarello, L., Piechocka-Trocha, A., Bashirova, A., Birnbaum, M. E., Carrington, M., Walker, B. D., & Gaiha, G. D. (2024). Polymorphic residues in HLA-B that mediate HIV control distinctly modulate peptide interactions with both TCR and KIR Molecules. Structure, 32(8).

Gordon, K. S., Perez, C. R., Garmilla, A., Lam, M. S. Y., Aw, J. J., Datta, A., Lauffenburger, D. A., Pavesi, A., & Birnbaum, M. E. (2024). Pooled screening for CAR function identifies novel IL13Rα2-targeted CARs for treatment of glioblastoma. bioRxiv.

Pandit, S., Smith, B. E., Birnbaum, M. E., & Brudno, Y. (2024). A biomaterial platform for T cell-specific gene delivery. Acta Biomaterialia, 177, 157–164.

Lu, R., Ang, Y. S., Cheung, K., Quek, K. Y., Sin, W., Lee, E., Lim, S. L., Yung, L. L., Birnbaum, M. E., Han, J., Cheow, L. F., & Zeming, K. K. (2024). iSECRETE: Integrating microfluidics and DNA proximity amplification for synchronous single‐cell activation and IFN‐γ secretion profiling. Advanced Science, 11(40).

Perez, C. R., Garmilla, A., Nilsson, A., Baghdassarian, H. M., Gordon, K. S., Lima, L. G., Smith, B. E., Maus, M. V., Lauffenburger, D. A., & Birnbaum, M. E. (2024). Library-based single-cell analysis of CAR signaling reveals drivers of in vivo persistence. bioRxiv.

Ramos, A., Koch, C. E., Liu-Lupo, Y., Hellinger, R. D., Kyung, T., Abbott, K. L., Fröse, J., Goulet, D., Gordon, K. S., Eidell, K. P., Leclerc, P., Whittaker, C. A., Larson, R. C., Muscato, A. J., Yates, K. B., Dubrot, J., Doench, J. G., Regev, A., Vander Heiden, M. G., Maus, M. V., Manguso, R. T., Birnbaum, M. E., & Hemann, M. T. (2023). Leukemia-intrinsic determinants of CAR-T response revealed by iterative in vivo genome-wide CRISPR screening. Nature Communications, 14(1).

Wu, T., Tan, J. H., Sin, W., Luah, Y. H., Tan, S. Y., Goh, M., Birnbaum, M. E., Chen, Q., & Cheow, L. F. (2023). Cell granularity reflects immune cell function and enables selection of lymphocytes with superior attributes for immunotherapy. Advanced Science, 10(28).

Huisman, B. D., Guan, N., Rückert, T., Garner, L., Singh, N. K., McMichael, A. J., Gillespie, G. M., Romagnani, C., & Birnbaum, M. E. (2023). High-throughput characterization of HLA-E-presented CD94/NKG2X ligands reveals peptides which modulate NK cell activation. Nature Communications, 14(1).

Nguyen, K. B., Roerden, M., Copeland, C. J., Backlund, C. M., Klop-Packel, N. G., Remba, T., Kim, B., Singh, N. K., Birnbaum, M. E., Irvine, D. J., & Spranger, S. (2023). Decoupled neoantigen cross-presentation by dendritic cells limits anti-tumor immunity against tumors with heterogeneous neoantigen expression. eLife, 12.

Li, X., Singh, N. K., Collins, D. R., Ng, R., Zhang, A., Lamothe-Molina, P. A., Shahinian, P., Xu, S., Tan, K., Piechocka-Trocha, A., Urbach, J. M., Weber, J. K., Gaiha, G. D., Takou Mbah, O. C., Huynh, T., Cheever, S., Chen, J., Birnbaum, M. E., Zhou, R., Walker, B. D., & Wang, J. (2023). Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide. Nature Communications, 14(1).

Huisman, B. D., Balivada, P. A., & Birnbaum, M. E. (2023). Yeast display platform with expression of linear peptide epitopes for high-throughput assessment of peptide-MHC-II binding. Journal of Biological Chemistry, 299(3), 102913.

Carter, B., Krog, J., Birnbaum, M. E., & Gifford, D. K. (2023). Machine learning model interpretations explain T cell receptor binding. bioRxiv.

Huisman, B. D., Dai, Z., Gifford, D. K., & Birnbaum, M. E. (2022). A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding. eLife, 11.

Gordon, K. S., Kyung, T., Perez, C. R., Holec, P. V., Ramos, A., Zhang, A. Q., Agarwal, Y., Liu, Y., Koch, C. E., Starchenko, A., Joughin, B. A., Lauffenburger, D. A., Irvine, D. J., Hemann, M. T., & Birnbaum, M. E. (2022). Screening for CD19-specific chimaeric antigen receptors with enhanced signalling via a barcoded library of intracellular domains. Nature Biomedical Engineering, 6(7), 855–866.

Grace, B. E., Backlund, C. M., Morgan, D. M., Kang, B. H., Singh, N. K., Huisman, B. D., Rappazzo, C. G., Moynihan, K. D., Maiorino, L., Dobson, C. S., Kyung, T., Gordon, K. S., Holec, P. V., Mbah, O. C., Garafola, D., Wu, S., Love, J. C., Wittrup, K. D., Irvine, D. J., & Birnbaum, M. E. (2022). Identification of highly cross-reactive mimotopes for a public T cell response in murine melanoma. Frontiers in Immunology, 13.

Holec, P. V., Camacho, K. V., Breuckman, K. C., Mou, J., & Birnbaum, M. E. (2022). Proteome-scale screening to identify high-expression signal peptides with minimal N-terminus biases via yeast display. ACS Synthetic Biology, 11(7), 2405–2416.

Huisman, B. D., Grace, B. E., Holec, P. V., & Birnbaum, M. E. (2022). Yeast display for the identification of peptide-MHC ligands of immune receptors. Methods in Molecular Biology, 263–291.

Dobson, C. S., Reich, A. N., Gaglione, S., Smith, B. E., Kim, E. J., Dong, J., Ronsard, L., Okonkwo, V., Lingwood, D., Dougan, M., Dougan, S. K., & Birnbaum, M. E. (2022). Antigen identification and high-throughput interaction mapping by reprogramming viral entry. Nature Methods, 19(4), 449–460.

Dai, Z., Huisman, B. D., Zeng, H., Carter, B., Jain, S., Birnbaum, M. E., & Gifford, D. K. (2021). Machine learning optimization of peptides for presentation by class II MHCs. Bioinformatics, 37(19), 3160–3167.

Kaseke, C., Park, R. J., Singh, N. K., Koundakjian, D., Bashirova, A., Garcia Beltran, W. F., Takou Mbah, O. C., Ma, J., Senjobe, F., Urbach, J. M., Nathan, A., Rossin, E. J., Tano-Menka, R., Khatri, A., Piechocka-Trocha, A., Waring, M. T., Birnbaum, M. E., Baker, B. M., Carrington, M., Walker, B. D., & Gaiha, G. D. (2021). HLA class-I-peptide stability mediates CD8+ T cell immunodominance hierarchies and facilitates HLA-associated immune control of HIV. Cell Reports, 36(2), 109378.

Pan, Y.-G., Aiamkitsumrit, B., Bartolo, L., Wang, Y., Lavery, C., Marc, A., Holec, P. V., Rappazzo, C. G., Eilola, T., Gimotty, P. A., Hensley, S. E., Antia, R., Zarnitsyna, V. I., Birnbaum, M. E., & Su, L. F. (2021). Vaccination reshapes the virus-specific T cell repertoire in unexposed adults. Immunity, 54(6).

Lin, X., George, J. T., Schafer, N. P., Ng Chau, K., Birnbaum, M. E., Clementi, C., Onuchic, J. N., & Levine, H. (2021). Rapid assessment of T-cell receptor specificity of the immune repertoire. Nature Computational Science, 1(5), 362–373.

Jan, M., Scarfò, I., Larson, R. C., Walker, A., Schmidts, A., Guirguis, A. A., Gasser, J. A., Słabicki, M., Bouffard, A. A., Castano, A. P., Kann, M. C., Cabral, M. L., Tepper, A., Grinshpun, D. E., Sperling, A. S., Kyung, T., Sievers, Q. L., Birnbaum, M. E., Maus, M. V., & Ebert, B. L. (2021). Reversible on- and off-switch chimeric antigen receptors controlled by Lenalidomide. Science Translational Medicine, 13(575).

Rappazzo, C. G., Huisman, B. D., & Birnbaum, M. E. (2020). Repertoire-scale determination of class II MHC peptide binding via yeast display improves antigen prediction. Nature Communications, 11(1).

Liu, G., Zeng, H., Mueller, J., Carter, B., Wang, Z., Schilz, J., Horny, G., Birnbaum, M. E., Ewert, S., & Gifford, D. K. (2019). Antibody complementarity determining region design using high-capacity machine learning. Bioinformatics, 36(7), 2126–2133.

Li, A., Herbst, R. H., Canner, D., Schenkel, J. M., Smith, O. C., Kim, J. Y., Hillman, M., Bhutkar, A., Cuoco, M. S., Rappazzo, C. G., Rogers, P., Dang, C., Jerby-Arnon, L., Rozenblatt-Rosen, O., Cong, L., Birnbaum, M., Regev, A., & Jacks, T. (2019). IL-33 signaling alters regulatory T cell diversity in support of tumor development. Cell Reports, 29(10).

Chu, N. D., Bi, H. S., Emerson, R. O., Sherwood, A. M., Birnbaum, M. E., Robins, H. S., & Alm, E. J. (2019). Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors. BMC Immunology, 20(1).

Holec, P. V., Berleant, J., Bathe, M., & Birnbaum, M. E. (2018). A Bayesian framework for high-throughput T cell receptor pairing. Bioinformatics, 35(8), 1318–1325.

D’Souza, M. P., Adams, E., Altman, J. D., Birnbaum, M. E., Boggiano, C., Casorati, G., Chien, Y., Conley, A., Eckle, S. B., Früh, K., Gondré-Lewis, T., Hassan, N., Huang, H., Jayashankar, L., Kasmar, A. G., Kunwar, N., Lavelle, J., Lewinsohn, D. M., Moody, B., Picker, L., Ramachandra, L., Shastri, N., Parham, P., McMichael, A. J., & Yewdell, J. W. (2019). Casting a wider net: Immunosurveillance by nonclassical MHC molecules. PLOS Pathogens, 15(2).

Clancy-Thompson, E., Devlin, C. A., Tyler, P. M., Servos, M. M., Ali, L. R., Ventre, K. S., Bhuiyan, M. A., Bruck, P. T., Birnbaum, M. E., & Dougan, S. K. (2018). Altered binding of tumor antigenic peptides to MHC class I affects CD8+ T cell–effector responses. Cancer Immunology Research, 6(12), 1524–1536.