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Shane Crotty, PhD

Professor Adjunct
Department of Immunology and Microbiology
California Campus
Scripps VIVO Scientific Profile
(858) 784-8104


Ph.D. (Biochemistry and Molecular Biology), University of California, San Francisco 2001
B.S. (Biology), Massachusetts Institute of Technology 1996
B.S. (Writing), Massachusetts Institute of Technology 1996

Professional Experience

2015-2017 Professor Adjunct, Immunology and Microbial Science (IMS), The Scripps Research Institute
2009-2014 Associate Professor, La Jolla Institute for Allergy and Immunology
2004-2010 Assistant Professor Adjunct, Department of Medicine, University of California, San Diego
2003-2009 Assistant Professor, La Jolla Institute for Allergy and Immunology
2001-2003 Postdoctoral Fellow in Immunology, Emory University
1995-1996 Research Technician, Massachusetts Institute of Technology

Selected References

All Publications

Upadhyay, A. A., Kauffman, R. C., Wolabaugh, A. N., Cho, A., Patel, N. B., Reiss, S. M., Havenar-Daughton, C., Dawoud, R. A., Tharp, G. K., Sanz, I., Pulendran, B., Crotty, S., et al. BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data. (2018). Genome Medicine, 10. PMCID: PMC5859752.

Crotty, S. Do memory CD4 T cells keep their cell-type programming: plasticity versus fate commitment? complexities of interpretation due to the heterogeneity of memory CD4 T cells, including T follicular helper cells. (2018). Cold Spring Harbor Perspectives in Biology, 10.

Klasse, P. J., Ketas, T. J., Cottrell, C. A., Ozorowski, G., Debnath, G., Camara, D., Francomano, E., Pugach, P., Ringe, R. P., LaBranche, C. C., van Gils, M. J., Bricault, C. A., et al. Epitopes for neutralizing antibodies induced by HIV-1 envelope glycoprotein BG505 SOSIP trimers in rabbits and macaques. (2018). PLoS Pathogens, 14. PMCID: PMC5841823.

Abbott, R. K., Lee, J. H., Menis, S., Skog, P., Rossi, M., Ota, T., Kulp, D. W., Bhullar, D., Kalyuzhniy, O., Havenar-Daughton, C., Schief, W. R., Nemazee, D., et al. Precursor Frequency and Affinity Determine B Cell Competitive Fitness in Germinal Centers, Tested with Germline-Targeting HIV Vaccine Immunogens. (2018). Immunity, 48(1), 133-+. PMCID:



Wang, D., Diao, H., Getzler, A. J., Rogal, W., Frederick, M. A., Milner, J., Yu, B., Crotty, S., Goldrath, A. W. & Pipkin, M. E. The transcription factor Runx3 establishes-chromatin accessibility of cis-regulatory landscapes that drive memory cytotoxic T lymphocyte formation. (2018). Immunity, 48(4), 659-674.

Pauthner, M., Havenar-Daughton, C., Sok, D., Nkolola, J. P., Bastidas, R., Boopathy, A. V., Carnathan, D. G., Chandrashekar, A., Cirelli, K. M., Cottrell, C. A., Eroshkin, A. M., Guenaga, J., et al. Elicitation of robust tier 2 neutralizing antibody responses in nonhuman primates by HIV envelope trimer immunization using optimized approaches. (2017). Immunity, 46(6), 1073-1088. PMCID: PMC5483234.

Kulp, D. W., Steichen, J. M., Pauthner, M., Hu, X., Schiffner, T., Liguori, A., Cottrell, C. A., Havenar-Daughton, C., Ozorowski, G., Georgeson, E., Kalyuzhniy, O., Willis, J. R., et al. Structure-based design of native-like HIV-1 envelope trimers to silence non-neutralizing epitopes and eliminate CD4 binding. (2017). Nature Communications, 8. PMCID: PMC5698488.

Havenar-Daughton, C., Lee, J. H. & Crotty, S. Tfh cells and HIV bnAbs, an immunodominance model of the HIV neutralizing antibody generation problem. (2017). Immunological Reviews, 275(1), 49-61.

Havenar-Daughton, C., Carnathan, D. G., Torrents de la Peña, A., Pauthner, M., Briney, B., Reiss, S. M., Wood, J. S., Kaushik, K., van Gils, M. J., Rosales, S. L., van der Woude, P., Locci, M., et al. Direct probing of germinal center responses reveals immunological features and bottlenecks for neutralizing antibody responses to HIV Env trimer. (2016). Cell Reports, 17(9), 2195-2209. PMCID: PMC5142765.

Crotty, S. & Pipkin, M. E. In vivo RNAi screens: concepts and applications. (2015). Trends in Immunology, 36(5), 315-322. PMCID: PMC4810674.