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Shannon Miller, PhD

Scripps Fellow
Department of Chemistry
California Campus
Laboratory Website
(858) 784-8103

Scripps Research Joint Appointments

Faculty, Graduate Program

Research Focus

The success of CRISPR gene therapies necessitates safe and efficient methods of in vivo administration. Our lab aims to bridge the gap between CRISPR technology development and therapeutic treatment by developing novel methods for the safe and efficient in vivo delivery of biomolecules. We use directed evolution and bioengineering to develop improved CRISPR technology and in vivo delivery methods to probe questions surrounding genome editing safety and serve as tools for the study and treatment of human disease.


Ph.D., Harvard University, 2022
B.S., University of Illinois Urbana-Champaign, 2016

Selected References

High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs. Huang, T.P., Heins, Z.J., Miller, S.M., Wong, B.G., Balivada, P.A., Wang, T., Khalil, A.S., Liu, D.R. Nat Biotechnol. 41. 96–107 (2023)

Base editing of haematopoietic stem cells rescues sickle cell disease in mice. Newby, G. A.*; Yen, J. S.*; Woodard, K. J.*; Mayuranathan, T.*; Lazzarotto, C. R.; Li, Y.; Sheppard-Tillman, H.; Porter, S. N.; Yau, Y.; Mayberry, K.; Everette, K. A.; Jang, Y.; Podracky, C. J.; Thaman, E.; Lechauve, C.; Sharma, A.; Henderson, J. M.; Richter, M. F.; Zhao, K. T.; Miller, S. M.; Wang, T.; Koblan, L. W.; McCaffrey, A. P.; Tisdale, J. F.; Kalfa, T. A.; Pruett-Miller, S. M.; Tsai, S. Q.; Weiss, M. J.; Liu, D. R. Nature. 595, 295-302 (2021).

Phage-assisted continuous and non-continuous evolution. Miller, S. M.; Wang, T; Liu, D. R.  Nature Protocols. 15, 4101-4127 (2020).

Continuous evolution of SpCas9 variants compatible with non-G PAMs. Miller, S. M.; Wang, T; Randolph, P.B.; Arbab, M; Shen, M.W.; Huang, T.P.; Matuszek, Z; Newby, G.A.; Rees, H.A; Liu, D.R. Nat. Biotechnol. 38, 471-481 (2020).

Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Huang, T. P.*; Zhao, K. T.*; Miller, S. M.; Gaudelli, N. M.; Oakes, B. L.; Fellmann, C.; Savage, D. F.; Liu, D. R. Nat. Biotechnol. 37, 626-631 (2019).

Simultaneous Targeting of Linked Loci in Mouse Embryos Using Base Editing. Lee, H. K.; Willi, M.; Smith, H. E.; Miller, S. M.; Liu, D. R.; Liu, C.; Hennighausen, L. Sci. Rep. 9, 1662 (2019).

Targeting Fidelity of Adenine and Cytosine Base Editors in Mouse Embryos. Lee, H. K.; Willi, M.; Miller, S. M.; Kim, S.; Liu, C; Liu, D. R.; Hennighausen, L. Nat. Commun. 9: 4804. 1-5 (2018).

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Hu, J. H.; Miller, S. M.; Geurts, M.; Tang, W.; Chen, L.; Sun, N.; Zeina, C.; Gao, X.; Rees, H.; Lin, Z.; Liu, D. R. Nature. 556, 57–63 (2018).

A manganese catalyst for highly reactive yet chemoselective intramolecular C(sp3)–H amination. Paradine, S. M.*; Griffin, J. R.*; Zhao, J.; Petronico, A. L.; Miller, S. M.; White, M. C. Nature Chemistry. 7, 987-994 (2015)