Publications

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Articles

7. Kim, Y.B., Pierce, E.B., Brown, M., Peterson, B.A., Sanford, D., Fear, J., Nicholl, D., San Pedro, E., Reynolds, G.M., Hunt, J.E., Schwark, D.G., Jali, S., Graham, N., Cesarz, Z., Chapman, T.A.L., Watts, J.M., Hummel, A.W. A novel mechanistic framework for precise sequence replacement using reverse transcriptase and diverse CRISPR-Cas systems. bioRxiv. doi: https://doi.org/10.1101/2022.12.13.520319 (2022).

Highlight: Expanding the use of reverse transcriptase at CRISPR-targeted sites with a new method broadly compatible with diverse CRISPR systems, including Type V systems.

6. Kim, Y.B.*, Zhao, K.T.*, Thompson, D.B., Liu, D.R. An anionic human protein mediates cationic liposome delivery of genome editing proteins into mammalian cells. Nat. Commun. 10 (1): 2905 (2019).

5. Komor, A.C., Zhao, K.T., Packer, M.S., Gaudelli, N.M., Waterbury, A.L., Koblan, L.W., Kim, Y.B., Badran, A.H., Liu, D.R. Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. Sci. Adv. 3: eaao4774 (2017).

4. Kim, Y.B., Komor, A.C., Levy, J.M., Packer, M.S., Zhao, K.T., Liu, D.R. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat. Biotechnol. 35, 371-376 (2017).

Highlight: Addressing key limitations of the cytosine base editor - increasing targeting scope and editing precision (2017). First example of deaminase engineering to refine base editing outcome.

3. Komor, A.C., Kim, Y.B., Packer, M.S., Zuris, J.A. & Liu, D.R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420-424 (2016).

Highlight: Invention of the original cytosine base editor.

2. Mazumder, M., Brechun, K.E., Kim, Y.B., Hoffmann, S.A., Chen, Y.Y., Keiski, C.L., Arndt, K.M., McMillen, D.R., Woolley, G.A. An Escherichia coli system for evolving improved light-controlled DNA-binding proteins. Protein Eng. Des. Sel. 9, 293-302 (2015).

1. Park, H., Hong, Y-L, Kim, Y.B., Tae-Lim Choi. Synthesis of Small and Large Fused Bicyclic Compounds by Tandem Dienyne Ring-Closing Metathesis. Organic Letters 12 (15), 3442-3445 (2010).

Patents and Patent Applications

15. Fusion proteins comprising an intein polypeptide and methods of use thereof. (2022)

14. Model editing systems and methods relating to the same. (2021)

13. Reporter constructs, compositions comprising the same, and methods of use thereof. (2021)

12. Compositions, systems, and methods for base diversification. (2021)

11. RNA and protein delivery methods, compositions, and components. (2020)

10. Compositions and methods for Type V CRISPR-Cas RNA-templated editing. WO2022098993A2 (2021)

9. Compositions, systems, and methods for base diversification. US20210238598, WO2021155109 (2020)

8. Suppression of shade avoidance response in plants. US202062968596, WO2021155084 (2020)

7. Compositions and methods for RNA-encoded DNA-replacement of alleles. US201962930836, WO2021092130 (2019)

6. Type V CRISPR-Cas base editors and methods of use thereof. US201962927914, WO2021087182 (2019)

5. Optimized CRISPR-Cas nucleases and base editors and methods of use thereof. US201962925422, WO2021081264 (2019)

4. Supernegatively charged proteins and uses thereof. US20210238598, WO2020154500 (2019)

3. Nucleobase editors comprising GeoCas9 and uses thereof. US201862752225, WO2020092453A1 (2018)

2. High efficiency base editors comprising gam. US201762551938, WO2019139645A2 (2017)

1. Nucleobase editors and uses thereof. US20170121693A1, WO2017070632A2 (2015)