Liu Group Publications
1. “Enzyme Mechanisms for Polycyclic Triterpene Formation” Wendt, K. U.; Schulz, G. E.; Corey, E. J.; Liu, D. R. Chem. Int. Ed. Engl. 39, 2813-2833 (2000).
2. “The Generality of DNA-Templated Synthesis as a Basis for Evolving Non-Natural Small Molecules.” Gartner, Z. J. and Liu, D. R. J. Am. Chem. Soc. 123, 6961-6963 (2001). PDF | SI | A highlight describing this work appears in Angew. Chem. Int. Ed. 41, 89-90 (2002). PDF
3. “An In Vivo Selection System for Homing Endonuclease Activity” Gruen, M.; Chang, K.; Serbanescu, I.; Liu, D. R. Nucleic Acids Res. 30, e29 (2002). PDF.
4. “Recent Advances in the In Vitro Evolution of Nucleic Acids” Bittker, J. A.; Phillips, K. J.; Liu, D. R. Opin. Chem. Biol., 6, 367-374 (2002). PDF
5. “Expanding the Reaction Scope of DNA-Templated Synthesis” Gartner, Z, J.; Kanan, M. W.; Liu, D. R. Angew. Chem. Int. Ed., 41, 1796-1800 (2002). PDF. This work is featured in an online Nature Science Update.
6. “Nucleic Acid Evolution and Minimization by Nonhomologous Random Recombination” Bittker, J. A.; Le, B. V.; Liu, D. R. Nat. Biotechnol. 20, 1024-1029 (2002). PDF
7. “Multistep Small-Molecule Synthesis Programmed by DNA Templates” Gartner, Z. J.; Kanan, M. W.; Liu, D. R. Am. Chem. Soc., 124, 10304-10306 (2002). News stories describing this work appear in Chem. & Eng. News 80 [34] 12 (2002), and in Science, 300, 242 (2003). PDF | SI This work is featured in Chem. & Eng. News 80 [34] 12 (2002) PDF, and in Science, 300, 242 (2003).
8. “Directing Otherwise Incompatible Reactions in a Single Solution By Using DNA-Templated Organic Synthesis” Calderone, C. T.; Puckett, J. W.; Gartner, Z. J.; Liu, D. R. Angew. Chem. Int. Ed. 41, 4104-4108 (2002). PDF | This work is featured as an Editor’s Choice in Science 298 [5598], 1517 (2002).
9. “Two Enabling Architectures for DNA-Templated Organic Synthesis” Gartner, Z. J.; Grubina, R.; Calderone, C. T.; Liu, D. R. Angew. Chem. Int. Ed. 42, 1370-1375 (2003). PDF | A Science and Technology Concentrate describing this work appears in Chem. & Eng. News 81 [13] 24 (2003). PDF
10. “In Vivo Evolution of an RNA-based Transcriptional Activator” Buskirk, A. R.; Kehayova, P. D.; Landrigan, A.; Liu, D. R. Biol. 10, 533-540 (2003). PDF | This paper is noted as an article of interest in Cell 113 (7) and is previewed in a separate article in Chem. Biol. 10, 584-585 (2003).
11. “Stereoselectivity in DNA-Templated Organic Synthesis and Its Origins” Li, X. and Liu, D. R. Am. Chem. Soc. 125, 10188-10189 (2003). PDF | SI
12. “Highly Sensitive In Vitro Selections for DNA-Linked Synthetic Small Molecules with Protein Binding Affinity and Specificity” Doyon, J. B.; Snyder, T. M.; Liu, D. R. Am. Chem. Soc. 125, 12372-12373 (2003). PDF | SI
13. “Efficient and Sequence-Specific DNA-Templated Polymerization of Peptide Nucleic Acid Aldehydes” Rosenbaum, D. M. and Liu, D. R. J. Am. Chem. Soc. 125, 13924-13925 (2003). PDF | SI | This work is highlighted in a Science and Technology story in Chem. & Eng. News 82 [3] 64 (2004). PDF
14. “Expanding the Genetic Code In Vitro andIn Vivo”Magliery, T. J.; Liu, D. R. The Genetic Code and the Origin of Life Ed. Ribas de Pouplana, L. Landes Bioscience and Springer, (2004).
15. “Translation of DNA into Synthetic N-Acyloxazolidines” Li, X.; Gartner, Z. J.; Tse, B. N.; Liu, D. R. Am. Chem. Soc. 126, 5090-5092 (2004). PDF | SI
16. “DNA-Templated Organic Synthesis: Nature’s Strategy for Controlling Chemical Reactivity Applied to Synthetic Molecules” Li, X.; Liu, D. R. Angew. Chem. Int. Ed. 43, 4848-4870 (2004). PDF | This paper was selected by the Angewandte Chemie Editorial Board as one of the 12 best Angewandte Chemie review articles in 2004.
17. “Directed Evolution of Protein Enzymes Using Nonhomologous Random Recombination” Bittker, J. A.; Le, B. V.; Liu, J. M.; Liu, D. R. Natl. Acad. Sci. USA 101, 7011-7016 (2004). PDF
18. “Engineering a Ligand-Dependent RNA Transcriptional Activator” Buskirk, A. R.; Landrigan, A.; Liu, D. R. Chem. Biol. 11, 1157-1163 (2004). PDF This work is featured in a Research Highlight in Nat. Methods 1, 6-7 (2004). PDF
19. “Directed Evolution of Ligand Dependence: Small Molecule-Activated Protein Splicing” Buskirk, A. R.; Ong, Y.-C.; Gartner, Z. J.; Liu, D. R. Natl. Acad. Sci. USA 101, 10505-10510 (2004). PDF
20. “DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles” Gartner, Z. J.; Tse, B. N.; Grubina, R.; Doyon, J. B.; Snyder, T. M.; Liu, D. R. Science 305, 1601-1605 (2004). PDF | SI
21. “Reaction Discovery Enabled by DNA-Templated Synthesis and In Vitro Selection” Kanan, M. W.; Rozenman, M. M.; Sakurai, K.; Snyder, T. M., Liu, D. R. Nature 431, 545-549 (2004). . PDF | SI | This work is featured in a news focus article in Science 305, 1558 (2004) PDF, in a Science and Technology Concentrate in Chem. & Eng. News 82 [40] 31 (2004) PDF, and in a News and Views commentary in Nat. Biotechnol. 22, 1378-1379 (2004). PDF.
22. “Nucleic Acid-Templated Synthesis as a Model System for Ancient Translation” Calderone, C. T. and Liu, D. R. Opin. Chem. Biol. 8, 645-653 (2004). PDF
23. “In Vitro Characterization of IroB, a Pathogen-Associated C-Glycosyltransferase” Fischbach, M. A.; Lin, H.; Liu, D. R.; Walsh, C. T. Natl. Acad. Sci. USA 102, 571-576 (2005). PDF
24.“Creating Small Molecule-Dependent Switches to Modulate Biological Functions” Buskirk, A. R. and Liu, D. R. Biol. 12, 151-161 (2005). PDF
25. “DNA-Templated Functional Group Transformations Enable Sequence-Programmed Synthesis Using Small-Molecule Reagents” Sakurai, K.; Snyder, T. M.; Liu, D. R. Am. Chem. Soc. 127, 1660-1661 (2005). PDF | SI
26. “Functional Dissection of sRNA Translational Regulators By Nonhomologous Random Recombination and In Vivo Selection” Liu, J. M.; Bittker, J. A.; Lonshteyn, M.; Liu, D. R. Biol. 12, 757-767 (2005). PDF | SI
27. “In Vitro Characterization of Salmochelin and Enterobactin Trilactone Hydrolases IroD, IroE, and Fes” Lin, H.; Fischbach, M. A.; Liu, D. R.; Walsh, C. T. Am. Chem. Soc. 127, 11075-11084 (2005). PDF
28. “Ordered Multistep Synthesis in a Single Solution Directed by DNA Templates” Snyder, T. M. and Liu, D. R. Chem. Int. Ed. 44, 7379-7382 (2005). PDF | SI
29. “Small-Molecule Diversification From Iterated Branching Reaction Pathways Enabled by DNA-Templated Synthesis” Calderone, C. T. and Liu, D. R. Chem. Int. Ed. 44, 7383-7386 (2005). PDF | SI
30. “DNA-Templated Synthesis in Organic Solvents” Rozenman, M.; Liu, D. R. ChemBioChem 7, 253-256 (2006). PDF
31. Enzymatic Tailoring of Enterobactin Alters Membrane Partitioning and Iron Acquisition” Luo, M.; Lin, H.; Fischbach, M. A.; Liu, D. R.; Walsh, C. T.; Groves, J. T. ACS Chem. Biol. 1, 29-32 (2006). PDF
32. “Directed Evolution and Substrate Specificity Profile of Homing Endonuclease I-SceI” Doyon, J.; Pattanayak, V.; Meyer, C. B.; Liu, D. R. Am. Chem. Soc. 128, 2477-2484 (2006). PDF | SI
33. “How Pathogenic Bacteria Evade Mammalian Sabotage in the Battle for Iron” Fischbach, M. A.; Lin, H.; Liu, D. R.; Walsh, C. T. Chem. Biol. 2, 132-138 (2006). PDF
34.“A Protein Interaction Surface in Nonribosomal Peptide Synthesis Mapped by Combinatorial Mutagenesis and Selection” Lai, J. R.; Fischbach, M. A.; Liu, D. R.; Walsh, C. T. Natl. Acad. Sci. USA 103, 5314-5319 (2006). PDF
35. “Control of Transcription Factor Activity and Osteoblast Differentiation in Mammalian Cells Using an Evolved Small-Molecule-Dependent Intein” Yuen, C. M.; Rodda, S. J.; Vokes, S. A.; McMahon, A. P.; Liu, D. R. J. Am. Chem. Soc. 128, 8939-8946 (2006). PDF. | This work is featured in a Science and Technology Concentrate in Chem. & Eng. News 84 [26], 34 (2006), as a Spotlight in ACS Chem. Biol. 1, 328 (2006), and as a News and Views article in Nature 442, 517-518 (2006).
36. “Bromoenterobactins as Potent Inhibitors of a Pathogen-Associated, Siderophore-Modifying C-Glycosyltransferase” Lin, H.; Fischbach, M. A.; Gatto Jr., G. J.; Liu, D. R.; Walsh, C. T. Am. Chem. Soc. 128, 9324-9325 (2006). PDF
37.“Localized Protein Interaction Surfaces on the EntB Carrier Protein Revealed by Combinatorial Mutagenesis and Selection” Lai, J. R.; Fischbach, M. A.; Liu, D. R.; Walsh, C. T. Am. Chem. Soc. 128, 11002-11003 (2006). PDF
38. “Binding and Stability Determinants of the PPARg Nuclear Receptor-Coactivator Interface as Revealed by Shotgun Alanine Scanning and In Vivo Selection” Phillips, K. J.; Rosenbaum, D. M.; Liu, D. R. Am. Chem. Soc. 128, 11298-11306 (2006). PDF
39. “The Pathogen-Associated iroA Gene Cluster Mediates Bacterial Evasion of Lipocalin 2” Fischbach, M.A.; Lin, H.; Zhou, L.; Yu, Y.; Abergel, R. J.; Liu, D. R.; Raymond, K. N.; Wanner, B. L.; Strong, R. K.; Walsh, C. T.; Aderem, A.; Smith, K. D. Natl. Acad. Sci. USA 103, 16502-16507 (2006). PDF
40.“In Vivo Evolution of an RNA-Based Transcriptional Silencing Domain in cerevisiae” Kehayova, P. D. and Liu, D. R. Chem. Biol. 14, 65-74 (2007). This work is featured in a Research Highlight in Nat. Methods 4, 297 (2007). PDF | This work is featured in a Research Highlight in Nat. Methods 4, 297 (2007). PDF
41. “Synthesis of Acyclic a,b-Unsaturated Ketones via Pd(II)-Catalyzed Intermolecular Reaction of Alkynamides and Alkenes” Momiyama, N.; Kanan, M. W.; Liu, D. R. Am. Chem. Soc. 129, 2230-2231 (2007). PDF | SI
42. “Solving Chemical Problems Through the Application of Evolutionary Principles” Rozenman, M. M.; McNaughton, B. R.; Liu, D. R. Opin. Chem. Biol. 11, 259-268 (2007). PDF
43. “Directed Evolution Can Rapidly Improve the Activity of Chimeric Assembly-Line Enzymes” Fischbach, M. A.; Lai, J. R.; Roche, E. D.; Walsh, C. T.; Liu. D. R. Natl. Acad. Sci. USA 104, 11951-11956 (2007). PDF
44. “Supercharging Proteins Can Impart Extraordinary Resilience” Lawrence, M. S.; Phillips, K. J.; Liu, D. R. J. Am. Chem. Soc. 129, 10110-10112 (2007). PDF | SI | This work is featured in a Research Highlight in Nature 448 973 (2007). PDF and as a News and Views article in Nature 449, 555 (2007). PDF
45.“Identification of Eukaryotic Promoter Regulatory Elements Using Nonhomologous Random Recombination” Doyon, J. B.; Liu, D. R. Nucleic Acids Res. 35, 5851-5860 (2007). PDF
46.“Dissecting Protein Structure and Function Using Directed Evolution” Yuen, C. M.; Liu, D. R. Methods 4, 995-997 (2007). PDF
47.“Discovery of a mRNA Mitochondrial Localization Element in Saccharomyces cerevisiae by Nonhomologous Random Recombination and In Vivo Selection” Liu, J. M.; Liu, D. R. Nucleic Acids Res. 35, 6750-6761 (2007). PDF
48. “Development and Initial Application of a Hybridization-Independent, DNA-Encoded Reaction Discovery System Compatible with Organic Solvents” Rozenman, M. M.; Kanan, M. W.; Liu, D. R. J. Am. Chem. Soc. 129, 14933-14938 (2007). PDF | SI | This work is featured in a Science and Technology Concentrate in Chem. & Eng. News 85 (47), 43.
49.“Effects of Template Sequence and Secondary Structure on DNA-Templated Reactivity” Snyder, T. M.; Tse, B. N.; Liu, D. R. Am. Chem. Soc. 130, 1392-1401 (2008). PDF | SI
50. “DNA-Templated Polymerization of Side-Chain-Functionalized Peptide Nucleic Acid Aldehydes” Kleiner, R. E.; Brudno, Y.; Birnbaum, M. E.; Liu, D. R. Am. Chem. Soc. 130, 4646-4659 (2008). PDF | SI
51. “Translation of DNA into a Library of 13,000 Synthetic Small-Molecule Macrocycles Suitable for In Vitro Selection” Tse, B. N.; Snyder, T. M.; Shen, Y.; Liu, D. R. Am. Chem. Soc. 130, 15611-15626 (2008). PDF | SI
52.“Recent Progress Toward the Templated Synthesis and Directed Evolution of Sequence-Defined Synthetic Polymers” Brudno, Y. and Liu, D. R. Biol. 16, 265-276 (2009). PDF
53. “Mammalian Cell Penetration, siRNA Transfection, and DNA Transfection by Supercharged Proteins” McNaughton, B. R.; Cronican, J. J.; Thompson, D. B.; Liu, D. R. Proc. Natl. Acad. Sci. USA 106, 6111-6116 (2009). PDF | SI | Supplemental Protocol. This work was featured as a Research Highlight in Nat. Methods 6, 322 (2009).
54. “A Chemical Screen for Biological Small Molecule-RNA Conjugates Reveals CoA-Linked RNA” Kowtoniuk, W. E.; Shen, Y.; Heemstra, J. M.; Agarwal, I.; Liu, D. R. Proc. Natl. Acad. Sci. USA 106, 7768-7773 (2009). PDF | SI| This work was featured in a news story in Chemistry World (PDF) (April 20, 2009), in a news story in Chem. & Eng. News 87[17] 9 (2009) PDF, in a Research Highlight in Nat. Chem. Biol. 5, 380-381 (2009). PDF, and in a Highlight in ChemBioChem 10, 2145-2146 (2009).
55. “Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by the MLL Fusion Partner TET1” Tahiliani, M.; Koh, K. P.; Shen, Y.; Pastor, W. A.; Bandukwala, H.; Brudno, Y.; Agarwal, S.; Iyer, L. M; Liu, D. R.; Aravind, L.; Rao, A. Science 324, 930-935 (2009). PDF | SI| This work was featured in a Spotlight in ACS Chem. Biol. 4, 315 (2009) PDF, in a Research Highlight in Nature 458, 1080 (2009). PDF , and in a Cover Story in C&E News 87 [37], 11 (2009).
56. “Reactivity-Dependent PCR: Direct, Solution-Phase In Vitro Selection for Bond Formation” Gorin, D. J.; Kamlet, A. S.; Liu, D. R. J. Am. Chem. Soc. 131, 9189-9191 (2009). PDF | SI| This work was featured in a news story in Chemistry World (June 18, 2009).
57. “Templated Synthesis of Peptide Nucleic Acids via Sequence-Selective Base-Filling Reactions” Heemstra, J. M.; Liu, D. R. Am. Chem. Soc. 131, 11347-11349 (2009). PDF
58. “LC/MS Analysis of Cellular RNA Reveals NAD-Linked RNA” Chen, Y. G.; Kowtoniuk, W. E.; Agarwal, I.; Shen, Y.; Liu, D. R. Chem. Biol. 5, 879-881 (2009). PDF | SI
59. “Photoswitching Mechanism of Cyanine Dyes” Dempsey, G. T.; Bates, M.; Kowtoniuk, W. E.; Liu, D. R.; Tsien, R. Y.; Zhuang, X. J. Am. Chem. Soc. 131, 18192-18193 (2009). PDF | This work was featured in a Science and Technology Concentrate in C&E News 87 [50], 34 (2009) PDF
60.“A Small-Molecule Inhibitor of Tgf-β Signaling Replaces Sox2 in Reprogramming by Inducing Nanog” Ichida, J. K.; Blanchard, J.; Lam, K.; Son, E. Y.; Chung, J. E.; Egli, D.; Loh, K. M.; Carter, A. C. ; Di Giorgio, F. P.; Koszka, K.; Huangfu, D.; Akutsu, H.; Liu, D. R.; Rubin, L. L.; Eggan, K. Cell Stem Cell 5, 491-503 (2009). PDF
61. “An In Vitro Translation, Selection, and Amplification System for Peptide Nucleic Acids” Brudno, Y.; Birnbaum, M. E.; Kleiner, R. E.; Liu, D. R. Nat. Chem. Biol. 6, 148-155 (2010). PDF | SI| This work was featured in a News and Views article in Nat. Chem. Biol. 6, 87-88 (2010) PDF, and was also featured in an article highlighting Nat. Chem. Biol. papers over the five-year history of the journal in Nat. Chem. Biol. 6, 387-389 (2010) PDF.
62. “The Behavior of 5-Hydroxymethylcytosine in Bisulfite Sequencing” Huang, Y.; Pastor, W. A.; Shen, Y.; Tahiliani, M.; Liu, D. R.; Rao, A. PLoS ONE 5, e8888 (2010). PDF
63 “Enhanced Functional Potential of Nucleic Acid Aptamer Libraries Patterned to Increase Secondary Structure” Ruff, K. M.; Snyder, T. M.; Liu, D. R. Am. Chem. Soc. 132, 9453-9464 (2010). PDF | SI
64. “Potent Delivery of Functional Proteins into Mammalian Cells in Vitro and in Vivo Using a Supercharged Protein” Cronican, J. J.; Thompson D. B.; Beier, K. T.; McNaughton, B. R.; Cepko, C. L.; Liu, D. R. ACS Chem. Biol. 5, 747-752 (2010). PDF
65.“In Vitro Selection of a DNA-Templated Small-Molecule Library Reveals a Class of Macrocyclic Kinase Inhibitors” Kleiner, R. E.; Dumelin, C.; Tiu, G. C.; Sakurai, K.; Liu, D. R. Am. Chem. Soc. 132, 11779-11791 (2010). PDF
66. “Autonomous Multistep Organic Synthesis in a Single Isothermal Solution Mediated by a DNA Walker” He, Y. and Liu, D. R. Nat. Nanotechnol. 5, 778-782 (2010). PDF | SI| This work was featured in a news story in Chemistry World (October 10, 2010) PDF in a News and Views article in Nat. Nanotechnol. 5, 760-761 (2010) PDF, and in a Research Highlight in Nat. Methods 7, 952 (2010) PDF.
67. “Interaction-Dependent PCR Identification of Ligand-Target Pairs from Libraries of Ligands and Libraries of Targets in a Single Solution-Phase Experiment” McGregor, L. M.; Gorin, D. J.; Dumelin, C. E.; Liu, D. R. Am. Chem. Soc. 132, 15522-15524 (2010). PDF | SI
68. “Molecules of Life: A General Education Approach to the Science of Living Systems” Tse, B. N.; Clardy, J.; Liu, D. R. in Science and the Educated American: A Core Component of Liberal Education, Meinwald, J. and Hildebrand, J.G. (Eds) Washington, DC: American Academy of Arts and Science pp 180-217 (2010)
69. “A Biomolecule-Compatible Visible Light-Induced Azide Reduction from a DNA-Encoded Reaction Discovery System” Chen, Y.; Kamlet, A. S.; Steinman, J. B.; Liu, D. R. Nat. Chem. 3, 146-153 (2011). PDF | SI
70. “A De Novo Protein Binding Pair by Computational Design and Directed Evolution” Karanicolas, J.; Corn, J. E.; Chen, I.; Joachimiak, L. A.; Dym, O.; Chung S.; Albeck, S.; Unger, T.; Hu, W.; Liu, G.; Delbecq, S.; Montelione, G.; Spiegel, C.; Liu, D. R.; Baker, D. Cell 42, 250-260 (2011). PDF
71. “A System for the Continuous Directed Evolution of Biomolecules” Esvelt, K. M.; Carlson, J. C.; Liu, D. R. Nature 472, 499–503 (2011). PDF | SI | This work was featured in a news story in C&E News 89 [16] (April 14, 2011), as a news story in the MIT Technology Review (April 18, 2011), in a News and Views article in Nat. Chem. Biol. 7, 252-253 (2011), in a feature article in BioTechniques, as a research highlight in Nat. Methods 8, 451 (2011), in a technology feature in Nat. Methods 8, 623 (2011), as a news story in SciBX 4 [18], 5 (2011), and as a news story in Ars Technica (May 15, 2011).
72. “Directed Evolution of a Small Molecule-Triggered Intein with Improved Splicing Properties in Mammalian Cells” Peck, S.; Chen, I.; Liu, D. R. Biol. 18, 619-630 (2011). PDF | SI
73. “Inhibition of Bacterial Conjugation by Phage M13 and Its Protein g3p: Quantitative Analysis and Model” Lin, A.; Jimenez J.; Derr, J.; Vera, P.; Manapat, M. L.; Esvelt, K. M.; Villanueva, L.; Liu, D. R.; Chen, I. A. PLoS One 6, e19991 (2011). | PDF | SI
74. “Opposing Effects if Tcf3 abd Tcf1 Control Wnt-Stimulation of Embryonic Stem Cell Self Renewal” Yi, F.; Pereira, L.; Hoffman, J. A.; Shy, B.; Yuen, C. M.; Liu, D. R.; Merrill, B. J. Nat. Cell Biol. 13, 762-770 (2011). PDF | SI
75. “A Sequential Strand-Displacement Strategy Enables Efficient Six-Step DNA-Templated Synthesis” He, Y., Liu, D. R. Am. Chem. Soc. 133, 9972-9975 (2011). PDF | SI
76. “A Class of Human Proteins that Deliver Functional Proteins into Mammalian Cells In Vitro and In Vivo” Cronican, J. J.; Beier, K. T.; Davis, T. N.; Tseng, J.; Li, W.; Thompson, D. B.; Shih, A. F.; Cepko, C. L.; Kung, A. L.; Zhou, Q.; Liu, D. R. Chem. Biol. 18, 833-838 (2011). This work was featured in SciBX 4 [31] (2011) [Bioworld] PDF | SI
77. “A General Strategy for the Evolution of Bond-Forming Enzymes Using Yeast Display” Chen, I.; Dorr, B. M.; Liu, D. R. Natl. Acad. Sci. USA 108, 11399-11404 (2011). This work was highlighted in a technology feature in Nat. Methods 8, 623 (2011). PDF | SI | This work was highlighted in a technology feature in Nat. Methods 8, 623 (2011).
78. “Small-Molecule Discovery from DNA-Encoded Chemical Libraries” Kleiner, R. E.; Dumelin, C. E.; Liu, D. R. Soc. Rev. 40, 5707-5717 (2011). PDF
79. “Revealing Off-Target Cleavage Specificities of Zinc Finger Nucleases by In Vitro Selection” Pattanayak, V.; Ramirez, C. L.; Joung, J. K.; Liu, D. R. Nat. Methods 8, 765-770 (2011). PDF, SI | This work was featured in a news story in the August 7, 2011 issue of Nature, in a Highlight in Nat. Genet., in a news story in C&E News, 89 [33], 8 (2011), in a news story in the August 7, 2011 issue of The Scientist, in a News and Views article in Nat. Methods 8, 725 (2011), and as a news story in the August 10, 2011 issue of BioWorld Today.
80. “DNA-Enabled Self-Assembly of Plasmonic Nanoclusters” Fan, J. A.; He, Y.; Bao, K.; Wu, C.; Bao, J.; Schade, N. B.; Manoharan, V. N.; Shvets, G.; Nordlander, P.; Liu, D. R.; Capasso, F. Nano Lett. 11, 4859-4864 (2011). PDF | SI
81. “Engineering and Identifying Supercharged Proteins for Macromolecule Delivery into Mammalian Cells” Thompson, D. B.; Cronican, J. J.; Liu, D. R. Methods in Enzymology 503, 293-319 (2012). PDF
82. “Highly Specific, Bisubstrate-Competitive Src Inhibitors From DNA-Templated Macrocycles” Georghiou, G.; Kleiner, R. E.; Pulkoski-Gross, M.; Liu, D. R.; Seeliger, M. A. Chem. Biol. 8, 366-374 (2012). PDF, SI
83. “Cellular Uptake Mechanisms and Endosomal Trafficking of Supercharged Proteins” Thompson, D. B.; Villaseñor, R.; Dorr, B. M.; Zerial, M.; Liu, D. R. Biol. 19, 831-843 (2012). PDF, SI
84. “Discovery and Biological Characterization of Geranylated RNA in Bacteria” Dumelin, C. E.; Chen. Y.; Leconte, A. M.; Chen. Y. G.; Liu, D. R. Nat. Chem. Biol. 8, 913-919 (2012). PDF, SI | This work was featured in a Science and Technology Concentrate in C&E News and in Nat. Rev. Microbiol. 10, 731 (2012).
85. “DNA Ligase-Mediated Translation of DNA Into Densely Functionalized Nucleic Acid Polymers” Hili, R.; Niu, J.; Liu, D. R. J. Am. Chem. Soc 135, 98-101 (2013). PDF, SI. This work was featured in a Spotlight in J. Am. Chem. Soc. 135, 1627 (2013).
86. “A Population-Based Experimental Model for Protein Evolution: Effects of Mutation Rate and Selection Stringency on Evolutionary Outcomes” Leconte, A. M.; Dickinson, B. C.; Yang, D. D.; Chen, I. A.; Allen, B.; Liu, D. R. Biochemistry 52, 1490-1499 (2013). PDF, SI
87. “Enzyme-Free Translation of DNA into Sequence-Defined Synthetic Polymers Structurally Unrelated to Nucleic Acids” Niu, J.; Hili, R.; Liu, D. R. Nat. Chem. 5, 282-292 (2013). PDF | SI. | This work was featured in a News & Views article in Nat. Chem. 5, 252-253 (2013), in a Science and Technology Concentrate in C&E News 91 [9], 45 (2013), in a news story in Chemistry World (March 3, 2013), and in a News & Views article in Nat. Biotechnol. 31, 613 (2013).
88. “Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA” Curtis, E. A. and Liu, D. R. Chem Biol. 20, 521-532 (2013). PDF, SI
89. “Experimental Interrogation of the Path Dependence and Stochasticity of Protein Evolution Using Phage-Assisted Continuous Evolution” Dickinson, B. C.; Leconte, A. M.; Allen, B.; Esvelt, K. M.; Liu, D. R. Natl. Acad. Sci. USA 110, 9007-9012 (2013). | PDF | SI
90. “Sequence-Controlled Polymers” Lutz, J.-F.; Ouchi, M.; Liu, D. R.; Sawamoto, M. Science 341, 628 (1238149-1 to 1238149-8 online) (2013). PDF
91. “High-Throughput Profiling of Off-Target DNA Cleavage Reveals RNA-Programmed Cas9 Nuclease Specificity” Pattanayak, V.; Lin, S.; Guilinger, J.P.; Ma, E.; Doudna, J. A.; Liu, D. R. Nat. Biotechnol. 31, 839-843 (2013). PDF | SI | This work was featured in a News & Views article in Nat. Biotechnol. 31, 807-809 (2013).
92.“In Silico Abstraction of Zinc Finger Nuclease Cleavage Profiles Reveals an Expanded Landscape of Off-Target Sites” Sander, J.; Ramirez, C.; Linder, S.; Pattanayak, V.; Shoresh, N.; Ku, M.; Foden, J.; Reyon, D.; Bernstein, B.; Liu, D. R.; Joung, J. K. Acids Res. 41, e181 (2013). PDF
93. “Negative Selection And Stringency Modulation in Phage-Assisted Continuous Evolution” Carlson, J. C.; Badran, A. H.; Nilo, D. A.; Liu, D. R. Chem. Biol. 10, 216-222 (2014). | PDF
94. “Immobilization of Actively Thromboresistant Assemblies on Sterile Blood-Contacting Surfaces” Qu Z.; Krishnamurthy, V.; Haller, C. A.; Dorr, B. M.; Marzec, U. M.; Hurst, S.; Hinds, M. T.; Hanson, S. R.; Liu, D. R.; Chaikof, E. L. Healthcare Mat. 3, 30-35 (2014). PDF
95. “Broad Specificity Profiling of TALENs Results in Engineered Nucleases with Improved DNA Cleavage Specificity” Guilinger, J. P.; Pattanayak, V.; Reyon, D.; Tsai, S. Q.; Sander, J. D.; Joung, J. K.; Liu, D. R. Methods 11, 429-435 (2014). PDF| SI
96. “Identification of Ligand-Target Pairs from Combined Libraries of Small Molecules and Unpurified Protein Targets in Cell Lysates” McGregor, L. M.; Jain, T.; Liu, D. R. Am. Chem. Soc. 136, 3264-3270 (2014). PDF
97. “Using DNA to Program Chemical Synthesis, Discover New Reactions, and Detect Ligand Binding” McGregor, L. M.; Liu, D. R. In A Handbook for DNA-Encoded Chemistry: Theory and Applications for Exploring Chemical Space and Drug Discovery. Goodnow, R.A., Ed.; Wiley: Hoboken pp. 377-415 (2014).
98. “Fusion of Catalytically Inactive Cas9 to FokI Nuclease Improves the Specificity of Genome Modification” Guilinger, J. P.; Thompson, D. B.; Liu, D. R. Biotechnol. 32, 577–582 (2014). This work was featured in a Research Highlight in Nat. Methods 11, 712 (2014). PDF | SI
99. “Anti-Diabetic Activity of Insulin-Degrading Enzyme Inhibitors Mediated by Multiple Hormones” Maianti, J. P.; McFedries, A.; Foda, Z. H.; Kleiner, R. E.; Du, X.-Q.; Leissring, M. A.; Tang, W.-J.; Charron, M. J.; Seeliger, M. A.; Saghatelian, A.; Liu, D. R. Nature 511, 94-98 (2014). PDF | SI | This work was featured in the Boston Globe, Nature News, Nat. Endocrinol., Cell Metabolism, C&E News, the MIT Technology Review, Endocrine News, Healthline, and other media outlets.
100.“A Naturally Occurring, Non-Canonical GTP Aptamer Made of Simple Tandem Repeats” Curtis, E. A. and Liu, D. R. RNA Biol. 11, 682-692 (2014). PDF
101. “Reprogramming the Specificity of Sortase Enzymes” Dorr, B. M.; Ham, H. O.; An, C.; Chaikof, E. L.; Liu, D. R. Natl. Acad. Sci. USA 111, 13343-13348 (2014). PDF, SI
102. “Electrophilic Activity-Based RNA Probes Reveal a Self-Alkylating RNA for RNA Labeling” McDonald, R. I.; Guilinger, J.P.; Mukherji, S.; Curtis, E.A.; Lee, W. I.; Liu, D. R. Chem. Biol. 10, 1049-1054 (2014). PDF | SI
103. “A System For the Continuous Directed Evolution of Proteases Rapidly Reveals Drug-Resistance Mutations” Dickinson, B. C.; Packer, M. S.; Badran, A. H.; Liu, D. R. Commun. 5, 5352 (2014). PDF | SI
104. “A DNA-Based Molecular Probe for Optically Reporting Cellular Traction Forces” Blakely, B. L.; Dumelin, C. E.; Trappmann, B.; McGregor, L.M.; Choi, C. K.; Anthony, P. C.; Duesterberg, V. K.; Baker, B. M.; Block, S. M.; Liu, D. R.; Chen. C. S. Methods 11, 1229-1232 (2014). PDF | SI
105. “Targeted Antithrombotic Protein Micelles” Kim, W.; Haller, C; Dai, E.; Wang, X.; Hagemeyer, C. E.; Liu, D. R.; Peter, K.; Chaikof, E. L. Chem. Int. Ed. 54, 1461-1465 (2014). PDF
106.“Determining the Specificities of TALENs, Cas9, and Other Genome Editing Enzymes” Pattanayak, V.; Guilinger, J. P.; Liu, D. R. Methods in Enzymology 546, 47-78 (2014). PDF
107. “Cationic Lipid-Mediated Delivery of Proteins Enables Efficient Protein-Based Genome Editing In Vitro and In Vivo” Zuris, J. A.; Thompson, D. B.; Shu, Y.; Guilinger, J. P.; Bessen, J. L.; Hu, J. H.; Maeder, M. L.; Joung, J. K.; Chen, Z.-Y.; Liu, D. R. Biotechnol. 33, 73-80 (2015). PDF | SI
108. “In Vivo Continuous Directed Evolution” Badran, A. H.; Liu, D. R. Opin. Chem. Biol. 24, 1-10 (2015). PDF
109. “Novel Selection Methods for DNA-Encoded Chemical Libraries” Chan, A. I.; McGregor, L. M.; Liu, D. R. Opin. Chem. Biol. 26, 55-61 (2015). PDF
110. “Small Molecule-Triggered Cas9 Protein with Improved Genome-Editing Specificity” Davis, K. M.; Pattanayak, V.; Thompson, D. B.; Zuris, J. A.; Liu, D. R. Chem. Biol. 11, 316-318 (2015). PDF, SI
111. “Methods for the Directed Evolution of Proteins” Packer, M. S. and Liu, D. R. Rev. Genetics 16, 379-394 (2015). PDF
112. “Continuous Directed Evolution of DNA-Binding Proteins to Improve TALEN Specificity” Hubbard, B. P.; Badran, A. H.; Zuris, J. A.; Guilinger, J. P.; Davis, K. M.; Tsai, S. Q.; Sander, J. D.; Joung, J. K.; Liu, D. R. Methods 12, 939-942 (2015). PDF | SI
113. “Development of Potent In Vivo Mutagenesis Plasmids with Broad Mutational Spectra” Badran, A. H. and Liu, D. R. Commun. 6, 8425 (2015). PDF | SI
114. “Discovery and Characterization of a Peptide That Enhances Endosomal Escape of Delivered Proteins In Vitro And In Vivo” Li, M.; Tao, Y.; Shu, Y.; LaRochelle, J. R.; Steinauer, A.; Thompson, D.; Schepartz, A.; Chen., Z.-Y.; Liu, D. R. Am. Chem. Soc. 137, 14084-14093 (2015). PDF
115. “Analytical Devices Based on Direct Synthesis of DNA on Paper” Glavan, A. C.; Niu, J.; Chen, Z.; Guder, F.; Cheng, C.-M.; Liu, D. R.; Whitesides, G. M. Chem. 88, 725-731 (2015). PDF
116. “Chemical Biology Approaches to Genome Editing: Understanding, Controlling, and Delivering Programmable Nucleases.” Hu, J. H.; Davis, K. M.; Liu, D. R. Cell Chem. Biol. 23, 57-73 (2016). PDF
117. “In Situ Regeneration of Bioactive Coatings Enabled by an Evolved Staphylococcus aureus Sortase A” Qu, Z.; Dorr, B. M.; Dai, E.; Haller, C. A.; Kim, W.; Ham, H. O.; Liu, D. R.; Chaikof, E. L. Commun. 7, 11140 (2016). PDF
118. “Efficient Delivery of Genome-Editing Proteins using Bioreducible Lipid Nanoparticles” Wang, M.; Zuris, J. A.; Meng, F.; Rees, H. A.; Deng, P.; Gao, X.; Pouli, D.; Wu, Q.; Georgakoudi, I.; Liu, D. R.; Xu, Q. Natl. Acad. Sci. USA 113, 2868-2873 (2016). PDF
119.“Programmable Editing of a Target Base in Genomic DNA Without Double-Stranded DNA Cleavage” Komor, A. C.; Kim, Y. B.; Packer, M. S.; Zuris, J. A.; Liu, D. R. Nature 533, 420-424 (2016). PDF | SI | Expanded Extended Data Figure 6
120.“Continuous Evolution of Bacillus thuringiensis Toxins Overcomes Insect Resistance” Badran, A. H.; Guzov, V. M.; Huai, Q.; Kemp, M. M.; Vishwanath, P.; Kain, W.; Nance, A.M.; Evdokimov, A.; Moshiri, F.; Turner, K. H.; Wang, P.; Malvar, T.; Liu, D. R. Nature 533, 58-63 (2016). PDF, SI
121. “Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein” Pak, C. W.; Kosno, M.; Holehouse, A. S.; Padrick, S. B.; Mittal, A.; Ali, R.; Yunus, A. A.; Liu, D.R.; Pappu, R. V.; Rosen, M. K. Cell 63, 72-85 (2016). PDF
122. “Structural and Biochemical Basis for Inhibition of Breast Cancer Cell Migration and Drug-Resistance Mutations by Src-Specific Macrocyclic Inhibitors” Aleem, A.; Georghiou, G.; Kleiner, R.; Guja, K.; Garcia-Diaz, M.; Miller, W. T.; Liu, D. R.; Seeliger, M. A. Cell Chem. Biol. 23, 1103-1112 (2016). PDF
123.“A Programmable Cas9-Serine Recombinase Fusion Protein That Operates on DNA Sequences in Mammalian Cells” Chaikind, B.; Bessen, J. L.; Thompson, D. B.; Hu, J. H.; Liu, D. R. Nucleic Acids Res. 44, 9758-9770 (2016). PDF | SI
124.“CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes” Komor, A. C.; Badran, A. H.; Liu, D. R. Cell 168, 20-36 (2017). PDF
125. “Increasing the Genome-Targeting Scope and Precision of Base Editing with Engineered Cas9-Cytidine Deaminase Fusions” Kim, Y. B.; Komor, A. C.; Levy, J. M.; Packer, M. S.; Zhao, K.T.; Liu, D. R. Biotechnol. 35, 371-376 (2017). PDF
126.“Improving the DNA Specificity and Applicability of Base Editing Through Protein Engineering and Protein Delivery” Rees, H. A.; Komor, A. C.; Yeh, W.-H.; Edge, A. S. B.; Liu, D. R. Commun. 8, 15790 (2017). PDF
127. “Aptazyme-Embedded Guide RNAs Enable Ligand-Responsive Genome Editing and Transcriptional Activation” Tang, W.; Hu, J. H.; Liu, D. R. Commun. 8, 15939 (2017). PDF
128.“Discovery of a Covalent Kinase Inhibitor from a DNA-Encoded Small-Molecule Library x Protein Library Selection” Chan, A. I.; McGregor, L. M.; Jain, R.; Liu, D. R. Am. Chem. Soc. 139, 10192-10195 (2017). PDF | SI
129.“Improved Base Excision Repair Inhibition and Bacteriophage Mu Gam Protein Yields C:G-to-T:A Base Editors with Higher Efficiency and Product Purity” 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. Adv. 3, eaao4774 (2017). PDF
130.“Phage-Assisted Continuous Evolution of Proteases with Altered Substrate Specificity” Packer, M. S.; Rees, H. A.; Liu, D. R. Commun. 8, 956 (2017). PDF | SI
131. “Nucleic Acid-Templated Synthesis of Sequence-Defined Synthetic Polymers” Chen, Z. and Liu, D. R. in Sequence-Controlled Polymers, ed. J. F. Lutz (Wiley) (2017).
132. “Continuous Directed Evolution of Aminoacyl-tRNA Synthetases” Bryson, D. I.; Fan C.; Guo, L.-T.; Miller, C.; Söll, D.; Liu, D. R. Chem. Biol. 13, 1253-1260 (2017). PDF
133. “Crystal Structures Reveal an Elusive Functional Domain of Pyrrolysyl-tRNA Synthetase” Suzuki, T.; Miller, C.; Guo, L.-T.; Ho, J. M. L.; Bryson, D. I.; Wang Y.-S.; Liu, D. R., and Söll, D. Chem. Biol. 13, 1261-1266 (2017). PDF
134. “Programmable Base Editing of A•T to G•C in Genomic DNA Without DNA Cleavage” Gaudelli, N. M.; Komor, A. C.; Rees, H. A.; Packer, M. S.; Badran, A. H.; Bryson, D. I.; Liu, D. R. Nature 551, 464-471 (2017). PDF | SI
135. “Development of a Formaldehyde Biosensor with Application to Synthetic Methylotrophy” Woolston, B. M.; Roth, T.; Kohale, I.; Liu, D. R.; Stephanopoulos, G. Bioeng. 115, 206-215 (2018). PDF
136. “Editing the Genome Without Double-Stranded DNA Breaks” Komor, A. C.; Badran, A. H.; Liu, D. R. ACS Chem. Biol. 13, 383-388 (2018). PDF.
137. “Treatment of Autosomal Dominant Hearing Loss by In Vivo Delivery of Genome Editing Agents” Gao, X.; Lamas, V.; Huang, M.; Yeh, W.-H.; Pan, B.; Hu, Y.-J.; Hu, J. H.; Thompson, D. B.; Shu, Y.; Li, Y.; Wang, H.; Yang, S.; Xu, Q.; Polley, D. B.; Liberman, M. C.; Kong, W.-J.; Holt, J. R.; Chen, Z.-Y.; Liu, D. R. Nature 553, 217-221 (2018). PDF | SI
138. “Evolution of Sequence-Defined Highly Functionalized Nucleic Acid Polymers” Chen, Z.; Lichtor, P. A.; Berliner, A. P.; Chen, J. C.; Liu, D. R. Chem. 10, 420-427 (2018). PDF | Nature Chem News and Views
139. “Rewritable Multi-Event Analog Recording in Bacterial and Mammalian Cells” Tang, W.; Liu, D. R. Science 360, eaap8992 (2018). PDF
140. “Evolved Cas9 Variants with Broad PAM Compatibility and High DNA Specificity” Hu, J. H.; Miller, S. M.; Geurts, M. H.; Tang, W.; Chen, L.; Sun, N.; Zeina, C.; Gao, X.; Rees. H. A.; Lin, Z.; Liu, D. R. Nature 556, 57-63 (2018). PDF | SI
141. “Ensemble CryoEM Elucidates the Mechanism of Insulin Capture and Degradation by Human Insulin Degrading Enzyme” Zhang, Z.; Liang, W. G.; Bailey, L. J.; Tan, Y. Z.; Wei, H.; Wang, A.; Farcasanu, M.; Woods, V. A.; McCord, L. A.; Lee, D.; Shang, W.; Deprez-Poulain, R.; Deprez, B.; Liu, D. R.; Koide, A.; Koide, S.; Kossiakoff, A. A.; Li, S.; Carragher, B.; Potter, C. S.; Tang, W.-J. eLife 7:e33572 (2018). PDF
142. “Second-Generation DNA-Templated Macrocycle Libraries for the Discovery of Bioactive Small Molecules” Usanov, D. L.; Chan, A. I.; Maianti, J. P.; Liu, D. R. Chem. 10, 704-714 (2018). PDF | SI
143. “In Vivo Base Editing of Post-Mitotic Sensory Cells” Yeh, W.-H.; Chiang, H.; Rees, H. A.; Edge, A. S.; Liu, D. R. Commun. 9, 2184 (2018). PDF
144. “Improving Cytidine and Adenine Base Editors by Expression Optimization and Ancestral Reconstruction” Koblan, L. W.; Doman, J. L.; Wilson, C.; Levy, J. M.; Tay, T.; Newby, G. A.; Maianti, J. P.; Raguram, A.; Liu, D. R. Biotechnol. 36, 843-846 (2018). PDF | SI
145. “Continuous Directed Evolution of Proteins with Improved Soluble Expression” Wang, T.; Badran, A. H.; Huang, T. P.; Liu, D. R. Chem. Biol. 14, 972-980 (2018). PDF | SI
146. “Green Fluorescent Proteins Engineered for Cartilage-Targeted Drug Delivery: Insights for Transport into Highly Charged Avascular Tissues” Krishnan, Y.; Rees, H. A.; Rossitto, C. P.; Kim, S.-E.; Hung, H.-H.; Frank, E. H.; Olsen, B. D.; Liu, D. R.; Hammond, P. T.; Grodzinsky, A. J. Biomaterials 183, 218-233 (2018). PDF | SI
147. “One-Pot Dual Labeling of IgG 1 and Preparation of C-to-C Fusion Proteins Through a Combination of Sortase A and Butelase 1” Harmand, T. J.; Bousbaine, D.; Chan, A.; Zhang, X.; Liu, D. R.; Tam, J. P.; Ploegh, H. L. Chem. 29, 3245-3249 (2018). PDF | SI
148. “Predictable and Precise Template-Free CRISPR Editing of Pathogenic Variants” Shen, M. W.; Arbab, M.; Hsu, J. Y.; Worstell, D.; Culbertson, S. J.; Krabbe, O.; Cassa, C. A.; Liu, D. R.; Gifford, D. K.; Sherwood, R. I. Nature 563, 646-651 (2018). PDF | SI
149. “Base Editing: Precision Chemistry on the Genome and Transcriptome of Living Cells” Rees, H. A. and Liu, D. R. Rev. Genet. 19, 770-788 (2018). PDF
150. “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. Commun 9, 4804 (2018). PDF| SI
151. “Adenine Base Editing in an Adult Mouse Model of Tyrosinemia” Song, C.-Q.; Jiang, T.; Richter, M.; Rhym, L. H.; Koblan, L. W.; Zafra, M. P.; Schatoff, E. M.; Cao, Y.; Dow L. E.; Zhu, L. J.; Anderson, D. G.; Liu, D. R.; Ying, H.; Xue, W. Biomed. Eng. 4, 125-130 (2020). PDF
152. “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. Rep. 9, 1662 (2019). PDF
153. “Accurate and Rapid Analysis of Genome Editing Data from Nucleases and Base Editors with CRISPResso2” Clement, K.; Rees, H. A.; Canver, M. C.; Gehrke, J. M.; Farouni, R.; Hsu, J. Y.; Cole, M. A.; Liu, D. R.; Joung, J. K.; Bauer, D. E.; Pinello, L. Biotechnol. 37, 224-226 (2019). PDF
154. “Adopt a Moratorium on Heritable Genome Editing” Lander, E.S.; Baylis, F.; Zhang, F.; Charpentier, E.; Berg, P.; Bourgain, C.; Friedrich, B.; Joung, J. K.; Li, J.; Liu, D.; Naldini, L.; Nie, J.-B.; Qui, R.; Schone-Seifer, B.; Shao, F.; Terry, S.; Wei, W.; Winnacker, E. Nature 567, 165-168 (2019). PDF
155. “Side-Chain Determinants of Biopolymer Function During Selection and Replication” Lichtor, P. A.; Chen, Z.; Elowe, N. H.; Chen, J. C.; Liu, D. R. Chem. Biol. 15, 419-426 (2019). PDF
156. “Phage-Assisted Evolution of Bacillus methanolicus Methanol Dehydrogenase 2” Roth, T. B.; Woolston, B. M.; Stephanopoulos, G.; Liu, D. R. ACS Syn. Biol. 8, 796-806 (2019). PDF
157. “A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9” Maji, B.; Gangopadhyay, S. A.; Lee, M.; Shi, M.; Wu P.; Heler, R.; Mok, B.; Lim, D.; Siriwardena, S.U.; Paul, B.; Dančík, V.; Vetere, A.; Mesleh, M. F.; Marraffini, L. A.; Liu, D. R.; Clemons, P. A.; Wagner, B. K.; Choudhary, A. Cell 177, 1067-1079 (2019). PDF
158. “High-Resolution Specificity Profiling and Off-Target Prediction for Site-Specific DNA Recombinases” Bessen, J. L.; Afeyan, L. K.; Dančík, C.; Koblan, L. W.; Thompson, D. B.; Leichner, C.; Clemons, P. A.; Liu, D. R. Commun. 10, 1937 (2019). PDF | SI
159. “Analysis and Minimization of Cellular RNA Editing by DNA Adenine Base Editors” Rees, H.A.; Wilson, C.; Doman, J. L.; Liu, D. R. Adv. 5, eaax5717 (2019). PDF
160. “Substrate-Selective Inhibitors that Reprogram the Activity of Insulin-Degrading Enzyme” Maianti, J. P.; Tan, G. A.; Vetere, A.; Welsh, A.; Wagner, B. K.; Seeliger, M. A.; Liu, D. R. Chem. Biol. 15, 565-574 (2019). PDF.
161. “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. Biotechnol. 37, 626-631 (2019). PDF | SI
162. “Development of hRad51–Cas9 Nickase Fusions that Mediate HDR Without Double-Stranded Breaks” Rees, H. A.; Yeh, W.-H.; Liu, D. R. Commun. 10, 2212 (2019). PDF
163. “An Anionic Human Protein Mediates Cationic Liposome Delivery of Genome Editing Proteins into Mammalian Cells” Kim Y. B.; Zhao, K. T.; Thompson, D. B.; Liu, D. R. Commun. 10, 2905 (2019). PDF
164. “Continuous Evolution of Base Editors with Expanded Target Compatibility and Improved Activity” Thuronyi, B. W.; Koblan, L. W.; Levy, J. M.; Yeh, W.-H.; Zheng, C.; Newby, G. A.; Wilson, C.; Bhaumik, M.; Shubina-Oleinik, O.; Holt, J. R.; Liu, D. R. Biotechnol. 37, 1070-1079 (2019). PDF, | SI
165. “Search-and-Replace Genome Editing Without Double-Strand Breaks or Donor DNA” Anzalone, A. V.; Randolph, P. B.; Davis, J. R.; Sousa, A. A.; Koblan, L. W.; Levy, J. M.; Chen, P. J.; Wilson, C.; Newby, G. A.; Raguram, A.; Liu, D. R. Nature 576, 149-157 (2019). PDF | SI
166. “Base Editor Correction of COL7A1 in Recessive Dystrophic Epidermolysis Bullosa Patient-Derived Fibroblasts and iPSCs” Osborn, M. J.; Newby, G. A.; Knipping, D.; McElroy, A. N.; Riddle, M.; Xia, L.; Chen, W.; C.; Eide, C.; Webber, B.R.; Wandall, H. H.; Dabelsteen, S.; Blazar, B. R.; Liu, D. R.; Tolar, J. Invest. Derm. 140, 338-347 (2019). PDF
167. “High-Throughput Analysis of the Activities of xCas9, SpCas9-NG, and SpCas9 at Matched and Mismatched Target Sequences in Human Cells” Kim, H. K.; Lee, S.; Kim, Y.; Park, J.; Min, S.; Choi, J. W.; Huang, T. P.; Yoon, S.; Liu, D. R.; Kim, H. H. Biomed. Eng. 4, 111-124 (2020). PDF
168. “Cytosine and Adenine Base Editing of the Brain, Liver, Retina, Heart and Skeletal Muscle of Mice Via Adeno-Associated Viruses” Levy, J. M.; Yeh, W.-H.; Pendse, N.; Davis, J. R.; Hennessey, E.; Butcher, R.; Koblan, L. W.; Comander, J.; Liu, Q.; Liu, D. R. Biomed. Eng. 4, 97-110 (2020). PDF | SI
169. “Evaluation and Minimization of Cas9-Independent Off-Target DNA Editing by Cytosine Base Editors” *Doman, J. L.; *Raguram, A.; Newby, G. A.; Liu, D. R. Biotechnol. 38, 620-628 (2020). PDF | SI
170. “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. Biotechnol. 38, 471-481 (2020). PDF | SI
171. “Prime Genome Editing in Rice and Wheat” Lin, Q.; Zong, Y.; Xue, C.; Wang, S.; Jin, S.; Zhu, Z.; Wang, Y.; Anzalone, A. V.; Raguram, A.; Doman. J. L.; Liu, D. R.; Gao, C. Biotechnol. 38, 582-585 (2020). PDF | SI
172. “The Developing Toolkit of Continuous Directed Evolution” Morrison, M. S; Podracky, C. J.; Liu, D. R. Chem Bio. 16, 610-619 (2020). PDF
173. “Glucose Response by Stem Cell-Derived β Cells In Vitro is Inhibited by a Bottleneck in Glycolysis” Davis, J. C.; Alves, T. C.; Helman, A.; Chen, J. C. ; Kenty, J. H.; Cardone, R. L.; Liu, D. R.; Kibbey, R .G.; Melton, D. A. Cell Rep. 31, 107623 (2020). PDF
174. “Chemical Modifications of Adenine Base Editor mRNA and Guide RNA Expand Its Application Scope” Jiang, T.; Henderson, J. M.; Coote, K.; Cheng, Y.; Valley, H. C.; Zhang, X.-O.; Wang, Q.; Rhym, L. H.; Cao, Y.; Newby, G. A.; Bihler, H.; Mense, M.; Weng, Z.; Anderson, D. G.; McCaffrey, A. P., Liu, D. R.; Xue, W. Commun. 11, 1979 (2020). PDF
175. “Phage-Assisted Evolution of an Adenine Base Editor with Enhanced Cas Domain Compatibility and Activity” Richter, M. F.; Zhao, K. T.; Eton, E.; Lapinaite, A.; Newby, G. A.; Thuronyi, B. W.; Wilson. C.; Koblan L. W.; Zeng, J.; Bauer, D. E.; Doudna, J. A.; Liu, D. R. Biotechnol. 38, 883-891 (2020). PDF | SI
176. “In Vivo Base Editing Restores Sensory Transduction and Transiently Improves Auditory Function in a Mouse Model of Recessive Deafness” Yeh, W.-H.; Shubina-Oleinik, O.; Levy, J. M.; Pan, B.; Newby, G. A.; Wornow, M.; Burt, R.; Chen, J. C.; Holt, J. R.; Liu, D. R. Trans. Med. 12, eaay9101 (2020). PDF | SI
177. “Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning” Arbab, M.; Shen, M. W.; Mok, B.; Wilson, C.; Matuszek, Z.; Cassa, C. A.; Liu, D. R. Cell 182, 463-480 (2020). PDF | SI
178. “Genome Editing with CRISPR-Cas Nucleases, Base Editors, Transposases, and Prime Editors” Anzalone, A. V.; Koblan, L. W.; Liu, D. R. Biotechnol. 38, 824-844 (2020). PDF | SI
179. “A Bacterial Cytidine Deaminase Toxin Enables CRISPR-Free Mitochondrial Base Editing” Mok, B. Y.; de Moraes, M. H.; Zeng, J.; Bosch, D. E.; Kotrys, A. V.; Raguram, A.; Hsu, F.; Radey, M. C.; Peterson, S. B.; Mootha, V. K.; Mougous, J. D.; Liu, D. R. Nature 583, 631-637 (2020).PDF | SI
180. “DNA Capture by a CRISPR-Cas9 Guided Adenine Base Editor” Lapinaite, A.; Knott, G. J.; Palumbo, C. M.; Lin-Shiao, E.; Richter, M. F.; Zhao, K. T.; Beal, P. A.; Liu, D. R.; Doudna, J. A. Science 369, 566-571 (2020).PDF | SI
181. “Programmable m6A Modification of Cellular RNAs with a Cas13-Directed Methyltransferase” Wilson, C.; Chen. P. J.; Miao, Z.; Liu, D. R. Biotechnol. 38, 1431-1440 (2020). PDF | SI
182. “Multimodal Small-Molecule Screening for Human Prion Protein Binders” Reidenbach, A. G.; Mesleh, M. F.; Casalena, D.; Vallabh, S. M.; Dahlin, J. L.; Leed, A. J.; Chan, A. I.; Usanov, D. L.; Yehl, J. B.; Lemke, C. T.; Campbell, A, J.; Shah, R. N.; Shrestha, O. K.; Sacher, J. R.; Rangel, V. L.; Moroco, J. A.; Sathappa, M.; Nonato, M. C.; Nguyen, K. T.; Wright, S. K.; Liu, D. R.; Wagner, F. F.; Kaushik, V. K.; Auld, D. S.; Schreiber, S. L.; Minikel, E. V. Biol. Chem. 295, 13516-13531 (2020). PDF | SI
183. “Phage-Assisted Continuous and Non-Continuous Evolution” Miller, S. M.; Wang, T.; Liu, D. R. Protocols 15, 4101-4127 (2020). PDF | SI
184. “Restoration of Visual Function in Adult Mice with an Inherited Retinal Disease via Adenine Base Editing” Suh, S.; Choi, E. H.; Leinonen, H.; Foik, A. T.; Newby, G. A.; Yeh, W.-H.; Dong, Z.; Kiser, P. D.; Lyon, D. C.; Liu, D. R.; Palczewski, K. Biomed. Eng. 5, 169-178 (2021). PDF | SI
185. “Precision Genome Editing Using Cytosine and Adenine Base Editors in Mammalian Cells” Huang, T. P.; Newby, G. A.; Liu, D. R. Protocols 16, 1089-1128 (2021). PDF | Supplementary Data & Tables.
186. “Laboratory Evolution of a Sortase Enzyme that Modifies Amyloid-β Protein” Podracky, C. J.; An. C.; DeSousa, A.; Dorr, B. M.; Walsh, D. M; Liu D. R. Chem. Biol. 17, 317-325 (2021). PDF | SI
187. “In Vivo Base Editing Rescues Hutchinson-Gilford Progeria Syndrome in Mice” Koblan L. W.; Erdos, M. R.; Wilson, C.; Cabral, W. A.; Levy, J. M.; Xiong, Z.-M.; Tavarez, U. L.; Davison, L.; Gete, Y. G.; Mao, X.; Newby, G. A.; Doherty, S. P.; Narisu, N.; Sheng, Q.; Krilow, C.; Lin, C. Y.; Gordon, L. B.; Cao, K.; Collins, F. S.; Brown, J. D.; Liu, D. R. Nature 589, 608-614 (2021). PDF | SI | “Base Editing in Progeria” NEJM Companion Paper
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190. “Phage-Assisted Evolution of Botulinum Neurotoxin Proteases with Reprogrammed Specificity” Blum, T. R.; Liu, H.; Packer, M. S.; Xiong, X.; Lee, P.-G.; Zhang, S.; Richter, M.; Dong, M.; Liu, D. R. Science 371, 803-810 (2021). PDF | SI | Insights:Perspectives
191. “Prime Editing in Mice Reveals the Essentiality of a Single Base in Driving Tissue-Specific Gene Expression” Gao, P.; Lyu, Q.; Ghanam, A. R.; Lazzarotto, C. R.; Newby G. A.; Zhang, W.; Choi, M.; Slivano, O.J.; Holden, K.; Walker II, J. A.; Kadina, A. P.; Munroe, R. J.; Abratte, C. M.; Schimenti, J. C.; Liu, D. R.; Tsai, S. Q.; Long, X.; Miano, J. M. Genome Biol. 22, 83 (2021). PDF
192. “The NIH Somatic Cell Genome Editing Program” Saha, K.; Sontheimer, E. J.; Brooks, P. J.; Dwinell, M. R.; Gersbach, C. A.; Liu, D.R.; Murray, S. A.; Tsai, S. Q.; Wilson, R. C.; Anderson, D. G. et al. Nature 592, 195-204 (2021). PDF
193. “Base Editing of Hematopoietic 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.; Yao, 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). PDF | SI
194. “Mechanisms of Angiogenic Incompetence in Hutchinson-Gilford Progeria via Downregulation of Endothelial NOS” Gete, Y. G.; Koblan, L. W.; Mao, X.; Trappio, M.; Mahadik, B.; Fisher, J. P.; Liu, D. R.; Cao, K. Aging Cell 20, e13388 (2021). PDF
195. “Efficient C•G-to-G•C Base Editors Developed Using CRISPRi Screens, Target-Library Analysis and Machine Learning” Koblan, L. W.; Arbab, M.; Shen, M. W.; Hussmann, J. A.; Anzalone, A. V.; Doman, J. L.; Newby, G. A.; Yang, D.; Mok, B.; Replogle, J. M.; Xu, A.; Sisley, T. A.; Weissman, J. S.; Adamson, B.; Liu, D. R. Biotechnol. 39, 1414-1425 (2021). PDF | SI
196. “Functional Correction of CFTR Mutations in Human Airway Epithelial Cells using Adenine Base Editors” Krishnamurthy, S.; Traore, S.; Cooney, A. L.; Brommel, C. M.; Kulhankova, K.; Sinn, P. L.; Newby, G. A.; Liu, D. R.; McCray, P. B. Acids Res. 49, 10558-10572 (2021). PDF
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198. “Reconstruction of Evolving Gene Variants and Fitness from Short Sequencing Reads” Shen, M. W.; Zhao, K. T.; Liu, D. R. Chem. Biol. 17, 1188-1198 (2021). PDF | SI
199. “Disulfide-Compatible Phage-Assisted Continuous Evolution in the Periplasmic Space” Morrison, M. S.; Wang, T.; Raguram, A.; Hemez, C.; Liu, D. R. Commun. 12, 5959 (2021). PDF | SI
200. “Enhanced Prime Editing Systems by Manipulating Cellular Determinants of Editing Outcomes” Chen. P. J.; Hussmann, J. A.; Yan, J.; Knipping, D.; Ravisankar, P.; Chen, P.-F.; Chen, C.; Nelson, J. W.; Newby G. A.; Sahin, M.; Osborn, M. J.; Weissman, J. S.; Adamson, B.; Liu, D. R. Cell 184, 5635-5652 (2021). PDF | SI
201. “Disruption of HIV-1 Co-Receptors CCR5 and CXCR4 in Primary Human T Cells and Hematopoietic Stem and Progenitor Cells Using Base Editing” Knipping, F.; Newby, G. A.; Eide, C. R.; McElroy, A. N.; Nielsen, S. C.; Smith, K.; Fang, Y.; Cornu, T. I.; Costa, C.; Gutierrez-Guerrero, A.; Bingea, S. P.; Feser, C. J.; Steinbeck, B.; Hippen, K. L.; Blazar, B. R.; McCaffrey, A.; Mussolino, C.; Verhoeyen, E.; Tolar, J., Liu, D. R.; Osborn, M. J. Ther. 30, 130-144 (2022). PDF
202. “Engineered pegRNAs Improve Prime Editing Efficiency” Nelson, J. W.; Randolph, P. B.; Shen, S. P.; Everette, K. A.; Chen, P. J.; Anzalone, A. V.; An, M.; Newby, G. A.; Chen. J. C.; Hsu, A.; Liu, D. R. Biotechnol. 40, 402-410 (2022). PDF | SI
203. “Programmable Deletion, Replacement, Integration, and Inversion of Large DNA Sequences with Twin Prime Editing” Anzalone, A. V.; Gao, X. D.; Podracky, C. J.; Nelson, A. T.; Koblan, L. W.; Raguram, A.; Levy, J. M.; Mercer, J. A., Liu, D. R. Biotechnol. 40, 731-740 (2022). PDF | SI
204. “Engineered Virus-Like Particles for Efficient In Vivo Delivery of Therapeutic Proteins” *Banskota, S.; *Raguram, A.; Sug, A.; Du, S. W.; Davis, J. R.; Choi, E. H.; Wang, X.; Nielsen, S. C.; Newby, G. A.; Randolph, P. B.; Osborn, M. J.; Musunuru, K.; Palczewski, K.; Liu, D. R. Cell 185, 250-265 (2022). PDF
205. “In Vivo Base Editing Rescues Cone Photoreceptors in a Mouse Model of Early-Onset Inherited Retinal Degeneration” Choi, E. H.; Suh, S.; Foik, A. T.; Leinonen, H.; Newby, G. A.; Gao, X. D.; Banskota, S.; Hoang, T.; Du, S.; Dong Z.; Raguram, A.; Kohli, S.; Blackshaw, S.; Lyon, D. C.; Liu, D. R.; Palczewski, K. Commun. 13, 1830 (2022). PDF | SI
206. “Prioritization of Autoimmune Disease-Associated Genetic Variants that Perturb Regulatory Element Activity in T Cells” Mouri, K.; Guo, M. H.; de Boer, C. G.; Lissner, M.M.; Harten, I.A.; Newby, G. A.; DeBerg, H.A.; Platt W.F.; Gentili, M.; Liu, D. R.; Campbell, D.J.; Hacohen, N.; Tewhey, R.; Ray, J. P. Genetics 54, 603-612 (2022). PDF | SI
207. “Precision Genome Editing in the Eye” Suh, S., Choi, E. H.; Raguram, A.; Liu, D. R.; Palczewski, K. Natl. Acad. Sci. USA 119, e2210104119 (2022). PDF
208. “CRISPR-Free Base Editors with Enhanced Activity and Expanded Targeting Scope in Mitochondrial and Nuclear DNA” Mok, B. Y.; Kotrys, A. V.; Raguram, A.; Huang, T. P.; Mootha, V. K.; Liu, D. R. Biotechnol. 40, 1378-1387 (2022). PDF | SI
209. “Therapeutic In Vivo Delivery of Gene Editing Agents” Raguram, A.; Banskota, S.; Liu, D. R. Cell 185, 2806-2827 (2022). PDF
210. “Generating Experimentally Unrelated Target Molecule-Binding Highly Functionalized Nucleic Acid Polymers Using Machine Learning” Chen, J. C.; Chen, J. P.; Shen M. W.; Wornow, M.; Bae, M.; Yeh, W.-H.; Hsu, A.; Liu, D. R. Commun. 13, 4541 (2022). PDF
211. “Efficient and Scalable Process to Produce Novel and Highly Bioactive Purified Cytosolic Crystals from Bacillus thuringiensis” Chicca, J.; Cazeault, N. R.; Rus, F.; Abraham, A.; Garceau, C.; Li, H.; Atwa, S. M.; Flanagan, K.; Soto, E. R.; Morrison, M. S.; Gazzola, D.; Hu, Y.; Liu, D. R.; Nielsen, M. K.; Urban Jr., J. F.; , Ostroff, G. R.; and Aroian, R. V. Spectrum 10, e02356-22 (2022). PDF | SI
212. “Designing and Executing Prime Editing Experiments in Mammalian Cells” Doman, J. L.; Sousa, A. A.; Randolph, P. B.; Chen. P. J.; Liu, D. R. Protocols 17, 2431–2468 (2022). PDF | SI
213. “Discovery and Molecular Basis of Subtype-Selective Cyclophilin Inhibitors” Peterson, A. A.; Rangwala, A. M.; Thakur, M. K.; Ward, P. S.; Hung, C.; Outhwaite, I. R.; Chan, A. I.; Usanov, D. L.; Mootha, V. K.; Seeliger, M. A.; Liu, D. R. Chem. Biol. 18, 1184–1195 (2022). PDF
214. “ABE8e Adenine Base Editor Precisely and Efficiently Corrects a Recurrent COL7A1 Nonsense Mutation” Sheriff, A.; Guri, I.; Zebrowska, P.; Llopis-Hernadez, V.; Brooks, I. R.; Tekkela, S.; Subramaniam, K.; Gebrezgabher, R.; Naso, G.; Petrova, A.; Balon, K.; Onoufriadis, A.; Kujawa, D.; Kotulska, M.; Newby, G.; Laczmanski, L.; Liu, D. R.; McGrath, J. A.; Jackow, J. Rep. 12, 19643 (2022). PDF | SI
215. “Efficient In Vivo Base Editing via Single Adeno-Associated Viruses with Size-Optimized Genomes Encoding Compact Adenine Base Editors” Davis, J. R.; Wang, X.; Witte, I.; Huang, T.P; Levy, J. M.; Raguram, A.; Banskota, S.; Seidah, N. G.; Musunuru, K.; Liu, D. R. Nat. Biomed. Eng. 6, 1272-1283 (2022). PDF | SI
216. “Prime Editing for Precise and Highly Versatile Genome Manipulation” Chen, P.J.; Liu, D. R. Nat. Rev. Genet. 24, 161-177 (2023). PDF
217. “In Vivo Base Editing by a Single I.V. Vector Injection for Treatment of Hemoglobinopathies” Li, C,; Georgakopoulou, A.; Newby, G. A.; Everette, K. A.; Nizamis, E.; Paschoudi, K.; Vlachaki, E.; Gil, S.; Anderson, A. K.; Koob, T.; Huang, L.; Wang, H.; Kiem, H.-P.; Liu, D. R.; Yannaki, E.; Lieber, A. Clin. Investig. Insight 7 (19): e162939. doi: 10.1172/jci.insight.162939 (2022) PDF | SI
218. “Compact Zinc Finger Base Editors that Edit Mitochondrial or Nuclear DNA In Vitro and In Vivo” Willis, J. C. W.; Silva-Pinheiro, P.; Widdup, L.; Minczuk, M.; Liu, D. R. Commun. 13, 7204 (2022). PDF | SI
219. “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. Biotechnol. 41, 96-107 (2023). PDF
220. “Efficient In Vivo Genome Editing Prevents Hypertrophic Cardiomyopathy in Mice” Reichart, D.; Newby, G. A.; Wakimoto, H.; Lun, M.; Gorham, J. M.; Curran, J. J.; Raguram, A.; DeLaughter, D. M.; Conner, D. A.; Marsiglia, J. D. C.; Kohli, S.; Chmatal, L.; Page, D. C.; Zabaleta, N.; Vandenberghe, L.; Liu, D. R.; Seidman, J. G.; Seidman, C. Med. 29, 412-421 (2023). PDF | SI
221. “In Vivo Base Editing by a Single I.V. Vector Injection for Treatment of Hemoglobinopathies” Li, C,; Georgakopoulou, A.; Newby, G. A.; Everette, K. A.; Nizamis, E.; Paschoudi, K.; Vlachaki, E.; Gil, S.; Anderson, A. K.; Koob, T.; Huang, L.; Wang, H.; Kiem, H.-P.; Liu, D. R.; Yannaki, E.; Lieber, A. Clin. Investig. Insight 7 (19): e162939. doi: 10.1172/jci.insight.162939 (2022). PDF | SI
222. “Evolution of an Adenine Base Editor into a Small, Efficient Cytosine Base Editor with Low Off-Target Activity” Neugebauer, M. E.; Hsu, A.; Arbab, M.; Krasnow, N. A.; McElroy, A. N.; Pandey, S.; Doman, J. L.; Huang, T.; Raguram, A.; Banskota, S.; Newby, G. A.; Tolar, J.; Osborn, M. J.; Liu, D. R. Biotechnol. 41, 673-685 (2023). PDF | SI
223. “In Vivo HSC Prime Editing Rescues Sickle Cell Disease in a Mouse Model” Li, C.; Georgakopoulou, A.; Newby, G. A.; Chen P. J.; Everette, K. A.; Paschoudi, K.; Vlachaki, E.; Gil, S.; Anderson, A. K.; Koob, T.; Huang, L.; Wang, H.; Kiem, H.-P.; Liu, D. R.; Yannaki, E.; Lieber, A. Blood 141, 2085-2099 (2023). [News & Views] | PDF | SI
224. “Human T Cell Generation Is Restored in CD3d Severe Combined Immunodeficiency Through Adenine Base Editing” McAuley, G. E.; Yiu, G.; Chang, P. C.; Newby, G. A.; Campo-Fernandez, B.; Fitz-Gibbon, S.; Wu, X.; Kang, S.-H. L.; Garibay, A.; Butler, J.; Christian, V.; Wong, R. L.; Everette, K. A.; Azzun, A.; Gelfer, H.; Seet, C. S.; Narendran, A.; Favela, L. M.; Romero, Z.; Wright, N.; Liu, D. R.; Crooks, G. M.; Kohn, D. B. Cell 186, 1398-1416 (2023). PDF | Cell Press Commentary
225. “Base Editing Rescue of Spinal Muscular Atrophy in Cells and in Mice” Arbab, M. Matuszek, Z.; Kray, K. M.; Du, A.; Newby, G. A.; Blatnik, A. J.; Raguram, A.; Richter, M. F.; Zhao, K. T.; Levy, J. M.; Shen. M. W.; Arnold, W. D.; Wang, D. ; Xie, J.; Gao, G.; Burghes, A. H. M.; Liu, D. R. Science 380, 6642, eadg6518 (2023). PDF | SI | [Videos]
226. “Ex Vivo Prime Editing of Patient Hematopoietic Stem Cells Rescues Sickle-Cell Disease Phenotypes After Engraftment in Mice” Everette, K. A.; Newby, G. A.; Levine, R. M.; Mayberry, K.; Jang, Y.; Mayuranathan, T.; Nimmagadda, N.; Dempsey, E.; Li, Y.; Bhoopalan, S. V.; Liu, X.; Davis, J. R.; Nelson, A. T.; Chen. P. J.; Sousa, A. A.; Cheng, Y.; Tisdale, J. F.; Weiss, M. J.; Yen. J. S.; Liu, D. R. Biomed. Eng. 7, 616–628 (2023). PDF | SI
227. “Massively Parallel Base Editing to Map Variant Effects in Human Hematopoiesis” Martin-Rufino, J. D.; Castano, N.; Pang, M.; Grody, E. I.; Joubran, S.; Caulier, A.; Wahlster, L.; Li, T.; Qiu, X.; Riera-Escandell, A. M.; Newby, G. A.; Al’Khafaji, A.; Chaudhary, S.; Black, S.; Weng, C.; Munson, G.; Liu, D. R.; Wlodarski, M. W.; Sims, K.; Oakley, J. H.; Fasano, R. M.; Xavier, R. J.; Lander, E. S.; Klein, D. E.; Sankaran, V. G. Cell 186, 2456-2474 (2023). PDF
228. “Rescue of Hearing by Adenine Base Editing in a Humanized Mouse Model of Usher Syndrome Type 1F” Peters, C. W.; Hanlon, K. S.; Ivanchenko, M. V.; Zinn, E.; Linarte, E. F.; Li, Y.; Levy, J. M.; Liu, D. R.; Kleinstiver, B. P.; Indzhykulian, A. A.; Corey, D. P. Ther. 31, 2439-2453 (2023). PDF
229. “Small-Molecule Discovery Through DNA-Encoded Libraries” Peterson, A. A. and Liu, D. R. Nat. Rev. Drug Disc. 22, 699–722 (2023). PDF
230. “Protospacer Modification Improves Base Editing of a Canonical Splice Site Variant and Recovery of CFTR Function in Human Airway Epithelial Cells” Joynt, A.T.; Kavanagh, E.W.; Newby, G.A.; Mitchell, S.; Eastman, A.C.; Paul, K.C.; Bowling, A.D.; Osorio, D.L.; Merlo, C.A.; Patel, S.U.; Raraigh, K.S.; Liu, D.R.; Sharma, N.; Cutting, G.R. Ther. Nuc. Acids. 33, 335-350 (2023). PDF | SI
231. “Potent and Uniform Fetal Hemoglobin Induction Via Base Editing” Mayuranathan, T.; Newby, G.A.; Feng, R.; Yao, Y.; Mayberry, K.D.; Lazzarotto, C.R.; Li, Y.; Levine, R.M.; Nimmagadda, N.; Dempsey, E.; Kang, G.; Porter, S.N.; Doerfler, P.A.; Zhang, J.; Jang, Y.; Chen, J.; Bell, H.W.; Crossley, M.; Velan Bhoopalan, S.; Sharma, A.; Tisdale, J.F.; Pruett-Miller, S.M.; Cheng, Y.; Tsai, S.Q.; Liu, D.R.; Weiss, M.J.; Yen, J.S. Gen.55, 1210–1220 (2023). PDF | SI
232. “Nonviral Base Editing of KCNJ13 Mutation Preserves Vision in a Model of Inherited Retinal Channelopathy” Kabra, M.; Shahi, P. K.; Wang, Y.; Sinha, D.; Spillane, A.; Newby, G. A.; Saxena, S.; Tong, Y.; Chang, Y.; Abdeen, A. A.; Edwards, K. L.; Theisen, C. O.; Liu, D. R.; Gamm, D. M.; Gong, S.; Saha, K.; Pattnaik, B. R. Clin. Investig. 133 (19): e171356 (2023). PDF | SI
233. “Treatment of Monogenic and Digenic Dominant Genetic Hearing Loss by CRISPR-Cas9 Ribonucleoprotein Delivery In Vivo” by Chen, Z.Y.; Tao, Y.; Lamas Alvarez, V.; Du, W.; Zhu, W.; Li, Y.; Whittaker, M.; Zuris, J.; Thompson, D.; Rameshbabu, A.P.; Shu, Y.; Gao, X.; Hu, J.; Pei, C.; Kong, W.J.; Liu, X.; Wu, H.; Kleinstiver, B.; Liu, D.R. Commun.14, 4928 (2023). PDF | SI
234. “Phage-Assisted Evolution and Protein Engineering Yield Compact, Efficient Prime Editors” *Doman, J.; *Pandey, S.; Neugebauer, M.E.; An, M.; Davis, J.R.; Randolph, P.B.; McElroy, A.; Gao, X.D.; Raguram, A.; Richter, M.F.; Everette, K.A.; Banskota, S.; Tian, K.; Tao, A.Y.; Tolar, J.; Osborn, M.J.; Liu, D. R. Cell 186, 3983-4002 (2023). PDF
235. “Assigning Functionality to Cysteines by Base Editing of Cancer Dependency Genes” Li, H.; Remsberg, J. R.; Won, S. J.; Zhao, K. T.; Huang, T. P.; Lu, B.; Simon, G. M.; Liu, D. R.; Cravatt, B. F. Chem. Biol. 19, 1320-1330 (2023). PDF | SI
236. “Reciprocal Mutations of Lung Tropic AAV Capsids Lead to Improved Transduction Properties” Cooney, A. L.; Brommel, C. M.; Traore, S.; Newby, G. A.; Liu, D. R.; McCray Jr, P. B.; Sinn, P. L. Frontiers in Genome Editing 5,1271813 (2023). PDF
237. “Shuttle Peptide Delivers Base Editor RNPs to Rhesus Monkey Airway Epithelial CellsIn Vivo” Kulhankova, K.; Traore, S.; Cheng, X.; Benk-Fortin, H.; Hallee, S.; Harvey, M.; Roberge, J.; Couture, F.; Kohli, S.; Gross, T.J.; Meyerholz, D.K.; Rettig, G.R.; Thommandru, B.; Kurgan, G.; Wohlford-Lenane, C.; Hartigan-O’Connor, D.J.; Yates, B.P.; Newby, G.A.; Liu, D.R.; Tarantal, A.F.; Guay, D.; McCray Jr., P.B. Commun. 14, 8051 (2023). PDF | SI
238. “Efficient Prime Editing in Mouse Brain, Liver and Heart with Dual AAVs” Davis, J. R.; Banskota, S.; Levy, J. M.; Newby, G. A.; Wang, X.; Anzalone, A. V.; Nelson, A. T.; Chen, P. J.; Hennes, A. D.; An, M.; Roh, H.; Randolph, P. B.; Musunuru, K.; Liu, D. R. Biotechnol. 42, 253-264 (2024). PDF | SI
239.“Self-Delivering, Chemically Modified CRISPR RNAs for AAV Co-Delivery and Genome Editing In Vivo” Zhang, H.; Kelly, K.; Lee, J.; Echeverria, D.; Cooper, D.; Panwala, R.; Chen, Z.; Gaston, N.; Newby, G.A.; Xie, J.; Liu, D.R.; Gao, G.; Wolfe, S.A.; Khvorova, A.; Watts, J.K.; Sontheimer, E.J. Acids Res., 52, 977-997 (2024). PDF
240. “Proteolysis Targeting Chimeras With Reduced Off-Targets” Nguyen, T. M.; Sreekanth, V.; Deb, A.; Kokkonda, P.; Tiwari, P. K.; Donovan, K.; Shoba, V.; Chaudhary, S. K.; Mercer, J. A. M.; Lai, S.; Sadagopan, A.; Jan, M.; Fischer, E. S.; Liu, D. R.; Ebert, B. L.; Choudhary, A. Chem. 16, 218-228 (2024). PDF | SI
241. “A Prime Editor Mouse to Model a Broad Spectrum of Somatic Mutations In Vivo” Ely, Z. A.; Mathey-Andrews, N.; Naranjo, S.; Gould, S. I.; Mercer, K. L.; Newby, G. A.; Cabana, C. M.; Rideout III, W. M.; Jaramillo, G. C.; Khirallah, J. M.; Holland, K.; Randolph, P. B.; Freed-Pastor, W. A.; Davis, J. R.; Kulstad, Z.; Westcott, P. M. K.; Lin, A.; Anzalone, A. V.; Horton, B. L.; Pattada, N. B.; Shanahan, S.-L.; Ye, Z.; Spranger, S.; Xu, Q.; Sanchez-Rivera, F. J.; Liu, D. R.; Jacks, T. Biotechnol. 42, 424-436 (2024). PDF | SI
242. “Adenine Transversion Editors Enable Precise, Efficient A•T-To-C•G Base Editing in Mammalian Cells and Embryos” Chen, L.; Hong, M.; Luan, C.; Gao, H.; Ru, G.; Guo, X.; Zhang, D.; Zhang, S.; Li, C.; Wu, J.; Randolph, P. B.; Sousa, A. A.; Qu, C.; Zhu, Y.; Guan, Y.; Wang, L.; Liu, M.; Feng, B.; Song, G.; Liu, D. R.; Li, D. Biotechnol. 42, 638-650 (2024). . PDF | SI
243. “Phage-Assisted Evolution of Highly Active Cytosine Base Editors with Enhanced Selectivity and Minimal Sequence Context Preference” Zhang, E.; Neugebauer, M. E.; Krasnow, N. A.; Liu, D. R. Commun. 15, 1697 (2024). PDF | SI
244. “Continuous Evolution of Compact Protein Degradation Tags Regulated by Selective Molecular Glues” Mercer, J. A. M.; DeCarlo, S. J.; Burman, S. S. R.; Sreekanth, V.; Nelson, A. T.; Hunkeler, M.; Chen. P. J.; Donovan, K. A.; Kokkonda, P.; Tiwari, P.; Shoba, V. M.; Deb. A.; Choudhary, A.; Fischer, E. S.; Liu, D. R. Science 383, 6688, eadk4422 (2024). PDF | SI
245. “Post-Translational Modification-Centric Base Editor Screens to Assess Phosphorylation Site Functionality In High-Throughput” Kennedy, P. H; Deh Sheikh, A. A; Balakar, M; Jones, A.C.; Olive, M.E.; Hegde, M.; Matias, M.I.; Pirete, N.; Burt, R.; Levy, J.; Little, T.; Hogan, P.G.; Liu, D.R.; Doench, J.G.; Newton, A.C.; Gottschalk, R.A.; De Boer, C.; Alarcon, S.; Newby, G.A.; Myers, S.; Meth. 21, 1033-1043 (2024). PDF | SI
246. “In Vivo Photoreceptor Base Editing Ameliorates Rhodopsin-E150K Autosomal-Recessive Retinitis Pigmentosa in Mice” Du., S.; Newby, G. A.; Salom, D.; Gao, F.; Menezes, C. R.; Suh S.; Choi, E. H.; Chen. P. Z.; Liu, D. R.; Palczewski, K. Natl. Acad. Sci. USA 121, e2416827121 (2024). PDF
247. “Amphiphilic Shuttle Peptide Delivers Base Editor Ribonucleoprotein to Correct the CFTR R553X Mutation in Well-Differentiated Airway Epithelial Cells” Kulhankova, K.; Cheng, A. X.; Traore, S.; Auger, M.; Pelletier, M.; Hervault, M.; Wells, K. D.; Green, J. A.; Byrne, A.; Nelson, B.; Sponchiado, M.; Boosani, C.; Heffner, C. S.; Snow, K. J.; Murray, S. A.; Villacreses, R. A.; Rector, M. V.; Gansemer, N. D.; Stoltz, D. A.; Allamargot, C.; Couture, F.; Hemez, C.; Hallée, S.; Barbeau, X.; Harvey, M.; Lauvaux, C.; Gaillet, B.; Newby, G. A.; Liu, D. R.; McCray Jr., P. B.; Guay, D. Nucleic Acids Res. 52, 11911-11925 (2024). PDF
248. “Engineered Virus-Like Particles for Transient Delivery of Prime Editor Ribonucleoprotein Complexes In Vivo” An, M.; Raguram, A.; Du, S. W.; Banskota, S.; Davis, J. R.; Newby, G. A.; Chen, P. Z.; Palczewski, K.; Liu, D. R. Biotechnol. 42, 1526–1537 (2024). PDF | SI
249. “Efficient Prime Editing in Two-Cell Mouse Embryos Using PEmbryo” Kim-Yip, R. P.; McNulty, R.; Joyce, B.; Mollica, A.; Chen. P. J.; Ravisankar, P.; Law, B. K.; Liu, D. R.; Toettcher, J. E.; Ivakine, E.; Posfai, E.; Adamson, B. Biotechnol. 42, 1822–1830 (2024). PDF | SI
250. “Introducing a Hemoglobin G-Makassar Variant in HSCs by In Vivo Base Editing Treats Sickle Cell Disease in Mice” Li, C.; Georgakopoulou, A.; Paschoudi, K.; Anderson, A. K.; Huang, L.; Gil, S.; Giannaki, M. G.; Vlachaki, E.; Newby, G. A.; Liu, D. R.; Yannaki, E.; Kiem, H.-P.; Lieber, A. Ther. 32(12), 4353-4371 (2024). PDF
251. “Bone-Marrow-Homing Lipid Nanoparticles for Genome Editing in Diseased and Malignant Haematopoietic Stem Cells” Lian, X.; Chatterjee S.; Sun, Y.; Dillard, S. A.; Moore, S.; Xiao, Y.; Bian, X.; Yamada, K.; Sung, Y.-C.; Levine, R. M.; Mayberry, K.; John, S.; Liu, X.; Smith, C.; Johnson, L. T.; Wang, X.; Zhang. C.C; Liu, D. R.; Newby, G. A.; Weiss, M. J.; Yen, J. S.; Siegwart, D. J. Nanotechnol. 19, 1409–1417 (2024). PDF
252. “Twin Prime Editing Mediated Exon Skipping/Reinsertion for Restored Collagen VII Expression in Recessive Dystrophic Epidermolysis Bullosa” Steinbeck, B. J.; Gao, X. D.; McElroy, A. N.; Pandey, S.; Doman, J. L.; Riddle, M. J.; Xia, L.; Chen. W.; Eide, C. R.; Lengert, A. H.; Han, S. W.; Blazar, B. R.; Wandall, H. H.; Dabelsteen, S.; Liu, D. R.; Tolar, J.; Osborn, M. J. Invest. Derm. 144(12), 2764-2777 (2024) . PDF
253. “High Throughput Evaluation of Genetic Variants with Prime Editing Sensor Libraries” Gould, S.I.; Wuest, A.N.; Dong, K.; Johnson, G.A.; Hsu, A.; Narendra, V.K.; Atwa, O.; Levine, S.S.; Liu, D.R.; Sanchez Rivera, F.J. Nat Biotechnol. 43, 1648-1662 (2025). PDF | SI
254. “Branched, Chemically Modified Poly(A) Tails Enhance the Translation Capacity of mRNA” Chen, H.; Liu, D.; Guo, J.; Aditham, A.; Zhou, Y.; Tian, J.; Luo, S.; Ren, J.; Hsu, A.; Huang, J.; Kostas, F.; Wu, M.; Liu, D. R.; Wang, X. Biotechnol. 43, 194–203 (2025). PDF | SI
255. “Efficient Site-Specific Integration of Large Genes in Mammalian Cells Via Continuously Evolved Recombinases and Prime Editing” Pandey, S.; Gao, X. D.; Krasnow, N. A.; McElroy, A.; Tao, Y. A.; Duby, J. E.; Steinbeck, B. J.; McCreary, J.; Pierce, S.; Tolar, J.; Meissner, T. B.; Chaikof, E. L.; Osborn, M. J.; Liu, D. R. Biomed. Eng. 9, 22–39 (2025). PDF | SI
256. “Systematic Optimization of Prime Editing for the Efficient Functional Correction of CFTR F508del in Human Airway Epithelial Cells” Sousa, A.A.; Hemez, C.; Lei, L.; Traore, S.; Kulhankova, K.; Newby, G. A.; Doman, J. L.; Oye, K.; Pandey, S.; Karp, Ph.H.; McCray Jr., P. B.; Liu, D. R. Biomed. Eng. 9, 7–21 (2025). PDF
257. “Safer and Efficient Base Editing and Prime Editing Via Ribonucleoproteins Delivered Through Optimized Lipid-Nanoparticle Formulations” Hołubowicz, R.; Du, S. W.; Felgner, J.; Smidak, R.; Choi, E. H.; Palczewska, G.; Menezes, C. R.; Dong, A.; Gao, F.; Medani, P.; Yan, A. L.; Hołubowicz, M. W.; Chen. P. Z.; Bassetto, M.; Risaliti, E.; Salom, D.; Workman, J. N.; Kiser, P. D.; Foik, A. T.; Lyon, D. C.; Newby, G. A.; Liu, D. R.; Felgner, P. L.; Palczewski, K. Biomed. Eng. 9, 57–78 (2025). PDF | SI
258. “Correcting a Pathogenic Mitochondrial DNA Mutation by Base Editing in Mice” Barrera-Paez, J. D.; Bacman, S. R.; Balla, T.; Van Booven, D.; Gannamedi, D. P.; Stewart, J. B.; Mok, B.; Liu, D. R.; Lombard, D. B.; Griswold, A. J.; Nedialkova, D. D.; Moraes, C. T. Transl. Med. 17, eadr0792 (2025). PDF | SI
259. “EvoAI Enables Extreme Compression and Reconstruction of the Protein Sequence Space” Ma. Z.; Li, W.; Shen. Y.; Xu, Y.; Liu, G.; Chang, J.; Li, Z.; Qin, H.; Tian, B.; Gong, H.; Liu, D. R.; Thuronyi, B. W.; Voigt, C. A.; Zhang, S. Meth. 22, 102–112 (2025). PDF
260. “In Vivo Base Editing of Angptl3 via Lipid Nanoparticles to Treat Cardiovascular Disease” Khirallah, J.; Bloomer, H.; Wich, D.; Huang, C.; Workman, J. N.; Li, Y.; Newby, G. A.; Liu, D. R.; Xu, Q. Ther. Nucl. Acids 36, 102486 (2025). PDF
261. “Modulating Collagen I Expression in Fibroblasts by CRISPR-Cas9 Base Editing of the Collagen 1A1 Promoter” Daliri, K.; Hescheler, J.; Newby, G. A.; Clement, K.; Liu, D. R.; Pfannkuche, K. J. Mol. Sci. 26, 3041 (2025).
262. “Directed Evolution of Engineered Virus-Like Particles with Improved Production and Transduction Efficiencies” Raguram, A.; An, M.; Chen. P. Z.; Liu, D. R. Biotechnol. 43, 1635-1647 (2025). PDF
263. “In Vivo Base Editing Extends Lifespan of a Humanized Mouse Model of Prion Disease” An, M.; Davis, J.R.; Levy, J.M.; Serack, F.E.; Harvey, JW.; Brauer, P.P.; Pirtle, C.P.; Berrios, K.N.; Newby, G.A.; Yeh, W.; Kamath, N.; Mortberg, M.; Lian, Y.; Howard, M.; DeSouza-Lenz, K.; Guzman, K.; Thai, A.; Graffman, S.; Laversenne, V.; Coffey, A.A.; Frei, J.; Pierce, S.E.; Safar, J.G.; Deverman, B.E.; Minikel, E.V.; Vallabh, S.M.; Liu, D.R. Med. 31, 1319–1328 (2025). PDF | SI || This work was featured as a “Research Highlight” in Nature Reviews Drug Discovery
264. “Adenine Base Editing Rescues Pathogenic Phenotypes in Tissue Engineered Vascular Model of Hutchinson-Gilford Progeria Syndrome” Abutaleb, N.; Gao, X.; Bedapudi, A.; Choi, L.; Shores, K.; Kennedy, C.; Duby, J.; Cao, K.; Liu, D.R.; Truskey, G. APL Bioeng.9, 016110 (2025). PDF
265. “In Vivo Prime Editing Rescues Photoreceptor Degeneration in Nonsense Mutant Retinitis Pigmentosa” Fu, Y.; He, X.; Ma, L.; Gao, X. D.; Liu, P.; Shi, H.; Chai, P.; Ge, S.; Jia, R.; Liu, D. R.; Fan, X.; Yang, Z. Commun. 16, 2394 (2025).
266. “Multiplex Base Editing to Protect from CD33 Directed Drugs for Immune and Gene Therapy” Borot, F.; Humbert, O.; Ehmsen, J. T.; Fields, E.; Kohli, S.; Radtke, S.; Swing, K.; Pande, D.; Enstrom, M. R.; Laszlo, G. S.; Mayuranathan, T.; Ali, A. M.; Weiss, M. J.; Yen, J. S.; Newby, G. A.; Walter, R. B.; Liu, D. R.; Mukherjee, S.; Kiem, H.-P. Commun. 16, 4899 (2025).
267. “Systematic Empirical Evaluation of Individual Base Editing Targets: Validating Therapeutic Targets in USH2A and Comparison of Methods” Tachida, Y.; Manian, K. V.; Butcher, R.; Levy, J. M.; Pendse, N.; Hennessey, E.; Liu, D. R.; Pierce, E. A.; Liu, Q.; Comander, J. Ther. 33, 1466-1484 (2025). PDF
268. “Programmable Gene Insertion in Human Cells with a Laboratory-Evolved CRISPR-Associated Transposase” Witte, I. P.; Lampe, G. D.; Eitzinger, S.; Miller, S. M.; Berrios, K. N.; McElroy, A. N.; King, R. T.; Stringham, O. G.; Gelsinger, S. R.; Vo, P. L. H.; Chen, A. T.; Tolar, J.; Osborn, M. J.; Sternberg, S. H.; Liu, D. R. Science 388, eadt5199 (2025). PDF || Nature Research Highlights
269. “Patient-Specific In Vivo Gene Editing to Treat a Rare Genetic Disease” Musunuru, K.; Grandinette, S.A.; Wang, X.; Hudson, T.R.; Briseno, K.; Berry, A.M.; Hacker, J.L.; Hsu, A.; Silverstein, R.A.; Hille, L.T.; Ogul, A.N.; Robinson-Garvin, N.A.; Small, J.C.; McCague, S.; Burke, S.M.; Wright, C.M.; Bick, S.; Indurthi, V.; Sharma, S.; Jepperson, M.; Vakulskas, C.A.; Collingwood, M.; Keogh, K.; Jacobi, A.; Sturgeon, M.; Brommel, C.; Schmaljohn, E.; Kurgan, G.; Osborne, T.; Zhang, H.; Kinney, K.; Rettig, G.; Barbosa, C.J.; Semple, S.C.; Tam, Y.K.; Lutz, C.; George, L.A.; Kleinstiver, B.P.; Liu, D.R.; Ng, K.; Kassim, S.H.; Giannikopoulous, P.; Alameh, M-G.; Urnov, F.D.; Ahrens-Nicklas, R.C., New England Journal of Medicine 392, 2235-2243 (2025). PDF
270. “Base Editing of Trinucleotide Repeats that Cause Huntington’s Disease and Friedreich’s Ataxia Reduces Somatic Repeat Expansions in Patient Cells and in Mice” Matuszek Z*, Arbab M*, Kesavan M, Hsu A, Roy J.C.L, Zhao J.; Yu, T.; Weisburd, B.; Newby, G.A.; Doherty, N.J.; Cristian, A.; Tao, A.; Fearnley, L.G.; Bahlo, M.; Rehm, H.L.; Xie, J.; Gao, G.; Mouro Pinto, R.; Liu, D.R. Genet. 57, 1437–1451 (2025). PDF || Nature News & Views
271. “In Vivo Prime Editing Rescues Alternating Hemiplegia of Childhood in Mice” Sousa, A.; Terrey, M.; Sakai, H. A.; Simmons, C. Q.; Arystarkhova, E.; Morsci, N. S.; Anderson, L. C.; Xie, J.; Suri-Payer, F.; Laux, L. C.; Roze, E.; Forlani, S.; Gao, G.; Frost, S.; Frost, N.; Sweadner, K. J.; George Jr., A. L.; Lutz, C.M.; Liu, D. R. Cell 188, 4275-4294 (2025). PDF | SI | Nature Research Highlights
272. “GFP-on Mouse Model for Interrogation of In Vivo Gene Editing” Dib, C.; Queenan, J.A.; Swartzrock, L.; Willner, H.; Denise, M.; Ahmed, N.; Zada, F.M.; Borges, B.; Charlesworth, C.T.; Lum, T.; Yates, B.P.; Kwon, C.Y.; Scorzo, A.V.; Davis, S.C.; Davis, J.R.; He, R.; Xie, J.; Gao, G.; MacKenzie, T.C.; Liu, D.R.; Newby, G.A.; Czechowicz, A.D. Comms. 16, 7017 (2025). PDF || SI
273. “Ultrasmall Chemogenetic Tags with Group-Transfer Ligands” Sreekanth, V.; Sindi, S. H.; Chaudhary, S. K.; Pergu, R.; Singh, P.; Karaj, E.; Siriwongsup, S.; Fung, J. E.; Deb, A.; DeCarlo, S. J.; Mercer, J. A. M.; Yamada, K.; Rodriguez, D.; Liu, D. R.; Choudhary, A. Chem. Int. Ed. Engl. 64, e202506997 (2025).
274. “Precisely Defining Disease Variant Effects in CRISPR-Edited Single Cells” Baglaenko, Y.; Mu, Z.; Curtis, M.; Mire, H. M.; Jayanthi, V.; Suqri, M. A.; Liu, C.; Agnew, R.; Nathan, A.; Mah-Som, A. Y.; Liu, D. R.; Newby, G. A. ; Raychaudhuri, S. Nature 646, 117-125 (2025).
275. “A Molecular Glue Approach to Control the Half-Life of CRISPR-Based Technologies” Sreekanth, V.; Jan, M.; Zhao, K. T.; Lim, D.; Siriwongsup, S.; Davis, J. R.; McConkey, M.; Kovalcik, V.; Barkal, S.; Law, B. K.; Fife, J.; Tian, R.; Vinyard, M.; Becerra, B.; Kampmann, M.; Sherwood, R. I.; Pinello, L.; Liu, D. R.; Ebert, B. L.; Choudhary, A. Am. Chem. Soc. 147, 23844–23856 (2025). PDF
276. “Engraftment and Persistence of HBB Base-Edited Hematopoietic Stem Cells in Nonhuman Primates” Radtke, S.; Fields, E.; Swing, K.; Kanestrom, G.; Yen, J. S.; Pande, D.; Enstrom, M. R.; Humbert, O.; Weiss, M. J.; Liu, D. R.; Newby, G. A.; Kiem, H.-P. Transl. Med. 17, eadn2601 (2025). PDF
277. “TIGER: A novel tdTomato In-Vivo Genome-Editing Reporter Mouse for Investigating Precision-Editor Delivery Approaches” Du, S.W.; Palczewska, G.; Dong, Z.; Lauterborn, J.C.; Kaipa, B.R.; Yan, A.L.; Holubowicz, R.; Ha, S.; Chen, P.Z.; Gall, C.M.; Zode, G.; Liu, D.R.; Palczewski, K. Natl. Acad. Sci USA 122, e2506257122 (2025). PDF
278. “Prime Editing-Installed Suppressor tRNAs for Disease-Agnostic Genome Editing” Pierce, S. E. ; Erwood, S.; Oye, K.; An, M.; Krasnow, N.; Zhang, E.; Raguram, A.; Seelig. D.; Osborn, M. J.; Liu, D. R. Nature 648, 191-202 (2025). PDF || SI || NEJM Highlight
279. “Scalable Purification Enables High-Quality Virus-Like Particles for Therapeutic Translation” Hołubowicz, R; Gao, F; Du, S; Rodrigues Menezes, C; Zhang, J; Hołubowicz, M; Chen, P; Armbrust, N; Geilenkeuser, J; Liu, D.R.; Truong, DJ; Westmeyer, G; Palczewska, G; Palczewski, K. J Biol. Chem. 301, 110946 (2025). PDF
280. “Self-Assembling Protein Nanoparticles for Cytosolic Delivery of Nucleic Acids and Proteins” Eweje, F.; Ibrahim. V.; Shajii, A.; Walsh, M. L.; Ahmad, K.; Alrefai, A.; Miyasato, D.; Davis, J. R.; Ham, H.; Li, K.; Roehrl, M.; Haller, C. A.; Liu, D. R.; Chen, J.; Chaikof, E. L. Nat. Biotechnol. 44 (4), 602-615 (2026). PDF
281.“In Vivo Base Editing Rescues Liver Pathophysiology and Peroxisome Dysfunction in a Mouse Model of Zellweger Spectrum Disorder” Gao, X.D.; Presa, M.; Duby, J.E.; Ryan, J.; Piec, P.A.; Hsu, A.; Banskota, S.; Jiang, A.Y.; Chen, L.; Newby, G.A.; DiPietro, E.; Levy, J.M.; Steele, B.H.; Lecordier, S.; Qin, F.; Moser, A.B.; Xie, J.; Gao, G.; Braverman, N.E.; Zuberi, A.R.; Hacia, J.G.; Lutz, C.M.; Liu, D.R. Nat Biomed. Eng. in press, online (2026). PDF || SI || [This work was highlighted in NEJM’s Clinical Applications of Biomedical Research “Gene Editing, Peroxisomal Disorders, and Treatments for Rare Disease“]
282. “In Vivo Adenine Base Editing Ameliorates Dravet Syndrome Phenotypes in a Mouse Model” Nelson, A. T.; Hill, S. F.; Simon, M.; Clatot, J.; Sakai, H. A.; Xie, J.; Sousa, A. A.; An, M.; Gao, G.; Lutz, C. M.; Goldberg, E. M.; Liu, D R. Science Transl. Med. in press, available online (2026). PDF || SI
283. “Directed Evolution of Small RNA-Stabilizing Motifs that Improve Prime Editing Efficiency” Sakai, H.A.; Pierce, S.E.; Jiang, A.Y. Cristian, A.; An, M.; Kim, C.R.; Ahmed, N.; Hemez, C.F. Tao, A.Y.; Zhang, E.; Wu, S.J.; Liu, D.R. Nature Biotechnology in press (2026). PDF || SI
284. “AI-guided Redesign of Laboratory-Evolved Reverse Transcriptases Enhances Prime Editing” Tao, A.Y.; Sakai, H.A.; Jiang, A.Y.; Krasnow, N.A.; Vaganov, V.S.; Shim, B.; Barsdale, Z.; Pandey, S.; Ahmed, N.; Na, M.; Liao, T-W.; Oye, K.; Cristian, A.; Zhang, E.; Xu, J.A.; Bulcaen, M.; Liu, D.R. Nature Biotechnology in press (2026). PDF || SI
285. “Prime Editing Removal of Trinucleotide Repeats Ameliorates Molecular Phenotypes in Friedreich’s Ataxia and Huntington’s Disease Models” Matuszek, Z.; Kesavan, M.; Hsu, A.; Roy, J.C.L.; Zhao, J.; Barsdale, Z.; Bulcean, M.; Newby, G.A.; Davis, J.R.; Doman, J.L.; Pandey, S.; Doherty, N.J.; Cristian, A.; Xie, J.; Gao, G.; Arbab, M.; Arlotta, P.; Mouro Pinto, R.; Liu, D.R. Biomed. Eng. in press (2026).
286. “Synonymous Editing Alters Ion Channel Function, Favoring Prime Editing for Retinal Disease Correction” Kabra, M.; Moosajee, M.; Navarrette, A.; Newby, G.A.; Rawding, P.; Xie, A.; Mechoulam, H.; Rivera, A.; Hung, A.; Tiwari, S.; Waxman, A.J.; Molugu, K.; Saha, K.; Gong, S.; Liu, D.R.; Pattnaik, B.R. J. Biol. Sci. 22, 4670-4690 (2026). PDF
287. “Efficient Prime Editing In Vivo and In Vitro Using Lipid Nanoparticles” Jiang, A.Y.; Cristian, A.; Brooks, D.L.; Feierman, E.R.; Chen, P.Z.; Whittaker, M.N.; Pierce, S.E.; Sakai, H.A.; Chen, H.; Liu, D.; Randolph, P.B.; Li, A.H.; Hsu, A.; Omo-Lamai, S.O.; Tao, A.Y.; Owusu-Amo, B.; Wang, X.; Musunuru, K.; Liu, D.R. Nature Nanotechnology, in press, available online (2026). PDF | SI
288. “Restoration of the immune system with base editing and non-genotoxic conditioning in a Rag2 point-mutant mouse model” Dib, C.; Queenan, J.A.; Willner, H.; Swartzrock, L.; Charlesworth, C.T.; Denise, M.; Davis, J.R.; Mepani, R.J.; Ho, K.; Castro, M.; Wilson, R.C.; Nakauchi, H.; Liu, D.R.; Czechowicz, A. Molecular Therapy, in press, available online (2026). PDF
289. “A Combinatorial Synthetic Strategy for Developing Genome-Editing Protein-Delivery Agents Targeting Mouse Retina” Zhang, J.; Holubowicz, R.; Smidak, R.; Hu, Y.; Du, W.W.; Felgner, J.H.; Palczewska, G.; Rodrigues, C.M.; Risaliti, E.; Dong, Z.; Ma, X.; Shayegan, M.H.; Chen, P.Z.; Xing, L.; Holubowicz, M.; Li, B.; Liu, D.R.; Felgner, P.L.; Tochtrop, G.P.; Palczewski, K.; Nature Communications, 7(17): 2479 (2026). PDF || SI
290. “Small-Molecule Binding and Sensing with a Designed Protein Family” Lee, G.R.; Pellock, S.; Norn, C.; Tischer, D.; Dauparas, J.; Anishchenko, I.; Mercer, J.; Kang, A.; Bera, A.; Nguyen, H.; Brackenbrough, E.; Sankaran, B.; Goreshnik, I.; Vafeados, D.; Roullier, N.; Han, H.; Coventry, B.; Haddox, H.; Liu, D.R.; Yeh, A.; Baker, D. Nature Communications, in press, available online (2026). PDF | SI
291. “AI-redesigned Starting Points and Outcomes Enhance Protein Evolution” Krasnow, N.A.; Xu, J.A.; Zhang, E.; Mahadeshwar, G.K.; Tao, A.Y.; McCreary, J.; Hemez, C.F.; Brown, L.E.; Jiang, W.; Liu, D.R. Nature, in press, online (2026). PDF || SI
292. “Evolution of Botulinum Neurotoxin Serotype X Proteases to Induce Inflammatory Cell Death in Cancer Cells” McCreary, J.; Hemez, C. F.; Raymond, M. H.; Blum, T. R.; Gonzalez-Valero, A.; Augustin, T. L.; Krasnow, N. A.; DeCarlo, S. J.; Qin, Y.; Rhee, K.; Jiang, W.; Ip, B. C.; Khalil, A. S.; Liu, D. R. Biotechnol. in press, online (2026). PDF || SI (Text, Tables & Video).
293. “Mechanistic Machine Learning for Prediction of Prime Editing Outcomes”Hsu, A.; Chen, P.J.; Li, A.H.; Hemez, C.F.; Gao, X.D.; Terrey, M.; Nelson, C.; Selvam, V.; Cristian, A.; McElroy, A.N.; Steinbeck, B.J.; Mahadeshwar, G.K.; Pandey, S.; Barsdale, Z.; Chen, P.Z.; Sousa, A.A.; Sakai, H.A.; Silverstein, R.A.; Morad, I.; Krueger, R.K.; Shen, M.W.; Kleinstiver, B.P.; Lutz, C.M.; Tolar, J.; Blazar, B.R.; Osborn, M.J.; Liu, D.R. Nature, in press, online (2026). PDF || SI (Text, Tables, Video 1 and Video 2).
294. “Virus-like Particles Enable Targeted Gene Engineering and Pooled CRISPR Screening in Primary Human Myeloid Cells” Jung, H.; Devant, P.; Ching, C.; Ota, M.; Dann, E.; Zhu, R.; Modak, C.; Vasquez-Ibarra, A.; Hamilton, J.R. Steinhart, Z.; Ngo, W.; Sandoval, L.; Jung, J.H.; Lee. J.H.J.; Xu, D.; An, M.; Urs, E.; Chen, P.A.; Allain, V.; Tada, T.; Gilbert, L.A.; Shy, B.R.; Pritchard, J.K.; Nunez, J.K.; Landau, N.R.; Liu, D.R.; Eyquem, J.; Doudna, J.A.; Marson, A.; Carnevale, J. Nature Biotechnology, in press, online (2026).
295. “Base editing reveals an essential role for NANOG in human embryogenesis”Bower, O.J.; Orsi, A.E.R.; McMahon, R.; Staneva, D.; Blagrove, J.R.; Singh, K.; Simon, C.S.; McCarthy, A.; Garcia, P.; Shaikly, V.; Taranissi, M.; Wilding, M.; Serhal, P.; Odia, R.A.; Vasilic, M.; Choudhary, M.; Papathanasiou, A.; Elder, K.; Snell, P.; Christie, L.; Arbab, M.; Liu, D.R.; Herbert, M.; Harasimov, K.; Niakan, K.K. Nature in press, online (2026). PDF
296. “Human Trilayer Engineered Blood Vessel Reveals Influence of Fibroblasts on Disease Progression in Model of Hutchinson-Gilford Progeria” Truskey, G.A.; Liu, D.R.; Gao, X.D.; Shores, K.L. Science Advances 12, eaeh3785 (2026). PDF
297. “Peptide-MHC-targeted Engineered Virus-like Particles Enable Selective Priming and Gene Editing of Tumor-specific T-cells“ Shim, B.H.; Zhao, H.; Queenan, J.A.; Smith, B.E.; Birnbaum, M.E.; Liu, D.R. Cell Reports, 45, 11750 (2026). PDF