Liu Group Publications

1. 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 This work reports the generality of DNA-templated synthesis, its distance independence, and a model translation of multiple DNA sequences into corresponding synthetic products in a manner suitable for in vitro selection and PCR amplification of templates encoding desired synthetic molecules.

2. 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 This paper describes a selection system that is the basis of ongoing efforts to evolve and understand homing endonucleases with novel substrate specificities.

3. Recent Advances in the In Vitro Evolution of Nucleic Acids. Bittker, J. A.; Phillips, K. J.; Liu, D. R. Curr. Opin. Chem. Biol.6, 367-374 (2002). PDF

4. 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. This paper reveals the potential of DNA to direct a wide range of synthetic organic reactions by reporting many new DNA-templated chemistries, including the first general carbon-carbon bond forming reactions (nitro-aldol, nitro-Michael, dipolar cycloadditions, Wittig olefinations, and Pd-mediated cross-couplings) templated by nucleic acids.

5. 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 This work describes a new method (NRR) for the diversification of nucleic acids that allows random recombination to take place between multiple unrelated DNA sequences, and demonstrates that NRR enables nucleic acid evolution, functional dissection, and minimization in ways not possible using existing diversification methods.

6. Multistep Small-Molecule Synthesis Programmed by DNA Templates. Gartner, Z. J.; Kanan, M. W.; Liu, D. R. J. Am. Chem. Soc.124, 10304-10306 (2002). PDF | SI News stories describing this work appear in Chem. & Eng. News 80 [34] 12 (2002) PDF, and in Science300, 242 (2003). This paper describes the development of linker and purification strategies that enable the products of DNA-templated reactions to serve as starting materials for subsequent DNA-templated transformations. These findings enable DNA sequences to be translated into structures of useful complexity.

7. Directing Otherwise Incompatible Reactions in a Single Solution 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). This paper describes a new mode of controlling reactivity in a DNA-templated format that is not possible using conventional synthesis approaches.

8. 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 This paper reports the development of two template architectures (omega and T) that expand the types of reactions that can be performed in a DNA-templated format.

9. In Vivo Evolution of an RNA Transcriptional Activator. Buskirk, A. R.; Kehayova, P. D.; Landrigan, A.; Liu, D. R. Chem. 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). This work describes the evolution from random RNA libraries expressed in yeast cells of a short RNA sequence that strongly activates gene transcription. The potency of this RNA rivals that of the most active known natural transcriptional activators (all of which are proteins). Its function was dissected using a combination of site-directed mutagenesis, additional evolution, and secondary structure prediction.

10. Stereoselectivity in DNA-Templated Organic Synthesis and Its Origins. Li, X. and Liu, D. R. J. Am. Chem. Soc. 125, 10188-10189 (2003). PDF | SI This paper reports the ability of DNA templates to induce stereoselectivity in DNA-templated reactions and traces the origins of this stereoselectivity to the macromolecular conformation of the DNA templates. These findings reveal the conditions under which DNA templates can perturb reaction outcomes beyond simple modulation of effective molarity.

11. 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. J. Am. Chem. Soc. 125, 12372-12373 (2003). PDF | SI This work describes the development of affinity and specificity selections for DNA-linked synthetic molecules such as those emerging from DNA-templated small molecule library synthesis.

12. Efficient and Sequence-Specific DNA-Templated Polymerization of PNA Aldehydes. Rosenbaum, D. M. and Liu, D. R. J. Am. Chem. Soc. 125, 13924-13925 (2003). PDF | SI This work reports the first efficient and sequence-specific translation of DNA templates into synthetic polymers of length similar to functional proteins. This work is highlighted in a Science and Technology story in Chem. & Eng. News 82 [3] 64 (2004). PDF

13. Expanding the Genetic Code In Vitro and In VivoMagliery, T. J.; Liu, D. R. The Genetic Code and the Origin of Life Ed. Ribas de Pouplana, L. Landes Bioscience and Springer, (2004).

14. Translation of DNA into Synthetic N-Acyloxazolidines. Li, X.; Gartner, Z. J.; Tse, B. N.; Liu, D. R. J. Am. Chem. Soc. 126, 5090-5092 (2004). PDF | SI Multistep DNA-templated synthesis was used to generate N-acyloxazolidines and macrocyclic N-acyloxazolidines. These structures represent the most complex synthetic small molecules to date translated from DNA.

15. 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 article reviews the growth of DNA-templated synthesis from its origins as a model system for self-replication to its recent development into a general way to control the reactivity of synthetic molecules using effective molarity.

16. Directed Evolution of Protein Enzymes Using Nonhomologous Random Recombination. Bittker, J. A.; Le, B. V.; Liu, J. M.; Liu, D. R. Proc. Natl. Acad. Sci. USA 101, 7011-7016 (2004). PDF The development and use of protein nonhomologous random recombination (protein NRR) to evolve active chorismate mutase protein enzymes with rearranged secondary structures are described in this work.

17. 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 This paper reports the use of RNA engineering and directed evolution methods to create an RNA-based transcriptional activator that is regulated by a cell-permeable synthetic small molecule.

18. Directed Evolution of Ligand Dependence: Small Molecule-Dependent Protein Splicing. Buskirk, A. R.; Ong, Y.-C.; Gartner, Z. J.; Liu, D. R. Proc. Natl. Acad. Sci. USA 101, 10505-10510 (2004). PDF The laboratory evolution of an intein that undergoes splicing only in the presence of a cell-permeable synthetic small molecule is described in this work. The evolved intein was used in living cells to render the function of four unrelated proteins dependent on the small molecule in a post-translational and dose-dependent manner.

19. 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

This work is featured as a Research Highlight in Nat. Biotechnol. 22, 1247 (2004). This paper describes the translation of a single-solution library of DNA templates into a library of corresponding synthetic small-molecule macrocycles, the in vitro selection of a single member of the DNA-templated library for its protein binding activity, and the amplification by PCR of the DNA encoding the active macrocycle.

20. 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. Here we report a new approach to reaction discovery that simultaneously evaluates many combinations of substrates in a single solution for bond-forming reactivity. Using this approach, we discovered an efficient and mild alkyne-alkene coupling reaction catalyzed by an inorganic Pd(II) salt that generates a trans-enone.

21. Nucleic Acid-Templated Synthesis as a Model System for Ancient Translation. Calderone, C. T. and Liu, D. R. Curr. Opin. Chem. Biol. 8, 645-653 (2004). PDF

22. In Vitro Characterization of IroB, a Pathogen-Associated C-Glycosyltransferase. Fischbach, M. A.; Lin, H.; Liu, D. R.; Walsh, C. T. Proc. Natl. Acad. Sci. USA 102, 571-576 (2004). PDF

23. Creating Small Molecule-Dependent Switches to Modulate Biological Functions. Buskirk, A. R. and Liu, D. R. Chem. Biol. 12 , 151-161 (2005). PDF

24. DNA-Templated Functional Group Transformations Enable Sequence-Programmed Synthesis Using Small-Molecule Reagents. Sakurai, K.; Snyder, T. M.; Liu, D. R. J. Am. Chem. Soc. 127, 1660-1661 (2005). PDF | SI

25. Functional Dissection of sRNA Translational Regulators Using Nonhomologous Random Recombination and In Vivo Selection. Liu, J.M.; Bittker, J.A.; Lonshteyn, M.; Liu, D. R. Chem. Biol. 12 , 757-767 (2005). PDF | SI

26. In Vitro Characterization of Salmochelin and Enterobactin Trilactone Hydrolases IroD, IroE, and Fes. Lin, H.; Fischbach, M. A.; Liu, D. R.; Walsh, C. T. J. Am. Chem Soc. 127, 11075-11084 (2005). PDF

27. Ordered Multistep Synthesis in a Single Solution Directed by DNA Templates. Snyder, T. M. and Liu, D. R. Angew. Chem. Int. Ed. 44, 7379-7382 (2005). PDF SI

28. Small-Molecule Diversification From Iterated Branching Reaction Pathways Enabled by DNA-Templated Synthesis. Calderone, C. T. and Liu, D. R. Angew. Chem. Int. Ed. 44, 7383-7386 (2005). PDF SI

29. DNA-Templated Synthesis in Organic Solvents. Rozenman, M. and Liu, D. R. ChemBioChem 7, 253-256 (2006). PDF

30. Enzymatic Tailoring of the Bacterial Siderophore Enterobactin Alters Membrane Partitioning and Iron Acquistion. Luo, M.; Lin, H.; Fischbach, M. A.; Liu, D. R.; Walsh, C. T.; Groves, J. T. ACS Chem. Biol. 1, 29-32 (2006). PDF

31. Directed Evolution and Substrate Specificity Profile of Homing Endonuclease I-SceI. Doyon, J. B.; Pattanayak, V.; Meyer, C. B; Liu, D. R. J. Am. Chem. Soc. 128, 2477-2484 (2006). PDF SI

32. How Pathogenic Bacteria Evade Mammalian Sabotage in the Battle for Iron. Fischbach, M. A.; Lin, H.; Liu, D. R.; Walsh, C. T. Nat. Chem. Biol. 2, 132-138 (2006). PDF

33. 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. Proc. Natl. Acad. Sci. 103 , 5314-5319 (2006). PDF

34. 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).

35. 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. J. Am. Chem. Soc. 128, 9324-9325 (2006). PDF

36. 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. J. Am. Chem. Soc. 128, 11002-11003 (2006). PDF

37. Binding and Stability Determinants of the PPARγ Nuclear Receptor/Coactivator Interface as Revealed by Shotgun Alanine Scanning and In Vivo Selection. Phillips, K. J.; Rosenbaum, D. M.; Liu, D. R. J. Am. Chem. Soc. 128, 11298-11306 (2006). PDF

38. 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. Proc. Natl. Acad. Sci. USA 103, 16502-16507 (2006). PDF

39. In Vivo Evolution of an RNA-Based Transcriptional Silencing Domain in S. cerevisiaeKehayova, P. D.; Liu, D. R. Chem. Biol. 14, 65-74 (2007). PDF This work is featured in a Research Highlight in Nat. Methods 4, 297 (2007). PDF

40. Synthesis of Acyclic α,β-Unsaturated Ketones via Pd(II)-Catalyzed Intermolecular Reaction of Alkynamides and Alkenes. Momiyama, N.; Kanan, M. W.; Liu, D. R. J. Am. Chem. Soc. 129, 2230-2231 (2007). PDF | SI

41. Solving Chemical Problems through the Application of Evolutionary Principles. Rozenman, M. M.; McNaughton, B. R.; Liu, D. R. Curr. Opin. Chem. Biol.11, 259-268 (2007). PDF

42. 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. Proc. Natl. Acad. Sci. USA 104, 11951-11956 (2007). PDF

43. Supercharging Proteins Can Impart Extraordinary Resilience. Lawrence, M. S.; Phillips, K. J.; Liu, D. R. J. Am. Chem. Soc. 129, 2230-2231 (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

44. Identification of Eukaryotic Promoter Regulatory Elements Using Nonhomologous Random Recombination. Doyon, J. B.; Liu, D. R. Nucleic Acids Res. 35, 5851-5860 (2007). PDF

45. Dissecting Protein Structure and Function using Directed Evolution. Yuen, C.M.; Liu, D. R. Nat. Methods 4, 995-997 (2007). PDF

46. 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

47. 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.

48. Effects of Template Sequence and Secondary Structure on DNA-Templated Reactivity. Snyder, T.M.; Tse, B.N.; Liu, D. R. J. Am. Chem. Soc. 130, 1392-1401 (2008). PDF | SI

49. DNA-Templated Polymerization of Side-Chain-Functionalized Peptide Nucleic Acid Aldehydes. Kleiner, R. E.; Brudno, Y.; Birnbaum, M. E.; Liu, D. R. J. Am. Chem. Soc. 130, 4646-4659 (2008). PDF | SI

50. 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. J. Am. Chem. Soc. 130, 15611-15626 (2008). PDF | SI

51. Recent Progress Towards the Templated Synthesis and Directed Evolution of Sequence-Defined Synthetic Polymers. Brudno, Y.; Liu, D. R. Chem. Biol 16, 265-276 (2009). PDF

52. 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)

53. 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).

54. 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).

55. 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).

56. Templated Synthesis of Peptide Nucleic Acids via Sequence-Selective Base-Filling Reactions. Heemstra, J. M.; Liu, D. R. J. Am. Chem. Soc 131, 11347-11349 (2009) PDF

57. LC/MS Analysis of Cellular RNA Reveals NAD-Linked RNA. Chen, Y. G.; Kowtoniuk, W. E.; Agarwal, I.; Shen, Y.; Liu, D. R. Nat. Chem. Biol. 5, 879-881 (2009) PDF | SI 

58. 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

59. 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.; Gi 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

60. An In Vitro Translation, Selection and Amplification System for Peptide Nucleic Acid. 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.

61. 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

62. Enhanced Functional Potential of Nucleic Acid Aptamer Libraries Patterned to Increase Secondary Structures. Ruff, K. M., Snyder, T. M., Liu, D. R. J. Am. Chem. Soc. 132, 9453-9464 (2010). PDF | SI

63. 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

64. In Vitro Selection of a DNA-Templated Small-Molecule Library Reveals a Class of Macrocyclic Kinase Inhibitors. Kleiner, R. E.; Dumelin, C.; Tiu, G.; Sakurai, K.; Liu, D. R. J. Am. Chem. Soc. 132, 11779-11791 (2010).PDF

65. 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.

66. Interaction-Dependent PCR Identified Target-Ligand Pairs from Libraries of Targets and Ligands. McGregor, L. M.; Gorin, D. J.; Dumelin, C. E.; Liu, D. R. J. Am. Chem. Soc. 132, 15522-15524 (2010).PDF | SI

67. 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)

68. 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 

69. De Novo Protein binding Pair by Computational Design and Directed Evolution. Karanicolas, J.; Corn, J. E.; Chen, I.; Joachimiak, L. A.; Dym, O.; Peck, S.; Albeck, S.; Unger, T.; Hu, W.; Liu, G.; Delbecq, S.; Monelione, G.; Spiegel, C.; Liu, D. R.; Baker, D. Mol. Cell 42 (2), 250-260 (2011). PDF

70. A System for the Continuous Directed Evolution of Biomolecules. Esvelt, K. M.; Carlson, J. C.; Liu, D. R. Nature 472, 499-503 (2011). This work was featured in a news story in C&E News 89 (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, as a news story in SciBX 4, 5 (2011), and as a news story in Ars Technica (May 15, 2011). PDFSI

71. Directed Evolution of a Small Molecule-Triggered Intein with Improved Splicing Properties in Mammalian Cells. Peck, S.; Chen, I.; Liu, D. R. Chem. Biol. 18 (5), 619-630 (2011). PDF, SI

72. 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 (5), e19991 (2011).PDF, SI

73. 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

74. A Sequential Strand-Displacement Strategy Enables Efficient Six-Step DNA-Templated Synthesis. He, Y.; Liu, D. R. J. Am. Chem. Soc. 133, 9972-9975 (2011). PDF, SI

75. 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

76. A General Strategy for the Evolution of Bond-Forming Enzymes Using Yeast Display. Chen, I.; Dorr, B. M.; Liu, D. R. Proc. Natl. Acad. Sci. USA 108 (28), 11399-11404 (2011). PDF, SI This work was highlighted in a technology feature in Nat. Methods 8, 623 (2011).

77. Small-Molecule Discovery from DNA-Encoded Chemical Libraries. Kleiner, R. E.; Dumelin, C. E.; Liu, D. R. Chem. Soc. Rev. 40, 5707-5717 (2011).PDF

78. 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 News89 [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.

79. 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

80. Engineering, Identifying, and Applying Supercharged Proteins for Macromolecule Delivery into Mammalian Cells. Thompson, D. B.; Cronican, J. J.; Liu, D. R. Methods Enzymol. 503, 293-319 (2012).PDF

81. Highly Specific Bisubstrate-Competitive Src Inhibitors from DNA-Templated Macrocycles. Georghiou, G.; Kleiner, R. E.; Pulkoski-Gross, M.; Liu, D. R.; Seeliger, M. A. Nat. Chem. Biol. 8, 366-374 (2012). PDF, SI

82. Cellular Uptake Mechanisms and Endosomal Trafficking of Supercharged Proteins. Thompson, D. B.; Villaseñor, R.; Dorr, B. M.; Zerial, M.; Liu, D. R. Chem. Biol. 19 (7), 831-843 (2012).PDF, SI

83. 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 (11), 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).

84. 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).

85. 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

86. 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)

87. Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA. Curtis, E. A.; Liu, D. R. Chem. Biol. 20, 521-532 (2013). PDF, SI

88. 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. Proc. Natl. Acad. Sci. USA 110, 9007-9012 (2013). PDF SI

89. Sequence-Controlled Polymers. Lutz, J.-F.; Ouchi, M.; Liu, D. R.; Sawamoto, M. Science 341, 628 (1238149-1 to 1238149-8 online) (2013).PDF

90. 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).

91. In Silico Abstractions of Zing Finger Nuclease Cleavage Profiles Reveals an Expanded Landscape of Off-Target Mutations. Sander, J.; Ramirez, C.; Linder, S.; Pattanayak, V.; Shoresh, N.; Ku, M.; Foden, J.; Reyon, D.; Bernstein, B.; Liu, D. R.; Joung, J. K. Nucleic Acids Res. 41, e181 (2013). PDF

92. Negative Selection And Stringency Modulation Enable Phage-Assisted Continuous Evolution (PACE) of Enzymes With Altered Specificity. Carlson, J. C.; Badran, A. H.; Nilo, D. A.; Liu, D. R. Nat. Chem. Biol. 10, 216-222 (2014). PDF

93. 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. Adv. Healthcare Mat. 3, 30-35 (2014). PDF

94. 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.Nat. Methods 11, 429-435 (2014).PDFSI

95. 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. J. Am. Chem. Soc. 136, 3264-3270 (2014).PDF

96. 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).

97. Fusion of Catalytically Inactive Cas9 to FokI Nuclease Improves the Specificity of Genome Modification. Guilinger, J. P.; Thompson, D. B.; Liu, D. R. Nat. Biotechnol. 32, 577-582 (2014).PDFSI

98. 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). PDFSI 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.

99. A Naturally Occurring, Non-Canonical GTP Aptamer Made of Simple Tandem Repeats. Curtis, E.A. and Liu, D.R. RNA Biol. 11:6 1-11 (2014).PDF

100. Reprogramming the Specificity of Sortase Enzymes. Dorr, B. M.; Ham, H. O.; An, C.; Chaikof, E. L.; Liu, D. R. Proc. Natl. Acad. Sci. USA 111, 13343-13348 (2014).PDFSI

101. 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. Nat. Chem. Biol. 10, 1049-1054 (2014).PDFSI

102. 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. Nat. Commun. 5, 5352 (2014).PDFSI

103. A DNA-Based Molecular Probe for Optically Reporting Cellular Traction Forces. Blakely, B. L.; Dumelin, C. E.; Choi, C. K.; Anthony, P. C.; Nguyen, V. K.; Baker, B. M.; Block, S. M.; Liu, D. R.; Chen, C. S. Nat. Methods 11, 1229-1232 (2014).PDFSI

104. Targeted Antithrombotic Protein Micelles. Kim, W.; Haller, C; Dai, E.; Wang, X.; Hagemeyer, C. E.; Liu, D. R. ; Peter, K.; Chaikof, E. L. Angew. Chem. Int. Ed. 54, 1461-1465 (2014).PDF

105. Determining the Specificities of TALENs, Cas9, and Other Genome Editing Enzymes. Pattanayak, V.; Guilinger, J. P.; Liu, D. R. Methods Enzymol. 546 47-78 (2014).PDF

106. 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. Nat. Biotechnol. 33, 73-80 (2014). PDFSI

107. In Vivo Continuous Directed Evolution. Badran, A. H.; Liu, D. R. Curr. Opin. Chem. Biol. 24, 1-10 (2014).PDF

108. Novel Selection Methods for DNA-Encoded Chemical Libraries. Chan, A. I.; McGregor, L. M.; Liu, D. R. Curr. Opin. Chem. Biol. 26, 55-61 (2015).PDF

109. Small Molecule-Triggered Cas9 Protein With Improved Genome-Editing Specificity. Davis, K. M.; Pattanayak, V.; Thompson, D. B.; Zuris, J. A.; Liu, D. R. Nat. Chem. Biol. 11,316-318 (2015).PDFSI

110. Methods for the Directed Evolution of Proteins. Packer, M. S. and Liu, D. R. Nat. Rev. Genetics 16 379-394 (2015).PDF

111. Continuous Directed Evolution of DNA-Binding Domains Generates TALENs With Improved DNA Cleavage 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. Nat. Methods 12, 939-942 (2015).PDFSI

112. Development of Potent In Vivo Mutagenesis Plasmids with Broad Mutational Spectra. Badran, A. H.. and Liu, D. R. Nat. Commun. 6 8425 (2015).PDFSI

113. 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. ; Thompson, D.; Schepartz, A.; Chen., Z.-Y.; Liu, D. R. J. Am. Chem. Soc.  (2015). PDF

114. 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. Anal. Chem. 88, 725-731 (2015).PDF

115. 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 (2015).PDF

116. 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. Nat. Commun. 7, 11140 (2016).PDF

117. 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. Proc. Natl. Acad. Sci. 113, 2868-2873 (2016).PDF

118. 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, SIExpanded Extended Data Figure 6

119. Continuous Evolution of B. thuringiensis Toxins Overcomes Insect Resistance. Badran, A. H.; Guzov, V. M.; Huai, Q.; Kemp, M. M.; Vishwanath, P.; Kain, W.; Evdokimov, A.; Moshiri, F.; Turner, K. H.; P.; Malvar, T.; Liu, D. R. Nature 533,58-63 (2016).PDFSI

120. 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. Mol. Cell 63, 72-85 (2016).PDF

121. 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, 1-10 (2016).PDF

122. 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).PDFSI

123. CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes. Komor, A.; Badran, A. H.; Liu, D. R. Cell 168, 20-36 (2017).PDF

124. 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.Nat. Biotechnol. 35 371-376 (2017). PDF

125. Improving the DNA Specificity and Applicability of Base Editing Through Protein Engineering and Protein Delivery In Vitro and In Vivo. Rees, H. A.; Komor, A. C.; Yeh, W.-H.; Edge, A. S. B.; Liu, D. R. Nat. Commun. 8, 15790 (2017).PDF

126. Aptazyme-Embedded Guide RNAs Enable Ligand-Responsive Genome Editing and Transcriptional Activation. Tang, W.; Hu, J. H.; Liu, D. R Nat. Commun. 8, 15939 (2017). PDF

127. 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. J. Am. Chem. Soc 139, 10192-10195 (2017). PDFSI

128. 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. Science Advances 3, eaao4774 (2017). PDF

129. Phage-Assisted Continuous Evolution of Proteases with Altered Substrate Specificity. Packer, M. S.; Rees, H. A.; Liu, D. R. Nat. Commun. 8, 956 (2017). PDFSI

130. 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).

131. Continuous directed evolution of aminoacyl-tRNA synthetases. Bryson, D. I.; Fan C.; Guo, L.-T.; Miller, C.; Söll, D.; Liu, D. R. Nat. Chem. Biol. 13, 1253-1260 (2017). PDF.

132. 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. Nat. Chem. Biol. 13, 1261-1266 (2017). PDF

133. 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). PDFSI

134. Development of a Formaldehyde Biosensor with Application to Synthetic Methylotrophy. Woolston, B. M.; Roth, T.; Kohale, I.; Liu, D. R.; Stephanopoulos, G. Biotechnol. Bioeng. 115, 206-215 (2017). PDF

135. 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.

136. Treatment of Autosomal Dominant Hearing Loss by In Vivo Delivery of Genome Editing Agents. Gao, X.; Tao, Y.; 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). PDFSI

137. Evolution of Sequence-Defined Highly Functionalized Nucleic Acid Polymers. Chen, Z.; Lichtor, P. A.; Berliner, A. P.; Liu, D. R. Nat. Chem. 15, 419-426 (2018). PDFNature Chem News and Views

138. Rewritable Multi-Event Analog Recording in Bacterial and Mammalian Cells. Tang, W.; Liu, D. R. Science 360, eaap8992 (2018). PDF

139. 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). PDFSI

140. 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

141. 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. Nat. Chem. 10, 704-714 (2018). PDF, SI

142. In Vivo Base Editing of Post-Mitotic Sensory Cells. Yeh, W.-H.; Chiang, H.; Rees, H. A.; Edge, A. S.; Liu, D. R. Nat. Commun. 9, 2184 (2018). PDF

143. 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. Nat. Biotechnol. 36, 843-846 (2018). PDFSI

144. Continuous Directed Evolution of Proteins with Improved Soluble Expression. Wang, T.; Badran, A. H.; Huang, T. P.; Liu, D. R. Nat. Chem. Biol. 14, 972-980 (2018). PDF SI

145. 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). PDFSI

146. 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. Bioconj. Chem. 29, 3245-3249 (2018). PDFSI

147. 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

148. Base Editing: Precision Chemistry on the Genome and Transcriptome of Living Cells. Rees, H. A. and Liu, D. R. Nat. Rev. Genet. 19, 770-788. (2018). PDF

149. 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). PDFSI

150. 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.; Doman, J.L.; Dow L. E.; Zhu, L. J.; Anderson, D. G.; Liu, D. R.; Ying, H.; Xue, W. Nat. Biomed. Eng. 36, 536-539 (2018).  PDF  News & Views

151. 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). PDF

152. CRISPResso2: Accurate and Rapid Analysis of Genome Editing Data from Nucleases and Base Editors.
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. Nat. Biotechnol. 37: 224-226 (2019).  PDF

153. 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 

154. Side-Chain Determinants of Biopolymer Function During Iterated Selection and Replication. Lichtor, P. A.; Chen, Z.; Elowe, N. H.; Chen, J. C.; Liu, D. R. Nat. Chem. Biol. 15, 419-426 (2019). PDF

155. 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

156. 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.; 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

157. 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 

158. Analysis and Minimization of Cellular RNA Editing by DNA Adenine Base Editors. Rees, H.A.; Wilson, C.; Doman, J.L.; Liu, D.R. Science Adv. 5, eaax5717 (2019). PDF

159. 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. Nat. Chem. Biol. 15, 565-574 (2019). PDF.

160 .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). PDF SI

161. Development of hRad51-Cas9 Nickase Fusions that Mediate HDR Without Double-Stranded Breaks. Rees, H. A.; Yeh, W.-H.,; Liu, D. R. Nat Commun. 10, 2212  (2019). PDF 

162.  An Anionic Human Protein that Mediates Potent Cationic Liposome Delivery of Genome Editing Proteins into Mammalian Cells. Kim Y. B.; Zhao, K. T.; Thompson, D. B.; Liu, D. R. Nat. Commun. 10, 2905  (2019). PDF

163. Continuous evolution of base editors with expanded target compatibility and improved activity. Thuronyi, B.W.; Koblan, L.W.; Levy, J.M.; Yeh, W.; Zheng, C.; Newby, G.A.; Wilson, C.; Bhaumik, M.; Shubina-Oleinik, O.; Holt, J.R.; Liu, D.R. Nat. Biotechnol. 37, 1070-1079 (2019). PDF, SI

164. 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,  576149157 (2019). PDF SI

165.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.; Nielsen, S. C.; Eide, C.; Dabelsteen, S.; Wandall, H. H.; Blazar, B. R.; Liu, D. R.; Tolar, J . Invest. Derm. 140, 338-347 (2020). PDF

166. 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. Biomol. Eng. 4, 111-124 (2020). PDF

167. 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. 1, 97-110 (2020). PDF SI

168. 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. Nat. Biotechnol. 38, 620-628 (2020). PDF SI

169. 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). PDF SI

170.  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. Nat Biotechnol. 38, 582-585 (2020). PDF SI

171. The Developing Toolkit of Continuous Directed Evolution. Morrison, M. S; Podracky, C. J.; Liu, D. R. Chem Bio. 16, 610-619 (2020). PDF

172. 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

173. 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. Nat. Commun. 11, 1979 (2020). PDF

174. 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. Nat. Biotechnol. 38, 883-891 (2020). PDF SI 

175.  In Vivo Postnatal Base Editing Restores Sensory Transduction and Transiently Improves Auditory Function in a Mouse Model of Recessive Deafness. Yeh, W.-H.; Shubina-Olenik, O.; Levy, J. M.; Pan, B.; Newby, G. A.; Wornow, M.; Burt, R.; Chen, J.C.; Holt, J. R.; Liu, D. R. Sci Trans. Med. 12, eaay9101 (2020). PDF. SI.

176. 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

177.  Genome Editing with CRISPR-Cas Nucleases, Base Editors, Transposases, and Prime Editors. Anzalone, A. V.; Koblan, L. W.; Liu, D. R. Nat. Biotechnol. 38, 824-844 (2020). PDF SI

178. 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; Radley, M.C; Peterson, S. B; Mootha, V.K; Mougous, J.D; Liu, D. R. Nature. 583, 631-637 (2020). PDF, SI

179. 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

180. Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase. Wilson, C*; Chen, P.J.;* Miao, Z; Liu, D.R. Nat. Biotechnol 38, 1431-1440 (2020). PDF SI

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

182. In Vivo Adenine Base Editing Corrects Hutchinson-Gilford Progeria Syndrome. Koblan L. W.; Erdos, M. R.; Wilson, C.; Cabral, W. A.; Levy, J. M.; Xiong, Z.-M.; Taarez, U. L.; Davison, L.; Gete, Y. G.; Mao, X.; Newby, G. A.; Doherty, S. P.; 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

183. Precision Genome Editing Using Cytosine and Adenine Base Editors. Huang, T. P.; Newby, G. A.; Liu, D. R. Nature Protocols 16, 1089-1128 (2021).  PDF  SI   Supplementary Data & Tables.

184. 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. Nat. Chem. Biol. 317-325 (2021) . PDF  SI

185. Phage-Assisted Evolution of Selective Botulinum Neurotoxin Proteases with Reprogrammed Substrate 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

185. 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

186. 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. Nat. Biomed. Eng. 5, 169-178 (2021). PDF  SI

187. PrimeDesign Software for Rapid and Simplified Design of Prime Editing Guide RNAs. Hsu, J. Y.; Anzalone, A. V.; Grünewald, J.; Lam, K. C.; Shen. M. W.; Liu, D. R.; Joung, J. K.; Pinello, L. Nat. Commun. 12, 1034 (2021). PDF

188. Massively Parallel Assessment of Human Variants with Base Editor Screens. Hanna, R.; Hegde, M.; Fagre, C.; DeWeirdt, P.; Sangree, A.; Szegletes, Z.; Griffith, A.; Feeley, M.; Sanson, K.; Baidi, Y.; Koblan, L.; Liu, D. R.; Neal, J.; Doench, J. Cell 184, 1064-1080 (2021). PDF

189. 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.; Holden, K.; Walker II, J. A.; Kadina, A. P.; Munrow, 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

190. 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

191. 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.; Sheppand-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

192. Mechanisms of Angiogenic Incompetence in iPSC-Derived Endothelial Cells of Hutchinson-Gilford Progeria Syndrome via Downregulation of Endothelial Nitric Oxide Synthase. 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

193. Efficient C•G-to-G•C Transversion 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. Nat. Biotechnol. in press, available online (2021). PDF

194. 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. Nucl. Acids Res. in press, available online (2021). PDF

195. In vivo Somatic Base Editing and Prime Editing.  Newby, G. A.; Liu, D. R. Molecular Therapy. in press, available online (2021). PDF

196. 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. Nat. Biotechnol. 40, 402-410 (2022). PDF SI

197. Reconstruction of evolving gene variants and fitness from short sequencing reads. Shen, M.W.; Zhao, K.T.; Liu, D.R. Nat. Chem Bio. 17, 1188–1198  (2021). PDF SI

198. Disulfide-compatible phage-assisted continuous evolution in the periplasmic space. Morrison, M.S.; Wang, T; Raguram, A; Hemez, C.; Liu, D.R. Nat. Commun. 12, 5959 (2021).  PDF SI

199. 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. 22, 5635–5652 (2021) PDF  SI

200. 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. Nat. Biotechnol. 40731–740 (2022)  PDF

201. Engineered virus-like particles for efficient in vivo delivery of therapeutic proteins. Banskota, S.*; Raguram, A.*; Suh, S.; 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

202. 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. Nat Biotechnol. (2022). in press, available online PDF SI

203. 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.; Neilsen, 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. Mol. Ther. 30, 130-144 (2022)

204. Experimental and Machine-Learning Discovery of Sequence-Defined Highly Functionalized Nucleic Acid Polymers that Bind a Target Small Molecule. Chen, J. C.; Chen, J. P.; Shen M. W.; Wornow, M.; Bae, M.; Ywh, W.-H.; Hsu, A.; Liu, D. R. in press, available online (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. Nat. Commun. 13, 1830 (2022)

206. Therapeutic In Vivo Delivery of Gene Editing Agents. Raguram, A.*; Banskota, S.*; Liu, D. R. Cell in press, available online (2022) PDF

207. Designing Prime Editing Experiments in Mammalian Cells. Doman, J. L.*; Sousa, A. A.*; Randolph, P. B.; Chen, P. J.; Liu, D. R. Nat. Protocols in press, available online (2022) PDF 

207. 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.P.; Huang, T.P.; Levy, J.M.; Raguram, A.; Banskota, S., Seidah, N.B; Musunuru, K.; Liu D.R. Nat. Biomed. Eng in press, available online (2022) PDF