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 Supplemental info 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 | Supplemental info 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 | Supplemental info 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 | Supplemental info 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 | Supplemental info 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 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).

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 | Supplemental info 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 | Supplemental info 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 | Supplemental info 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 | Supplemental info

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 | Supplemental info

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 Supplemental info

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 Supplemental info

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 Supplemental info

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. cerevisiae.
Kehayova, 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 | Supplemental info

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 | Supplemental info . 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 | Supplemental info

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 | Supplemental info

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 | Supplemental info

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 | Supplemental info

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 | Supplemental Info | 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 | Supplemental Info 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 | Supplemental Info. 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 | Supplemental Info. 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 | Supplemental Information

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 | Supplemental Information. 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 | Supplemental Info

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 | Supplemental Information. 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 | Supplemental Information

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 | Supplemental Information

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). PDFSupp

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).PDFSupp

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).PDFSupp

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). PDFSupp 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).PDFSupp

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).PDFSupp

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).PDFSupp

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).PDFSupp

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).PDFSupp

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).PDFSupp

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).PDFSupp

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

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).PDFSuppExpanded 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).PDFSupp

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).PDFSupp

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). PDFSupp

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). PDFSupp

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). PDFSupp

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). PDFSupp

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). PDFSupp

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). PDFSupp

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). PDFSupp

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). PDFSupp

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). PDFSupp

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, Supp

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). PDFSupp

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.; Dow L. E.; Zhu, L. J.; Anderson, D. G.; Liu, D. R.; Ying, H.; Xue, W. 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 PDF (2019).

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

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. in press, available online (2019). 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. in press, available online (2019). 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. in press, available online (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. in press, available online (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. in press, available online  (2020). PDF SI

170. 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. in press, available online (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. in press, available online  (2020). PDF SI 

172.  In Vivo Postnatal Base Editing Rescues Hearing 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. Trans. Med. in press (2020).

173. Continuous Directed Evolution: From Concept to Toolbox Morrison, M. S; Podracky, C. J.; Liu, D. R. Chem Bio. in press (2020).

174.  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. submitted (2020).

175. Genome Editing with CRISPR-Cas Nucleases, Base Editors, Transposases, and Prime Editors Anzalone, A. V.; Koblan, L. W.; Liu, D. R. submitted (2020).