Articles (*corresponding author)


Molina RS (co-first), Rix G (co-first), Mengiste AA, Álvarez B, Seo D, Chen H, Hurtado JE, Zhang Q, García-García JD, Heins ZJ, Almhjell PJ, Arnold FH, Khalil AS, Hanson AD, Dueber JE, Schaffer DV, Chen F, Kim S, Fernández LÁ, Shoulders MD, *Liu CC. In vivo hypermutation and continuous evolution with cellular systems. Nature Reviews Methods Primers 2:36 (2022).

Harvey EP (co-first), Shin J-E (co-first), Skiba MA (co-first), Nemeth GR, Hurley JD, Wellner A, Shaw AY, Miranda VG, Min JK, Liu CC, *Marks DS, *Kruse AC. An in silico Method to Assess Antibody Fragment Polyreactivity. bioRxiv (2022). See Preprint.


*Loveless TB (co-first), Carlson CK (co-first), Hu VJ, Dentzel Helmy CA, Liang G, Ficht M, Singhai A, *Liu CC. Molecular Recording of Sequential Cellular Events into DNA. bioRxiv (2021). See Preprint.

*Liu CC. Sense and Sense Ability in a Synthetic Genetic Code. New England Journal of Medicine 385, 1045-1048 (2021).

Garcia-Garcia JD, Van Gelder K, Joshi J, Bathe U, Leong BJ, Bruner SD, Liu CC, *Hanson AD. Using Continuous Directed Evolution to Improve Enzymes for Plant Applications. Plant Physiology 188, 1-13 (2021).

Javanpour AA, *Liu CC. Evolving Small-Molecule Biosensors with Improved Performance and Reprogrammed Ligand Specificity using OrthoRep. ACS Synthetic Biology 10, 2705-2714 (2021).

Wellner A (co-first), McMahon C (co-first), Gilman MSA, Clements JR, Clark S, Nguyen KM, Ho MH, Hu VJ, Shin J-E, Feldman J, Hauser BM, Caradonna TM, Wingler LM, Schmidt AG, Marks DS, Abraham J, *Kruse AC, *Liu CC. Rapid Generation of Potent Antibodies by Autonomous Hypermutation in Yeast. Nature Chemical Biology 17, 1057-1064 (2021).

Rix G, *Liu CC. Systems for in vivo Hypermutation: a Quest for Scale and Depth in Directed Evolution. Current Opinion in Chemical Biology 64, 20-26 (2021).

Loveless TB, Grotts JH, Schechter MW, Forouzmand E, Carlson CK, Agahi BS, Liang G, Ficht M, Liu B, Xie X, *Liu CC. Lineage Tracing and Analog Recording in Mammalian Cells by Single-Site DNA Writing. Nature Chemical Biology 17, 739-747 (2021).

Jensen ED, Ambri F, Bendtsen MB, Javanpour AA, Liu CC, *Jensen MK, Keasling JD. Integrating Continuous Hypermutation with High-Throughput Screening for Optimization of cis,cis-Muconic Acid Production in Yeast. Microbial Biotechnology 14, 2617-2626 (2021).


Rix G, Watkins-Dulaney EJ, Almhjell PJ, Boville CE, Arnold FH, *Liu CC. Scalable, Continuous Evolution for the Generation of Diverse Enzyme Variants Encompassing Promiscuous Activities. Nature Communications 11, 5644 (2020).

*Garcia-Garcia JD, *Joshi J, *Patterson JA, Trujillo-Rodriguez L, Reisch CR, Javanpour AA, Liu CC, Hanson AD. Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study. Life, 10, 178 (2020).

Zhong Z, Wong BG, Ravikumar A, Arzumanyan GA, *Khalil AS, *Liu CC. Automated Continuous Evolution of Proteins in vivo. ACS Synthetic Biology, 9, 1270-1276 (2020).

*Liu CC. A New Path to Tyrosine Sulfation. Nature Chemical Biology, 16, 365-366 (2020).


Wellner A, Ravikumar A, *Liu CC. Continuous Evolution of Proteins in vivo. In H. Zhao (Ed.), Protein Engineering. Wiley-VCH, Accepted (2019).

Javanpour AA, *Liu CC. Genetic Compatibility and Extensibility of Orthogonal Replication. ACS Synthetic Biology, 8, 1249-1256 (2019).

*Loveless TB, *Liu CC. Viewpoint: Synthetic Epigenetics to Engineer Regulation. Biochemistry, 58, 1558-1559 (2019).

Zhong Z, *Liu CC. Probing Pathways of Adaptation with Continuous Evolution. Current Opinion in Systems Biology, 14, 18-24 (2019).


Zhong Z, Ravikumar A, *Liu CC. Tunable Expression Systems for Orthogonal DNA Replication. ACS Synthetic Biology, 7, 2930-2934 (2018).

Ravikumar A, Arzumanyan GA, Obadi MKA, Javanpour AA, *Liu CC. Scalable, Continuous Evolution of Genes at Mutation Rates Above Genomic Error Thresholds. Cell, 175, 1946-1957 (2018).

Arzumanyan GA, Gabriel KN, Ravikumar A, Javanpour AA, *Liu CC. Mutually Orthogonal DNA Replication Systems in vivo. ACS Synthetic Biology, 7, 1722-1729 (2018).

Li X, Hitomi J, *Liu CC. Characterization of a Sulfated Anti-HIV Antibody using an Expanded Genetic Code. Biochemistry, 57, 2903-2907 (2018).

Li X, *Liu CC. Site-Specific Incorporation of Sulfotyrosine Using an Expanded Genetic Code. Methods Molecular Biology, 1728, 191-200 (2018).

*Liu CC, *Jewett MC, *Chin JW, *Voigt CA. Toward an Orthogonal Central Dogma. Nature Chemical Biology, 14, 103-106 (2018).


Schwessinger B, Li X, Ellinghaus TL,…*Liu CC, *Ronald PC. A Second-Generation Expression System for Tyrosine-Sulfated Proteins and its Application in Crop Protection. Integrative Biology, 8, 542-545 (2016).


Pruitt R et al. (29 authors total). The Rice Immune Receptor XA21 Recognizes a Tyrosine-Sulfated Protein from a Gram-Negative Bacterium. Science Advances, 1, e1500245 (2015).

Ravikumar A, *Liu CC. Biocontainment through Reengineered Genetic Codes. ChemBioChem, 16, 1149-1151 (2015).


Li X, *Liu CC. Biological Applications of Expanded Genetic Codes. ChemBioChem, 15, 2335-2341 (2014).

Ravikumar A, Arrieta A, *Liu CC. An Orthogonal DNA Replication System in Yeast. Nature Chemical Biology, 10, 175-177 (2014).


Chen M, Wang L, Liu CC, *Nie Q. Noise Attenuation in the ON and OFF States of Biological Switches. ACS Synthetic Biology, 2, 587-593 (2013).

Guimares JC, Liu CC, *Arkin AP. From Biological Parts to Circuit Design. In H. Zhao (Ed.), Synthetic Biology (pp. 63-77). London: Academic Press (2013).

Before 2013

Liu CC, Qi L, Lucks JB, Segall-Shapiro TH, Wang D, Mutalik VK, *Arkin AP. An Adaptor from Translational to Transcriptional Control Enables Predictable Assembly of Complex Regulation. Nature Methods, 9, 1088-1094 (2012).

Qi L, Lucks JB, Liu CC, Mutalik VK, *Arkin AP. Engineering Naturally Occurring Trans-Acting Non-Coding RNAs to Sense Cellular Signals. Nucleic Acids Research, 40, 5775-5786 (2012).

*Liu CC, Qi L, Yanofsky C, *Arkin AP. Regulation of Transcription by Unnatural Amino Acids. Nature Biotechnology, 29, 164-168 (2011).

*Liu CC, *Arkin AP. The Case for RNA. Science, 330, 1185-1186 (2010).

*Liu CC, *Schultz PG. Adding New Chemistries to the Genetic Code. Annual Reviews of Biochemistry, 70, 413-444 (2010).

Liu CC, Cellitti SE, Geierstanger BH, *Schultz PG. Efficient Expression of Tyrosine-Sulfated Proteins in E. coli using an Expanded Genetic Code. Nature Protocols, 4, 1784-1789 (2009).

Liu CC, Choe H, Farzan M, Smider VV, *Schultz PG. Mutagenesis and Evolution of Sulfated Antibodies using an Expanded Genetic Code. Biochemistry, 48, 8891-8898 (2009).

Mills JH, Lee HS, Liu CC, Wang J, *Schultz PG. A Genetically Encoded Direct Sensor of Antibody-Antigen Interactions. Chembiochem, 10, 2162-2164 (2009).

Liu CC, Mack AV, Brustad E, Mills JH, Groff D, *Smider VV, *Schultz PG. Evolution of Proteins with Genetically Encoded “Chemical Warheads”. Journal of the American Chemical Society, 131, 9616-9617 (2009).

Liu CC, Mack AV, Tsao M, Mills JH, Lee H, Choe H, Farzan M, *Schultz PG, *Smider VV. Protein Evolution with an Expanded Genetic Code. Proceedings of the National Academy of Sciences, 105, 17688-17693 (2008).

Liu CC, Brustad E, *Liu W, *Schultz PG. Crystal Structure of a Biosynthetic Sulfo-hirudin Complexed to Thrombin. Journal of the American Chemical Society, 129, 10648-10649 (2007).

*Liu CC, *Schultz PG. Recombinant Expression of Selectively Sulfated Proteins in E. coli. Nature Biotechnology, 24, 1436-1440 (2006).

Andreana PR, Liu CC, *Schreiber SL. Stereochemical Control of the Passerini Reaction. Organic Letters, 6, 4231-4233 (2004).