Articles (*corresponding author)

2022

Kellogg EH, Gootenberg J, Abudayyeh O, Wong ASL, Dahlman JE, Lapinaite A, Myhrvold C, Liu CC, Hsu PD, Mali P, Qi LS. What are the current bottlenecks in developing and applying CRISPR technologies? Cell Systems 13, 589-593 (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. Nature Communications 13, 7554 (2022).

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).

2021

*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).

2020

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).

2019

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).

2018

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).

2016

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).

2015

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).

2014

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).

2013

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).