1.      Quinn,J.Y., Cox,R.S., Adler,A., Beal,J., Bhatia,S., Cai,Y., Chen,J., Clancy,K., Galdzicki,M., Hillson,N.J., et al. (2015) SBOL Visual: A Graphical Language for Genetic Designs. PLoS Biology, 13, e1002310.


2.      Shen,Y., Stracquadanio,G., Wang,Y., Yang,K., Mitchell,L.A., Xue,Y., Cai,Y., Chen,T., Dymond,J.S., Kang,K., et al. (2015) SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Research, 10.1101/gr.193433.115.


3.      Kanigowska P, Shen Y, Zheng Y, Rosser S, Cai Y (2015) Smart DNA Fabrication Using Sound Waves: Applying Acoustic Dispensing Technologies to Synthetic Biology. Journal of the Association for Laboratory Automation. (Corresponding Author)


4.      Guo Y, Dong J, Zhou T, Auxillos J, Li T, et al. (2015) YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae. Nucleic Acids Res. (Corresponding Author)


5.      Mitchell LA, Chuang J, Agmon N, Khunsriraksakul C, Phillips NA, et al. (2015) Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae. Nucleic Acids Res.


6.      Agmon N, Mitchell LA, Cai Y, Ikushima S, Chuang J, et al. (2015) Yeast Golden Gate (yGG) for efficient assembly of S. cerevisiae transcription units. ACS Synth Biol.


7.      Cai Y, Agmon N, Choi WJ, Ubide A, Stracquadanio G, et al. (2015) Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes. Proceedings of the National Academy of Sciences. (Corresponding Author)



8.      Trubitsyna M, Michlewski G, Cai Y, Elfick A, French CE (2014) PaperClip: rapid multi-part DNA assembly from existing libraries. Nucleic acids research.


9.      Scher E, Luo Y, Berliner A, Olguin C, Cai Y (2014) GenomeCarver: harvesting genetic parts from genomes to support biological design automation. 6th International Workshop on Bio-Design Automation. (Corresponding Author)



10.  Liao C, Cai Y (2014) Towards Modeling Automation for Synthetic Biology. A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems: Springer Netherlands. pp. 201-217. (Corresponding Author)


11.  Cai Y, Ellis T (2014) The Sixth International Meeting on Synthetic Biology (SB6. 0) Special Issue Editorial. ACS Synthetic Biology 3: 107-107. (Corresponding Author)



12.  Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, et al. (2014) Total synthesis of a functional designer eukaryotic chromosome. Science 344: 55-58.



13.  Mitchell LA, Cai Y, Taylor M, Noronha AM, Chuang J, et al. (2013) Multichange Isothermal Mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA. ACS synthetic biology 2: 473-477. (co-First author)



14.  Wilson ML, Cai Y, Hanlon R, Taylor S, Chevreux B, et al. (2012) Sequence verification of synthetic DNA by assembly of sequencing reads. Nucleic acids research. (co-First author)


15.  Galdzicki M, Wilson M, Rodriguez CA, Pocock MR, Oberortner E, et al. (2012) Synthetic Biology Open Language (SBOL) Version 1.1. 0.



16.  Boeke J, Mitchell L, Cai Y, Stracquadanio G, Chuang J, et al. (2012) Yeast Golden Gate: Standardized Assembly of S. cerevisiae Transcriptional Units.



17.  Cai Y, Boeke JD (2011) Genome remodeling. Nature Biotechnology 29: 807-808.


18.  Beal J, Phillips A, Densmore D, Cai Y (2011) High-level programming languages for biomolecular systems. Design and analysis of biomolecular circuits: Springer New York. pp. 225-252.



19.  Cai Y, Wilson ML, Peccoud J (2010) GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic acids research 38: 2637-2644.


20.  Cai Y (2010) GenoCAD: linguistic approaches to synthetic biology: Virginia Polytechnic Institute and State University.



21.  Czar MJ, Cai Y, Peccoud J (2009) Writing DNA with GenoCAD™. Nucleic acids research 37: W40-W47.


22.  Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS computational biology 5: e1000529.





24.  Peccoud J, Blauvelt MF, Cai Y, Cooper KL, Crasta O, et al. (2008) Targeted development of registries of biological parts. PLoS One 3: e2671.



25.  French C, Nicholson J, Bizzari F, Aleksic J, Cai Y, et al. (2007) Arsenic biosenseor: a step further. BMC Systems Biology 1: S11.


26.  Cai Y, Hartnett B, Gustafsson C, Peccoud J (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23: 2760-2767.



27.  Cai Y, Davidson B, Ma H, French C (2007) Modeling the arsenic biosensor system. BMC Systems Biology 1: P83.


28.  Aleksic J, Bizzari F, Cai Y, Davidson B, De Mora K, et al. (2007) Development of a novel biosensor for the detection of arsenic in drinking water. IET Synthetic Biology 1: 87-90.


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