Publications

48. Luo Z, Wang L, Wang Y, Zhang W, Guo Yakun, Shen Y, Jiang L, Wu Q, Zhang C, Cai Y, Dai J (2017). Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES. Nature Communications. 2017, doi: 10.1038/s41467-017-00806-y. [In press]. (Corresponding author).

47. Xie ZX., Liu D., Li BZ., Zhao M., Zeng BX., Wu Y., Shen Y., Lin T., Yang P., Dai J., Cai Y., Yang H., Yuan YJ (2017). Design and chemical synthesis of eukaryotic chromosomes. Chemical Society Reviews. 2017 Nov 2. doi: 10.1039/c7cs00208d. [Epub ahead of print]. PMID: 29094136.

46. Craig T, Holland R, D'Amore R, Johnson JR, McCue HV, West A, Zulkower V, Tekotte H, Cai Y, Swan D, Davey RP, Hertz-Fowler C, Hall A, Caddick M (2017). Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus. ACS Synth Biol. 2017 Sep 13. doi: 10.1021/acssynbio.7b00212. [Epub ahead of print]. PMID: 28877583.

45. Dai J., Cai Y., Yuan Y, Yang H, Boeke J. (2017), Whole genome synthesis: from poliovirus to synthetic yeast. Quantitative Biology. 2017, 5(1): 105-109. doi 10.1007/s40484-017-0101-x.

44. Liu W, Tuck LR, Wright JM, Cai Y (2017). Using purified tyrosine site-specific recombinases in vitro to rapidly construct and diversify metabolic pathways. Methods Mol Biol. 2017, 1642:285-302. doi: 10.1007/978-1-4939-7169-5_18. (Corresponding author). PMID: 28815507.

43. Jia B, Qi H, Li BZ, Pan S, Liu D, Liu H, Cai Y, Yuan YJ (2017). Orthogonal ribosome bio- firewall. ACS Synth Biol. 2017 Aug 7. doi: 10.1021/acssynbio.7b00148. [Epub ahead of print]. PMID: 28783349

42. Ting Yuan, Yakun Guo, Junkai Dong, Tianyi Li, Tong Zhou, Kaiwen Sun, Mei Zhang, Qingyu Wu, Zhen Xie, Yizhi Cai, Limin Cao, Junbiao Dai. (2017), Construction, characterization and application of a genome-wide promoter library in Saccharomyces cerevisiae. Frontiers of Chemical Science and Engineering. doi: 10.1007/s11705-017-1621-7.

41. Zahn, et al. (2017), Building on nature's design. Science. 2017 Mar 10; 355 (6329): 1038- 1039. doi: 10.1126/science.355.6329.1038. PMID: 28280198.

40. Martella, A, Matjusaitis, M, Auxillos, J, Pollard, S, Cai, Y. (2017), EMMA: an Extensible Mammalian Modular Assembly toolkit for the rapid design and production of diverse expression vectors. ACS Synthetic Biology. (Corresponding author). PMID: 28418644.

39. Shen et al. (2017), A 770kb fully synthetic yeast chromosome II reveals genomic plasticity and robustness through deep functional profiling. Science. 2017 Mar 10;355(6329). pii: eaaf4791. doi: 10.1126/science.aaf4791. (Corresponding author). PMID: 28280153.

38. Richardson, et al. (2017), Design of a synthetic yeast genome. Science. 2017 Mar 10;355(6329):1040-1044. doi: 10.1126/science.aaf4557. PMID: 28280199.

37. Guillaume et al. (2017), 3D organization of synthetic and scrambled chromosomes. Science. 2017 Mar 10;355(6329). pii: eaaf4597. doi: 10.1126/science.aaf4597. PMID: 28280150.

36. Xie, et al. (2017), Synthetic chromosome V: Behavior of ring derivatives and approaching a variant-free designer chromosome. Science. 2017 Mar 10;355(6329). pii: eaaf4704. doi: 10.1126/science.aaf4704. PMID: 28280151.

35. Mitchell, et al. (2017), Synthesis, debugging and consolidation of synthetic chromosomes in yeast: synVI and beyond. Science. 2017 Mar 10;355(6329). pii: eaaf4831. doi: 10.1126/science.aaf4831.PMID: 28280154.

34. Zhang, et al. (2017), Synthetic yeast chromosome XII: morphing species identity. Science. 2017 Mar 10;355(6329). pii: eaaf3981. doi: 10.1126/science.aaf3981. PMID: 28280149.

33. Wu, et al. (2017), Bug-mapping and fitness testing of chemically synthesized chro- mosome X in Yeast. Science. 2017 Mar 10;355(6329). pii: eaaf4791. doi: 10.1126/sci- ence.aaf4791. PMID: 28280153.

32. Cai Y., Dai J. (2017), Methods to Synthesize Large DNA Fragments for a Synthetic YeastGenome. Cold Spring Harb Protoc. 2017 Mar 1;2017(3):pdb.prot080978. doi: 10.1101/pdb.prot080978 (Corresponding author). PMID: 28250211

31. Agmon, et al. (2017), Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1470- E1479. doi: 10.1073/pnas.1621250114. PMID: 28174266

30. Walker RS, Cai Y (2016). The Fifth Annual Sc2.0 and Synthetic Genomes Conference: Syn- thetic Genomes in High Gear. ACS Synthetic Biology (Corresponding Author). PMID: 27633830

29. Ellis T, Cai Y (2016). Synthetic Biology in Europe Special Issue Editorial. ACS Synthetic Biology (Corresponding Author). PMID: 27764945

28. Qin, Y., Tan, C., Lin, J., Qin, Q., He, J., Wu, Q., Cai, Y., et al. (2016) EcoExpress-Highly Efficient Construction and Expression of Multicomponent Protein Complexes in Escherichia coli. ACS Synthetic Biology. PMID: 27345099.

27. Martella A, Pollard SM, Dai J, Cai Y (2016). Mammalian Synthetic Biology: Time for Big MACs. ACS Synthetic Biology. 21;5(10):1040-1049. PMID: 27076218

26. Boeke, J., Church, G., Hessel, A., Kelley NJ., Arkin, A., Cai, Y., et al. (2016) GENOME ENGINEERING. The Genome Project-Write. Science. PMID: 27256881.

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

24. 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

23. 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)

22. 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)

21. 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.

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

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

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

17. 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)

16. 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)

15. 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)

14. 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)

12. 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)

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

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

9. 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.

8. 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.

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

6. 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.

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

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

3. 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.

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

1. 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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