Publications

@article{xllzz17:chem_soc_rev,

title = {Design and chemical synthesis of eukaryotic chromosomes},

author = {Z. X. Xie and D. Liu and B. Z. Li and M. Zhao and B. X. Zeng and Y. Wu and Y. Shen and T. Lin and P. Yang and Y. Cai and J. Dai and H. Yang and Y. J. Yuan},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Chemical Society Reviews},

volume = {46},

pages = {7191--7207},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zzllw17:science,

title = {Engineering the ribosomal DNA in a megabase synthetic chromosome},

author = {W. Zhang and G. Zhao and Z. Luo and Y. Lin and L. Wang and Y. Guo and A. Wang and S. Jiang and Q. Jiang and Y. Wang and J. Gong and S. Hou and J. Huang and T. Li and Y. Qin and J. Dong and Q. Qin and J. Zhang and X. Zou and L. Zhao and X. He and Y. Xiao and M. Xu and E. Cheng and N. Huang and T. Zhou and Y. Shen and R. Walker and Y. Luo and Z. Kuang and L. A. Mitchell and K. Yang and S. M. Richardson and Y. Wu and B. Z. Li and Y. J. Yuan and J. Lin and H. Yang and G. Q. Chen and Q. Wu and J. S. Bader and Y. Cai and J. D. Boeke and J. Dai},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Science},

volume = {355},

number = {6329},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bchka16:science,

title = {GENOME ENGINEERING. The Genome Project-Write},

author = {J. D. Boeke and G. Church and A. Hessel and N. J. Kelley and A. Arkin and Y. Cai and R. Carlson and V. W. Cornish and A. Chakravarti and L. Holt and F. J. Isaacs and T. Kuiken and M. Lajoie and T. Lessor and M. T. Maurano and J. Lunshof and L. A. Mitchell and J. Rine and S. Rosser and N. E. Sanjana and P. A. Silver and D. Valle and H. Wang and J. C. Way and L. Yang},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Science},

volume = {353},

number = {6329},

pages = {126--127},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ec16:acs_synthbio,

title = {Synthetic Biology in Europe},

author = {T. Ellis and Y. Cai},

year  = {2016},

date = {2016-01-01},

journal = {ACS Synthetic Biology},

volume = {5},

number = {10},

pages = {1033},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kszrc16:jlabauto,

title = {Smart DNA Fabrication Using Sound Waves: Applying Acoustic Dispensing Technologies to Synthetic Biology},

author = {P. Kanigowska and Y. Shen and Y. Zheng and S. Rosser and Y. Cai},

year  = {2016},

date = {2016-01-01},

journal = {Journal of Laboratory Automation},

volume = {21},

number = {1},

pages = {49--56},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mpdc16:acs_synthbio,

title = {Mammalian Synthetic Biology: Time for Big MACs},

author = {A. Martella and S. M. Pollard and J. Dai and Y. Cai},

year  = {2016},

date = {2016-01-01},

journal = {ACS Synthetic Biology},

volume = {5},

number = {10},

pages = {1040--1049},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{qtlqh16:acs_synthbio,

title = {EcoExpress-Highly Efficient Construction and Expression of Multicomponent Protein Complexes in Escherichia coli},

author = {Y. Qin and C. Tan and J. Lin and Q. Qin and J. He and Q. Wu and Y. Cai and Z. Chen and J. Dai},

year  = {2016},

date = {2016-01-01},

journal = {ACS Synthetic Biology},

volume = {5},

number = {11},

pages = {1239--1246},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sswym16:gr,

title = {SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes},

author = {Y. Shen and G. Stracquadanio and Y. Wang and K. Yang and L. A. Mitchell and Y. Xue and Y. Cai and T. Chen and J. S. Dymond and K. Kang and J. Gong and X. Zeng and Y. Zhang and Y. Li and Q. Feng and X. Xu and J. Wang and J. Wang and H. Yang and J. D. Boeke and J. S. Bader},

year  = {2016},

date = {2016-01-01},

journal = {Genome Research},

volume = {26},

number = {1},

pages = {36--49},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wc16:acs_synthbio,

title = {The Fifth Annual Sc2.0 and Synthetic Genomes Conference: Synthetic Genomes in High Gear},

author = {R. S. Walker and Y. Cai},

year  = {2016},

date = {2016-01-01},

journal = {ACS Synthetic Biology},

volume = {5},

number = {9},

pages = {920--922},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{amcic15:acs_synthbio,

title = {Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units},

author = {N. Agmon and L. A. Mitchell and Y. Cai and S. Ikushima and J. Chuang and A. Zheng and W. J. Choi and J. A. Martin and K. Caravelli and G. Stracquadanio and J. D. Boeke},

year  = {2015},

date = {2015-01-01},

urldate = {2015-01-01},

journal = {ACS Synthetic Biology},

volume = {4},

number = {7},

pages = {853--859},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cacus15:pnas,

title = {Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes},

author = {Y. Cai and N. Agmon and W. J. Choi and A. Ubide and G. Stracquadanio and K. Caravelli and H. Hao and J. S.Bader and J. D. Boeke},

year  = {2015},

date = {2015-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {112},

number = {6},

pages = {1803--1808},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gdzal15:nar,

title = {YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae},

author = {Y. Guo and J. Dong and T. Zhou and J. Auxillos and T. Li and W. Zhang and L. Wang and Y. Shen and Y. Luo and J. Lin and Y.Zheng and G. Q. Chen and Q. Wu and Y. Cai and J. Dai},

year  = {2015},

date = {2015-01-01},

urldate = {2015-01-01},

journal = {Nucleic Acids Research},

volume = {43},

number = {13},

pages = {e88},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mcakp15:nar,

title = {Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae},

author = {L. A. Mitchell and J. Chuang and N. Agmon and C. Khunsriraksakul and N. A. Phillips and Y. Cai and D. M. Truong and A. Veerakumar and Y. Wang and M. Mayorga and P. Blomquist and P. Sadda and J. Trueheart and J. D. Boeke},

year  = {2015},

date = {2015-01-01},

journal = {Nucleic Acids Research},

volume = {43},

number = {13},

pages = {6620--6630},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{qcabb15:plosbio,

title = {SBOL Visual: A Graphical Language for Genetic Designs},

author = {J. Y. Quinn and R. S. Cox and A. Adler and J. Beal and S. Bhatia and Y. Cai and J. Chen and K. Clancy and M. Galdzicki and N. J. Hillson and N. Le Novère and A. J. Maheshwari and J. A. McLaughlin and C. J. Myers and U. P and M. Pocock and C. Rodriguez and L. Soldatova and G. B. Stan and N. Swainston and A. Wipat and H. M. Sauro},

year  = {2015},

date = {2015-01-01},

volume = {13},

number = {12},

pages = {e1002310},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ammrs14:science,

title = {Total synthesis of a functional designer eukaryotic chromosome},

author = {N. Annaluru and H. Muller and L. A. Mitchell and S. Ramalingam and G. Stracquadanio and S. M.Richardson and J. S. Dymond and Z. Kuang and L. Z. Scheifele and E. M. Cooper and Y. Cai and K. Zeller and N. Agmon and J. S. Han and M. Hadjithomas and J. Tullman and K. Caravelli and K. Cirelli and Z. Guo and A. Yeluru and V. London and S. Murugan and K. Kandavelou and N. Agier and G. Fischer and K. Yang and J. A. Martin and M. Bilgel and P. Bohutski and K. M. Boulier and B. J. Capaldo and J. Chang and K. Charoen and W. J. Choi and P. Deng and J. E. DiCarlo and J. Doong and J. Dunn and J. I. Feinberg and C. Fernandez and C. E. Floria and D. Gladowski and P. Hadidi and I. Ishizuka and J. Jabbari and C. Y. Lau and P. A. Lee and D. Lin S.Li and M. E. Linder and J. Ling and J. Liu and J. Liu and M. London and H. Ma and J. Mao and J. E.McDade and A. McMillan and A. M. Moore and W. C. Oh and Y. Ouyang and R. Patel and M. Paul and L. C.Paulsen and J. Qiu and A. Rhee and M. G. Rubashkin and I. Y. Soh and N. E. Sotuyo and V. Srinivas and A. Wong and A. Suarez and R. Wong and W. R. Xie and Y. Xu and A. T. Yu and R. Koszul and J. S. Bader and J. D.Boeke and S. Chandrasegaran},

year  = {2014},

date = {2014-01-01},

urldate = {2014-01-01},

journal = {Science},

volume = {344},

number = {6179},

pages = {55--58},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ce14:acs_synthbio,

title = {The Sixth International Meeting on Synthetic Biology (SB6.0) special issue editorial},

author = {Y. Cai and T. Ellis},

year  = {2014},

date = {2014-01-01},

journal = {ACS Synthetic Biology},

volume = {3},

number = {3},

pages = {107},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tmcef14:nar,

title = {PaperClip: rapid multi-part DNA assembly from existing libraries},

author = {M. Trubitsyna and G. Michlewski and Y. Cai and A. Elfick and C. E. French},

year  = {2014},

date = {2014-01-01},

journal = {Nucleic Acids Res},

volume = {42},

number = {20},

pages = {e154},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mctnc13:acs_synthbio,

title = {Multichange isothermal mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA},

author = {L. A. Mitchell and Y. Cai and M. Taylor and A. M. Noronha and J. Chuang and L. Dai and J. D. Boeke},

year  = {2013},

date = {2013-01-01},

journal = {ACS Synthetic Biology},

volume = {2},

number = {8},

pages = {473--477},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wchtc13:nar,

title = {Sequence verification of synthetic DNA by assembly of sequencing reads},

author = {M. L. Wilson and Y. Cai and R. Hanlon and S. Taylor and B. Chevreux and J. C. Setubal and B. M. Tyler and J. Peccoud},

year  = {2013},

date = {2013-01-01},

journal = {Nucleic Acids Research},

volume = {41},

number = {1},

pages = {e25},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cb11:nature_biot,

title = {Genome remodeling},

author = {Y. Cai and J. D. Boeke},

year  = {2011},

date = {2011-01-01},

journal = {Nature Biotechnology},

volume = {29},

number = {9},

pages = {807--808},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cwp10:nar,

title = {GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs},

author = {Y. Cai and M. L. Wilson and J. Peccoud},

year  = {2010},

date = {2010-01-01},

journal = {Nucleic Acids Research},

volume = {38},

number = {8},

pages = {2637--2644},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{clap09:ploscb,

title = {Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars},

author = {Y. Cai and M. W. Lux and L. Adam and J. Peccoud},

year  = {2009},

date = {2009-10-01},

journal = {PLoS Computational Biology},

volume = {5},

number = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ccp09:nar,

title = {Writing DNA with GenoCAD},

author = {M. J. Czar and Y. Cai and J. Peccoud},

year  = {2009},

date = {2009-01-01},

journal = {Nucleic Acids Research},

volume = {37},

pages = {W40--W47},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pbccc08:plosone,

title = {Targeted development of registries of biological parts},

author = {J. Peccoud and M. F. Blauvelt and Y. Cai and K. L. Cooper and O. Crasta and E. C. DeLalla and C. Evans and O. Folkerts and B. M. Lyons and S. P. Mane and R. Shelton and M. A. Sweede and S. A. Waldon},

year  = {2008},

date = {2008-01-01},

journal = {PLoS ONE},

volume = {3},

number = {7},

pages = {e2671},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chgp07:bio,

title = {A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts},

author = {Y. Cai and B. Hartnett and C. Gustafsson and J. Peccoud},

year  = {2007},

date = {2007-01-01},

journal = {Bioinformatics},

volume = {23},

number = {20},

pages = {2760--2767},

keywords = {},

pubstate = {published},

tppubtype = {article}

}