Publications

@article{lygjy18:scls,

title = {Whole genome engineering by synthesis},

author = {Z. Luo and Q. Yang and B. Geng and S. Jiang and S. Yang and X. Li and Y. Cai and J. Dai},

doi = {doi.org/10.1007/s11427-018-9403-y},

year  = {2018},

date = {2018-12-01},

urldate = {2018-12-01},

journal = {Science China Life Sciences},

volume = {61},

number = {12},

pages = {1515--1527},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{avumc18:front_bioeng_biotech,

title = {Hydrogen Peroxide-Based Fluorometric Assay for Real-Time Monitoring of SAM-Dependent Methyltransferases},

author = {M. K. Akhtar and D. Vijay and S. Umbreen and C. J. McLean and Y. Cai and D. J. Campopiano and G. J.Loake},

doi = {10.3389/fbioe.2018.00146},

year  = {2018},

date = {2018-10-01},

journal = {Frontiers in Bioengineering and Biotechnology},

volume = {6},

pages = {146},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sdc18:co_chembio,

title = {Synthetic genomics: a new venture to dissect genome fundamentals and engineer new functions},

author = {D. Schindler and J. Dai and Y. Cai},

doi = {10.1016/j.cbpa.2018.04.002},

year  = {2018},

date = {2018-10-01},

urldate = {2018-10-01},

journal = {Current Opinion in Chemical Biology},

volume = {46},

pages = {56--62},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lccd18:metab_eng,

title = {Artificial Protein Scaffold System (AProSS): An efficient method to optimize exogenous metabolic pathways in Saccharomyces cerevisiae},

author = {T. Li and X. Chen and Y. Cai and J. Dai},

doi = {doi.org/10.1016/j.ymben.2018.07.006},

year  = {2018},

date = {2018-09-01},

urldate = {2018-09-01},

journal = {Metabolic Engineering},

volume = {49},

pages = {13--20},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{llwpt18:nature_comm,

title = {Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods},

author = {W. Liu and Z. Luo and Y. Wang and N. T. Pham and L. Tuck and I. Pérez-Pi and L. Liu and Y. Shen and C. French and M. Auer and J. Marles-Wright and J. Dai and Y. Cai},

doi = {doi.org/10.1038/s41467-018-04254-0},

year  = {2018},

date = {2018-05-22},

urldate = {2018-05-22},

journal = {Nature Communications},

volume = {9},

pages = {1936},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lwwzg18:nature_comm,

title = {Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES},

author = {Z. Luo and L. Wang and Y. Wang and W. Zhang and Y. Guo and Y. Shen and L. Jiang and Q. Wu and C. Zhang and Y. Cai and J. Dai},

doi = {doi.org/10.1038/s41467-017-00806-y},

year  = {2018},

date = {2018-05-22},

urldate = {2018-05-22},

journal = {Nature Communications},

volume = {9},

pages = {1930},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{galdc18:methods_enzym,

title = {YeastFab: High-Throughput Genetic Parts Construction, Measurement, and Pathway Engineering in Yeast},

author = {E. Garcia-Ruiz and J. Auxillos and T. Li and J. Dai and Y. Cai},

doi = {10.1016/bs.mie.2018.05.003},

year  = {2018},

date = {2018-01-01},

journal = {Methods in Enzymology},

volume = {608},

pages = {277--306},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chdjm17:acs_synthbio,

title = {Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus},

author = {T. Craig and R. Holland and R. D’Amore and J. R. Johnson and H. V. McCue and A. West and V. Zulkower and H. Tekotte and Y. Cai and D. Swan and R. P. Davey and C. Hertz-Fowler and A. Hall and M. Caddick},

doi = {doi.org/10.1021/acssynbio.7b00212},

year  = {2017},

date = {2017-09-06},

urldate = {2017-09-06},

journal = {ACS Synthetic Biology},

volume = {6},

number = {12},

pages = {2273--2280},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ltwc17:methods_molec_bio,

title = {Using Purified Tyrosine Site-Specific Recombinases In Vitro to Rapidly Construct and Diversify Metabolic Pathways},

author = {W. Liu and L. R. Tuck and J. M. Wright and Y. Cai},

doi = {10.1007/978-1-4939-7169-5_18},

year  = {2017},

date = {2017-08-17},

urldate = {2017-08-17},

journal = {Methods in Molecular Biology},

volume = {1642},

pages = {285--302},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jqlpl17:acs_synthbio,

title = {Orthogonal Ribosome Biofirewall},

author = {B. Jia and H. Qi and B. Z. Li and S. Pan and D. Liu and H. Liu and Y. Cai and Y. J. Yuan},

doi = {doi.org/10.1021/acssynbio.7b00148},

year  = {2017},

date = {2017-08-07},

urldate = {2017-08-07},

journal = {ACS Synthetic Biology},

volume = {6},

number = {11},

pages = {2108--2117},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{dcyyb17:quantitative_biology,

title = {Whole genome synthesis:  from poliovirus to synthesis yeast},

author = {J. Dai and Y. Cai and Y. Yuan and H. Yang and J. D. Boeke},

doi = {10.1007/s40484-017-0101-x},

year  = {2017},

date = {2017-03-30},

journal = {Quantitative Biology},

volume = {5},

issue = {1},

pages = {105--109},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mmsyz17:science,

title = {3D organization of synthetic and scrambled chromosomes},

author = {G. Mercy and J. Mozziconacci and V. F. Scolari and K. Yang and G. Zhao and A. Thierry and Y. Luo and L. A. Mitchell and M. Shen and Y. Shen and R. Walker and W. Zhang and Y. Wu and Z. X. Xie and Z. Luo and Y. Cai and H. Yang and J. Dai and Y. J. Yuan and J. D. Boeke and J. S. Bader and H. Muller and R. Koszul},

doi = {10.1126/science.aaf4597},

year  = {2017},

date = {2017-03-10},

urldate = {2017-03-10},

journal = {Science},

volume = {355},

number = {6329},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mwskw17:science,

title = {Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond},

author = {L. A. Mitchell and A. Wang and G. Stracquadanio and Z. Kuang and X. Wang and K. Yang and J. A. Martin and S.Richardson and Y. Zhao and R. Walker and Y. Luo and H. Dai and K. Dong and Z. Tang and Y. Cai and Y. Yang and A. Heguy and B. Ueberheide and D. Fenyö and J. Dai and J. S. Bader and J. D. Boeke},

doi = {10.1126/science.aaf4831},

year  = {2017},

date = {2017-03-10},

urldate = {2017-03-10},

journal = {Science},

volume = {355},

number = {6329},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{swcgg17:science,

title = {Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome},

author = {Y. Shen and Y. Wang and T. Chen and F. Gao and J. Gong and D. Abramczyk and R. Walker and H. Zhao and W. Liu and S. Chen and Y. Luo and C. A. Müller and A. Paul-Dubois-Taine and B. Alver and G. Stracquadanio and L. A. Mitchell and Z. Luo and Y. Fan and B. Zhou and B. Wen and F. Tan and Y. Wang and J. Zi and Z. Xie and B. Li and K. Yang and S. M. Richardson and H. Jiang and C. E. French and C. A. Nieduszynski and R. Koszul and A. L.Marston and Y. Yuan and J. Wang and J. S. Bader and J. Dai and J. D. Boeke and X. Xu and Y. Cai and H. Yang},

doi = {10.1126/science.aaf4791},

year  = {2017},

date = {2017-03-10},

urldate = {2017-03-10},

journal = {Science},

volume = {355},

number = {6329},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wlzmx17:science,

title = {Bug mapping and fitness testing of chemically synthesized chromosome X},

author = {Y. Wu and B. Z. Li and M. Zhao and L. A. Mitchell and Z. X. Xie and Q. H. Lin and X. Wang and W. H. Xiao and Y. Wang and X. Zhou and H. Liu and X. Li and M. Z. Ding and D. Liu and L. Zhang and B. L. Liu and X. L. Wu and F. F. Li and X. T. Dong and B. Jia and W. Z. Zhang and G. Z. Jiang and Y. Liu and X. Bai and T. Q. Song and S. J. Zhou and Y. Chen and R. Y. Zhu and F. Gao and Z. Kuang and X. Wang and M. Shen and K. Yang and S. M. Richardson and G. Stracquadanio and Y. Lin and L. Wang and R. Walker and Y. Luo and P. S. Ma and Y. Cai and H. Yang and J. Dai and J. S. Bader and J. D. Boeke and Y. J. Yuan},

doi = {10.1126/science.aaf4706},

year  = {2017},

date = {2017-03-10},

urldate = {2017-03-10},

journal = {Science},

volume = {353},

number = {6329},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{xlmwq17:science,

title = {"Perfect" designer chromosome V and behavior of a ring derivative},

author = {Z. X. Xie and B. Z. Li and L. A. Mitchell and Y. Wu and X. Qi and Z. Jin and B. Jia and X. Wang and B. X. Zeng and H. M. Liu and X. L. Wu and Q. Feng and W. Z. Zhang and W. Liu and M. Z. Ding and X. Li and G. R. Zhao and J. J. Qiao and J. S. Cheng and M. Zhao and Z. Kuang and X. Wang and J. A. Martin and G. Stracquadanio and K. Yang and X. Bai and J. Zhao and M. L. Hu and Q. H. Lin and W. Q. Zhang and M. H. Shen and S. Chen and W. Su and E. X. Wang and R. Guo and F. Zhai and X. J. Guo and H. X. Du and J. Q. Zhu and T. Q. Song and J. J. Dai and F. F. Li and G. Z. Jiang and S. L. Han and S. Y. Liu and Z. C. Yu and X. N. Yang and K. Chen and C. Hu and D. S. Li and N. Jia and Y. Liu and L. T. Wang and S. Wang and X. T. Wei and M. Q. Fu and L. M. Qu and S. Y. Xin and T. Liu and K. R. Tian and X. N. Li and J. H. Zhang and L. X. Song and J. G. Liu and J. F. Lv and H. Xu and R. Tao and Y. Wang and T. T. Zhang and Y. X. Deng and Y. R. Wang and T. Li and G. X. Ye and X. R. Xu and Z. B. Xia and W. Zhang and S. L. Yang and Y. L. Liu and W. Q. Ding and Z. N. Liu and J. Q. Zhu and N. Z. Liu and R. Walker and Y. Luo and Y. Wang and Y. Shen and H. Yang and Y. Cai and P. S. Ma and C. T. Zhang and J. S. Bader and J. D. Boeke and Y. J. Yuan},

doi = {10.1126/science.aaf4704},

year  = {2017},

date = {2017-03-10},

urldate = {2017-03-10},

journal = {Science},

volume = {355},

number = {6329},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cd17:csh_proto,

title = {Methods to Synthesize Large DNA Fragments for a Synthetic Yeast Genome},

author = {Y. Cai and J. Dai},

doi = {10.1101/pdb.prot080978},

year  = {2017},

date = {2017-03-01},

urldate = {2017-03-01},

journal = {Cold Spring Harbor Protocols},

volume = {2017},

number = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{atysi17:pnas,

title = {Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae},

author = {N. Agmon and Z. Tang and K. Yang and B. Sutter and S. Ikushima and Y. Cai and K. Caravelli and J. A. Martin and X. Sun and W. J. Choi and A. Zhang and G. Stracquadanio and H. Hao and B. P. Tu and D. Fenyö and J. S. Bader and J. D. Boeke},

doi = {doi.org/10.1073/pnas.1621250114},

year  = {2017},

date = {2017-02-07},

urldate = {2017-02-07},

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

volume = {114},

pages = {1470-- 1479},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mmapc17:acs_synthbio,

title = {EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors},

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

doi = {doi.org/10.1021/acssynbio.7b00016},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {ACS Synthetic Biology},

volume = {6},

number = {7},

pages = {1380--1392},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{rmsyd17:science,

title = {Design of a synthetic yeast genome},

author = {S. M. Richardson and L. A. Mitchell and G. Stracquadanio and K. Yang and J. S. Dymond and J. E. DiCarlo and D. Lee and C. L. Huang and S. Chandrasegaran and Y. Cai and J. D. Boeke and J. S. Bader},

doi = {doi.org/10.1126/science.aaf4557},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Science},

volume = {355},

number = {6329},

pages = {1040--1044},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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},

doi = {doi.org/10.1039/C7CS00208D},

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},

doi = {10.1126/science.aaf3981},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Science},

volume = {355},

number = {6329},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ygdlz17:frontier_chem_sci_eng,

title = {Construction, characterization and application of a genome-wide promoter library in Saccharomyces cerevisiae},

author = {T. Yuan and Y. Guo and J. Dong and T. Li and T. Zhou and K. Sun and M. Zhang and Q. Wu and Z. Xie and Y. Cai and L. Cao and J. Dai},

doi = {10.1007/s11705-017-1621-7},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Frontiers of Chemical Science and Engineering},

volume = {11},

issue = {1},

pages = {107--116},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ec16:acs_synthbio,

title = {Synthetic Biology in Europe},

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

doi = {10.1021/acssynbio.6b00265},

year  = {2016},

date = {2016-10-21},

urldate = {2016-10-21},

journal = {ACS Synthetic Biology},

volume = {5},

number = {10},

pages = {1033},

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},

doi = {doi.org/10.1021/acssynbio.6b00227},

year  = {2016},

date = {2016-09-16},

urldate = {2016-09-16},

journal = {ACS Synthetic Biology},

volume = {5},

number = {9},

pages = {920--922},

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},

doi = {doi.org/10.1021/acssynbio.5b00291},

year  = {2016},

date = {2016-06-26},

urldate = {2016-06-26},

journal = {ACS Synthetic Biology},

volume = {5},

number = {11},

pages = {1239--1246},

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},

doi = {doi.org/10.1126/science.aaf6850},

year  = {2016},

date = {2016-06-02},

urldate = {2016-06-02},

journal = {Science},

volume = {353},

number = {6329},

pages = {126--127},

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},

doi = {doi.org/10.1021/acssynbio.6b00074},

year  = {2016},

date = {2016-04-13},

urldate = {2016-04-13},

journal = {ACS Synthetic Biology},

volume = {5},

number = {10},

pages = {1040--1049},

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},

doi = {10.1177/2211068215593754},

year  = {2016},

date = {2016-02-01},

urldate = {2016-02-01},

journal = {Journal of Laboratory Automation},

volume = {21},

number = {1},

pages = {49--56},

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},

doi = {10.1101/gr.193433.115},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Genome Research},

volume = {26},

number = {1},

pages = {36--49},

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},

urldate = {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},

doi = {10.1093/nar/gks908},

year  = {2013},

date = {2013-01-01},

urldate = {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},

doi = {10.1093/nar/gkp361},

year  = {2009},

date = {2009-01-01},

urldate = {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{fnbac07:bmc_systems_biology,

title = {Arsenic biosenseor: a step further},

author = {C. French and J. Nicholson and F. Bizzari and J. Aleksic and Y. Cai and S. L. Seshasayee and S. Ivakhno and B. Davidson and J. Wilson and K. de Mora and H. Ma and L. Kozma-Bognar and A. Elfick},

doi = {10.1186/1752-0509-1-S1-S11},

year  = {2007},

date = {2007-05-08},

urldate = {2007-05-08},

journal = {BMC Systems Biology},

volume = {1},

number = {S11},

issue = {Supplement 1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cdmf07:bmc_systems_biology,

title = {Modeling the arsenic biosensor system},

author = {Y. Cai and B. Davidson and H. Ma and C. French},

doi = {10.1186/1752-0509-1-S1-P83},

year  = {2007},

date = {2007-05-08},

urldate = {2007-05-08},

journal = {BMC Systems Biology},

volume = {1},

number = {P83},

keywords = {},

pubstate = {published},

tppubtype = {article}

}