Publications

@article{lcmcd24:quant_biology,

title = {Recent technology advancements in large-scale DNA assembly},

author = {J. Li and L. Cheng and Y. Ma and Y. Cai and J. Dai},

doi = {doi.org/10.1002/qub2.79},

year  = {2024},

date = {2024-12-17},

journal = {Quantitative Biology},

volume = {e79},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{aabbc24:science,

title = {Confronting risks of mirror life},

author = {K. P. Adamala and D. Agashe and Y. Belkaid and D. M. De C. Bittencourt and Y. Cai and M. W. Chang and I. A. Chen and G. M. Church and V. S. Cooper and M. M. Davis and N. K. Devaraj and D. Endy and K. M. Esvelt and J. I. Glass and T. W. Hand and T. V. Inglesby and F. J. Isaacs and W. G. James and J. D. G. Jones and M. S. Kay and R. E. Lenski and C. Liu and R. Medzhitov and M. L. Nicotra and S. B. Oehm and J. Pannu and D. A. Relman and P. Schwille and J. A. Smith and H. Suga and J. W. Szostak and N. J. Talbot and J. M. Tiedje and J. C. Venter and G. Winter and W. Zhang and X. Zhu and M. T. Zuber},

doi = {doi.org/10.1126/science.ads9158},

year  = {2024},

date = {2024-12-12},

urldate = {2024-12-12},

journal = {Science},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zwhaf24:nature_communications,

title = {The de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging},

author = {C. Zhou and Y. Wang and Y. Huang and Y. An and X. Fu and D. Yang and Y. Wang and J. Zhang and L. A. Mitchell and J. S. Bader and Y. Cai and J. Dai and J. D. Boeke and Z. Cai and Z. Xie and Y. Shen and W. Huang},

doi = {doi.org/10.1038/s41467-024-54130-3},

year  = {2024},

date = {2024-11-22},

journal = {Nature Communications},

volume = {15},

issue = {10139},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jdcc24:nature_review_genetics,

title = {The design and engineering of synthetic genomes},

author = {J. S. James and J. Dai and W. L. Chew and Y. Cai},

doi = {10.1038/s41576-024-00786-y},

year  = {2024},

date = {2024-11-06},

urldate = {2024-11-06},

journal = {Nature Reviews Genetics},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zkccx24:microbiological_research,

title = {Challenges to rhizobial adaptability in a changing climate: Genetic engineering solutions for stress tolerance},

author = {Y. Zhang and Y.-S. Ku and T.-Y. Cheung and S.-S. Cheng and D. Xin and K. Gombeau and Y. Cai and H.-M. Lam and T.-F. Chan},

doi = {doi.org/10.1016/j.micres.2024.127886},

year  = {2024},

date = {2024-08-31},

urldate = {2024-08-31},

journal = {Microbiological Research},

volume = {288},

issue = {127886},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bb24:genetics,

title = {Build-A-Genome and the “awesome power of undergraduates”},

author = {J. D. Boeke and {the Build-A-Genome Course}},

doi = {doi.org/10.1093/genetics/iyae083},

year  = {2024},

date = {2024-08-04},

urldate = {2024-08-04},

journal = {Genetics},

volume = {227},

number = {iyae083},

issue = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jbc24:gen_biotechnology,

title = {Yeasty HAC Does the Trick},

author = {J. S. James and A. Ballerini and Y. Cai},

doi = {10.1089/genbio.2024.0026},

year  = {2024},

date = {2024-06-22},

urldate = {2024-06-22},

journal = {GEN Biotechnology},

volume = {3},

issue = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{omc24:current_opinion_biotech,

title = {Searching for the optimal microbial factory: high-throughput biosensors and analytical techniques for screening small molecules},

author = {E. O'Connor and J. Micklefield and Y. Cai},

doi = {10.1016/j.copbio.2024.103125},

year  = {2024},

date = {2024-06-01},

urldate = {2024-06-01},

journal = {Current Opinion in Biotechnology},

volume = {87},

issue = {103125},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{swc24:cell_reports_methods,

title = {Methodological advances enabled by the construction of a synthetic yeast genome},

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

doi = {10.1016/j.crmeth.2024.100761},

year  = {2024},

date = {2024-04-22},

journal = {Cell Reports Methods},

volume = {4},

number = {100761},

issue = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hfsth24:faraday_discuss,

title = {An Efficient Pyrrolysyl-tRNA Synthetase for Economical Production of MeHis-containing Enzymes},

author = {A. E. Hutton and J. Foster and J. E. J. Sanders and C. J. Taylor and S. A. Hoffmann and Y. Cai and S. L. Lovelock and A. P. Green},

doi = {doi.org/10.1039/D4FD00019F},

year  = {2024},

date = {2024-03-07},

urldate = {2024-03-07},

journal = {Faraday Discussions},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{fsmsc24:life_medicine,

title = {When synthetic biology meets medicine},

author = {Y. Feng and C. Su and G. Mao and B. Sun and Y. Cai and J. Dai and Y. Ma},

doi = {doi.org/10.1093/lifemedi/lnae010},

year  = {2024},

date = {2024-03-06},

urldate = {2024-03-06},

journal = {Life Medicine},

volume = {3},

number = {lnae010},

issue = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jcwzz24:cell_reports,

title = {High plasticity of ribosomal DNA organization in budding yeast},

author = {S. Jiang and Z. Cai and Y. Wang and C. Zeng and J. Zhang and W. Yu and C. Su and S. Zhao and Y. Cheng and Y. Shen and Y. Ma and Y. Cai and J. Dai},

doi = {doi.org/10.1016/j.celrep.2024.113742},

year  = {2024},

date = {2024-02-27},

journal = {Cell Reports},

volume = {43},

number = {113742},

issue = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hc24:nature_communications,

title = {Engineering stringent genetic biocontainment of yeast with a protein stability switch},

author = {S. A. Hoffmann and Y. Cai},

doi = {doi.org/10.1038/s41467-024-44988-8},

year  = {2024},

date = {2024-02-05},

journal = {Nature Communications},

volume = {15},

issue = {1060},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{czlhl24:nature_communications,

title = {Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae},

author = {L. Cheng and S. Zhao and T. Li and S. Hou and Z. Luo and J. Xu and W. Yu and S. Jiang and M. Monti and D. Schindler and W. Zhang and C. Hou and Y. Ma and Y. Cai and J. D. Boeke and J. Dai},

doi = {doi.org/10.1038/s41467-023-44511-5},

year  = {2024},

date = {2024-01-26},

journal = {Nature Communications},

volume = {15},

number = {770},

issue = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fmmbn24:fems_yeast_res,

title = {Heterologous pulcherrimin production in Saccharomyces cerevisiae confers inhibitory activity on Botrytis conidiation},

author = {F. M. Freimoser and M. Mahler and M. McCullough and A. O. Brachmann and L. Nägeli and M. Hilber-Bodmer and J. Piel and S. Hoffmann and Y. Cai},

doi = {doi.org/10.1093/femsyr/foad053},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {FEMS Yeast Research},

volume = {24},

issue = {foad053},

pages = {1--8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jlwyz23:nature_comm,

title = {Building a eukaryotic chromosome arm by de novo design and synthesis},

author = {S. Jiang and Z. Luo and J. Wu and K. Yu and S. Zhao and Z. CAi and W. Yu and H. Wang and L. Cheng and Z. Liang and H. Gao and M. Monti and D. Schindler and L. Huang and C. Zeng and W. Zhang and C. Zhou and Y. Tang and T. Li and Y. Mz and Y. Cai and J. D. Boeke and Q. Zhao and J. Dai},

doi = {doi.org/10.1038/s41467-023-43531-5},

year  = {2023},

date = {2023-11-30},

urldate = {2023-11-30},

journal = {Nature Communications},

volume = {14},

number = {7886},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{swjbw23:cell,

title = {Design, construction, and functional characterization of a tRNA neochromosome in yeast},

author = {D. Schindler and R. S. K. Walker and S. Jiang and A. N. Brooks and Y. Wang and C. A. Müller and C. Cockram and Y. Luo and A. Garcia and D. Schraivogel and J. Mozziconacci and N. Pena and M. Assari and M. d. C. S. Olmos and Y. Zhao and A. Ballerini and B. A. Blout and J. Cai and L. Ogunlana and W. Liu and K. Jönsson and D. Abramczyk and E. Garcia-Ruiz and T. W. Turowski and R. Swidah and T. Ellis and T. Pan and F. Antequera and Y. Shen and C. A. Nieduszynski and R. Koszul and J. Dai and L. M. Steinmetz and J. D. Boeke and Y. Cai},

doi = {doi.org/10.1016/j.cell.2023.10.015},

year  = {2023},

date = {2023-11-24},

urldate = {2023-11-24},

journal = {Cell},

volume = {186},

issue = {24},

pages = {5237--5253},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fksjl23:cell_genomics,

title = {Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration},

author = {J. L. Foo and S. Kitano and A. V. Susanto and Z. Jin and Y. Lin and Z. Luo and L. Huang and Z. Liang and L. A. Mitchell and K. Yang and A. Wong and Y. Cai and J. Cai and G. Stracquadanio and J. S. Bader and J. D. Boeke and J. Dai and M. W. Chang},

doi = {10.1016/j.xgen.2023.100435},

year  = {2023},

date = {2023-11-08},

urldate = {2023-11-08},

journal = {Cell Genomics},

volume = {3},

number = {100435},

issue = {11},

key = {fksjl23:cell_genomics},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bldjs23:cell_genomics,

title = {Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics},

author = {B. A. Blout and X. Lu and M. R. M. Driessen and D. Jovicevic M. I. Sanchez and K. Ciurkot and Y. Zhao and S. Lauer and R. M. McKiernan and G.-O. F. Gowers and F. Sweeney and V. Fanfani and E. Lobzaev and K. Palacios-Flores and R. S. K. Walker and A. Hesketh and J. Cai and S. G. Oliver and Y. Cai and G. Stracquadanio and L. A. Mitchell and J. S. Bader and J. D. Boeke and T. Ellis},

doi = {doi.org/10.1016/j.xgen.2023.100418},

year  = {2023},

date = {2023-11-08},

urldate = {2023-11-08},

journal = {Cell Genomics},

volume = {3},

number = {100418},

issue = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wkxwl23:cell_genomics,

title = {Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects},

author = {T. C. Williams and H. Kroukamp and X. Xu and E. L. I. Wightman and B. Llorente and A. R. Borneman and A. C. Carpenter and N. Van Wyk and F. Meier and T. R. V. Collier and M. I. Espinosa and E. L. Daniel and R. S. K. Walker and Y. Cai and H. K. M. Nevalainen and N. C. Curach and I. W. Deveson and T. R. Mercer and D. L. Johnson and L. A. Mitchenll and J. S. Bader and G. Stracquadanio and J. D. Boeke and H. D. Goold and I. S. Pretorius and I. T. Paulsen},

doi = {doi.org/10.1016/j.xgen.2023.100379},

year  = {2023},

date = {2023-11-08},

journal = {Cell Genomics},

volume = {3},

number = {100379},

issue = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sgwwz23:cell_genomics,

title = {Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast},

author = {Y. Shen and F. Gao and Y. Wang and Y. Wang and J. Zheng and J. Gong and J. Zhang and Z. Luo and D. Schindler and Y. Deng and W. Ding and T. Lin and R. Swidah and H. Zhao and S. Jiang and C. Zeng and S. Chen and T. Chen and Y. Wang and Y. Luo and L. Mitchell and J. S. Bader and G. Zhang and X. Shen J. Wang and X. Fu and J. Dai and J. D. Boeke and H. Yang and X. Xu and Y. Cai},

doi = {doi.org/10.1016/j.xgen.2023.100364},

year  = {2023},

date = {2023-11-08},

urldate = {2023-11-08},

journal = {Cell Genomics},

volume = {3},

number = {100364},

issue = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{dypcs23:cell_genomics,

title = {A spotlight on global collaboration in the Sc2.0 yeast consortium},

author = {J. Dai and H. Yang and I. S. Pretorius and Y. Cai and Y. Shen and M. Chang and Y. Yuan},

doi = {doi.org/10.1016/j.xgen.2023.100441},

year  = {2023},

date = {2023-11-08},

journal = {Cell Genomics},

volume = {3},

number = {100441},

issue = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zchly23:cell_genomics,

title = {Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions},

author = {Y. Zhao and C. Coelho and A. L. Hughes and L. Lazar-Stefanita and S. Yang and A. N. Brooks and R. S. K. Walker and W. Zhang and S. Lauer and C. Hernandez and J. Cai and L. A. Mitchell and N. Agmon and Y. Shen and J. Sall and V. Fanfani and A. Jalan and J. Rivera and F.-X. Liang and J. S. Bader and G. Stracquadanio and L. M. Steinmetz and Y. Cai and J. D. Boeke},

doi = {doi.org/10.1016/j.cell.2023.09.025},

year  = {2023},

date = {2023-11-08},

journal = {Cell},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doc23:gen_biotechnology,

title = {Cellular Surveillance: DNA-Based Recording to Monitor and Memorize Biological Events},

author = {G. David and R. T. O'Keefe and Y. Cai},

doi = {doi:10.1089/genbio.2023.0018},

year  = {2023},

date = {2023-06-19},

urldate = {2023-06-19},

journal = {GEN Biotechnology},

volume = {2},

number = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hdddk23:iscience,

title = {Safety by design: Biosafety and biosecurity in the age of synthetic genomics},

author = {S. A. Hoffmann and J. Diggans and D. Densmore and J. Dai and T. Knight and E. Leproust and J. D. Boeke and N. Wheeler and Y. Cai},

doi = {10.1016/j.isci.2023.106165},

year  = {2023},

date = {2023-03-17},

journal = {iScience},

volume = {26},

issue = {3},

pages = {106165},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hc22:biorxiv,

title = {Engineering stringent genetic biocontainment of yeast with a protein stability switch},

author = {S. A. Hoffmann and Y. Cai},

doi = {10.1101/2022.11.24.517818 },

year  = {2022},

date = {2022-11-24},

journal = {bioRxiv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jlyzc22:biorxiv,

title = {Reconstruct a eukaryotic chromosome arm by de novo design and synthesis},

author = {S. Jiang and Z. Luo and K. Yu and S. Zhao and Z. Cai and W. Yu and H. Wang and L. Cheng and Z. Liang and H. Gao and M. Monti and D. Schindler and L. Huang and C. Zeng and W. Zhang and C. Zhou and Y. Tang and T. Li and Y. Ma and Y. Cai and J. D. Boeke and J. Dai},

doi = {10.1101/2022.10.04.509869 },

year  = {2022},

date = {2022-10-04},

journal = {bioRxiv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{swjbw22:biorxiv,

title = {Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast},

author = {D. Schindler and R. S. K. Walker and S. Jiang and A. N. Brooks and Y. Wang and C. A. Müller and C. Cockram and Y. Luo and A. García and D. Schraivogel and J. Mozziconacci and B. A. Blount and J. Cai and L. Ogunlana and W. Liu and K. Jönsson and D. Abramczyk and E. Garcia-Ruiz and T. W. Turowski and R. Swidah and T. Ellis and F. Antequera and Y. Shen and C. A. Nieduszynski and R. Koszul and J. Dai and L. M. Steinmetz and J. D. Boeke and Y. Cai},

doi = {10.1101/2022.10.03.510608 },

year  = {2022},

date = {2022-10-03},

urldate = {2022-10-03},

journal = {bioRxiv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sgwwz22:biorxiv,

title = {Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast},

author = {Y. Shen and F. Gao and Y. Wang and Y. Wang and J. Zheng and J. Gong and J. Zhang and Z. Luo and D. Schindler and Y. Deng and W. Ding and T. Lin and R. Swidah and H. Zhao and S. Jiang and C. Zeng and S. Chen and T. Chen and Y. Wang and Y. Luo and L. Mitchell and J. S. Bader and G. Zhang and X. Shen and J. Wang and X. Fu and J. Dai and J. D. Boeke and H. Yang and X. Xu and Y. Cai},

doi = {10.1101/2022.09.01.506252},

year  = {2022},

date = {2022-09-01},

urldate = {2022-09-01},

journal = {bioRxiv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wkxwl22:biorxiv,

title = {Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements},

author = {T. C. Williams and H. Kroukamp and X. Xu and E. L. I. Wightman and B. Llorente and A. R. Borneman and A. C. Carpenter and N. V. Wyk and M. I. Espinosa and E. L. Daniel and R. S. K. Walker and Y. Cai and H. K. M. Nevalainen and N. C. Curach and I. W. Deveson and T. R. Mercer and D. L. Johnson and L. A. Mitchell and J. S. Bader and G. Stracquadanio and J. D. Boeke and H. D. Goold and I. S. Pretorius and I. T. Paulsen},

doi = {10.1101/2022.07.22.501046 },

year  = {2022},

date = {2022-07-22},

journal = {bioRxiv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bldjs22:biorxiv,

title = {Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand},

author = {B. A. Blount and X. Lu and M. R. M. Driessen and D. Jovicevic and M. I. Sanchez and K. Ciurkot and Y. Zhao and S. Lauer and R. M. McKiernan and G.-O. F. Gowers and F. Sweeney and V. Fanfani and E. Lobzaev and K. Palacios-Flores and R. Walker and A. Hesketh and S. G. Oliver and Y. Cai and G. Stracquadanio and L. A. Mitchell and J. S. Bader and J. D. Boeke and T. Ellis},

doi = {10.1101/2022.07.15.500197 },

year  = {2022},

date = {2022-07-15},

journal = {bioRxiv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zchly22:biorxiv,

title = {Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions},

author = {Y. Zhao and C. Coelho and A. L. Hughes and L. Lazar-Stefanita and S. Yang and A. N. Brooks and R. S. K. Walker and W. Zhang and S. Lauer and C. Hernandez and L. A. Mitchell and N. Agmon and Y. Shen and J. Sall and V. Fanfani and A. Jalan and J. Rivera and F.-X. Liang and G. Stracquadanio and L. M. Steinmetz and Y. Cai and J. D. Boeke},

doi = {10.1101/2022.04.11.486913},

year  = {2022},

date = {2022-04-11},

urldate = {2022-04-11},

journal = {bioRxiv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{shgc22:co_biotech,

title = {New Opportunities for Genetic Code Expansion in Synthetic Yeast},

author = {J. Sanders and S. A. Hoffmann and A. P. Green and Y. Cai},

doi = {10.1016/j.copbio.2022.102691},

year  = {2022},

date = {2022-02-10},

urldate = {2022-02-10},

journal = {Current Opinion in Biotechnology},

volume = {75},

number = {102691},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jjmlf22:acs_synthbio,

title = {Automation and Expansion of EMMA Assembly for Fast-Tracking Mammalian System Engineering},

author = {J. S. James and S. Jones and A. Martella and Y. Luo and D. I. Fisher and Y. Cai},

doi = {doi.org/10.1021/acssynbio.1c00330},

year  = {2022},

date = {2022-01-21},

urldate = {2022-01-21},

journal = {ACS Synthetic Biology},

volume = {11},

number = {2},

pages = {587--595},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ljjmc22:acs_synthbio,

title = {EMMA-CAD: Design Automation for Synthetic Mammalian Constructs},

author = {Y. Luo and J. S. James and S. Jones and A. Martella and Y. Cai},

doi = {doi.org/10.1021/acssynbio.1c00433},

year  = {2022},

date = {2022-01-20},

urldate = {2022-01-20},

journal = {ACS Synthetic Biology},

volume = {11},

number = {2},

pages = {579--586},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lyxms21:gb,

title = {Compacting a synthetic yeast chromosome arm},

author = {Z. Luo and K. Yu and S. Xie and M. Monti and D. Schindler and Y. Fang and S. Zhao and Z. Liang and S. Jiang and M. Luan and C. Xiao and Y. Cai and J. Dai},

doi = {doi.org/10.1186/s13059-020-02232-8},

year  = {2021},

date = {2021-01-04},

urldate = {2021-01-04},

journal = {Genome Biology},

volume = {22},

number = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{osmsd21:bio_basel,

title = {SCRaMbLE: A Study of Its Robustness and Challenges through Enhancement of Hygromycin B Resistance in a Semi-Synthetic Yeast},

author = {J. Y. Ong and R. Swidah and M. Monti and D. Schindler and J. Dai and Y. Cai},

doi = {10.3390/bioengineering8030042},

year  = {2021},

date = {2021-01-01},

journal = {Bioengineering (Basel)},

volume = {8},

number = {3},

pages = {42},

keywords = {},

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tppubtype = {article}

}

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title = {The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing},

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doi = {doi.org/10.1038/s41587-020-0655-4},

year  = {2020},

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journal = {Nature Biotechnology},

volume = {38},

pages = {1021--1024},

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title = {Sc3.0: revamping and minimizing the yeast genome},

author = {J. Dai and J. D. Boeke and Z. Luo and S. Jiang and Y. Cai},

doi = {doi.org/10.1186/s13059-020-02130-z},

year  = {2020},

date = {2020-08-13},

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journal = {Genome Biology},

volume = {21},

number = {205},

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}

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title = {SpEDIT: A fast and efficient CRISPR/Cas9 method for fission yeast},

author = {S. Torres-Garcia and L. Pompeo and L. Eivers and B. Gaborieau and S. A. White and A. L. Pidoux and P. Kanigowska and I. Yaseen and Y. Cai and R. C. Allshire},

doi = {10.12688/wellcomeopenres.16405.1},

year  = {2020},

date = {2020-01-01},

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journal = {Wellcome Open Research},

volume = {5},

pages = {274},

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}

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title = {Probing eukaryotic genome functions with synthetic chromosomes},

author = {Z. Luo and S. A. Hoffmann and S. Jiang and Y. Cai and J. Dai},

doi = {10.1016/j.yexcr.2020.111936},

year  = {2020},

date = {2020-01-01},

journal = {Experimental Cell Research},

volume = {390},

number = {1},

pages = {111936},

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}

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title = {Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories},

author = {Y. Zhao and Z. Yao and D. Ploessl and S. Ghosh and M. Monti and D. Schindler and M. Gao and Y. Cai and C. Yang and M. Qiao and M. Cao and Z. Shao},

doi = {10.1021/acssynbio.0c00123},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {ACS Synthetic Biology},

volume = {9},

number = {7},

pages = {1736--1752},

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}

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title = {Improving Chromosome Synthesis with a Semiquantitative Phenotypic Assay and Refined Assembly Strategy},

author = {Y. Lin and X. Zou and Y. Zheng and Y. Cai and J. Dai},

doi = {doi.org/10.1021/acssynbio.8b00505},

year  = {2019},

date = {2019-09-18},

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journal = {ACS Synthetic Biology},

volume = {8},

number = {10},

pages = {2203--2211},

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}

@article{hcccc19:nature_comm,

title = {Building a global alliance of biofoundries},

author = {N. Hillson and M. Caddick and Y. Cai and J. A. Carrasco and M. W. Chang and N. C. Curach and D. J. Bell and R. Le Feuvre and D. C. Friedman and X. Fu and N. D. Gold and M. J. Herrgard and M. B. Holowko and J. R.Johnson and R. A. Johnson and J. D. Keasling and R. I. Kitney and A. Kondo and C. Liu and V. J. J. Martin and F. Menolascina and C. Ogino and N. J. Patron and M. Pavan and C. L. Poh and I. S. Pretorius and S. J.Rosser and N. S. Scrutton and M. Storch and H. Tekotte and E. Travnik and C. E. Vickers and W. S. Yew and H. Zhao and Y. Yuan and P. S. Freemont},

doi = {doi.org/10.1038/s41467-019-10079-2},

year  = {2019},

date = {2019-05-09},

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journal = {Nature Communications},

volume = {10},

pages = {2040},

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}

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title = {Multiplex Genome Engineering for Optimizing Bioproduction in Saccharomyces cerevisiae},

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

doi = {doi.org/10.1021/acs.biochem.8b01086},

year  = {2019},

date = {2019-02-28},

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journal = {Biochemistry},

volume = {58},

number = {11},

pages = {1492--1500},

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}

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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},

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journal = {Science China Life Sciences},

volume = {61},

number = {12},

pages = {1515--1527},

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}

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

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doi = {10.3389/fbioe.2018.00146},

year  = {2018},

date = {2018-10-01},

journal = {Frontiers in Bioengineering and Biotechnology},

volume = {6},

pages = {146},

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}

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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},

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journal = {Current Opinion in Chemical Biology},

volume = {46},

pages = {56--62},

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}

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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},

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journal = {Metabolic Engineering},

volume = {49},

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}

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

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date = {2018-05-22},

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journal = {Nature Communications},

volume = {9},

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

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

year  = {2018},

date = {2018-05-22},

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journal = {Nature Communications},

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

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

year  = {2018},

date = {2018-01-01},

journal = {Methods in Enzymology},

volume = {608},

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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},

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date = {2017-09-06},

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journal = {ACS Synthetic Biology},

volume = {6},

number = {12},

pages = {2273--2280},

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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},

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journal = {Methods in Molecular Biology},

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}

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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},

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journal = {ACS Synthetic Biology},

volume = {6},

number = {11},

pages = {2108--2117},

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}

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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},

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pages = {105--109},

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

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doi = {10.1126/science.aaf4597},

year  = {2017},

date = {2017-03-10},

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journal = {Science},

volume = {355},

number = {6329},

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

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volume = {355},

number = {6329},

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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},

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date = {2017-03-10},

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volume = {355},

number = {6329},

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

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doi = {10.1126/science.aaf4706},

year  = {2017},

date = {2017-03-10},

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volume = {353},

number = {6329},

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

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doi = {10.1126/science.aaf4704},

year  = {2017},

date = {2017-03-10},

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volume = {355},

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

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doi = {10.1101/pdb.prot080978},

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date = {2017-03-01},

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journal = {Cold Spring Harbor Protocols},

volume = {2017},

number = {3},

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

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

year  = {2017},

date = {2017-02-07},

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

volume = {114},

pages = {1470-- 1479},

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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},

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journal = {ACS Synthetic Biology},

volume = {6},

number = {7},

pages = {1380--1392},

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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},

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date = {2017-01-01},

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journal = {Science},

volume = {355},

number = {6329},

pages = {1040--1044},

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

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

year  = {2017},

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journal = {Chemical Society Reviews},

volume = {46},

pages = {7191--7207},

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

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doi = {10.1126/science.aaf3981},

year  = {2017},

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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},

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journal = {Frontiers of Chemical Science and Engineering},

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title = {Synthetic Biology in Europe},

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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},

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journal = {ACS Synthetic Biology},

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

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

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journal = {ACS Synthetic Biology},

volume = {5},

number = {11},

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

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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}

}

@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}

}

@article{abcdm07:iet_synth_biology,

title = {Development of a Novel Biosensor for the Detection of Arsenic in Drinking Water},

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

doi = {10.1049/iet-stb:20060002},

year  = {2007},

date = {2007-01-01},

urldate = {2007-01-01},

journal = {IET Synthetic Biology},

volume = {1},

number = {40940},

pages = {87--90},

keywords = {},

pubstate = {published},

tppubtype = {article}

}