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

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

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

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