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Publications


2024

Jiang, S.; Cai, Z.; Wang, Y.; Zeng, C.; Zhang, J.; Yu, W.; Su, C.; Zhao, S.; Cheng, Y.; Shen, Y.; Ma, Y.; Cai, Y.; Dai, J.

High plasticity of ribosomal DNA organization in budding yeast Cover Journal Article

In: Cell Reports, vol. 43, iss. 2, no. 113742, 2024.

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Hoffmann, S. A.; Cai, Y.

Engineering stringent genetic biocontainment of yeast with a protein stability switch Journal Article

In: Nature Communications, vol. 15, iss. 1060, 2024.

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

Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae Journal Article

In: Nature Communications, vol. 15, iss. 1, no. 770, 2024.

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Freimoser, F. M.; Mahler, M.; McCullough, M.; Brachmann, A. O.; Nägeli, L.; Hilber-Bodmer, M.; Piel, J.; Hoffmann, S.; Cai, Y.

Heterologous pulcherrimin production in Saccharomyces cerevisiae confers inhibitory activity on Botrytis conidiation Journal Article

In: FEMS Yeast Research, vol. 24, iss. foad053, pp. 1–8, 2024.

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2023

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

Design, construction, and functional characterization of a tRNA neochromosome in yeast Cover Journal Article

In: Cell, vol. 186, iss. 24, pp. 5237–5253, 2023.

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

Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration Journal Article

In: Cell Genomics, vol. 3, iss. 11, no. 100435, 2023.

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

Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics Journal Article

In: Cell Genomics, vol. 3, iss. 11, no. 100418, 2023.

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

Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects Journal Article

In: Cell Genomics, vol. 3, iss. 11, no. 100379, 2023.

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

Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast Cover Journal Article

In: Cell Genomics, vol. 3, iss. 11, no. 100364, 2023.

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Dai, J.; Yang, H.; Pretorius, I. S.; Cai, Y.; Shen, Y.; Chang, M.; Yuan, Y.

A spotlight on global collaboration in the Sc2.0 yeast consortium Journal Article

In: Cell Genomics, vol. 3, iss. 11, no. 100441, 2023.

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

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions Journal Article

In: Cell, 2023.

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David, G.; O'Keefe, R. T.; Cai, Y.

Cellular Surveillance: DNA-Based Recording to Monitor and Memorize Biological Events Journal Article

In: GEN Biotechnology, vol. 2, no. 3, 2023.

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Hoffmann, S. A.; Diggans, J.; Densmore, D.; Dai, J.; Knight, T.; Leproust, E.; Boeke, J. D.; Wheeler, N.; Cai, Y.

Safety by design: Biosafety and biosecurity in the age of synthetic genomics Journal Article

In: iScience, vol. 26, iss. 3, pp. 106165, 2023.

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2022

Hoffmann, S. A.; Cai, Y.

Engineering stringent genetic biocontainment of yeast with a protein stability switch Journal Article

In: bioRxiv, 2022.

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

Reconstruct a eukaryotic chromosome arm by de novo design and synthesis Journal Article

In: bioRxiv, 2022.

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

Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast Journal Article

In: bioRxiv, 2022.

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

Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast Journal Article

In: 2022.

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

Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements Journal Article

In: bioRxiv, 2022.

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

Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand Journal Article

In: bioRxiv, 2022.

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

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions Journal Article

In: bioRxiv, 2022.

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Sanders, J.; Hoffmann, S. A.; Green, A. P.; Cai, Y.

New Opportunities for Genetic Code Expansion in Synthetic Yeast Journal Article

In: Current Opinion in Biotechnology, vol. 75, no. 102691, 2022.

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James, J. S.; Jones, S.; Martella, A.; Luo, Y.; Fisher, D. I.; Cai, Y.

Automation and Expansion of EMMA Assembly for Fast-Tracking Mammalian System Engineering Journal Article

In: ACS Synthetic Biology, vol. 11, no. 2, pp. 587–595, 2022.

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Luo, Y.; James, J. S.; Jones, S.; Martella, A.; Cai, Y.

EMMA-CAD: Design Automation for Synthetic Mammalian Constructs Journal Article

In: ACS Synthetic Biology, vol. 11, no. 2, pp. 579–586, 2022.

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2021

Ong, J. Y.; Swidah, R.; Monti, M.; Schindler, D.; Dai, J.; Cai, Y.

SCRaMbLE: A Study of Its Robustness and Challenges through Enhancement of Hygromycin B Resistance in a Semi-Synthetic Yeast Journal Article

In: Bioengineering (Basel), vol. 8, no. 3, pp. 42, 2021.

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Luo, Z.; Yu, K.; Xie, S.; Monti, M.; Schindler, D.; Fang, Y.; Zhao, S.; Liang, Z.; Jiang, S.; Luan, M.; Xiao, C.; Cai, Y.; Dai, J.

Compacting a synthetic yeast chromosome arm Journal Article

In: Genome Biology, vol. 22, no. 5, 2021.

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2020

Torres-Garcia, S.; Pompeo, L.; Eivers, L.; Gaborieau, B.; White, S. A.; Pidoux, A. L.; Kanigowska, P.; Yaseen, I.; Cai, Y.; Allshire, R. C.

SpEDIT: A fast and efficient CRISPR/Cas9 method for fission yeast Journal Article

In: Wellcome Open Research, vol. 5, pp. 274, 2020.

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Dai, J.; Boeke, J. D.; Luo, Z.; Jiang, S.; Cai, Y.

Sc3.0: revamping and minimizing the yeast genome Journal Article

In: Genome Biology, vol. 21, no. 205, 2020.

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Luo, Z.; Hoffmann, S. A.; Jiang, S.; Cai, Y.; Dai, J.

Probing eukaryotic genome functions with synthetic chromosomes Journal Article

In: Experimental Cell Research, vol. 390, no. 1, pp. 111936, 2020.

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MacKay, M. J.; Hooker, A. C.; Afshinnekoo, E.; Salit, M.; Kelly, J.; Feldstein, J. V.; Haft, N.; Schenkel, D.; Nambi, S.; Cai, Y.; Zhang, F.; Church, G.; Dai, J.; Wang, C. L.; Levy, S.; Huber, J.; Ji, H. P.; Kriegel, A.; Wyllie, A. L.; Mason, C. E.

The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing Journal Article

In: Nature Biotechnology, vol. 38, pp. 1021–1024, 2020.

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Swidah, R.; Auxillos, J.; Liu, W.; Jones, S.; Chan, T. F.; Dai, J.; Cai, Y.

SCRaMbLE-in: A Fast and Efficient Method to Diversify and Improve the Yields of Heterologous Pathways in Synthetic Yeast Book Section

In: DNA Cloning and Assembly, vol. 2205, pp. 305–327, 2020.

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Zhao, Y.; Yao, Z.; Ploessl, D.; Ghosh, S.; Monti, M.; Schindler, D.; Gao, M.; Cai, Y.; Yang, C.; Qiao, M.; Cao, M.; Shao, Z.

Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories Journal Article

In: ACS Synthetic Biology, vol. 9, no. 7, pp. 1736–1752, 2020.

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2019

Auxillos, J. Y.; Garcia-Ruiz, E.; Jones, S.; Li, T.; Jiang, S.; Dai, J.; Cai, Y.

Multiplex Genome Engineering for Optimizing Bioproduction in Saccharomyces cerevisiae Journal Article

In: Biochemistry, vol. 58, no. 11, pp. 1492–1500, 2019.

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

Building a global alliance of biofoundries Journal Article

In: Nature Communications, vol. 10, pp. 2040, 2019.

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Jones, S.; Martella, A.; Cai, Y.

EMMA assembly explained: A step-by-step guide to assemble synthetic mammalian vectors Book Chapter

In: vol. 617, Chapter 18, pp. 463–493, 2019.

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Lin, Y.; Zou, X.; Zheng, Y.; Cai, Y.; Dai, J.

Improving Chromosome Synthesis with a Semiquantitative Phenotypic Assay and Refined Assembly Strategy Journal Article

In: ACS Synthetic Biology, vol. 8, no. 10, pp. 2203–2211, 2019.

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2018

Akhtar, M. K.; Vijay, D.; Umbreen, S.; McLean, C. J.; Cai, Y.; Campopiano, D. J.; J.Loake, G.

Hydrogen Peroxide-Based Fluorometric Assay for Real-Time Monitoring of SAM-Dependent Methyltransferases Journal Article

In: Frontiers in Bioengineering and Biotechnology, vol. 6, pp. 146, 2018.

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Schindler, D.; Dai, J.; Cai, Y.

Synthetic genomics: a new venture to dissect genome fundamentals and engineer new functions Journal Article

In: Current Opinion in Chemical Biology, vol. 46, pp. 56–62, 2018.

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Garcia-Ruiz, E.; Auxillos, J.; Li, T.; Dai, J.; Cai, Y.

YeastFab: High-Throughput Genetic Parts Construction, Measurement, and Pathway Engineering in Yeast Journal Article

In: Methods in Enzymology, vol. 608, pp. 277–306, 2018.

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Li, T.; Chen, X.; Cai, Y.; Dai, J.

Artificial Protein Scaffold System (AProSS): An efficient method to optimize exogenous metabolic pathways in Saccharomyces cerevisiae Journal Article

In: Metabolic Engineering, vol. 49, pp. 13–20, 2018.

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

Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods Journal Article

In: Nature Communications, vol. 9, pp. 1936, 2018.

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Luo, Z.; Wang, L.; Wang, Y.; Zhang, W.; Guo, Y.; Shen, Y.; Jiang, L.; Wu, Q.; Zhang, C.; Cai, Y.; Dai, J.

Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES Journal Article

In: Nature Communications, vol. 9, pp. 1930, 2018.

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Luo, Z.; Yang, Q.; Geng, B.; Jiang, S.; Yang, S.; Li, X.; Cai, Y.; Dai, J.

Whole genome engineering by synthesis Journal Article

In: Science China Life Sciences, vol. 61, no. 12, pp. 1515–1527, 2018.

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2017

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

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus Journal Article

In: ACS Synthetic Biology, vol. 6, no. 12, pp. 2273–2280, 2017.

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Dai, J.; Cai, Y.; Yuan, Y.; Yang, H.; Boeke, J. D.

Whole genome synthesis: from poliovirus to synthesis yeast Journal Article

In: Quantitative Biology, vol. 5, iss. 1, pp. 105–109, 2017.

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

3D organization of synthetic and scrambled chromosomes Journal Article

In: Science, vol. 355, no. 6329, 2017.

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

Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond Journal Article

In: Science, vol. 355, no. 6329, 2017.

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

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome Cover Journal Article

In: Science, vol. 355, no. 6329, 2017.

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

Bug mapping and fitness testing of chemically synthesized chromosome X Journal Article

In: Science, vol. 353, no. 6329, 2017.

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

"Perfect" designer chromosome V and behavior of a ring derivative Journal Article

In: Science, vol. 355, no. 6329, 2017.

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

Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae Journal Article

In: Proceedings of the National Academy of Sciences, vol. 114, pp. 1470– 1479, 2017.

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Cai, Y.; Dai, J.

Methods to Synthesize Large DNA Fragments for a Synthetic Yeast Genome Journal Article

In: Cold Spring Harbor Protocols, vol. 2017, no. 3, 2017.

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Jia, B.; Qi, H.; Li, B. Z.; Pan, S.; Liu, D.; Liu, H.; Cai, Y.; Yuan, Y. J.

Orthogonal Ribosome Biofirewall Journal Article

In: ACS Synthetic Biology, vol. 6, no. 11, pp. 2108–2117, 2017.

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Liu, W.; Tuck, L. R.; Wright, J. M.; Cai, Y.

Using Purified Tyrosine Site-Specific Recombinases In Vitro to Rapidly Construct and Diversify Metabolic Pathways Journal Article

In: Methods in Molecular Biology, vol. 1642, pp. 285–302, 2017.

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Martella, A.; Matjusaitis, M.; Auxillos, J.; Pollard, S. M.; Cai, Y.

EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors Journal Article

In: ACS Synthetic Biology, vol. 6, no. 7, pp. 1380–1392, 2017.

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

Design of a synthetic yeast genome Journal Article

In: Science, vol. 355, no. 6329, pp. 1040–1044, 2017.

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

Design and chemical synthesis of eukaryotic chromosomes Journal Article

In: Chemical Society Reviews, vol. 46, pp. 7191–7207, 2017.

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

Engineering the ribosomal DNA in a megabase synthetic chromosome Journal Article

In: Science, vol. 355, no. 6329, 2017.

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Yuan, T.; Guo, Y.; Dong, J.; Li, T.; Zhou, T.; Sun, K.; Zhang, M.; Wu, Q.; Xie, Z.; Cai, Y.; Cao, L.; Dai, J.

Construction, characterization and application of a genome-wide promoter library in Saccharomyces cerevisiae Journal Article

In: Frontiers of Chemical Science and Engineering, vol. 11, iss. 1, pp. 107–116, 2017.

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2016

Ellis, T.; Cai, Y.

Synthetic Biology in Europe Journal Article

In: ACS Synthetic Biology, vol. 5, no. 10, pp. 1033, 2016.

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

GENOME ENGINEERING. The Genome Project-Write Journal Article

In: Science, vol. 353, no. 6329, pp. 126–127, 2016.

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Kanigowska, P.; Shen, Y.; Zheng, Y.; Rosser, S.; Cai, Y.

Smart DNA Fabrication Using Sound Waves: Applying Acoustic Dispensing Technologies to Synthetic Biology Journal Article

In: Journal of Laboratory Automation, vol. 21, no. 1, pp. 49–56, 2016.

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Martella, A.; Pollard, S. M.; Dai, J.; Cai, Y.

Mammalian Synthetic Biology: Time for Big MACs Journal Article

In: ACS Synthetic Biology, vol. 5, no. 10, pp. 1040–1049, 2016.

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Qin, Y.; Tan, C.; Lin, J.; Qin, Q.; He, J.; Wu, Q.; Cai, Y.; Chen, Z.; Dai, J.

EcoExpress-Highly Efficient Construction and Expression of Multicomponent Protein Complexes in Escherichia coli Journal Article

In: ACS Synthetic Biology, vol. 5, no. 11, pp. 1239–1246, 2016.

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

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes Journal Article

In: Genome Research, vol. 26, no. 1, pp. 36–49, 2016.

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Walker, R. S.; Cai, Y.

The Fifth Annual Sc2.0 and Synthetic Genomes Conference: Synthetic Genomes in High Gear Journal Article

In: ACS Synthetic Biology, vol. 5, no. 9, pp. 920–922, 2016.

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2015

Agmon, N.; Mitchell, L. A.; Cai, Y.; Ikushima, S.; Chuang, J.; Zheng, A.; Choi, W. J.; Martin, J. A.; Caravelli, K.; Stracquadanio, G.; Boeke, J. D.

Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units Journal Article

In: ACS Synthetic Biology, vol. 4, no. 7, pp. 853–859, 2015.

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Cai, Y.; Agmon, N.; Choi, W. J.; Ubide, A.; Stracquadanio, G.; Caravelli, K.; Hao, H.; S.Bader, J.; Boeke, J. D.

Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes Journal Article

In: Proceedings of the National Academy of Sciences, vol. 112, no. 6, pp. 1803–1808, 2015.

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

YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae Journal Article

In: Nucleic Acids Research, vol. 43, no. 13, pp. e88, 2015.

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

Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae Journal Article

In: Nucleic Acids Research, vol. 43, no. 13, pp. 6620–6630, 2015.

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

SBOL Visual: A Graphical Language for Genetic Designs Journal Article

In: vol. 13, no. 12, pp. e1002310, 2015.

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2014

Liao, C.; Cai, Y.

Towards Modeling Automation for Synthetic Biology Book Chapter

In: Kulkarni, V. V>; Stan, G. -B.; Raman, K. (Ed.): A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems, pp. 201–217, 2014.

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Scher, E.; Luo, Y.; Berliner, A. J.; Quinn, J.; Olguin, C.; Cai, Y.

GenomeCarver: harvesting genetic parts from genomes to support biological design automation Conference

International Workshop on BioDesign Automation 2014, 2014.

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

Total synthesis of a functional designer eukaryotic chromosome Journal Article

In: Science, vol. 344, no. 6179, pp. 55–58, 2014.

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Cai, Y.; Ellis, T.

The Sixth International Meeting on Synthetic Biology (SB6.0) special issue editorial Journal Article

In: ACS Synthetic Biology, vol. 3, no. 3, pp. 107, 2014.

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Trubitsyna, M.; Michlewski, G.; Cai, Y.; Elfick, A.; French, C. E.

PaperClip: rapid multi-part DNA assembly from existing libraries Journal Article

In: Nucleic Acids Res, vol. 42, no. 20, pp. e154, 2014.

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2013

Mitchell, L. A.; Cai, Y.; Taylor, M.; Noronha, A. M.; Chuang, J.; Dai, L.; Boeke, J. D.

Multichange isothermal mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA Journal Article

In: ACS Synthetic Biology, vol. 2, no. 8, pp. 473–477, 2013.

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Wilson, M. L.; Cai, Y.; Hanlon, R.; Taylor, S.; Chevreux, B.; Setubal, J. C.; Tyler, B. M.; Peccoud, J.

Sequence verification of synthetic DNA by assembly of sequencing reads Journal Article

In: Nucleic Acids Research, vol. 41, no. 1, pp. e25, 2013.

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2011

Beal, J.; Phillips, A.; Densmore, D.; Cai, Y.

High-Level Programming Languages for Biomolecular Systems Book Chapter

In: Koeppl, H.; Setti, G.; di Bernardo, M.; Densmore, D. (Ed.): Design and Analysis of Biomolecular Circuits, 2011.

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Cai, Y.; Boeke, J. D.

Genome remodeling Journal Article

In: Nature Biotechnology, vol. 29, no. 9, pp. 807–808, 2011.

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2010

Cai, Y.; Wilson, M. L.; Peccoud, J.

GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs Journal Article

In: Nucleic Acids Research, vol. 38, no. 8, pp. 2637–2644, 2010.

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2009

Cai, Y.; Lux, M. W.; Adam, L.; Peccoud, J.

Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars Journal Article

In: PLoS Computational Biology, vol. 5, no. 10, 2009.

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Czar, M. J.; Cai, Y.; Peccoud, J.

Writing DNA with GenoCAD Journal Article

In: Nucleic Acids Research, vol. 37, pp. W40–W47, 2009.

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2008

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

Targeted development of registries of biological parts Journal Article

In: PLoS ONE, vol. 3, no. 7, pp. e2671, 2008.

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2007

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

Arsenic biosenseor: a step further Journal Article

In: BMC Systems Biology, vol. 1, iss. Supplement 1, no. S11, 2007.

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Cai, Y.; Davidson, B.; Ma, H.; French, C.

Modeling the arsenic biosensor system Journal Article

In: BMC Systems Biology, vol. 1, no. P83, 2007.

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Cai, Y.; Hartnett, B.; Gustafsson, C.; Peccoud, J.

A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts Journal Article

In: Bioinformatics, vol. 23, no. 20, pp. 2760–2767, 2007.

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

Development of a Novel Biosensor for the Detection of Arsenic in Drinking Water Journal Article

In: IET Synthetic Biology, vol. 1, no. 40940, pp. 87–90, 2007.

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