Cailab

To close the gap between design and fabrication in synthetic biology, we are proposing to automate the DNA synthesis process, utilizing liquid handling robots and other laboratory automation equipment.

Moreover, we are part of the international synthetic yeast consortium (Sc2.0, www.syntheticyeast.org), which aims to re-design and synthesize a designer yeast genome de novo

THE LAB

Postdoctoral research associate

Lab technician

Aileen Greig

Dr. Andrea Martella

Dr. Dariusz Abramczyk

Postdoctoral research associate

PhD student

Postdoctoral research associate

Dr. Eva Garcia-Ruiz

Chantal Yue Shen

Emily Scher

PhD student

PhD student

Jamie Auxillos

Katarina Jonsson

Olivia Wei Liu

PhD student

PhD student

Paulina Kanigowska

Roy Walker

PhD student

Cailab

Synthetic Genomics

P

ABOUT PATRICK CAI

Patrick is Chancellor's Fellow at the University of Edinburgh, overseeing a research group of 18 researchers. He is the international coordinator of the Synthetic Yeast Genome Project, which involves over 10 top universities across the world and a research portfolio of $20M. His research interests centre around creating synthetic yeast genomes, developing computer aided DNA design and automated DNA synthesis.

The Lab

Publications

Contact

About

CONTACT US

yizhi.cai@ed.ac.uk

+44 (0) 131 651 3348

Daniel Rutherford Building G.24
School of Biological Sciences
University of Edinburgh
The King's Buildings
Edinburgh EH9 3BF

PUBLICATIONS

Sc2.0 project

Synthetic Chromosomes

DNA design

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NEWS & TALKS

News & Talks

Cai Y, Wilson ML, Peccoud J (2010) GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic acids research 38: 2637-2644.

Cai Y (2010) GenoCAD: linguistic approaches to synthetic biology: Virginia Polytechnic Institute and State University.

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Czar MJ, Cai Y, Peccoud J (2009) Writing DNA with GenoCAD™. Nucleic acids research 37: W40-W47.

Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS computational biology 5: e1000529.

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Peccoud J, Cai Y (2008) SOFTWARE FOR DESIGN AND VERIFICATION OF SYNTHETIC GENETIC CONSTRUCTS. US Patent App. 12/058,712.

Peccoud J, Blauvelt MF, Cai Y, Cooper KL, Crasta O, et al. (2008) Targeted development of registries of biological parts. PLoS One 3: e2671.

French C, Nicholson J, Bizzari F, Aleksic J, Cai Y, et al. (2007) Arsenic biosenseor: a step further. BMC Systems Biology 1: S11.

Cai Y, Hartnett B, Gustafsson C, Peccoud J (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23: 2760-2767.

Cai Y, Davidson B, Ma H, French C (2007) Modeling the arsenic biosensor system. BMC Systems Biology 1: P83.

Aleksic J, Bizzari F, Cai Y, Davidson B, De Mora K, et al. (2007) Development of a novel biosensor for the detection of arsenic in drinking water. IET Synthetic Biology 1: 87-90.

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Cai Y, Boeke JD (2011) Genome remodeling. Nature Biotechnology 29: 807-808.

Beal J, Phillips A, Densmore D, Cai Y (2011) High-level programming languages for biomolecular systems. Design and analysis of biomolecular circuits: Springer New York. pp. 225-252.

Wilson ML, Cai Y, Hanlon R, Taylor S, Chevreux B, et al. (2012) Sequence verification of synthetic DNA by assembly of sequencing reads. Nucleic acids research. (co-First author)

Galdzicki M, Wilson M, Rodriguez CA, Pocock MR, Oberortner E, et al. (2012) Synthetic Biology Open Language (SBOL) Version 1.1. 0.

Boeke J, Mitchell L, Cai Y, Stracquadanio G, Chuang J, et al. (2012) Yeast Golden Gate: Standardized Assembly of S. cerevisiae Transcriptional Units.

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Mitchell LA, Cai Y, Taylor M, Noronha AM, Chuang J, et al. (2013) Multichange Isothermal Mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA. ACS synthetic biology 2: 473-477. (co-First author)

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Trubitsyna M, Michlewski G, Cai Y, Elfick A, French CE (2014) PaperClip: rapid multi-part DNA assembly from existing libraries. Nucleic acids research.

Scher E, Luo Y, Berliner A, Olguin C, Cai Y (2014) GenomeCarver: harvesting genetic parts from genomes to support biological design automation. 6th International Workshop on Bio-Design Automation. (Corresponding Author)

Liao C, Cai Y (2014) Towards Modeling Automation for Synthetic Biology. A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems: Springer Netherlands. pp. 201-217. (Corresponding Author)

Cai Y, Ellis T (2014) The Sixth International Meeting on Synthetic Biology (SB6. 0) Special Issue Editorial. ACS Synthetic Biology 3: 107-107. (Corresponding Author)

Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, et al. (2014) Total synthesis of a functional designer eukaryotic chromosome. Science 344: 55-58.

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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., et al. (2015) SBOL Visual: A Graphical Language for Genetic Designs. PLoS Biology, 13, e1002310.

Shen,Y., Stracquadanio,G., Wang,Y., Yang,K., Mitchell,L.A., Xue,Y., Cai,Y., Chen,T., Dymond,J.S., Kang,K., et al. (2015) SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Research, 10.1101/gr.193433.115.

Kanigowska P, Shen Y, Zheng Y, Rosser S, Cai Y (2015) Smart DNA Fabrication Using Sound Waves: Applying Acoustic Dispensing Technologies to Synthetic Biology. Journal of the Association for Laboratory Automation. (Corresponding Author)

Guo Y, Dong J, Zhou T, Auxillos J, Li T, et al. (2015) YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae. Nucleic Acids Res. (Corresponding Author)

Mitchell LA, Chuang J, Agmon N, Khunsriraksakul C, Phillips NA, et al. (2015) Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae. Nucleic Acids Res.

Agmon N, Mitchell LA, Cai Y, Ikushima S, Chuang J, et al. (2015) Yeast Golden Gate (yGG) for efficient assembly of S. cerevisiae transcription units. ACS Synth Biol.

Cai Y, Agmon N, Choi WJ, Ubide A, Stracquadanio G, et al. (2015) Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes. Proceedings of the National Academy of Sciences. (Corresponding Author)