2024
The de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging Journal Article
In: Nature Communications, vol. 15, iss. 10139, 2024.
The design and engineering of synthetic genomes Journal Article
In: Nature Reviews Genetics, 2024.
Challenges to rhizobial adaptability in a changing climate: Genetic engineering solutions for stress tolerance Journal Article
In: Microbiological Research, vol. 288, iss. 127886, 2024.
Build-A-Genome and the “awesome power of undergraduates” Journal Article
In: Genetics, vol. 227, iss. 4, no. iyae083, 2024.
Yeasty HAC Does the Trick Journal Article
In: GEN Biotechnology, vol. 3, iss. 3, 2024.
Searching for the optimal microbial factory: high-throughput biosensors and analytical techniques for screening small molecules Journal Article
In: Current Opinion in Biotechnology, vol. 87, iss. 103125, 2024.
Methodological advances enabled by the construction of a synthetic yeast genome Journal Article
In: Cell Reports Methods, vol. 4, iss. 4, no. 100761, 2024.
An Efficient Pyrrolysyl-tRNA Synthetase for Economical Production of MeHis-containing Enzymes Journal Article Forthcoming
In: Faraday Discussions, Forthcoming.
When synthetic biology meets medicine Journal Article
In: Life Medicine, vol. 3, iss. 1, no. lnae010, 2024.
High plasticity of ribosomal DNA organization in budding yeast Cover Journal Article
In: Cell Reports, vol. 43, iss. 2, no. 113742, 2024.
Engineering stringent genetic biocontainment of yeast with a protein stability switch Journal Article
In: Nature Communications, vol. 15, iss. 1060, 2024.
Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae Journal Article
In: Nature Communications, vol. 15, iss. 1, no. 770, 2024.
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.
2023
Building a eukaryotic chromosome arm by de novo design and synthesis Journal Article
In: Nature Communications, vol. 14, no. 7886, 2023.
Design, construction, and functional characterization of a tRNA neochromosome in yeast Cover Journal Article
In: Cell, vol. 186, iss. 24, pp. 5237–5253, 2023.
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.
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.
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.
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.
A spotlight on global collaboration in the Sc2.0 yeast consortium Journal Article
In: Cell Genomics, vol. 3, iss. 11, no. 100441, 2023.
Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions Journal Article
In: Cell, 2023.
Cellular Surveillance: DNA-Based Recording to Monitor and Memorize Biological Events Journal Article
In: GEN Biotechnology, vol. 2, no. 3, 2023.
Safety by design: Biosafety and biosecurity in the age of synthetic genomics Journal Article
In: iScience, vol. 26, iss. 3, pp. 106165, 2023.
2022
Engineering stringent genetic biocontainment of yeast with a protein stability switch Journal Article
In: bioRxiv, 2022.
Reconstruct a eukaryotic chromosome arm by de novo design and synthesis Journal Article
In: bioRxiv, 2022.
Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast Journal Article
In: bioRxiv, 2022.
Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements Journal Article
In: bioRxiv, 2022.
Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand Journal Article
In: bioRxiv, 2022.
Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions Journal Article
In: bioRxiv, 2022.
New Opportunities for Genetic Code Expansion in Synthetic Yeast Journal Article
In: Current Opinion in Biotechnology, vol. 75, no. 102691, 2022.
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.
EMMA-CAD: Design Automation for Synthetic Mammalian Constructs Journal Article
In: ACS Synthetic Biology, vol. 11, no. 2, pp. 579–586, 2022.
2021
Compacting a synthetic yeast chromosome arm Journal Article
In: Genome Biology, vol. 22, no. 5, 2021.
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.
2020
The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing Journal Article
In: Nature Biotechnology, vol. 38, pp. 1021–1024, 2020.
In: DNA Cloning and Assembly, vol. 2205, pp. 305–327, 2020.
Sc3.0: revamping and minimizing the yeast genome Journal Article
In: Genome Biology, vol. 21, no. 205, 2020.
SpEDIT: A fast and efficient CRISPR/Cas9 method for fission yeast Journal Article
In: Wellcome Open Research, vol. 5, pp. 274, 2020.
Probing eukaryotic genome functions with synthetic chromosomes Journal Article
In: Experimental Cell Research, vol. 390, no. 1, pp. 111936, 2020.
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.
2019
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.
Building a global alliance of biofoundries Journal Article
In: Nature Communications, vol. 10, pp. 2040, 2019.
Multiplex Genome Engineering for Optimizing Bioproduction in Saccharomyces cerevisiae Journal Article
In: Biochemistry, vol. 58, no. 11, pp. 1492–1500, 2019.
EMMA assembly explained: A step-by-step guide to assemble synthetic mammalian vectors Book Chapter
In: vol. 617, Chapter 18, pp. 463–493, 2019.
2018
Whole genome engineering by synthesis Journal Article
In: Science China Life Sciences, vol. 61, no. 12, pp. 1515–1527, 2018.
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.
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.
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.
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.
Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES Journal Article
In: Nature Communications, vol. 9, pp. 1930, 2018.
YeastFab: High-Throughput Genetic Parts Construction, Measurement, and Pathway Engineering in Yeast Journal Article
In: Methods in Enzymology, vol. 608, pp. 277–306, 2018.
2017
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.
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.
Orthogonal Ribosome Biofirewall Journal Article
In: ACS Synthetic Biology, vol. 6, no. 11, pp. 2108–2117, 2017.
Whole genome synthesis: from poliovirus to synthesis yeast Journal Article
In: Quantitative Biology, vol. 5, iss. 1, pp. 105–109, 2017.
3D organization of synthetic and scrambled chromosomes Journal Article
In: Science, vol. 355, no. 6329, 2017.
Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond Journal Article
In: Science, vol. 355, no. 6329, 2017.
Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome Cover Journal Article
In: Science, vol. 355, no. 6329, 2017.
Bug mapping and fitness testing of chemically synthesized chromosome X Journal Article
In: Science, vol. 353, no. 6329, 2017.
"Perfect" designer chromosome V and behavior of a ring derivative Journal Article
In: Science, vol. 355, no. 6329, 2017.
Methods to Synthesize Large DNA Fragments for a Synthetic Yeast Genome Journal Article
In: Cold Spring Harbor Protocols, vol. 2017, no. 3, 2017.
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.
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.
Design of a synthetic yeast genome Journal Article
In: Science, vol. 355, no. 6329, pp. 1040–1044, 2017.
Design and chemical synthesis of eukaryotic chromosomes Journal Article
In: Chemical Society Reviews, vol. 46, pp. 7191–7207, 2017.
Engineering the ribosomal DNA in a megabase synthetic chromosome Journal Article
In: Science, vol. 355, no. 6329, 2017.
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.
2016
Synthetic Biology in Europe Cover Journal Article
In: ACS Synthetic Biology, vol. 5, no. 10, pp. 1033, 2016.
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.
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.
GENOME ENGINEERING. The Genome Project-Write Journal Article
In: Science, vol. 353, no. 6329, pp. 126–127, 2016.
Mammalian Synthetic Biology: Time for Big MACs Journal Article
In: ACS Synthetic Biology, vol. 5, no. 10, pp. 1040–1049, 2016.
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.
SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes Journal Article
In: Genome Research, vol. 26, no. 1, pp. 36–49, 2016.
2015
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.
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.
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.
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.
SBOL Visual: A Graphical Language for Genetic Designs Journal Article
In: vol. 13, no. 12, pp. e1002310, 2015.
2014
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.
GenomeCarver: harvesting genetic parts from genomes to support biological design automation Conference
International Workshop on BioDesign Automation 2014, 2014.
Total synthesis of a functional designer eukaryotic chromosome Journal Article
In: Science, vol. 344, no. 6179, pp. 55–58, 2014.
The Sixth International Meeting on Synthetic Biology (SB6.0) special issue editorial Cover Journal Article
In: ACS Synthetic Biology, vol. 3, no. 3, pp. 107, 2014.
PaperClip: rapid multi-part DNA assembly from existing libraries Journal Article
In: Nucleic Acids Res, vol. 42, no. 20, pp. e154, 2014.
2013
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.
Sequence verification of synthetic DNA by assembly of sequencing reads Journal Article
In: Nucleic Acids Research, vol. 41, no. 1, pp. e25, 2013.
2011
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.
Genome remodeling Journal Article
In: Nature Biotechnology, vol. 29, no. 9, pp. 807–808, 2011.
2010
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.
2009
Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars Journal Article
In: PLoS Computational Biology, vol. 5, no. 10, 2009.
Writing DNA with GenoCAD Journal Article
In: Nucleic Acids Research, vol. 37, pp. W40–W47, 2009.
2008
Targeted development of registries of biological parts Journal Article
In: PLoS ONE, vol. 3, no. 7, pp. e2671, 2008.
2007
Arsenic biosenseor: a step further Journal Article
In: BMC Systems Biology, vol. 1, iss. Supplement 1, no. S11, 2007.
Modeling the arsenic biosensor system Journal Article
In: BMC Systems Biology, vol. 1, no. P83, 2007.
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.
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.