Voigt Lab


Burén S., Young E.M., Sweeny E.A., López-Torrejón G., Veldhuizen M., Voigt C.A., & Rubio L.M. (2016).
Formation of Nitrogenase NifDK Tetramers in the Mitochondria of Saccharomyces cerevisiae.
ACS Synthetic Biology, DOI: 10.1021/acssynbio.6b00371

Guo C.J., Chang F.Y., Wyche T.P., Backus K.M., Acker T.M., Funabashi M., Taketani M., Donia M.S., Nayfach S., Pollard K.S., Craik C.S., Cravatt B.F., Clardy J., Voigt C.A., & Fischbach M.A. (2017).
Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.
Cell, DOI: http://dx.doi.org/10.1016/j.cell.2016.12.021


Woodruff L.B., Gorochowski T.E., Roehner N., Mikkelsen T.S., Densmore D., Gordon D.B., Nicol R., & Voigt C.A. (2016).
Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration.
Nucleic Acids Research, DOI: 10.1093/nar/gkw1226

Der B.S., Glassey E., Bartley B.A., Enghuus C., Goodman D.B., Gordon D.B., Voigt C.A., & Gorochowski T.E. (2016).
DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data.
ACS Synthetic Biology, DOI: 10.1021/acssynbio.6b00252

Fernández-Rodríguez, & Voigt C.A. (2016).
Post-translational control of genetic circuits using Potyvirus proteases.
Nucleic Acids Research, DOI: 10.1093/nar/gkw537

Elbaz J., Yin P., & Voigt C.A. (2016).
Genetic encoding of DNA nanostructures and their self-assembly in living bacteria.
Nature Communications, DOI: 10.1038/ncomms11179

Mus F., Crook M.B., Garcia K., Garcia Costas A., Geddes B.A., Kouri E.D., Paramasivan P., Ryu MH., Oldroyd G.E., Poole P.S., Udvardi M.K., Voigt C.A., Ané J.M., & Peters J.W. (2016).
Symbiotic Nitrogen Fixation and Challenges to Extending it to Non-Legumes.
Applied Environmental Microbiology, DOI: 10.1128/AEM.01055-16

Roehner N., Young E., Voigt C.A., Gordon D.B., & Densmore D. (2016).
Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems.
ACS Synthetic Biology, DOI: 10.1021/acssynbio.5b00232

Nielsen A.A.K., Der B.S., Shin J., Vaidyanathan P., Paralanov V., Strychalski E.A., Ross D., Densmore D., & Voigt C.A. (2016).
Genetic circuit design automation.
Science, DOI: 10.1126/science.aac7341

Smanski M.J., Zhou H., Claesen J., Shen B., Fischbach M.A., & Voigt C.A. (2016).
Synthetic biology to access and expand nature's chemical diversity.
Nature Reviews Microbiology, DOI: 10.1038/nrmicro.2015.24

Brophy, J.A., & Voigt, C.A. (2016).
Antisense transcription as a tool to tune gene expression.
Molecular Systems Biology, DOI: 10.15252/msb.20156540


Patrick, W.G., Nielsen, A.A.K., Keating, S.J., Levy, T.J., Wang, C.-W., Rivera, J.J., Mondragon-Palomino, O., Carr, P.A., Voigt, C.A., Oxman, N., & D.S. Kong (2015).
DNA Assembly in 3D Printed Fluidics.
PLOS ONE, DOI: 10.1371/journal.pone.0143636

Fernández-Rodríguez, J., Yang, L., Gorochowski, T.E., Gordon, B., & C.A. Voigt (2015).
Memory and combinatorial logic based on DNA inversions: dynamics and evolutionary stability.
ACS Synthetic Biology, DOI: 10.1021/acssynbio.5b00170

Zhou, H., Vonk, B., Roubos, J.A., Bovenberg, R.A., & C.A. Voigt (2015).
Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor.
Nucleic Acids Res, doi: 10.1093/nar/gkv1071

*Mimee, M., *Tucker, A., Voigt, C.A. & T.K. Lu (2015).
Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota.
Cell Systems, doi: 10.1016/j.cels.2015.06.001

Caliando, B.J. & C.A. Voigt (2015).
Targeted DNA degradation using a CRISPR device stably carried in the host genome.
Nature Communications, doi: 10.1038/ncomms7989

Geddes, B.A., Ryu, M., Mus, F., Costas, A.G., Peters, J.W., Voigt, C.A., &P. Poole (2015).
Use of plant colonizing bacteria as chassis for transfer of N2-fixation to cereals.
Current Opinion in Biotechnology, doi:10.1016/j.copbio.2015.01.004


Nielsen, A.A.K. &C.A. Voigt (2014).
Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks.
Molecular Systems Biology, doi: 10.15252/msb.20145735

Smanski, M.J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L.B.A., Giannoukos, G., Ciulla, D., Busby, M., Calderon, J., Nicol, R., Gordon, D.B., Densmore, D., &C.A. Voigt (2014).
Functional optimization of gene clusters by combinatorial design and assembly.
Nature Biotechnology, doi: 10.1038/nbt.3063

Stanton, B.C., Siciliano, V., Ghodasara, A.N., Wroblewska, L., Clancy, K., Trefzer, A.C., Chesnut, J., Weiss, R., &C.A. Voigt (2014).
Systematic transfer of prokaryotic sensors and circuits to mammalian cells.
ACS Synthetic Biology, doi: 10.1021/sb5002856

Yang, L., Nielsen, A.A.K., Fernandez-Rodriguez, J., McClune, C.J., Laub, M.T., &C.A. Voigt (2014).
Permanent genetic memory with >1-byte capacity.
Nature Methods, doi: 10.1038/nmeth.3147

Segall-Shapiro, T.H., Meyer, A.J., Ellington, A.D., Sontag, E.D. & C.A. Voigt (2014).
A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase.
Molecular Systems Biology, doi: 10.15252/msb.20145299

Brophy, J.A.N. & C.A. Voigt (2014).
Principles of Genetic Circuit Design.
Nature Methods, 101: 508-520.

Church, G.M., Elowitz, M.B., Smolke, C.D., Voigt, C.A., & R. Weiss (2014).
Realizing the potential of synthetic biology.
Nature Reviews Molecular Cell Biology, 15: 289-294..

Stanton, B.C., Nielsen, A.A.K., Tamsir, A., Clancy, K., Peterson, T., & C.A. Voigt (2014).
Genomic mining of prokaryotic repressors for orthogonal logic gates.
Nature Chemical Biology, 10: 99-105.


*Nielsen, A.A.K., *Segall-Shapiro, T.H., & C.A. Voigt (2013).
Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression.
Current Opinion in Chemical Biology, 17(6): 878-892.

*Rhodius, V.A., *Segall-Shapiro, T.H., Sharon, B.D., Ghodasara, A., Orlova, E., Tabakh, H., Burkhardt, D.H., Clancy, K., Peterson, T.C., Gross, C.A., & C.A. Voigt (2013).
Design of orthogonal genetic switches based on a crosstalk map of sigmas, anti-sigmas, and promoters.
Molecular Systems Biology, 9(1): 1-13.

*Moser, F., *Horwitz, A., Chen, J., Lim, W.A., & C.A. Voigt (2013).
A genetic sensor for strong methylating compounds.
ACS Synthetic Biology, 2(10): 614-614.

Chen, Y.-J., Liu, P., Nielsen, A.A.K., Brophy, J.A.N., Clancy, K., Peterson, T., & C.A. Voigt (2013).
Characterization of 582 natural and synthetic terminators and quantification of their design constraints.
Nature Methods, 10: 659-664.


Chen, Y.-J., Clancy, K., & C.A. Voigt (2012).
"Biophysical Models to Predict the Function of Genetic Parts."
in Quantitative Biology From Molecular to Cellular Systems, ed. Michael E. Wall, Taylor & Francis.

Lou, C., Stanton, B.C., Chen, Y.-J., Munsky, B., & C.A. Voigt (2012).
Ribozyme-based insulator parts buffer synthetic circuits from genetic context.
Nature Biotechnology, 30: 1137-1142.

Moon, T.S., Lou, C., Tamsir, A., Stanton, B.C., & C.A. Voigt (2012).
Genetic programs constructed from layered logic gates in single cells.
Nature, 491: 249-253.

Moser, F., Broers, N., Hartmans, S., Tamsir, A., Kerkman, R., Roubos, J.A., Bovenberg, R., & C.A. Voigt (2012).
Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors.
ACS Synth. Biol., 1(11): 555-564.

Temme, K., Hill, R., Segall-Shapiro, T.H., Moser, F., & C.A. Voigt (2012).
Modular control of multiple pathways using engineered orthogonal T7 polymerases
Nucleic Acids Research, 40(17): 8773-8781.

*Temme, K., *Zhao, D., & C.A. Voigt (2012).
Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca.
Proc. Natl. Acad. Sci., 109(18): 7085-7090.


Clarke E.J. & C.A. Voigt (2011).
Characterization of combinatorial patterns generated by multiple two-component sensors in E. coli that respond to many stimuli.
Biotechnology & Bioengineering, 108(3): 666-675.

Moon, T.S., Clarke E.J., Groban, E.S., Tamsir, A., Clark, R.M., Eames, M., Kortemme, T., & C.A.Voigt (2011).
Construction of a Genetic Multiplexer to Toggle between Chemosensory Pathways in Escherichia coli.
J. Molec. Biol., 406(2): 245-227.

Tabor J.J., Levskaya A. & C.A. Voigt (2011).
Multichromatic control of gene expression in Escherichia coli.
Journal of Molecular Biology, 405(2): 315-324.

Tamsir A., Tabor J.J. & C.A. Voigt (2011).
Robust multicellular computing using genetically encoded NOR gates and chemical 'wires.'
Nature, 469(7329): 212-215.

Toettcher, J.E., Voigt, C.A., Weiner, O.D. & W.A. Lim (2011).
The promise of optogenetics in cell biology: interrogating molecular circuits in space and time.
Nature Methods, 8(1): 35-38.


Clancy, K., & C.A. Voigt (2010).
Programming cells: towards an automated 'Genetic Compiler'.
Curr. Opin. Biotechnol. 21(4):572-81.

Fischbach, M., & C.A. Voigt (2010).
Prokaryotic gene clusters: a rich toolbox for synthetic biology.
Biotechnol J., 5(12):1277-96.

Widmaier D. & C.A. Voigt (2010).
Quantification of the physiochemical constraints on the export of spider silk proteins by Salmonella type III secretion.
Microbial Cell Factories, 9: 78.


Bayer, T.S., Widmaier, D.M., Temme, K., Mirsky, E.A., Santi, D.V., & C.A. Voigt (2009).
Microbial conversion of biomass to methyl halides.
JACS, 131 (18): 6508-6515.

Groban, E.S., Clarke, E.J., Salis, H., Miller, S.M., & C.A. Voigt (2009).
Kinetic buffering of crosstalk between bacterial two-component sensors.
Journal of Molecular Biology, 390 (3): 380-393.

Levskaya, A., Weiner, O.D., Lim, W.A., & C.A. Voigt (2009).
Spatiotemporal control of cell signalling using a light-switchable protein interaction.
Nature, 461(7266):997-1001.

Salis, H., Tamsir, A. & C.A. Voigt (2009).
Engineering Bacterial Signals and Sensors.
Collin M, Schuch R (eds): Bacterial Sensing and Signaling. Contrib Microbiol. Basel, Karger, 16: 194-225.

Salis, H., Mirsky, E. & C.A. Voigt (2009).
Automated design of synthetic ribosome binding sites to control protein expression.
Nature Biotechnology, 27(10):946-50.

Tabor, J.J., Salis, H., Simpson, Z.B., Chevalier, A.A., Levskaya, A., Marcotte, E., Voigt, C.A., & Ellington, A.D. (2009).
A Synthetic Genetic Edge Detection Program.
Cell, 137 (7): 1271-1281.

Widmaier, D., Tullman-Ercek, D., Mirsky, E., Hill, R., Govindarajan, S., Minshull, J., & C.A.Voigt (2009).
Engineering the Salmonella type III secretion system to export spider silk monomers.
Molecular Systems Biology, 5: 309.


Temme, K., Salis, H., Tullman-Erck, D. Levskaya, A., Hong, S-H., & C.A.Voigt (2008).
Induction and relaxation dynamics of the regulatory network controlling the type III secretion system encoded within Salmonella pathogenicity island.
Journal of Molecular Biology, 377 (1): 47-61.

Voigt, C.A. (2008).
Life from information.
Nature Methods, 5(1):27-8.


Anderson, JC, Voigt, CA, & Arkin, AP. (2007).
Environmental signal integration by a modular AND gate.
Molecular Systems Biology, 3: 133.


Anderson, J. C., Clarke, E. J., Arkin, A. P., & Voigt, C. A. (2006)
Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria.
Journal of Molecular Biology, 355(4): 619-627.

Voigt C.A. (2006).
Genetic parts to program bacteria.
Curr Opin Biotechnol. 17(5):548-57.


Levskaya, A., Chevalier, A. A., Tabor, J. J., Simpson, Z. B., Lavery, L. A., Levy, M., Davidson, E. A., Scouras, A., Ellington, A. D., Marcotte, E. M., & Voigt, C. A. (2005).
Synthetic biology: Engineering Escherichia coli to see light.
Nature, 438: 441-442.

Voigt, C. A., and Keasling, J. D. (2005).
Programming Cellular Function. (meeting review)
Nature Chemical Biology, 1: 304-307.

Voigt C. A., Wolf D. M., & Arkin A. P. (2005).
The Bacillus subtilis sin operon: An evolvable network motif.
Genetics, 169 (3): 1187-1202.


Otey C. R., Silberg J. J., Voigt C. A., Endelman J. B., Bandara G., & Arnold F. H.
Functional evolution and structural conservation in chimeric cytochromes P450: Calibrating a structure-guided approach.
Chemistry & Biology, 11 (3): 309-318.


Meyer, M. M., Silberg, J. J., Voigt, C. A., Endelman, J. B., Mayo, S. L., Wang, Z-G., & Arnold, F. H.
Library analysis of SCHEMA-guided protein recombination.
Protein Science, 12: 1686-1693.


Bolon, D. N., Voigt, C. A., & Mayo, S. L.
De novo design of biocatalysts.
Curr. Opin. Chem. Biol., 6: 125-129.

Voigt, C. A., Martinez, C., Mayo, S.L., Wang, Z-.G., & Arnold, F.H. (2002)
Protein building blocks preserved by recombination.
Nature Structural Biology, 9: 553-558.

Voigt, C. A.
Computationally optimizing the directed evolution of proteins.
Thesis, California Institute of Technology.


Voigt, C. A., Mayo, S.L., Arnold, F.H., & Wang, Z-.G.
Computational method to reduce the search space of directed protein evolution.
Proc. Natl. Acad. Sci. USA, 98: 3778-3783.

Voigt, C. A., Mayo, S.L., Arnold, F.H., & Wang, Z-.G.
Computationally focusing the directed evolution of proteins.
J. Cellular Biochem., Supp 37: 58-63.


Voigt, C. A., Gorden, D. B., & Mayo, S. L.
Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design.
Journal of Molecular Biology, 299: 789-803.


Voigt, C. A., & Ziff, R. M.
Epidemic analysis of the oxygen poisoning critical point in the Ziff- Gulari-Barshad model.
Physical Review E, 56: R6241-R6244.

Voigt, C. A., & Ziff, R. M.
Dynamic behavior of the monomer-monomer surface reaction model with adsorbate interactions.
Journal of Chemical Physics, 107: 7397-7401.

Sythetic Biology Center at MIT MIT Department of Bioengineering MIT
Synthetic Biology Center @ MIT Department of Biological Engineering Massachusetts Institute of Technology