Voigt Lab

2018

Segall-Shapiro T.H., Sontag E.D., & Voigt C.A. (2018)
Engineered promoters enable constant gene expression at any copy number in bacteria.
Nature Biotechnology, DOI: 10.1038/nbt.4111

Cox R.S., Madsen C., McLaughlin J., Nguyen T., Roehner N., Bartley B., Bhatia S., Bissell M., Clancy K., Gorochowski T., Grünberg R., Luna A., Le Novere N., Pocock M., Sauro H., Sexton J.T., Stan G.B., Tabor J.J, Voigt C.A., Zundel Z., Myers C., Beal J., & Wipat A. (2018)
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.
Journal of Integrative Bioinformatics, DOI: 10.1515/jib-2017-0074

Casini A., Chang F.Y., Eluere R., King A., Young E.M., Dudley Q.M., Karim A., Pratt K., Bristol C., Forget A., Ghodasara A., Warden-Rothman R., Gan R., Cristofaro A., Espah Borujeni A., Ryu M.H., Li J., Kwon Y.C., Wang H., Tatsis E., Rodriguez-Lopez C., O'Connor S., Medema M.H., Fischbach M., Jewett M.C., Voigt C.A., & Gordon D.B. (2018)
A pressure test to make 10 molecules in 90 days: External evaluation of methods to engineer biology.
Journal of the American Chemical Society, DOI: 10.1021/jacs.7b13292

Liu C.C., Jewett M.C., Chin J.W., & Voigt C.A. (2018)
Toward an orthogonal central dogma.
Nature Chemical Biology, DOI: 10.1038/nchembio.2554

2017

Gorochowski T.E., Espah Borujeni A., Park Y., Nielsen A.A.K., Zhang J., Der B.S., Gordon D.B., & Voigt C.A. (2017)
Genetic circuit characterization and debugging using RNA-seq.
Molecular Systems Biology, DOI: 10.15252/msb.20167461

Bhatia S.P., Smanski M.J., Voigt C.A., & Densmore D.M. 2017)
Genetic Design via Combinatorial Constraint Specification.
ACS Synthetic Biology, DOI: 10.1021/acssynbio.7b00154

Ghodasara A., & Voigt C.A. (2017)
Balancing gene expression without library construction via a reusable sRNA pool.
Nucleic Acids Research, DOI: 10.1093/nar/gkx530

Fernandez-Rodriguez J., Moser F., Song M., & Voigt C.A. (2017)
Engineering RGB color vision into Escherichia coli.
Nature Chemical Biology, DOI: 10.1038/nchembio.2390

Song M., Sukovich D.J., Ciccarelli L., Mayr J., Fernandez-Rodriguez J., Mirsky E.A., Tucker A.C., Gordon D.B., Marlovits T.C., & Voigt C.A. (2017)
Control of type III protein secretion using a minimal genetic system.
Nature Communications, DOI: 10.1038/ncomms14737

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: 10.1016/j.cell.2016.12.021

2016

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

2015

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

2014

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.

2013

*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.

2012

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.

2011

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.

2010

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.

2009

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.

2008

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.

2007

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

2006

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.

2005

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.

2004

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.

2003

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.

2002

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.

2001

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.

2000

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.

1997

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