2023

Lin, G.M.,& Voigt, C.A. (2023)
Design of a redox-proficient Escherichia coli for screening terpenoids and modifying cytochrome P450s
Nature Catalysis https://doi.org/10.1038/s41929-023-01049-5

King, A.M., Zhang, Z., Glassey, E., Siuti, P., Clardy, J. & Voigt, C.A. (2023)
Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra
Nature Microbiology https://doi.org/10.1038/s41564-023-01524-6

Nou, X.A., & Voigt, C.A. (2023)
Sentinel cells programmed to respond to environmental DNA including human sequences
Nature Chemical Biology https://doi.org/10.1038/s41589-023-01431-1

Triassi, A., Fields, B.D., Monahan, C.A., Means, J.M., Park, Y., Doosthosseini, H., Padmakumar, J.P., Isabella, V.M., & Voigt, C.A. (2023)
Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden
Cell Systems https://doi.org/10.1016/j.cels.2023.05.004

Schimunek, J., ... Voigt, C.A., ...Varnek, A. (2023)
A community effort to discover small molecule SARS-CoV-2 inhibitors
ChemRxiv https://doi.org/10.26434/chemrxiv-2023-1d5w8

Park, J.H., Bassalo, M.C., Lin, G-M., Chen, Y., Doosthosseini, H., Schmitz, J., Roubous, J.A., & Voigt, C.A. (2023)
Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis
ACS Synthetic Biology https://doi.org/10.1021/acssynbio.2c00607

Bird, L.J., Leary, D.H., Hervey, J., Compton, J., Phillips, D., Tender, L.M., Voigt, C.A., & Glaven, S.M. (2023)
Marine Biofilm Engineered to Produce Current in Response to Small Molecules
ACS Synthetic Biology https://doi.org/10.1021/acssynbio.2c00417

Levin, I., Liu, M., Voigt, C.A., & Coley, C. (2023)
Merging enzymatic and synthetic chemistry with computational synthesis planning
Nature Communications https://doi.org/10.1038/s41467-022-35422-y

Chemla, Y., Dorfan, Y., Yannai, A., Meng, D., Cao, P., Glaven, S., Gordon, D.B., Elbaz., & Voigt, C.A. (2023)
Parallel engineering of environmental bacteria and performance over years under jungle-simulated conditions
Plos One https://doi.org/10.1371/journal.pone.0278471

2022

Glassey, E., King, A.M., Anderson, D.A., Zhang, Z., & Voigt, C.A. (2022)
Functional expression of diverse post-translational peptide-modifying enzymes in Escherichia coli under uniform expression and purification conditions
PLOS ONE https://doi.org/10.1371/journal.pone.0266488

Haskett, T.L., Paramasivan, P., Mendes, M.D., Green, P., Geddes, B.A., Knights, H.E., Jorrin, B., Ryu, M-H., Brett, P., Voigt, C.A., Oldroyd G.E.D., & Poole, P.S. (2022)
Engineered plant control of associative nitrogen fixation
Proceedings of the National Academy of Sciences https://doi.org/10.1073/pnas.2117465119

Jones, T.S., Oliveira S.M.D., Myers, C.J., Voigt, C.A. & Densmore, D. (2022)
Genetic circuit design automation with Cello 2.0
Nature Protocols https://doi.org/10.1038/s41596-021-00675-2

McBee, R.M., Lucht, M., Mukhitov, N., Richardson, M., Srinivasan, T., Meng, D., Chen, H., Kaufman, A., Reitman, M., Munck, C., Schaak, D., Voigt, C.A. & Wang, H. (2022)
Engineering living and regenerative fungal–bacterial biocomposite structures
Nature Materials https://doi.org/10.1038/s41563-021-01123-y

Vaiana, C.A., Kim, H., Cottet, J., Oai, K., Ge, Z., Conforti, K., King, A.M., Meyer, A.J., Chen, H., Voigt, C.A. & Buie, C. (2022)
Characterizing chemical signaling between engineered “microbial sentinels” in porous microplates
Molecular Systems Biology https://doi.org/10.15252/msb.202110785

Eslami, M., Borujeni, A.E., Eramian, H., Weston, M., Zheng, G., Urrutia, J., Corbet, C., Becker, D., Maschhoff, P., Clowers, K., Cristofaro, A., Doost Hosseini, H., Gordon, D.B., Dorfan, Y., Singer, J., Vaughn, M., Gaffney, N., Fonner, J., Stubbs, J., Voigt, C.A. & Yeung, E. (2022)
Prediction of whole-cell transcriptional response with machine learning
Bioinformatics https://doi.org/10.1093/bioinformatics/btab676

Chen, T., Al-Radhawi, M.A., Voigt, C.A. & Sontag, E.D. (2022)
A synthetic distributed genetic multi-bit counter
iScience https://doi.org/10.1016/j.isci.2021.103526

2021

King, A.M., Anderson, D.A., Glassey, E., Segall-Shapiro, T.H., Zhang, Z., Niquille, D.L., Embree, A.C., Pratt, K., Williams, T.L., Gordon, D.B.,& Voigt, C.A.(2021)
Selection for constrained peptides that bind to a single target protein
Nature Communications https://doi.org/10.1038/s41467-021-26350-4

Anderson, D.A. & Voigt, C.A. (2021)
Competitive dCas9 binding as a mechanism for transcriptional control
Molecular Systems Biology https://doi.org/10.15252/msb.202110512

Becker, M.H., Brophy, J.A.N., Barrett, K., Bronikowski, E., Evans, M., Glassey, E., Kaganer, A.W., Klocke, B., Lassiter, E., Meyer, A.J., Muletz-Wolz, C.R., Fleischer, R.C., Voigt, C.A. & Gatwicke, B.(2021)
Genetically modifying skin microbe to produce violacein and augmenting microbiome did not defend Panamanian golden frogs from disease
ISME Communications https://doi.org/10.1038/s43705-021-00044-w

Pandey, R.P., Casini, A., Voigt, C.A., & Gordon, D.B.(2021)
Four-Step Pathway from Phenylpyruvate to Benzylamine, an Intermediate to the High-Energy Propellant CL-20
ACS Synthetic Biology https://doi.org/10.1021/acssynbio.1c00021

Zhang, J., Hernandez-Gordillo, V., Trapecar, M., Wright, C., Taketani, M., Schneider, K., Chen, W.L.K., Stas, E., Breault, D.T., Carrier, R.L., Voigt, C.A., & Griffith, L.G. (2021)
Coculture of primary human colon monolayer with human gut bacteria
Nature Protocols https://doi.org/10.1038/s41596-021-00562-w

Cha, T-C., Tsedev, U., Ransil, A., Embree, A., Gordon, D.B., Belcher, A.M., & Voigt, C.A. (2021)
Genetic Control of Aerogel and Nanofoam Properties, Applied to Ni–MnO_X Cathode Design
Advanced Functional Materials https://doi.org/10.1002/adfm.202010867

Chang, F.-Y., Siuti, P., Laurent, S., Williams, T., Glassey, E., Sailer, A.W., Gordon, D.B., Hemmerle, H., & Voigt, C.A. (2021)
Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids
Nature Microbiology https://doi.org/10.1038/s41564-021-00910-2

Shao, B., Rammohan, J., Anderson, D.A., Alperovich, N., Ross, D., & Voigt, C.A. (2021)
Single-cell measurement of plasmid copy number and promoter activity
Nature Communications DOI: https://doi.org/10.1038/s41467-021-21734-y

Meng, D., Mukhitov, N., Neitzey, D., Lucht, M., Schaak, D.D.,& Voigt, C.A. (2021)
Rapid and simultaneous screening of pathway designs and chassis organisms, applied to engineered living materials
Metabolic Engineering DOI: https://doi.org/10.1016/j.ymben.2021.01.006

Zhong-Johnson, E.Z.L., Voigt, C.A.,& Sinskey, A.J. (2021)
An absorbance method for analysis of enzymatic degradation kinetics of poly(ethylene terephthalate) films
Nature Scientific Reports DOI: https://doi.org/10.1038/s41598-020-79031-5

Eslami, M., Borujeni, A.E., Doosthosseini, H., Vaughn, M., Eramian, H., Clowers, K., Gordon, D.B., Gaffney, N., Weston, M., Becker, D., Dorfan, Y., Fonner, J., Urrutia, J., Corbet, C., Zheng, G., Stubbs, J., Cristofaro, A., Maschhoff, P., Singer, J., Voigt, C.A., & Yeung, E. (2021)
Prediction of Whole-Cell Transcriptional Response with Machine Learning
bioRxiv DOI: https://doi.org/10.1101/2021.04.30.442142

... Voigt, C.A. ... (2021)
Voices of chemical biology
Nature Chemical Biology DOI: https://doi.org/10.1038/s41589-020-00714-1

2020

Voigt, C.A. (2020)
Synthetic biology 2020–2030: six commercially-available products that are changing our world
Nature Communications DOI: https://doi.org/10.1038/s41467-020-20122-2

Chen, Y., Zhang, S., Young, E.M., Jones, T.S., Densmore, D., & Voigt, C.A. (2020)
Genetic circuit design automation for yeast
Nature Microbiology DOI: https://doi.org/10.1038/s41564-020-0757-2

Furubayashi, M., Wallace, A.K., González, L.M., Jahnke, J.P., Hanrahan, B.M., Payne, A.L., Stratis-Cullum, D.N., Gray, M.T., Liu, H., Rhoads, M.K., & Voigt, C.A. (2020)
Genetic Tuning of Iron Oxide Nanoparticle Size, Shape, and Surface Properties in Magnetospirillum magneticum
Advanced Functional Materials DOI: https://doi.org/10.1002/adfm.202004813

Borujeni, A.E., Zhang, J., Doosthosseini, H., Nielsen, A.A.K., & Voigt, C.A. (2020)
Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage
Nature Communications DOI: https://doi.org/10.1038/s41467-020-18630-2

Yates, M.D., Bird, L.J., Eddie, B.J., Onderko, E.L., Voigt, C.A., & Glaven, S.M. (2020)
Nanoliter scale electrochemistry of natural and engineered electroactive bacteria
Bioelectrochemistry DOI: https://doi.org/10.1016/j.bioelechem.2020.107644

Zhang, J., Huang, Y.-J., Yoon, J.Y., ... Voigt, C.A., Carrier, R.L., Trumper, D.L., & Griffith, L.G.(2020)
Primary Human Colonic Mucosal Barrier Crosstalk with Super Oxygen-Sensitive Faecalibacterium prausnitzii in Continuous Culture
Clinical and Translational Resource and Technology Insights

Fontanarrosa, P., Doosthosseini, H., Borujeni, A.E., Dorfan, Y., Voigt, C.A., & Myers, C. (2020)
Genetic Circuit Dynamics: Hazard and Glitch Analysis
ACS Synthetic Biology DOI: https://doi.org/10.1021/acssynbio.0c00055

Park, Y., Borujeni, A.E., Gorochowski, T.E., Shin, J., & Voigt, C.A.(2020)
Precision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads
Molecular Systems Biology DOI: https://doi.org/10.15252/msb.20209584

Phillips, D.A., Bird, L.J., Eddie, B.J., Yates, M.D., Tender, L.M., Voigt, C.A., & Glaven, S.M. (2020)
Activation of Protein Expression in Electroactive Biofilms
ACS Synthetic Biology DOI: https://doi.org/10.1021/acssynbio.0c00278

Burrows, C.J., Huang, J., Wang, S., ... Voigt, C.A., ... Laskin, J. (2020)
Confronting Racism in Chemistry Journals
ACS Synthetic Biology DOI: https://doi.org/10.1021/acsanm.0c01653

Baig, H., Fontanarrosa, P., Kulkarni, V., ... Voigt, C.A., Wipat, A., Zong, D., Zundel, Z., Beal, J., & Myers, C. (2020)
Synthetic biology open language visual (SBOL visual) version 2.2
Journal of Integrative Bioinformatics DOI: https://doi.org/10.1515/jib-2020-0014

Taketani, M., Zhang, J., Zhang, S., Triassi, A.J., Huang, Y.-J., Griffith, L.G., & Voigt, C.A. (2020)
Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron
Nature Biotechnology DOI: https://doi.org/10.1038/s41587-020-0468-5

Al-Radhawi, M.A., Tran, A.P., Ernst, E.A., Chen, T., Voigt, C.A., & Sontag, E.D. (2020)
Distributed implementation of Boolean functions by transcriptional synthetic circuits
bioRxiv DOI: https://doi.org/10.1101/2020.04.21.053231

Shin, J,. Zhang, S., Der, B.S., Nielsen, A.A.K., & Voigt C.A. (2020)
Programming Escherichia coli to function as a digital display
Mol Syst Biol DOI: https://doi.org/10.15252/msb.20199401

Alon, D.M., Voigt C.A., & Elbaz, J. (2020)
Engineering a DNAzyme-Based Operon System for the Production of DNA Nanoscaffolds in Living Bacteria
ACS Synthetic Biology DOI: https://doi.org/10.1021/acssynbio.9b00415

González, L.M., Mukhitov, N., & Voigt C.A. (2020)
Resilient living materials built by printing bacterial spores
Nature Chemical Biology DOI: https://doi.org/10.1038/s41589-019-0412-5

Liu C-T., Helfrich E.J.N., Lin G-M., Moore, C., Voigt C.A, & Clardy, J. (2020)
P60: Functional characterization of a novel Actinobacterial diterpene biosynthetic gene cluster
3rd International Conference on Natural Product Discovery and Development in the Genomic Era

Schuerle S., Furubayashi M., Soleimany A.P., Gwisai T., Huang W., Voigt C.A.,& Bhatia S.N. (2020)
Genetic Encoding of Targeted Magnetic Resonance Imaging Contrast Agents for Tumor Imaging
ACS Synthetic Biology DOI: https://doi.org/10.1021/acssynbio.9b00416

2019

Soo Hoo Smith R., Bader C., Sharma S., Kolb D., Tang T-C, Hosny A., Moser F., Weaver J.C., Voigt C.A., & Oxman N. (2019)
Hybrid Living Materials: Digital Design and Fabrication of 3D Multimaterial Structures with Programmable Biohybrid Surfaces
Advanced Functional Materials DOI: https://doi.org/10.1002/adfm.201907401

Ryu M-H., Zhang J., Toth T., Khokhani D., Geddes B.A., Mus F., Garcia-Costas A., Peters J.W., Poole P.S>, Ane J-M., & Voigt C.A. (2019)
Control of nitrogen fixation in bacteria that associate with cereals.
Nature Microbiology DOI: https://doi.org/10.1038/s41564-019-0631-2

Buren S., Pratt K., Jiang X., Guo Y., Jiminez-Vicente E., Echavarri-Erasun C., Dean D.R., Saaem I.,Gordon D.B.,Voigt C.A., & Rubio L.M. (2019)
Biosynthesis of the nitrogenase active-site cofactor precursor NifB-co in Saccharomyces cerevisiae
Proceedings of the National Academy of Sciences DOI: https://doi.org/10.1073/pnas.1904903116

Helfrich E.J.N., Lin G-M., Voigt C.A.,& Clardy, J. (2019)
Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering
Beilstein Journal of Organic Chemistry DOI: 10.3762/bjoc.15.283

Meyer A., Saaem I., Silverman A., Varaljay V.A., Mickol R., Blum S., Tobias A.V., Schwalm III N.D., Mojadedi W., Onderko, E., Bristol C., Liu S., Pratt K., Casini A., Eluere R., Moser F., Drake C., Gupta M., Kelley-Loughnane N., Lucks J.P., Akingbade K.L., Lux M.P., Glaven, S., Crookes-Goodson W., Jewett M.C., Gordon D.B., & Voigt C.A. (2019)
Organism Engineering for the Bioproduction of the Triaminotrinitrobenzene (TATB) Precursor Phloroglucinol (PG)
ACS Synthetic Biology DOI: https://doi.org/10.1021/acssynbio.9b00393

McClune C., Alvarez-Buylla A., Voigt C.A., & Laub M.T. (2019)
Engineering orthogonal signalling pathways reveals the sparse occupancy of sequence space
Nature DOI: https://doi.org/10.1038/s41586-019-1639-8

Beal J., Nguyen T., Gorochowski T., Goni-Moreno A., Scott-Brown J., McLaughlin J. A, Madsen C., Aleritsch B., Bartley B., Bhakta S., Missell M., Castillo-Hair S.M., Clancy K., Luna A., Le Novere N., Palchick Z., Pocock M., Sauro H., Sexton J.T., Tabor J., Voigt C.A., Zundel Z., Myers C.J. & Wipat A. (2019)
Communicating Structure and Function in Synthetic Biology Diagrams
ACS Synthetic Biology DOI: 10.1021/acssynbio.9b00139

Moser F., Tham E., González L.M., Lu T.K., & Voigt C.A. (2019)
Light‐Controlled, High‐Resolution Patterning of Living Engineered Bacteria Onto Textiles, Ceramics, and Plastic.
Advanced Functional Materials, DOI: 10.1002/adfm.201901788

Lin G.-M., Warden-Rothman R., & Voigt C.A. (2019)
Retrosynthetic design of metabolic pathways to chemicals not found in nature.
Current Opinion in Systems Biology, DOI: 10.1016/j.coisb.2019.04.004

2018

Moser F., Espah Borujeni A., Ghodasara A.N., Cameron E., Park Y., & Voigt C.A. (2018)
Dynamic control of endogenous metabolism with combinatorial logic circuits.
Molecular Systems Biology, DOI: 10.15252/msb.20188605

Meyer A.J., Segall-Shapiro T.H., Glassey E., Zhang J., & Voigt C.A. (2018)
Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors.
Nature Chemical Biology, DOI: 10.1038/s41589-018-0168-3

Zhang S. & Voigt C.A. (2018)
Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design.
Nucleic Acids Research, DOI: 10.1093/nar/gky884

Andrews L.B., Nielsen A.A.K., & Voigt C.A. (2018)
Cellular checkpoint control using programmable sequential logic.
Science, DOI: 10.1126/science.aap8987

Brophy, J.A., Triassi A.J., Adams B.L., Renberg R.L., Stratis-Cullum D.N., Grossman A.D., & Voigt C.A. (2018)
Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria.
Nature Microbiology, DOI: 10.1038/s41564-018-0216-5

Nielsen A.A.K., & Voigt C.A. (2018)
Deep learning to predict the lab-of-origin of engineered DNA.
Nature Communications, DOI: 10.1038/s41467-018-05378-z

Young E.M., Zhao Z., Gielesen B.E.M., Wu L., Gordon D.B., Roubos J.A., & Voigt C.A. (2018)
Iterative algorithm-guided design of massive strain libraries, applied to itaconic acid production in yeast.
Metabolic Engineering, DOI: 10.1016/j.ymben.2018.05.002

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.