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2024

211

Rezvani, R.N., Aw, R., Chan, W., Satish, K., Chen, H., Lavy, A., Rimal, S., Patel, D.A., Kvam, E., Karim. A.S., Krüger, A., Kightlinger, W.K., Jewett, M.C. 2024. Scalable cell-free production of active T7 RNA polymerase. https://www.biorxiv.org/content/10.1101/2024.11.19.623967v1

210

Baranowski, C., Martin, H.G., Oyarzún, D., Petzold, C., Nikolados, E-M., Jaaks-Kraatz, S., Gaber, A., Chalkley, R., Scannell, D., Sevey, R., Jewett, M.C., Kelly, P., DeBenedictis, E. 2024. Can protein expression be “solved”? https://zenodo.org/records/13940346.

209

Hunt, A.C., Rasor, B.J., Seki, K., Ekas, H.M., Warfel, K.F., Karim, A.S., and Jewett, M.C. 2024. Cell-free gene expression: methods and applications. Chemical Reviews. In press.

208

Brown, D.M., Phillips, D.A., Garcia, D., Arce, A., Lucci, T., Davies, J., Mangini, J., Rhea, K., Lee, M.S., Wang, B., Biondo, J., Perdue, D.L., Thavarajah, W., Karim, A.S., Lux, M., Jewett, M.C., Miklos, A.E., Lucks, J.B. 2024. Semi-automated production of cell-free biosensors. BioRxiv. doi.org/10.1101/2024.10.13.618078.

207

Ekas, H.M., Wang, B., Silverman, A.D., Lucks, J.B., Karim, A.S., and Jewett, M.C. 2024. An automated, cell-free workflow for transcription factor engineering. ACS Synthetic Biology. In press.

206

Sotomayor, B., Donahue, T.C., Mahajan, S.P., Taw, M.N., Hulbert, S.W., Bidstrup, E.J., Pang, A., Yang, X., Azadi, P., Gray, J.J., Jewett, M.C., Wang, L-X., and DeLisa, M.P. 2024. Glycosylation of full-length IgG antibodies in bacteria enabled by a single-subunit oligosaccharyltransferase from Desulfovibrio marinus. BioRxiv: 10.1101/2024.08.12.607630

205

Landwehr, G.M., Vogeli, B., Tian, C., Singal, B., Gupta, A., Lion, R., Sargent, E.H., Karim, A.S., and Jewett, M.C. 2024. A synthetic cell-free pathway for biocatalytic upgrading of one-carbon substrates. https://www.biorxiv.org/content/10.1101/2024.08.08.607227v1

204

Landwehr, G.M., Bogart, J.W., Magalhaes, C., Hammarlund, E.G., A. Karim, A.S., and Jewett, M.C. 2024. Accelerated enzyme engineering by machine-learning guided cell-free expression. https://www.biorxiv.org/content/10.1101/2024.07.30.605672v1

203

Wong, D.A., Cabezas, M.D., Daniel-Ivad, M., Prasanna, D.V., Fernandez, R., Nicol, R., Balskus, E.P., Karim, A.S. and Jewett, M.C. 2024. A cell-free workflow for detecting and characterizing RiPP recognition element-precursor peptide interactions.

202

Ekas, H.M., Wang, B., Silverman, A.D., Lucks, J.B., Karim, A.S., and Jewett, M.C. 2024. Engineering a PbrR-based biosensor for cell-free detection of lead at the legal limit. ACS Synthetic Biology. In press.

201

Alejo, J.L., Girodat, D., Hammerling, M.J., Willi, J.A., Jewett, M.C., Engelhart, A.E., and Adamala, K.P. 2024. Alternate conformational trajectories in protein synthesis. PLOS Computational Biology. 20: e1012319.

200

Willi, J.A., Karim, A.S., and Jewett, M.C. 2024. Cell-free translation quantification via a fluorescent minihelix. ACS Synthetic Biology. 13: 2253–2259.

199

Collins, M.C., Lau, M., Ma, W., Shen, A., Wang, B.W., Cai, S, Russa, M.L., Jewett, M.C., and Qi, L.S. 2024. CRISPRkit: A frugal gene editing and regulation kit for equitable and accessible education. Nature Communications. 15: 6563.

198

Palma, J., Bunyatov, M., Hulbert, S., Jewett, M.C., and DeLisa, M.P. 2024. Bacterial glycoengineering: cell based and cell-free routes for producing biopharmaceuticals with customized glycosylation. Current Opinion in Chemical Biology. 81: 10250.

197

DeWinter, M.A., Wong, D.A., Fernandez, R., Kightlinger, W., Thames, A.H., DeLisa, M.P., and Jewett, M.C. 2024. Establishing a cell-free glycoprotein synthesis system for enzymatic N-GlcNAcylation. ACS Chemical Biology. 19: 1570–1582.

196

Liu, W-Q., Ji, X., Ba, F., Zhang, Y., Xu, H., Huang, S., Zheng, X., Liu, Y., Ling, S., Jewett, M.C, and Li., J. 2024. Cell-free biosynthesis and engineering of ribosomally synthesized lanthipeptides. Nature Communications. 15: 4336.

195

Clark, L., Voigt, C.A., and Jewett, M.C. 2024. Establishing a high yielding chloroplast cell-free system for prototyping genetic parts. ACS Synthetic Biology. 13: 2402–2411.

194

Böhm, C.V., Inckemann, R., Burgis, M., Baumann, J., Brinkmann, C.K., Lipińska, K.E., Gilles, S., Freudigmann, J., Seiler, V., Clark, L.G., Jewett, M.C., Voll, L.M., and Niederholtmeyer, H. 2024. Chloroplasts cell-free systems as rapid prototyping platforms for high-throughput part characterization. ACS Synthetic Biology. 13: 2412–2424.

193

Karim, A.S., Brown, D.M., Archuleta, C.M., Grannan, S., Aristilde, L., Goyal, Y., Leonard, J.N., Mangan, N.M., Prindle, A., Rocklin, G.J., Tyo, K.J., Zoloth, L., Jewett, M.C., Calkins, S., Kamat, N.,Tullman-Ercek, D., and Lucks, J.B. 2024. Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists. Nature Communications. 15: 5425.

192

Jensen, R.O., Schulz, F., Roux, S., Klingeman, D.M., Reynoso, V., Winkler, J., Nagaraju, S., Mitchell, W.P., Moraïs, S., Tissera, S.D., Shapiro, N., Ivanova, N., Reddy, T.B.K., Mizrahi, I., Utturkar, S., Bayer, E.A., Woyke, T., Mouncey, N.J., , Jewett, M.C., Simpson, S.D., Köpke, M., Jones, D.T.,,and Brown, S.D. 2024. Phylogenomics and genetic analysis of solvent-producing Clostridium species. Scientific Data. 11: 432.

191

Kofman, C., Willi, J.A., Karim, A.S., and Jewett, M.C. 2024. Ribosome pool engineering increases protein biosynthesis yields. ACS Central Science. 10:871–881. (Highlighted in C&E News).

190

Lin, L., Kightlinger, W., Warfel, K., Jewett, M.C., and Mrksich, M. 2024. Using high- throughput experiments to engineer N-glycosyltransferases with altered specificities. ACS Synthetic Biology. 13:1290-1302.

189

Rothschild, L.J., Averesch, Nils, J.H., Strychalski, E., Moser, F., Glass, J.I., Perez, R.C., Yekinni, I.O., Rothschild-Mancinelli, B., Roberts Kingman, G.A., Wu, F., Waeterschoot, J., Ioannou, I.A., Jewett, M.C., Liu, A.P., Noireaux, V., Sorenson, C., and Adamala, K.P. 2024. Building synthetic cells – from the technology infrastructure to cellular entities. ACS Synthetic Biology. 13:974-997. (Highlighted by NASA).

188

Kocalar, S., Miller, B.M., Huang, A., Gleason, E., Martin, K., Foley, K., Copeland, D.S., Jewett, M.C., Saavedra, E.A., and Kraves, S. 2024. Validation of cell-free protein synthesis aboard the International Space Station. ACS Synthetic Biology. 13: 942–950.

187

Steinküher, J., Peruzzi, J.A., Krüger, K., Jacobs, M.L., Jewett, M.C., and Kamat, N.P. 2024. Improving cell-free expression of membrane proteins by tuning ribosome co-translational membrane association and nascent chain aggregation. ACS Synthetic Biology. 13: 29–140.

2023

186

Hulbert, S.W., Desai, P., Jewett, M.C., DeLisa, M.P., Williams, A.J. 2023. Glycovaccinology: The design and engineering of carbohydrate-based vaccine components. Biotechnology Advances. 108234.

185

Yia, X., Rasor, B.J.,, Boadi, N., Louie, K., Northern, T.R., Karim, A.S., Jewett, M.C., and Alper, H.A. 2023. Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping. Metabolic Engineering. 80:241-253.

184

Thames, A.H. Rische, C.H., Yun Cao, Y., Krier-Burris, R.A., Kuang, F.L., Hamilton, R.G., Bronzert, C., Bochner, B.S., and Jewett, M.C. 2023. A cell-free protein synthesis platform to produce a clinically relevant allergen panel. ACS Synthetic Biology. 12:2252-2261.

183

Jung, K.J., Rasor, B.J., Rybnicky, G.A., Silverman, A.D., Standevene, J., Kuhn, R., Granitoh, T., Ekas, H.M., Wang, B.M., Karim, A.S., Lucks, J.B., and Jewett, M.C. 2023. At-home, cell-free synthetic biology education modules for transcriptional regulation and environmental water quality monitoring. ACS Synthetic Biology. 12:2909-2921.

182

Thames, A.H., Moons, S.J., Wong, D.A., Boltje, T.J., Bochner, B.S., and Jewett, M.C. 2023. GlycoCAP: A cell-free, bacterial glycosylation platform for building clickable azido-sialoglycoproteins. Glycobiology. ACS Synthetic Biology. 12:1264-1274.

181

Seki, K., Galindo, J.L., Karim, A.S., and Jewett, M.C. 2023. A cell-free gene expression platform for discovering and characterizing stop codon suppressing tRNAs. ACS Chemical Biology. 18:1324–1334.

180

Hunt, A.C., Vögeli, B., Kightlinger, W.K., Yoesep, D.J., Krüger, A., and Jewett, M.C. 2023. A high-throughput, automated, cell-free expression and screening platform for antibody discovery. Nature Communications. 14:3897.

179

Stark, J.C., Jaroentomeecha, T., Warfel., K.F., Hershewe, J.M., DeLisa, M.P., and Jewett, M.C. 2023. Rapid biosynthesis of glycoprotein therapeutics and vaccines from freeze-dried bacterial cell lysates. Nature Protocols. 18:1-25.

178

DeWinter, M.A., Thames, A.H., Guerrero, L., Kightlinger, W.K., Karim, A.S., and Jewett, M.C. 2023. Point-of-care peptide hormone production enabled by cell-free protein synthesis. ACS Synthetic Biology. 12:1216-1226.

177

Rasor, B.J., Karim, A.S., Alper, H.A., and Jewett, M.C. 2023. Cell extracts from bacteria and yeast retain metabolic activity after extended storage and repeated thawing. ACS Synthetic Biology. 12:904-908.

176

Warfel, K.F., Laigred, E., Sobol, S.E., Gillone, E., Varrote, A., Renaudted, O., Dejeud, J., Jewett, M.C., and Imbertye, A. 2023. Cell-free expression and characterization of multivalent rhamnose-binding lectins using biolayer interferometry. Glycobiology. 33:358-363.

175

Williams, A.J., Warfel, K.T., Desai, P., Li, J., Jen-Jie Lee, J.J., Wong, D.A., Sobol, S.E., Jewett, M.C., Chang, Y.F., and DeLisa, M.P. 2023. A low-cost recombinant glycoconjugate vaccine confers immunogenicity and protection against enterotoxigenic Escherichia coli infections in mice. Frontiers in Microbiology. 10:1085887.

174

Kruger, A., Watkins, A.M., Wellington-Oguri, R., Romano, J., Kofman, C., DeFoe, A., Kim, Y., Anderson-Lee, J., Fisker, E., Townley, J., Eterna participants, d’Aquino, A.E., Das, R., and Jewett, M.C. 2023. Community science designed ribosomes with beneficial phenotypes. Nature Communications.14: 961

173

Rasor, B.J., Chirania, P., Rybnicky, G.A., Giannone, R.J., Engle, N.L., Tschaplinski, T.J., Karim, A.S., Hettich, R.L.,, and Jewett, M.C., 2023. Mechanistic insights into cell-free gene expression through an integrated -omics analysis of extract processing methods. ACS Synthetic Biology. 12:405-418

172

Martin, J., Rasor, B., DeBonis, J., Karim, A.S., Jewett, M.C., Broadbelt, L.J., and Tyo, K.E.J. 2023. A dynamic kinetic model captures cell-free metabolism for improved butanol production. Metabolic Engineering. 76:133-145.

171

Lee, H., Willi, J.A., Cho, N., Kim, I., Jewett, M.C., and Lee, J. 2023. Cell-free biosynthesis of peptidomimetics. Biotechnology and Bioprocess Engineering. 1-17.

170

Warfel, K.T., Williams, A., Wong, D.A., Sobol, S.E., Desaie, P., Chang Y-F, Karim, A.S., DeLisa, M.P., and Jewett, M.C. 2023. A low-cost, thermostable, cell-free protein synthesis platform for on-demand production of glycoconjugate vaccines. ACS Synthetic Biology. 12:95–107.

2022

169

Chung, S.S., Bidstrup, E.J., Hershewe, J.M., Warfel, K.F., Jewett, M.C., and DeLisa, M.P. 2022. Ribosome stalling of N-linked glycoproteins in cell-free extracts. ACS Synthetic Biology. 11: 3892–3899.

168

Schachner, L. F., Des Soye, B., Ro, S., Kenney, G. E., Ives, A. N., Su, T., Goo, Y.A., Jewett., M.C., Rosenzweig, A. C., and Kelleher, N. L. 2022. Revving an engine of human metabolism: Activity enhancement of Triosephosphate Isomerase via hemi-phosphorylation. ACS Chemical Biology. 17: 2769–2780.

167

Gowland, S. and Jewett., M.C. 2022. Mobile translation systems generate genomically engineered Escherichia coli cells with improved growth phenotypes. ACS Synthetic Biology. 11: 2969–2978.

166

Nielsen, M.I., de Haan, N., Kightlinger, W., Ye, Z., Dabelsteen, S., Li, M., Jewett., M.C., Bagdonaite, I., Vakhrushev, S.Y., and Wandall, H.S. 2022. Global mapping of GalNAc-T isoform-specificities and O-glycosylation site-occupancy in a tissue-forming human cell line. Nature Communications. 13:6257

165

Koo., C., Hershewe, J.M., Jewett, M.C., and Rosenzweig, A.C. 2022. Cell-free protein synthesis of particulate methane monooxygenase into nanodiscs. ACS Synthetic Biology. 11: 4009–4017.

164

Nogle, R., Nagaraju, S., Utturkar, S.M., Giannone, R.J., Reynoso, V., Leang, C., Hettich, R., Mitchell, W.P., Simpson, S.D., Jewett, M.C., Köpke, M., Brown, S. 2022. Clostridium autoethanogenum isopropanol production via native plasmid pCA replicon. Frontiers in Bioengineering and Biotechnology. 10:932363

163

Lee, J., Coronado, J.N., Cho, N., Lim, J., Hosford, B.M., Seo, S., Kim, D.S., Kofman, C., Moore, J.S., Ellington, A.E., Anslyn, E.V., and Jewett, M.C. 2022. Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro. Nature Communications. 13: 6322.

162

Kofman, C., Watkins, A.M., Kim, D.S., Wooldredge, A.C., Karim, A.S., Das, D., and Jewett, M.C. 2022. Computationally-guided design and selection of ribosomal active site mutants with high activity. Nucleic Acids Research. 50: 13143–13154.

161

Gan, R., Cabezas, M.D., Pan, M., Zhang, H., Hu, G., Clark, L.G., Jewett, M.C., and Nicol, R. 2022. High-throughput regulatory part prototyping and analysis by cell-free protein synthesis and droplet microfluidics. ACS Synthetic Biology. 11: 2108-2120. (On the cover)

160

Jaroentomeechai, T., Liu, Y., Young, O., Bhawal, R., Wilson, J.D., Chapla, D.G., Li, M., Jewett, M.C., Moremen, K.W., Mizrachi, D., and DeLisa, M.P. 2022. A universal glycoenzyme biosynthesis pipeline that enables efficient cell-free remodeling of glycans. Nature Communications. 13: 6325.

159

Vögeli, B., Schulz, L., Garg, S., Tarasava, K., Clomburg, J.M., Lee, S.H., Gonnot, A., Moully, E.H., Kimmel, B.R., Mrksich, M., Karim, A.S., Gonzalez, R., Köpke, M., and Jewett, M.C. 2022. Cell-free prototyping enables implementation of optimized reverse b-oxidation pathways in heterotrophic and autotrophic bacteria. Nature Communications. 13: 3058.

158

Agarwal, D.K., Hunt, A.C., Shekhawat, G.S., Carter, L., Chan, S., Wu, K., Cao, L., Baker, D., Lorenzo-Redondo, R., Ozer, E.A., Simons, L. M., Hultquist, J. F., Jewett, M.C., and Dravid, V.P. 2022. Rapid and sensitive detection of antigen from SARS-CoV-2 variants of concern by a multivalent minibinder-functionalized nanomechanical sensor. Analytical Chemistry. 94: 8105-8109.

157

Charna, A.K.R., Des Soye, B.J., Ioanni Ntai, I., Kelleher, N.L., and Jewett, M.C. 2022. An efficient cell-free protein synthesis platform for the incorporation of pyrrolysine-based non-canonical amino acids. Biotechnology Journal. 17: e2200096.

156

Rybnicky, G.A., Dixon, R.A., Kuhn, R.M., Karim, A.S., and Jewett, M.C. 2022. Development of a freeze-dried CRISPR-Cas12 sensor for detecting Wolbachia in the secondary science classroom. ACS Synthetic Biology. 11: 835–842.

155

Rybnicky, G.A., Fackler, N.A., Karim., A.S., Köpke, M., and Jewett, M.C. 2022. Spacer2PAM: A computational framework for identification of functional PAM sequences for endogenous CRISPR systems. Nucleic Acids Research. gkac142.

154

Zubi, Y.S., Seki, K., Ying Li, Y., Hunt, A., Liu, B., Roux, B., Jewett, M.C., and Lewis, J.C. 2022. Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches. Nature Communications. 13: 1864.

153

Hunt, A.C., Case, J.B., Park, Y.J., Cao, L., Wu, K., Walls, A.C., Liu, Z., Bowen, J., Yeh, H.W., Saini, S., Helms, L., Zhao, Y.T., Starr, T.N., Goreshnik, I., Kozodoy, L., Carter, L., Ravichandran, R., Green, L.B., Matochko, W.L., Thomson, C.A., Vögeli, B., Krüger-Gericke, A., VanBlargan, L.A.,Chen, R.E., Ying, B., Bailey, A.L., Kafai, N.M., Boyken, S., Ljubetič, A., Edman, N., Ueda, G., Chow, C., Addetia, A., Panpradist, N., Gale, M., Freedman, B., Lutz, B., Bloom, J.D., Ruohola-Baker, H., Whelan, S., Stewart, L., Diamond, M.S., Veesler, D., Jewett, M.C., and Baker, D. 2022. Multivalent designed proteins protect against SARS-CoV-2 variants of concern. Science Translational Medicine. 14: eabn1252.

152

Mills, C.E., Waltmann, C., Archer, A., Kennedy, N.W., Abrahamson, C.H., Jackson, A., Shirman, S., Jewett, M.C., Mangan, N.M., Olvera de la Cruz, M., and Tullman-Ercek, D. 2022. Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphology. Nature Communications. 13: 3746.

151

Kennedy, N.W., Mills, C.E., Abrahamson, C.H., Archerc, A.G, Shirman, S., Jewett, M.C., Mangan, N.M., and Tullman-Ercek, D. 2022. Linking the Salmonella enterica 1,2-propanediol utilization bacterial microcompartment shell to the enzymatic core via the shell protein PduB. J. Bacteriology. 204: e00576.

150

Harbaugh, S., Silverman, A.D., Chushak, Y., Zimlich, K., Wolfe, M., Thavarajah, W., Jewett, M.C., Lucks, J.B., Chavez, J. 2022. Engineering a synthetic dopamine-responsive riboswitch for in vitro biosensing. ACS Synthetic Biology. 11: 2275–2283.

149

Tarasava, K., Lee, S.H., Chen, J., Köpke, M., Jewett, M.C., and Gonzalez, R. 2022. Reverse β-oxidation pathways for efficient chemical production. Journal of Industrial Microbiology and Biotechnology. kuac003.

148

Kim, D.S., Watkins, A., Bidstrup, E., Lee, J., Topkar, V., Schwarz, K.J., Kofman, C.,Schwarz, K.J., Liu, Y., Pintilie, G., Roney, E., Das, R., and Jewett, M.C. 2022. 3D-structure-guided evolution of a ribosome with tethered subunits. Nature Chemical Biology. 18: 990–998.

147

Liew, F., Nogle, R., Abdalla, T., Rasor, B.J., Canter, C., Jensen,R.O., Wang, L., Strutz, J., Chirania, P., Tissera, S.D., Mueller, A.P., Ruan, Z., Gao, A., Tran, L., Bromley,, Leang, C., Jewett, M.C., and Köpke, M. 2022. Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale. Nature Biotechnology. 40: 335–344. (On the cover. Highlighted in Science, Nature, News and Views, Chemistry World, Chemical and Engineering News)

2021

146

Perez, J.G., Carlson, E.D., Weisser, O., Kofman, C., Seki, K., Des Soye, B.J., Karim, A.S., and Jewett, M.C. 2021. Improving genomically recoded Escherichia coli to produce proteins containing non canonical amino acids. Biotechnology Journal. 2100330.

145

Rasor, B.J., Yi, X., Brown, H., Alper, H.S., and Jewett, M.C. 2021. An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts. Nature Communications. 12: 5139.

144

Kofman, C., Lee, J., and Jewett, M.C. 2021. Engineering molecular translation systems. Cell Systems. 12(6): 595-607.

141

Hammerling, M.J., Warfel, K.F., and Jewett, M.C. 2021. Lyophilization of premixed COVID 19 diagnostic RT-qPCR reactions for rapid assembly and long-term stability. Biotechnology Journal. 16: 2000572.

140

Hershewe, J.M., Warfel, K.F., Iyera, S.M., Peruzzi, J.A., Sullivan, C.J., Rothe, E.W., DeLisa, M.P., Kamat, N.P., and Jewett, M.C. 2021. Improving cell-free glycoprotein synthesis by characterizing and enriching native membrane vesicles. Nature Communications. 12: 1-2664.

139

Lee, L., Schwarz, K.J., Yu, H., Krüger, A., Anslyn, E.V., Ellington, A.D., Moore, J.S., and Jewett, M.C. 2021. Ribosome-mediated incorporation of fluorescent amino acids into peptides in vitro. Chemical Communications. 57: 2661-2664.

138

Rasor, B.J., Vögeli, B., Landwehr, G.M., Bogart, J.W., Karim, A.S., and Jewett, M.C. 2021. Toward sustainable, cell-free biomanufacturing. Current Opinion in Biotechnology. 69: 136-144.

137

Stark, J.C., Jaroentomeechai, T., Moeller, T.D., Hershewe, J.M., Warfel, K.F., Moricz, B.S., Martini, A.M., Dubner, R.S., Hsu, K.J., Stevenson, T.C., Jones, B.D., DeLisa, M.P., and Jewett, M.C. 2021. On-demand, biomanufacturing of protective conjugate vaccines. Science Advances. 7(6): EABE9444. (On the cover; Highlighted in Vice, DDN, Biopharma Reporter)

136

Liu, Y., Davis, R.G., Thomas, P.M., Kelleher, N.L., and Jewett, M.C. 2021. In vitro constructed ribosomes enable multi-site incorporation of non-canonical amino acids into proteins. Biochemistry. 60(3): 161-169.

2020

135

Hammerling, M.J., Yoesep, D.J., and Jewett, M.C. 2020. Single enzyme RT-PCR of full-length ribosomal RNA. Synthetic Biology OUP. 5(1): ysaa028.

134

Danielson, N., McKay, S., Bloom, P., Dunn, J., Jakel, N., Bauer, T., Hannon, J., Jewett, M.C., and Shanks, B. 2020. Industrial biotechnology—an industry at an inflection point. Industrial Biotechnolgy. 16(6): 321-332.

133

Gupta, M.K., Wagner,D.T., and Jewett, M.C. 2020. Engineered proteins as multifunctional materials. MRS Bulletin. 45(12): 999-1004.

132

Hershewe, J.M., Wiseman, W.D., Kath, J.E., Buck, C.C., Gupta, M.K., Dennis, P.B., Naik, R.R., and Jewett, M.C. 2020. Characterizing and controlling nanoscale self-assembly of suckerin-12. ACS Synthetic Biology. 9(12): 3388-3399.

131

Hershewe, J.M., Kightlinger, W., and Jewett, M.C. 2020. Cell-free systems for accelerating glycoprotein expression and biomanufacturing. Journal of Industrial Microbiology and Biotechnology. 47(11): 977-991. (On the cover)

130

Lee, J., Schwarz, K.J., Kim, D.S., Moore, J.S., and Jewett, M.C. 2020. Ribosome mediated polymerization of long chain carbon and cyclic amino acids into peptides in vitro. Nature Communications. 11: 4304. (Highlighted in C&E News).

129

Bogart, J.W., Cabezas, M.D., Vögeli, B., Wong, D., Karim, A.S., and Jewett, M.C. 2020. Cell-free exploration of the natural product chemical space. ChemBioChem. 22(1): 84-91.

128

Karim, A.S., Liew, F.E., Garg, S., Vögeli, B., Rasor, B.J., Gonnot, A., Pavan, M., Juminaga, A., Simpson, S.D., Köpke, M., and Jewett, M.C. 2020. Modular cell-free expression plasmids to accelerate biological design in cells. Synthetic Biology OUP. 5(1): ysaa019.

127

Zhu, B., Gan, R., Cabezas, M.D., Kojima, T., Nicol, R., Jewett, M.C. and Nakano, H. 2020. Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins. Bioengineering and Biotechnology. 117(12): 3849-3857.

126

Liu, W.Q., Wu, C., Jewett, M.C., and Li, J. 2020. Cell-free protein synthesis enables one-pot cascade biotransformation in an aqueous-organic biphasic system. Biotechnology and Bioengineering. 117(12): 4001-4008.

125

Thames, A.H., Wolniak, K.L., Stupp, S.I., and Jewett, M.C. 2020. Principles learned from the international race to develop a safe and effective COVID-19 vaccine. ACS Central Science. 6: 1341-1347.

124

Jaroentomeechai, T., Taw, M.N., Li, M., Aquino, A., Agashe, N., Chung, S., Jewett, M.C., and DeLisa, M.P. 2020. Cell-free synthetic glycobiology: Designing and engineering glycomolecules outside of living cells. Frontiers in Chemistry. 8: 645.

123

Grubbe, W.S., Rasor, B.J., Krüger, A., Jewett, M.C., and Karim, A.S. 2020. Cell-free styrene biosynthesis at high titers. Metabolic Engineering. 61: 89-95.

122

Dudley, Q.M., Karim, A.S., Nash, C.J., and Jewett, M.C. 2020. Cell-free prototyping of limonene biosynthesis using cell-free protein synthesis. Metabolic Engineering. 61: 251-260.

121

Kightlinger, W., Warfel, K., DeLisa, M.P., and Jewett, M.C. 2020. Synthetic Glycobiology: Parts, Systems, and Applications. ACS Synthetic Biology. 9: 1534-1562.

120

Krüger, A., Mueller, A.P., Rybnicky, G.A., Engle, N.L., Yang, Z.K., Tschaplinski, T.J., Simpson, S.D., Köpke, M., and Jewett, M.C. 2020. Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways. Metabolic Engineering. 62: 95-105.

119

Karim, A.S., Dudley, Q.M., Juminaga, A., Yuan, Y., Crowe, S.A., Heggestad, J.T., Garg, S., Abdalla, T., Grubbe, W., Rasor, B., Coar, D., Torculas, M., Krein, M., Liew, F., Quattlebaum, A., Jensen, R.O., Stuart, J., Simpson, S.D., Köpke, M., and Jewett, M.C. 2020. In vitro prototyping and rapid optimization of biosynthetic enzymes for cellular design. Nature Chemical Biology. 16: 912-919. (On the cover)

118

Lee, J., Torres, R., Kim, D.S., Byrom, M., Ellington, A.D., and Jewett, M.C. 2020. Ribosomal incorporation of cyclic b-amino acids into peptides using in vitro translation. Chemical Communications. 56: 5597-5600. (On the cover)

117

Whitehead, T.A., Banta, S., Bentley, W.E., Betenbaugh, M.J., Chane, C., Clark, D.S., Hoeslig, C., Jewett, M.C., Junkeri, B., Koffas, M., Kshirsagark, R., Lewis, A., Lid, C.T., Maranas, C., Papoutsakis, E., Prather K.J., Schaffer, S., Segatori. L., and Wheeldon, I. 2020. The importance and future ofbiochemical engineering. Biotechnology and Bioengineering. 117(8): 2305-2318.

116

Zhuang, L., Huang, S., Liu, W.Q., Karim, A.S., Jewett, M.C., and Li, J. 2020. Total in vitro biosynthesis of the nonribosomal macrolactone peptide valinomycin. Metabolic Engineering. 60: 37-44.

115

Kennedy, N.W., Hershewe, J.M., Nichols, T.M., Roth, E.W., Wilke, C.D., Jewett, M.C., and Tullman-Ercek, D. 2020. Apparent size and morphology of bacterial microcompartments varies with technique. PLOS One. 15(3): e0226395.

114

Thavarajah, W., Verosloff, M.S., Jung, J.K., Alam, K.K., Miller, J.D., Jewett, M.C., Young, S.L., and Lucks, J.B. 2020. A primer on emerging field-deployable synthetic biology tools for democratizing global water quality monitoring. NPJ Clean Water. 3:18.

113

Aleksashin, N.A., Szal, T., d’Aquino, A.E., Jewett, M.C., and Mankin, A.M. 2020. A fully orthogonal system for protein synthesis in bacterial cells. Nature Communications. 11:1858.

112

Silverman, A.D., Akova, U., Alam, K.K., Jewett, M.C., and Lucks, J.B. 2020. Design and optimization of a cell-free atrazine biosensor. ACS Synthetic Biology. 9: 671–677.

111

Chen, Z., Kibler, R.D., Hunt, A., Busch, F., Pearl, J., Jia, M., VanAernum, Z.L., Wicky, B.I.M., Dods, G., Liao, H., El-Samad, H., Stamatoyannopoulos, J., Wysocki, V.H., Jewett, M.C., Boyken, S.E., and Baker, D. 2020. De novo design of protein logic gates. Science. 368: 78-84.

110

Lin, L., Kightlinger, W., Parhu, S.K., Hockenberry, A.J., Li, C., Wang, L.-X., Jewett, M.C. and Mrksich, M. 2020. Sequential glycosylation of protein via substrate specific N-glycosyltransferases. ACS Central Science. 6: 144-154.

109

Hammerling, M.J., Fritz, B.R., Yoesep, D.J., Kim, D.S., Carlson, E.D., and Jewett, M.C. 2020. In vitro ribosome synthesis and evolution through ribosome display. Nature Communications. 11: 1108.

108

Kay, J.E. and Jewett, M.C. 2020. A cell-free system for production of 2,3-butanediol is robust to growth-toxic compounds. Metabolic Engineering Communications. 10: e00114.

107

Hammerling, M.J., Krüger, A., and Jewett, M.C. 2020. Strategies for in vitro engineering of the translation machinery. Nucleic Acids Research. 48(3): 1068-1083.

106

Silverman, A.D., Karim, A.S., and Jewett, M.C. 2020. Cell-free gene expression systems: An expanded repertoire of applications. Nature Reviews Genetics. 21: 151-170.

105

Techner, J.M., Kightlinger, W., Lin, L., Hershewe, J., Ramesh, A., DeLisa, M.P., Jewett, M.C., and Mrksich, M. 2020. High-throughput synthesis and analysis of intact glycoproteins using SAMDI-MS. Analytical Chemistry. 92(2): 1963-1971.

104

d’Aquino, A.E., Azim, T., Aleksashin, N.A., Hockenberry, A.J., and Jewett, M.C. 2020. Mutational characterization and mapping of the 70S ribosome active site. Nucleic Acids Research. gkaa001.

103

Thavarajah, W., Silverman, A.D., Verosloff, M.S., Kelley-Loughnane, N., Jewett, M.C., and Lucks, J.B. 2020. Point-of-use detection of environmental fluoride via an engineered cell-free riboswitch-based biosensor. ACS Synthetic Biology. 9(1):10-18.

102

Liu, X., Silverman, A.D., Alam, K.K., Iverson, E., Lucks, J.B., Jewett, M.C., and Raman, S. 2020. Design of a transcriptional biosensor for the portable, on-demand detection of cyanuric acid. ACS Synthetic Biology. 9(1): 84-94.

2019

101

Meyer, A., Saaem, I., Silverman, A.D., Varaljay, V., Mikol, R., Blum, S., Onderko, E., Bristol, C., Liu, S., Pratt, K., Casini, A., Eluere, R., Moser, F., Servinksy, M., Lucks, J.B., Lux, M., Glaven, S., Crookes-Goodson, W., Jewett, M.C., Gordon, D.B., and Voigt, C.A. 2019. Organism engineering for the bioproduction of the triaminotrinitrobenzene (TATB) precursor phloroglucinol (PG). ACS Synthetic Biology. 8(12): 2746-2755.

100

Kightlinger, W., Duncker, K., Ramesh, A., Thames, A., Natarajan, A., Stark, J.C., Yang, A., Lin, L., Mrksich, M., DeLisa, M.P., and Jewett, M.C. 2019. A cell-free biosynthesis platform for modular construction of protein glycosylation pathways. Nature Communications. 10: 5404.

99

Karim, A.S., Rasor, B.J., and Jewett, M.C. 2019. Enhancing control of cell-free metabolism through pH modulation. Synthetic Biology. ysz027.

98

Lee, J., Schwieter, K.E., Watkins, A.M., Kim, D.S., Yu, H., Schwarz, K.J., Lim, J., Coronado, J., Byrom, M., Anslyn, E.V., Ellington, A.D., Moore, J.S., and Jewett, M.C. 2019. Expanding the limits of the second genetic code with ribozymes. Nature Communications. 10: 5097.

97

Des Soye, B.J., Gerbasi, V.R., Thomas, P.M., Kelleher, N.L., and Jewett, M.C. 2019. A highly productive, one-pot cell-free protein synthesis platform based on genomically recoded Escherichia coli. Cell Chemical Biology. 26: 1–12.

96

Carlson, E.D., d’Aquino, A.E., Kim, D.S., Fulk, E.M., Hoang, K., Szal, T., Mankin, A.S., and Jewett, M.C. 2019. Engineered ribosomes with tethered subunits for expanding biological function. Nature Communications. 10: 3920.

95

McNerney, M.P., Zhang, Y., Steppe, P., Silverman, A.D., Jewett, M.C., and Styczynski, M.P. 2019. Point-of-care biomarker quantification enabled by sample-specific calibration. Science Advances. 5 (9): EAAX4473.

94

Yesselman, J.D., Eiler, D., Carlson, E.D., Gotrik, M.R., d’Aquino, A.E., Ooms, A.N., Kladwang, W., Shi, X., Costantino, D., Carlson, P.D., Lucks, J.B., Herschlag, D., Jewett, M.C., Kieft, J.S., and Das, R. 2019. Computational design of three-dimensional RNA structure and function. Nature Nanotechnology. 14: 866-873.

93

O’Kane, P.T., Dudley, Q.M., McMillan, A.K., Jewett, M.C., and Mrksich, M. 2019. High-throughput mapping of CoA metabolites by SAMDI-MS to optimize the cell-free biosynthesis of HMG-CoA. Science Advances. 5(6): EAAW9180.

92

Stark, J.C., Huang, A., Hsu, K.J., Dubner, R.S., Forbrook, J., Marshalla, S., Rodriguez, F., Washington, M., Rybnicky, G.A., Nguyen, P.Q., Hasselbacher, B., Jabri, R., Kamran, R., Koralewski, V., Wightkin, W., Martinez, T., and Jewett, M.C. 2019. BioBits Health: Exploring engineering, biology, andhuman health with fluorescent readouts. ACS Synthetic Biology. 8(5): 1001-1009.

91

Silverman, A.D., Kelley-Loughnane, N., Lucks, J.B., and Jewett, M.C. 2019. Deconstructing cell-free extract preparation for in vitro activation of transcriptional genetic circuitry. ACS Synthetic Biology. 8(2): 403-414.

90

Dudley, Q.M., Nash, C.J., and Jewett, M.C. 2019. Cell-free biosynthesis of limonene using enzyme enriched Escherichia coli lysates. Synthetic Biology. 4(1): ysz003.

89

Aleksashin, N.A., Leppik, M., Hockenberry, A.J., Klepacki, D., Vázquez-Laslop, N., Jewett, M.C., Remme, J., and Mankin, A.S. 2019. Assembly and functionality of the ribosome with tethered subunits. Nature Communications. 10: 930.

88

Levine, M.Z., Gregorio, N.E., Jewett, M.C., Watts, K.R., and Oza, J.P. 2019. Escherichia coli-based cell-free protein synthesis: Protocols for a robust, flexible, and accessible platform technology. The Journal of Visualized Experiments. e58882.

2018

87

Bundy, B.C., Hunt, J.P., Jewett, M.C., Swartz, J.R., Wood, D.W., Rao, G., and Frey, D.D. 2018. Cell-free biomanufacturing. Current Opinion in Chemical Engineering. 22: 177-183.

86

Caschera, F., Karim, A.S., Gazzolae, G., d’Aquino, A.E., Packard, N.H., and Jewett, M.C. 2018. High-throughput optimization cycle of a cell-free ribosome assembly and protein synthesis system. ACS Synthetic Biology. 7: 2841-2853.

85

Des Soye, B.J., Davidson, S.R., Weinstock, M.T., Gibson, D.G., and Jewett, M.C. 2018. Establishing a high-yielding cell-free protein synthesis platform derived from Vibrio natriegens. ACS Synthetic Biology. 7(9): 2245-2255.

84

Quillin, S.J., Hockenberry, A.J., Jewett, M.C., and Seifert, H.S. 2018. Neisseria gonorrhoeae exposed to sublethal levels of hydrogenperoxide mounts a complex transcriptional response. mSystems. 3(5): e00156-18.

83

Hockenberry, A.J., Amaral, L.A.N., Jewett, M.C., and Wilke, C.O. 2018. Within-gene Shine-Dalgarno sequences are not selected for function. Molecular Biology and Evolution. 35(10): 2487-2498.

82

Karim, A.S. and Jewett, M.C. 2018. Cell-free synthetic biology for pathway prototyping. Methods in Enzymology. 608: 31-57.

81

Jaroentomeechai, T., Stark, J.C., Natarajan, A., Glasscock, C., Yates, L., Hsu, K.J., Mrksich, M., Jewett, M.C., and DeLisa, M.P. 2018. Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery. Nature Communications. 9: 2686. (Highlighted in Chemical and Engineering News)

80

Stark, J.C., Huang, A., Nguyen, P.Q., Dubner, R.S., Hsu, K.J., Ferrante, T., Anderson, M., Kanapskyte, A., Mucha, Q., Packett, J.S., Patel, P., Patel, R., Qaq, D., Zondor, T., Burke, J., Martinez, T., Miller-Berry, A., Puppala, A., Reichert, K., Schmid, M., Brand, L., Hill, L.R., Chellaswamy, J.F., Faheem, N., Fetherling, S., Gong, E., Gonzalzles, E.M., Granito, T., Koritsaris, J., Nguyen, B., Ottman, S., Palffy, C., Patel, A., Skweres, S., Slaton, A., Woods, T., Donghia, N., Pardee, K., Collins, J.J., and Jewett, M.C. 2018. BioBits Bright: A fluorescent synthetic biology education kit. Science Advances. EAAT5107.

79

Huang, A., Nguyen, P.Q., Stark, J.C., Takahasi, M.K., Donghia, N., Ferrante, T., Dy, A.J., Hsu, K.J., Dubner, R.S., Pardee, K., Jewett, M.C., and Collins, J.J. 2018. BioBits Explorer: A modular synthetic biology education kit. Science Advances. EAAT5105.

78

Wang, H., Li, J., and Jewett, M.C. Development of a Pseudomonas putida cell-free protein synthesis platform for rapid screening of gene regulatory elements. 2018. Synthetic Biology. 3: ysy003.

77

d’Aquino, A.E., Kim, D.S., and Jewett, M.C. 2018. Engineered ribosomes for basic science and synthetic biology. Annual Review of Chemical and Biomolecular Engineering. 9: 311-340.

76

Casini, A., Chang, F-Y., Eluere, R., King, A.M., 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.,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. JACS. 140: 4302-4316.

75

Kightlinger, W., Lin, L., Rosztoczy, M., DeLisa, M.P., Mrksich, M., and Jewett, M.C. 2018. Design of glycosylation sites by rapid synthesis and analysis of glycosyltransferase. Nature Chemical Biology. 14: 627-635.

74

Martin, R.W., Des Soye, B.J., Kwon, Y.C., Kay, J., Davis, R.G., Thomas, P.M., Marcum, R.D., Majewska, N.I., Chen, C.X., Weiss, M.G., Stoddart, A.E., Amiram, M., Charna, A.K., Isaacs, F.J., Kelleher, N.L., Hong, S.H., and Jewett, M.C. 2018. Cell-free protein synthesis from genomically recoded bacteria enables multi-site incorporation of non-canonical amino acids. Nature Communications. 9: 1203.

73

Kakkar, N., Perez, J.G., Liu, W., Jewett, M.C., van der Donk, W.A. 2018. Incorporation of non-proteinogenic amino acids in class I and II lantibiotics. ACS Chemical Biology. 13: 951-957.

72

Aebersold, R., Agar, J.N., Amster, J., Baker, M., Bertozzi, C.R., Boja, E.S., Costello, C.E., Cravatt, B.F., Fenselau, C., Garcia, B., Ge, Y., Gunawardena, J., Hendrickson, R.C., Hergenrother, P.J., Huber, C., Ivanov, A.R., Jensen, O., Jewett, M.C., Kelleher, N.L., Kiessling, L.L., Krogan, N.J., Larsen, M.R., Loo, J.A., Loo, R.R., Lundberg, E., MacCoss, M., Mallick, P., Mootha, V.K., Mrksich, M., Muir, T.W., Patrie, S.M., Pesavento, J.J., Pitteri, S.J., Rodriguez, H., Saghatelian, A., Sandoval, W., Schlüter, H., Sechi, A., Sheeley, D.M., Slavoff, S.A., Smith, L.M., Snyder, M.P., Thomas, P.M., Uhlen, M., van der Donk, W.A., van Eyk, J.E., Vidal, M., Walt, D.R., White, F.M., Williams, E.R., Wohlschlager, T., Wysocki, V.H., Yates, N.A., Young, N.L., and Zhang, B. 2018. How many human proteoforms are there? Nature Chemical Biology. 14(3): 206-214.

71

Liu, S.S., Hockenberry, A.J., Lancichinetti, A., Jewett, M.C., and Amaral, L.A.N. 2018. A novel framework for evaluating the performance of codon usage bias metrics. Journal of the Royal Society Interface. 15: 20170667.

70

Liu, C.C., Jewett, M.C., Chin, J.W., and Voigt, C.A. 2018. Toward an orthogonal central dogma. Nature Chemical Biology. 14: 103-106.

69

Schoborg, J.A., Hershewe, J., Stark, J.C., Kightlinger, W., Kath, J.E., Jaroentomeechai, T., Natarajan, A., DeLisa, M.P., and Jewett, M.C. 2018. A cell-free platform for rapid synthesis and testing of active oligosaccharyltransferases. Biotechnology and Bioengineering. 115 (3): 739-750.

68

Li, J., Wang, H., and Jewett, M.C. 2018. Expanding the palette of Streptomyces-based cell-free protein synthesis systems with enhanced yields. Biochemical Engineering Journal. 130: 29-33.

67

Hockenberry, A.J., Stern, A.J., Amaral, L.A.N., and Jewett, M.C. 2018. Diversity of translation initiation mechanisms across bacterial species is driven by environmental conditions and growth demands. Molecular Biology and Evolution. 35 (3): 582-592.

66

Karim, A.S., Heggestad, J.T., Crowe, S.A., and Jewett, M.C. 2018. Controlling cell-free metabolism through physiochemical perturbations. Metabolic Engineering. 45: 86-94.

2017

65

Jaroentomeechai, T., Zheng, X., Hershewe, J., Stark, J.C., Jewett, M.C., and DeLisa, M.P. 2017. A pipeline for interrogating and engineering single-subunit oligosaccharyltransferases. Methods in Enzymology, Chemical Glycobiology. 597: 55-81.

64

Li, J., Haas, W., Jackson, K., Kuru, E., Jewett, M.C., Fan, Z.H., Gygi, S., Church, G.M. 2017. Cogenerating synthetic parts toward a self-replicating system. ACS Synthetic Biology. 6(7): 1327-1336.

63

Martin, R.W., Majewska, N.I., Chen, C.X., Albanetti, T.E., Jimenez, R.B., Schmelzer, A.E., Jewett, M.C., and Roy, V. 2017. Development of a CHO-based cell-free platform for synthesis of active monoclonal antibodies. ACS Synthetic Biology. 6(7): 1370-1379. (Accompanied by C&E News article)

62

Liu, Y., Kim, D.S., and Jewett, M.C. 2017. Repurposing ribosomes for synthetic biology. Current Opinion in Chemical Biology. 40: 87-94.

61

Li, J., Wang, H., Kwon, Y.C., and Jewett, M.C. 2017. Establishing a high yielding Streptomyces-based cell-free protein synthesis system. Biotechnology and Bioengineering. 114: 1343-1353.

60

Gan, R., Perez, J.G., Carlson, E.D., Ntai, I., Isaacs, F.J., Kelleher, N.L., and Jewett, M.C. 2017. Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins. Biotechnology and Bioengineering. 114: 1074-1086. (Spotlight article)

59

Hockenberry, A.J., Pah, A.R., Jewett, M.C., and Amaral, L.A.N. 2017. Leveraging genome-wide datasets to quantify the functional role of the anti-Shine-Dalgarno sequence in regulating translation efficiency. Open Biology. 7: 160239.

2016

58

Liu, S.S., Hockenberry, A.J., Lancichinetti, A., Jewett, M.C., and Amaral, L.A.N. 2016. NullSeq: A tool for generating random coding sequences with amino acid and GC constraints. PLOS Computational Biology. 12(11): e1005184.

57

Goering, A.W., Li, J., McClure, R.A., Thomson, R., Jewett, M.C., and Kelleher, N.L. 2016. In vitro reconstruction of nonribosomal peptide biosynthesis directly from using cell-free protein synthesis. ACS Synthetic Biology. 6: 39-44.

56

Dudley, Q.M., Anderson, K.C., and Jewett, M.C. 2016. Cell-free mixing of Escherichia coli crude extracts to prototype and rationally engineer high-titer mevalonate synthesis. ACS Synthetic Biology. 5: 1578-1588.

55

Yang, C., Hockenberry, A.J., Jewett, M.C., and Amaral, L.A.N. 2016. Depletion of Shine Dalgarno sequences within coding regions is expression dependent. G3: Genes, Genomes, Genetics. 6(11): 3467-3474.

54

Caschera, F., Lee, J.W., Ho, K.K.Y., Liu, A.P., and Jewett, M.C. 2016. Cell-free compartmentalized protein synthesis inside double emulsion templated liposomes with in vitro synthesized and assembled ribosomes. Chemical Communications. 52: 5467-5469.

53

Karim, A.S. and Jewett, M.C. 2016. A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery. Metabolic Engineering. 36:116-126. (Top download)

52

Schoborg, J.A., Clark, L.G., Choudury, A., Hodgman, C.E., and Jewett, M.C. 2016. Yeast knockout library allows for efficient testing of genomic mutations for cell-free protein synthesis. Synthetic and Systems Biotechnology. 1: 2-6.

51

Gan, R. and Jewett, M.C. 2016. Evolution of translation initiation sequences with in vivo functionality using in vitro yeast ribosome display. Biotechnology and Bioengineering. 113: 1777-1786. (Spotlight article)

50

Sullivan, C.J., Pendleton, E.D., Sasmor, H.H., Hicks, W.L., Farnum, J.B., Muto, M., Amendt, E.M., Schoborg, J.A., Martin, R.W., Clark, L.G., Anderson, M.J., Choudhury, A., Fior, R., Lo, Y.H., Griffey, R.H., Chappell, S.A., Jewett, M.C., Mauro, V.P., and Dresios, J. 2016. A cell-free expression and purification process for rapid production of protein biologics. Biotechnology Journal. 11: 238-248.

49

Li, J., Lawton, T.J., Kostecki, J.S., Nisthal, A., Fang, J., Mayo, S.L., Rosenzweig, A.C., and Jewett, M.C. 2016. Cell-free protein synthesis enables high yielding synthesis of an active multicopper oxidase. Biotechnology Journal. 11: 212-218. (On the cover)

2015

48

Amiram, M., Haimovich, A.D., Fan, C., Wang, Y.S., Aerni, H.R., Ntai, I., Moonan, D.W., Ma, N.J., Rovner, A.J., Hong, S.H., Kelleher, N.L., Goodman, A.L., Jewett, M.C., Söll, D., Rinehart, J., and Isaacs, F.J. 2015. Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nature Biotechnology. 33: 1272-1279.

47

Kay, J.E. and Jewett, M.C. 2015. Lysate of engineered Escherichia coli supports high-level conversion of glucose to 2,3-butanediol. Metabolic Engineering. 30: 133-142.

46

Orelle, C., Carlson, E.D., Szal, T., Florin, T., Jewett, M.C., and Mankin, A.S. 2015. Protein synthesis by ribosomes with tethered subunits. Nature. 524: 119-124. (Accompanied by News and Views article, Highlighted in Nature News, Chemistry & Biology, The Scientist, Chemical & Engineering News, The Verge, Scientific American, Nature Methods, Recommended by Faculty of 1000)

45

Oza, J.P., Aerni, H.R., Pirman, N.L., Barber, K.W., ter Haar, C.M., Rogulina, S., Amrofell, M.B., Isaacs, F.J., Rinehart, J., and Jewett, M.C. 2015. Robust production of recombinant phosphoproteins using cell-free protein synthesis. Nature Communications. 6: 8168.

44

Fritz, B.R., Jamil, O.K., and Jewett, M.C. 2015. Implications of macromolecular crowding and reducing conditions for in vitro ribosome construction. Nucleic Acids Research. 43: 4774-4784.

43

Moatsou, D., Li, J., Ranji, A., Pitto-Barry, A., Ntai, I., Jewett, M.C., and O’Reilly, R.K. 2015. Reversible self-assembly of temperature-responsive protein-polymer conjugates. Bioconjugate Chemistry. 26: 1890-1899. (On the cover)

42

Heinzelman, P., Schoborg, J.A., and Jewett, M.C. 2015. pH responsive granulocyte colony stimulating factor variants with implications for treating Alzheimer’s disease and other central nervous system disorders. Protein Engineering Design and Selection. 28: 481-489.

41

Des Soye, B., Patel, J., Isaacs, F.J., and Jewett, M.C. 2015. Repurposing the translation apparatus for synthetic biology. Current Opinion in Chemical Biology. 28: 83-90.

40

Anderson, M.J., Stark, J.C., Hodgman, C.E., and Jewett, M.C. 2015. Energizing yeast cell-free protein synthesis with glucose metabolism. FEBS Letters. 589: 1723-1727.

39

Ploskon, E., Wagner, S., Ellington, A.D., Jewett, M.C., O’Reilly, R., and Booth, P. 2015. Controlled assembly of artificial protein-protein complexes via DNA duplex formation. Bioconjugate Chemistry. 26: 427-434.

38

Kwon, Y.C. and Jewett, M.C. 2015. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Scientific Reports. 5: 8663. (Editor’s choice)

37

Hong, S.H., Kwon, Y.C., Martin, R.W., Des Soye, B.J., de Paz, A.M., Swonger, K.N., Ntai, I., Kelleher, N.L., and Jewett, M.C. 2015. Improving cell-free protein synthesis through genome engineering of Escherichia coli lacking release factor 1. ChemBioChem. 16: 844-853. (On the inside cover)

36

Dudley, Q.M., Karim, A.S., and Jewett, M.C. 2015. Cell-free metabolic engineering: Biomanufacturing beyond the cell. Biotechnology Journal. 10: 69-82. (Top Download 2014-2015)

35

Liu, Y., Fritz, B.R., Anderson, M.J., Schoborg, J.A., and Jewett, M.C. 2015. Characterizing and alleviating substrate limitations for improved in vitro ribosome construction. ACS Synthetic Biology. 4: 454-462.

2014

34

Hodgman, C.E. and Jewett, M.C. 2014. Characterizing IGR IRES-mediated translation initiation for use in yeast cell-free protein synthesis. New Biotechnology. 31: 499-505.

33

Hong, S.H., Kwon, Y.C., and Jewett, M.C. 2014. Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis. Frontiers in Chemistry. 2: 34.

32

Choudury, A., Hodgman, C.E., Anderson, M., and Jewett, M.C. 2014. Evaluating fermentation effects on cell growth and crude extract metabolic activity for improved yeast cell-free protein synthesis. Biochemical Engineering Journal. 91: 140-148.

31

Hockenberry, A.J., Sirer, M.A., Amaral, L.A.N., and Jewett, M.C. 2014. Quantifying position-dependent codon usage bias. Molecular Biology and Evolution. 31: 1880-1893.

30

Fritz, B.R. and Jewett, M.C. 2014. The impact of transcriptional tuning on in vitro integrated rRNA transcription and ribosome construction. Nucleic Acids Research. 42: 6774-6785.

29

Palmer, M.J. and Jewett, M.C. 2014. Enabling a next generation of synthetic biology community organization and leadership. ACS Synthetic Biology. 3: 117-120.

28

Gan, R. and Jewett, M.C. 2014. A combined cell-free transcription-translation system from Saccharomyces cerevisiae for rapid and robust protein synthesis. Biotechnology Journal. 9: 641-651. (Top 10 cited article published in 2014)

27

Hong, S.H., Ntai, I., Haimovich, A.D., Kelleher, N.L., Isaacs, F.J., and Jewett, M.C. 2014. Cell-free protein synthesis from a release factor 1 deficient Escherichia coli activates efficient and multiple site-specific non-standard amino acid incorporation. ACS Synthetic Biology. 3: 398–409. (On the cover)

2013

26

Schoborg, J.A., Hodgman, C.E., Anderson, M.J., and Jewett, M.C. 2013. Substrate replenishment and byproduct removal improve yeast cell-free protein synthesis. Biotechnology Journal. 9: 630-640.

25

Kang, Y., Lu, A., Ellington, A.D., Jewett, M.C., and O’Reilly, R.K. 2013. Effect of complementary nucleobase interactions on the copolymer composition of RAFT copolymerizations. ACS Macromolecules. 2: 581-586.

24

Hodgman, C.E. and Jewett, M.C. 2013. Optimized extract preparation methods and reaction conditions for improved yeast cell-free protein synthesis. Biotechnology and Bioengineering. 10: 2643-2654.

23

Jewett, M.C., Fritz, B.R., Timmerman, L.E., and Church, G.M. 2013. In vitro integration of ribosomal RNA synthesis, ribosome assembly, and protein synthesis. Molecular Systems Biology. 9: 678.

22

Jewett, M.C., Workman, C.T., Nookaew, I., Pizarro, F.P., Hellgren, L., and Nielsen, J. 2013. Mapping condition-dependent regulation of lipid metabolism in Saccharomyces cerevisiae. G3: Genes, Genomes, Genetics. 3: 1979-1995.

2012

21

Hockenberry, A.J. and Jewett M.C. 2012. Synthetic in vitro circuits. Current Opinion in Chemical Biology. 16: 253-259.

20

Harris, D.C. and Jewett M.C. 2012. Cell-free biology: Exploiting the interface between synthetic biology and synthetic chemistry. Current Opinion in Biotechnology. 5: 672-678.

19

Carlson, E.D., Gan, R., Hodgman, C.E., and Jewett M.C. 2012. Cell-free protein synthesis: Applications come of age. Biotechnology Advances. 30: 1185-1194.

18

Hodgman, C.E. and Jewett, M.C. 2012. Cell-free synthetic biology: Thinking outside the cell. Metabolic Engineering. 14: 261–269. (Top Download: Sep 1, 2011 – May 31, 2012)

17

Wang, H.H., Huang, P-Y., Xu, G., Haas, W., Marblestone, A., Li, J., Gygi, S., Forster, A.C., Jewett, M.C., and Church, G.M. 2012. In vivo tagging of enzyme ensembles with MAGE for in vitro single-pot multi-enzyme catalysis. ACS Synthetic Biology. 1: 43-52.

2004-2011

16

Isaacs, F.J., Carr, P.A., Wang, H.H., Sterling, B., Lajoie, M.J., Kraal, L., Tolonen, A., Reppas, N.B., Emig, C.J., Bang, D., Hwang, S.J., Jewett, M.C., Jacobson, J.M., and Church, G.M. 2011. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science. 333: 348-353.

15

Fritz, B.R., Timmerman, L.E., Daringer, N.M., Leonard, J.N., and Jewett, M.C. 2010. Biology by design: From top to bottom… and back. Journal of Biomedicine and Biotechnology. 232016.

14

Jewett, M.C. and Forster, A.C. 2010. Update on designing and building minimal cells. Current Opinion in Biotechnology. 21: 697-703.

13

Usaite, R., Jewett, M.C., Oliveira, A.P., Yates, J.R., Olsson, L., and Nielsen, J. 2009. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Molecular Systems Biology. 5: 319. (Top 10 Download in 2009)

12

Moxley, J.F., Jewett, M.C., Antoniewicz, M.R., Villas-Boas, S.G., Alper, H.S., Wheeler, R.T., Tong, L., Hinnebusch, A.G., Ideker, T., Nielsen, J., and Stephanopoulos, G.N. 2009. Linking high resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. PNAS. 106: 6477-6482. (On the Cover: Complex Systems: From Chemistry to Systems Biology Special Feature; Faculty of 1000 Biology)

11

Jewett, M.C., Miller, M.L., Chen, Y., and Swartz, J.R. 2009. Continued protein synthesis at low [ATP] and [GTP] enables cell adaptation during starvation. Journal of Bacteriology. 191: 1083-1091.

10

Jewett, M.C., Calhoun, K.A., Voloshin, A., Wuu, J.J., and Swartz, J.R. 2008. An integrated cell-free metabolic platform for protein production and synthetic biology. Molecular Systems Biology. 4: 220. (Top 10 Download in 2008)

9

Pizarro, F.J., Jewett, M.C., Nielsen, J., and Agosin, E. 2008. Physiological and transcriptional mapping of evolutionary differences between commercial and laboratory Saccharomyces cerevisiae strains. Applied Environmental Microbiology. 74: 6358-6368.

8

Nookaew, N., Jewett, M.C., Meechai, A., Thammarongtham, C., Laoteng, K., Cheevadhanarak, S., Nielsen, J., and Bhumiratana, S. 2008. The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: A scaffold to query lipid metabolism. BMC Systems Biology. 2: 71. (Highly accessed)

7

Fazio, A., Jewett, M.C., Daran-Lapujade, P., Mustacchi, R., Usaite, R., Pronk, J.T., Workman, C.T., and Nielsen, J. 2008. Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design. BMC Genomics. 9: 341. (Highly accessed)

6

Nielsen, J. and Jewett, M.C. 2008. The impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Research. 8: 122-131.

5

Jewett, M.C., Hofmann, G., and Nielsen, J. 2006. Fungal metabolite analysis in genomics and phenomics. Current Opinion in Biotechnology. 17: 191-197.

4

Jewett, M.C., Oliveira, A.P., Patil, K.R., and Nielsen, J. 2005. The role of high-throughput transcriptome analysis in metabolic engineering. Biotechnology and Bioprocess Engineering. 10: 385-399.

3

Jewett, M.C. and Swartz, J.R. 2004. Substrate replenishment extends protein synthesis with an in vitro system designed to mimic the cytoplasm. Biotechnology and Bioengineering. 87: 465-472.

2

Jewett, M.C. and Swartz, J.R. 2004. Mimicking the Escherichia coli cytoplasmic environment activates long-lived and efficient protein synthesis. Biotechnology and Bioengineering. 86: 19-26.

1

Jewett, M.C. and Swartz, J.R. 2004. Rapid expression and purification of 100 nmol quantities of active protein using cell-free protein synthesis. Biotechnology Progress. 20: 102-109.

Book Chapters

12

Bidstrup, E., Kwon, Y.H., Kim, K., Bandi, C.K., Aw, R., Jewett, M.C., and. DeLisa, M.P. 2023. Cell-Free Systems for the Production of Glycoproteins, in Recombinant Glycoproteins: Methods and Protocols, Methods in Molecular Biology, vol. 2762, Steven B. Bradfute, editor.

11

Rasor, B.J., Vogeli, B., Jewett, M.C., and Karim, A.S. 2021. Cell-free protein synthesis for high-throughput biosynthetic pathway prototyping, in Cell-Free Gene Expression: Methods in Molecular Biology, Vol. 2433, Ashty S. Karim and Michael C. Jewett, editors. 199-215.

10

Lee, J., Kim, D.S., and Jewett, M.C. 2020. Recent advances in engineering ribosomes for natural product biosynthesis, in Comprehensive Natural Products III: Chemistry and Biology, Chaitan Khosla, Jay Keasling, and Sean Brady, editors. Elsevier. 6: 377-397.

9

Schoborg, J.A. and Jewett, M.C. 2018. Cell-free protein synthesis: An emerging technology for understanding, harnessing, and expanding the capabilities of biological systems, in Synthetic Biology, Christina Smolke, editor. Wiley Biotechnology Series. 8: 309-330.

8

Karim, A.S., Dudley, Q.M., and Jewett, M.C. 2017. Cell-free synthetic systems for metabolic engineering and biosynthetic pathway prototyping, in Industrial Biotechnology, James C. Liao, Christoph Wittman, editors. Wiley Biotechnology Series. 125-148.

7

Perez, J.G., Stark, J.C., and Jewett, M.C. 2016. Cell-free synthetic biology: Engineering beyond the cell, in Synthetic Biology, J. Craig Venter, Daniel Gibson, Hamilton Smith, Clyde Hutchison, editors. Cold Spring Harbor Laboratory Press. a023853.

6

Ranji, A., Wu, J.C., Bundy, B.C., and Jewett, M.C. 2013. Transforming synthetic biology with cell-free systems, in Synthetic Biology, Huimin Zhao, editor. Waltham, MA, Elsevier. 277-301.

5

Oliveira, A.P., Jewett, M.C., and Nielsen, J. 2007. From gene expression to metabolic fluxes, in Introduction to Systems Biology, Sangdun Choi, editor. Totowa, NJ, Humana Press Inc. 37-68.

4

Nielsen J. and Jewett, M.C. 2007. The role of metabolomics in systems biology, in Metabolomics: A powerful tool in systems biology, Jens Nielsen, Michael C. Jewett, editors. Topics in Current Genetics Series. Heidelberg, Germany, Springer. 1-10.

3

Jewett, M.C., Hansen, M.E., and Nielsen J. 2007. Data acquisition, analysis, and mining: Integrative tools for discerning metabolic function in Saccharomyces cerevisiae, in Metabolomics: A powerful tool in systems biology, Jens Nielsen, Michael C. Jewett, editors. Topics in Current Genetics Series. Heidelberg, Germany, Springer. 159-187.

2

Swartz, J.R., Jewett, M.C., and Woodrow, K.A. 2004. Cell-free protein synthesis with prokaryotic combined transcription-translation, in Recombinant Protein Protocols: Methods in Molecular Biology Series, Paulina Balbas, Argelia Lorence, editors. Totowa, NJ, Humana Press Inc. 267: 169-182.

1

Jewett, M.C., Voloshin, A., and Swartz, J.R. 2002. Prokaryotic systems for in vitro Expression, in Gene Cloning and Expression Technologies, Michael Weiner, Quinn Lu, editors. Westborough, MA, Eaton Publishing. 391-411.

Patents

21

Jewett, M.C. Dudley. Q.M., Li, J., and Karim, A. 2024. Cell-free protein synthesis driven metabolic engineering. US Patent 11,913,052.

20

Kightlinger, W., Lin, L., Mrksich, M., and Jewett, M.C. 2024. Design of protein glycosylation sites by rapid expression and characterization of N-glycosyltransferases. U.S. Patent No. 11,898,187.

19

Jewett, M.C., Lee, J., Schwieter, K.E., and Moore, J. 2023. Expanding chemical substrates for genetic code reprogramming. U.S. Patent No. 11,814,621.

18

Jewett, M.C. Hershewe, J., and Stark, J.C. 2023. Methods for co-activating in vitro non-standard amino acid incorporation and glycosylation in crude cell lysates. U.S. Patent No. 11,725,224.

17

Jewett, M.C., Stark, J.C., DeLisa, M.P., and Jaroentomeechai, T. 2022. Compositions and methods for rapid in vitro synthesis of bioconjugate vaccines in vitro via production and N-glycosylation of protein carriers in detoxified prokaryotic cell lysates. U.S. Patent No. 11,530,432.

16

Jewett, M.C. Davidson, S., and Des Soye, B. 2019.Cell-free protein synthesis platform derived from cellular extracts of Vibrio natriegens. U.S. Patent No. 11,673,921.

15

Jewett, M.C., Stark, J.C., DeLisa, M.P., and Jaroentomeechai, T. 2023. Method for rapid in vitro synthesis of glycoproteins via recombinant production of N-glycosylated proteins in prokaryotic cell lysates. U.S. Patent No. 11,542,538.

14

Jewett, M.C., Stark, J.C., DeLisa, M.P., and Jaroentomeechai, T. 2022. Cell-free glycoprotein synthesis (CFGpS) in prokaryotic cell lysates enriched with components for glycosylation. U.S. Patent No. 11,453,901.

13

Jewett, M.C., Carlson, E.D., Orelle, C., dAquino, A.E., Kim, D.S., Szal, T., and Mankin, A.S. 2020. Ribosomes with tethered subunits. U.S. Patent No. 10,590,456.

12

Jewett, M.C. and Karim, A. 2020. Cell-free protein synthesis driven metabolic engineering for the production of 1-butanol. U.S. Patent No. 10,577,632.

11

Jewett, M.C. and Des Soye, B. 2019. Genomically recoded organisms lacking release factor 1 (RF1) and engineered to express a heterologous RNA polymerase. U.S. Patent No. 10,465,221.

10

Jewett, M.C. and Fritz, B.R. 2019. Method to in vitro ribosome synthesis and evolution. U.S. Patent No. 10,457,932.

9

Jewett, M.C., Stark, J.C., DeLisa, M.P., and Jaroentomeechai, T. 2018. Method for rapid in vitro synthesis of glycoproteins via recombinant production of N-glycosylated proteins in prokaryotic cell lysates. U.S. Patent No. 10,829,795.

8

Jewett, M.C., Hong, S.H., Kwon, Y.C., Martin, R.W., and Des Soye, B.J. 2018. Platforms for cell-free protein synthesis comprising extracts from genomically recoded E. coli strains having genetic knock-out mutations in release factor 1 (RF-1) and endA. U.S. Patent No. 10,118,950.

7

Jewett, M.C., Fritz, B.R., Timmerman, L.E., and Liu, Y. 2018. Improved methods for making ribosomes. U.S. Patent No. 10,017,728.

6

Jewett, M.C., Schoborg, J.A., and Hodgman, C.E. 2018. Substrate replenishment and byproduct removal improve yeast cell-free protein synthesis. U.S. Patent No. 9,951,392.

5

Jewett, M.C., Hodgman, C.E., and Gan, R. 2016. Methods for cell-free protein synthesis. U.S. Patent No. 9,528,137.

4

Swartz, J.R., Calhoun, K.A., and Jewett, M.C. 2016. Methods of in vitro protein synthesis. U.S. Patent No. 9,410,170.

3

Swartz, J.R. and Jewett, M.C. 2013. Methods of in vitro protein synthesis. U.S. Patent No. 8,357,529.

2

Bond, R., Jewett, M.C., McAuliffe, J.C., and Ward, D.E. 2010. Biocomposite comprising co-precipitate of enzyme, silicate and polyamine. U.S. Patent No. 7,642,077.

1

Swartz, J.R. and Jewett, M.C. 2008. Methods of in vitro protein synthesis. U.S. Patent No. 7,338,789.