Our publications

Check out all our most up-to-date list of publications on Google Scholar.

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Publications

2025

Characterizing and engineering post-translational modifications with high-throughput cell-free expression
Wong, Derek A; Shaver, Zachary M; Cabezas, Maria D; Daniel-Ivad, Martin; Warfel, Katherine F; Prasanna, Deepali V; Sobol, Sarah E; Fernandez, Regina; Tobias, Fernando; Filip, Szymon K; et al.
Nature communications, 16(1), 7215
A scalable cell-free manufacturing platform for two-step bioproduction of immunogenic conjugate vaccines
Wong, Derek A; Aw, Rochelle; Hulbert, Sophia W; Qin, Yufan; Shaver, Zachary M; Myers, Kathryn A; Karim, Ashty S; DeLisa, Matthew P; Jewett, Michael C
bioRxiv, 2025.08.05.668792
Active learning-guided optimization of cell-free biosensors for lead testing in drinking water
Wang, Brenda M; Chiang, Nicole; Ekas, Holly M; Brown, Dylan M; Dildine, Garrett; Lucci, Tyler J; Feng, Siyuang; Bly, Vanessa; Gaillard, Jean-François; Lucks, Julius B; et al.
bioRxiv, 2025.08.20.671382
Design-driven optimization of low-cost reagent formulations for reproducible and high-yielding cell-free gene expression
Olsen, Meagan L; Copeland, Caroline E; Sundberg, Chad A; Aw, Rochelle; Shaver, Zachary M; Rao, Govind; Swartz, James R; Karim, Ashty S; Jewett, Michael C
bioRxiv, 2025.08.01.668204
Semiautomated Production of Cell-Free Biosensors
Brown, Dylan M; Phillips, Daniel A; Garcia, David C; Arce, Anibal; Lucci, Tyler; Davies Jr, John P; Mangini, Jacob T; Rhea, Katherine A; Bernhards, Casey B; Biondo, John R; et al.
ACS synthetic biology, 14(3), 979-986
Scalable Cell‐Free Production of Active T7 RNA Polymerase
Rezvani, Ryan N; Aw, Rochelle; Chan, Wei; Satish, Krishnathreya; Chen, Han; Lavy, Adi; Rimal, Swechha; Patel, Divyesh A; Rao, Govind; Swartz, James R; et al.
Biotechnology and Bioengineering
Cell-Free Expression of Soluble Leafhopper Proteins from Brochosomes
Lay, Caleb G; Burks, Gabriel R; Li, Zheng; Barrick, Jeffrey E; Schroeder, Charles M; Karim, Ashty S; Jewett, Michael C
ACS synthetic biology, 14(3), 987-994
Accelerated enzyme engineering by machine-learning guided cell-free expression
Landwehr, Grant M; Bogart, Jonathan W; Magalhaes, Carol; Hammarlund, Eric G; Karim, Ashty S; Jewett, Michael C
Nature communications, 16(1), 865
Systems and methods for cell-free iterative site saturation mutagenesis and its application for the directed evolution of enzymes catalyzing unnatural reactions
Jewett, Micahel C; Bogart, Jonathan W; Landwehr, Grant M; Karim, Ashty Stephen
US Patent App. 18/878,530

2021 – 2024

Cell-free gene expression: methods and applications
Hunt, Andrew C; Rasor, Blake J; Seki, Kosuke; Ekas, Holly M; Warfel, Katherine F; Karim, Ashty S; Jewett, Michael C
Chemical Reviews, 125(1), 91-149
An automated cell-free workflow for transcription factor engineering
Ekas, Holly M; Wang, Brenda; Silverman, Adam D; Lucks, Julius B; Karim, Ashty S; Jewett, Michael C
ACS synthetic biology, 13(10), 3389-3399
Engineering a PbrR-based biosensor for cell-free detection of lead at the legal limit
Ekas, Holly M; Wang, Brenda; Silverman, Adam D; Lucks, Julius B; Karim, Ashty S; Jewett, Michael C
ACS synthetic biology, 13(9), 3003-3012
A synthetic cell-free pathway for biocatalytic upgrading of one-carbon substrates
Landwehr, Grant M; Vogeli, Bastian; Tian, Cong; Singal, Bharti; Gupta, Anika; Lion, Rebeca; Sargent, Edward H; Karim, Ashty S; Jewett, Michael C
bioRxiv
Cell-free translation quantification via a fluorescent minihelix
Willi, Jessica A; Karim, Ashty S; Jewett, Michael C
ACS synthetic biology, 13(7), 2253-2259
Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists
Karim, Ashty S; Brown, Dylan M; Archuleta, Chloé M; Grannan, Sharisse; Aristilde, Ludmilla; Goyal, Yogesh; Leonard, Josh N; Mangan, Niall M; Prindle, Arthur; Rocklin, Gabriel J; et al.
Nature communications, 15(1), 5425
Ribosome Pool Engineering Increases Protein Biosynthesis Yields
Kofman, Camila; Willi, Jessica A; Karim, Ashty S; Jewett, Michael C
ACS Central Science, 10(4), 871-881
Cell-free protein synthesis driven metabolic engineering
Jewett, Michael Christopher; Karim, Ashty Stephen; Li, Jian; Dudley, Quentin
US Patent 11,913,052
Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping
Yi, Xiunan; Rasor, Blake J; Boadi, Nathalie; Louie, Katherine; Northen, Trent R; Karim, Ashty S; Jewett, Michael C; Alper, Hal S
Metabolic Engineering, 80, 241-253
A rapid cell-free expression and screening platform for antibody discovery
Hunt, Andrew C; Vögeli, Bastian; Hassan, Ahmed O; Guerrero, Laura; Kightlinger, Weston; Yoesep, Danielle J; Krüger, Antje; DeWinter, Madison; Diamond, Michael S; Karim, Ashty S; et al.
Nature communications, 14(1), 3897
A Cell-Free Gene Expression Platform for Discovering and Characterizing Stop Codon Suppressing tRNAs
Seki, Kosuke; Galindo, Joey L; Karim, Ashty S; Jewett, Michael C
ACS chemical biology, 18(6), 1324-1334
Cell extracts from bacteria and yeast retain metabolic activity after extended storage and repeated thawing
Rasor, Blake J; Karim, Ashty S; Alper, Hal S; Jewett, Michael C
ACS synthetic biology, 12(3), 904-908
Mechanistic insights into cell-free gene expression through an integrated-omics analysis of extract processing methods
Rasor, Blake J; Chirania, Payal; Rybnicky, Grant A; Giannone, Richard J; Engle, Nancy L; Tschaplinski, Timothy J; Karim, Ashty S; Hettich, Robert L; Jewett, Michael C
ACS synthetic biology, 12(2), 405-418
At-home, cell-free synthetic biology education modules for transcriptional regulation and environmental water quality monitoring
Jung, Jaeyoung K; Rasor, Blake J; Rybnicky, Grant A; Silverman, Adam D; Standeven, Janet; Kuhn, Robert; Granito, Teresa; Ekas, Holly M; Wang, Brenda M; Karim, Ashty S; et al.
ACS synthetic biology, 12(10), 2909-2921
Point-of-care peptide hormone production enabled by cell-free protein synthesis
DeWinter, Madison A; Thames, Ariel Helms; Guerrero, Laura; Kightlinger, Weston; Karim, Ashty S; Jewett, Michael C
ACS synthetic biology, 12(4), 1216-1226
A dynamic kinetic model captures cell-free metabolism for improved butanol production
Martin, Jacob P; Rasor, Blake J; DeBonis, Jonathon; Karim, Ashty S; Jewett, Michael C; Tyo, Keith EJ; Broadbelt, Linda J
Metabolic Engineering, 76, 133-145
Computationally-guided design and selection of high performing ribosomal active site mutants
Kofman, Camila; Watkins, Andrew M; Kim, Do Soon; Willi, Jessica A; Wooldredge, Alexandra C; Karim, Ashty S; Das, Rhiju; Jewett, Michael C
Nucleic acids research, 50(22), 13143-13154
A low-cost, thermostable, cell-free protein synthesis platform for on-demand production of conjugate vaccines
Warfel, Katherine F; Williams, Asher; Wong, Derek A; Sobol, Sarah E; Desai, Primit; Li, Jie; Chang, Yung-Fu; DeLisa, Matthew P; Karim, Ashty S; Jewett, Michael C
ACS synthetic biology, 12(1), 95-107
Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria
Vögeli, Bastian; Schulz, Luca; Garg, Shivani; Tarasava, Katia; Clomburg, James M; Lee, Seung Hwan; Gonnot, Aislinn; Moully, Elamar Hakim; Kimmel, Blaise R; Tran, Loan; et al.
Nature communications, 13(1), 3058
Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences
Rybnicky, Grant A; Fackler, Nicholas A; Karim, Ashty S; Köpke, Michael; Jewett, Michael C
Nucleic acids research, 50(6), 3523-3534
Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale
Liew, Fungmin Eric; Nogle, Robert; Abdalla, Tanus; Rasor, Blake J; Canter, Christina; Jensen, Rasmus O; Wang, Lan; Strutz, Jonathan; Chirania, Payal; De Tissera, Sashini; et al.
Nature biotechnology, 40(3), 335-344
Cell-free protein synthesis for high-throughput biosynthetic pathway prototyping
Rasor, Blake J; Vögeli, Bastian; Jewett, Michael C; Karim, Ashty S
Cell-Free Gene Expression: Methods and Protocols, 199-215
Improving genomically recoded Escherichia coli to produce proteins containing non‐canonical amino acids
Perez, Jessica G; Carlson, Erik D; Weisser, Oliver; Kofman, Camila; Seki, Kosuke; Des Soye, Benjamin J; Karim, Ashty S; Jewett, Michael C
Biotechnology journal, 17(4), 2100330
Development of a freeze-dried CRISPR-Cas12 sensor for detecting wolbachia in the secondary science classroom
Rybnicky, Grant A; Dixon, Radeen A; Kuhn, Robert M; Karim, Ashty S; Jewett, Michael C
ACS synthetic biology, 11(2), 835-842
Cell-Free Gene Expression
Karim, Ashty S; Jewett, Michael C
Methods in Molecular Biology
Modular, cell-free protein expression vectors to accelerate biological design in cells
Jewett, Michael C; Karim, Ashty S; Koepke, Michael; Juminaga, Darmawi; Liew, Fungmin
Patent
Analysis of the innovation trend in cell-free synthetic biology
Meyer, Conary; Nakamura, Yusuke; Rasor, Blake J; Karim, Ashty S; Jewett, Michael C; Tan, Cheemeng
Life, 11(6), 551
Toward sustainable, cell-free biomanufacturing
Rasor, Blake J; Vögeli, Bastian; Landwehr, Grant M; Bogart, Jonathan W; Karim, Ashty S; Jewett, Michael C
Current Opinion in Biotechnology, 69, 136-144
Cell‐free exploration of the natural product chemical space
Bogart, Jonathan W; Cabezas, Maria D; Vögeli, Bastian; Wong, Derek A; Karim, Ashty S; Jewett, Michael C
ChemBioChem, 22(1), 84-91

2020 and Before

Modular cell-free expression plasmids to accelerate biological design in cells
Karim, Ashty S; Liew, Fungmin; Garg, Shivani; Vögeli, Bastian; Rasor, Blake J; Gonnot, Aislinn; Pavan, Marilene; Juminaga, Alex; Simpson, Séan D; Köpke, Michael; et al.
Synthetic Biology, 5(1), ysaa019
In vitro prototyping of limonene biosynthesis using cell-free protein synthesis
Dudley, Quentin M; Karim, Ashty S; Nash, Connor J; Jewett, Michael C
Metabolic Engineering, 61, 251-260
Total in vitro biosynthesis of the nonribosomal macrolactone peptide valinomycin
Zhuang, Lei; Huang, Shuhui; Liu, Wan-Qiu; Karim, Ashty S; Jewett, Michael C; Li, Jian
Metabolic engineering, 60, 37-44
Cell-free styrene biosynthesis at high titers
Grubbe, William S; Rasor, Blake J; Krüger, Antje; Jewett, Michael C; Karim, Ashty S
Metabolic Engineering, 61, 89-95
Cell-free gene expression: an expanded repertoire of applications
Silverman, Adam D; Karim, Ashty S; Jewett, Michael C
Nature Reviews Genetics, 21(3), 151-170
Enhancing control of cell-free metabolism through pH modulation
Karim, Ashty S; Rasor, Blake J; Jewett, Michael C
Synthetic Biology, 5(1), ysz027
In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design
Karim, Ashty S; Dudley, Quentin M; Juminaga, Alex; Yuan, Yongbo; Crowe, Samantha A; Heggestad, Jacob T; Abdalla, Tanus; Grubbe, William; Rasor, Blake; Coar, Dave; et al.
Nature Chemical Biology, 16, 912-919
Cell-free protein synthesis driven metabolic engineering for the production of 1-butanol
Jewett, Michael Christopher; Karim, Ashty Stephen
US Patent 10,577,632
High-throughput optimization cycle of a cell-free ribosome assembly and protein synthesis system
Caschera, Filippo; Karim, Ashty S; Gazzola, Gianluca; d’Aquino, Anne E; Packard, Norman H; Jewett, Michael C
ACS synthetic biology, 7(12), 2841-2853
Cell-free synthetic biology for pathway prototyping
Karim, Ashty S; Jewett, Michael C
Methods in enzymology, 608, 31-57
A pressure test to make 10 molecules in 90 days: external evaluation of methods to engineer biology
Casini, Arturo; Chang, Fang-Yuan; Eluere, Raissa; King, Andrew M; Young, Eric M; Dudley, Quentin M; Karim, Ashty; Pratt, Katelin; Bristol, Cassandra; Forget, Anthony; et al.
Journal of the American Chemical Society, 140(12), 4302-4316
Controlling cell-free metabolism through physiochemical perturbations
Karim, Ashty S; Heggestad, Jacob T; Crowe, Samantha A; Jewett, Michael C
Metabolic engineering, 45, 86-94
A Cell-Free Framework for Rapid Enzymatic Pathway Prototyping and Discovery
Karim, Ashty Stephen
Ph.D. Thesis, Northwestern University
Cell‐free synthetic systems for metabolic engineering and biosynthetic pathway prototyping
Karim, Ashty S; Dudley, Quentin M; Jewett, Michael C
Industrial Biotechnology: Microorganisms, 1, 125-148
A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery
Karim, Ashty S; Jewett, Michael C
Metabolic engineering, 36, 116-126
Cell‐free metabolic engineering: biomanufacturing beyond the cell
Dudley, Quentin M; Karim, Ashty S; Jewett, Michael C
Biotechnology journal, 10(1), 69-82
Design of synthetic yeast promoters via tuning of nucleosome architecture
Curran, Kathleen A; Crook, Nathan C; Karim, Ashty S; Gupta, Akash; Wagman, Allison M; Alper, Hal S
Nature communications, 5(1), 4002
Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications
Curran, Kathleen A; Karim, Ashty S; Gupta, Akash; Alper, Hal S
Metabolic engineering, 19, 88-97
Metabolic engineering of muconic acid production in Saccharomyces cerevisiae
Curran, Kathleen A; Leavitt, John M; Karim, Ashty S; Alper, Hal S
Metabolic engineering, 15, 55-66
Characterization of plasmid burden and copy number in Saccharomyces cerevisiae for optimization of metabolic engineering applications
Karim, Ashty S; Curran, Kathleen A; Alper, Hal S
FEMS yeast research, 13(1), 107-116