Publications

Wagner L, Jules M, and Borkowski O*.  What remains from living cells in bacterial lysate-based cell-free systems. Computational and Structural Biotechnology Journal. 2023 May. DOI:10.1016/j.csbj.2023.05.025 | https://pubmed.ncbi.nlm.nih.gov/37333859/ 

Borkowski O, Koch M, Zettor A, Pandi A, Batista AC, Soudier P, and Faulon JL. Large scale active-learning-guided exploration for in vitro protein production optimization. Nat Commun. 2020 Apr 20;11(1):1872. DOI:10.1038/s41467-020-15798-5 | PubMed ID:32312991 

Pandi A, Grigoras I, Borkowski O*, and Faulon JL*. Optimizing Cell-Free Biosensors to Monitor Enzymatic Production. ACS Synth Biol. 2019 Aug 16;8(8):1952-1957. DOI:10.1021/acssynbio.9b00160 | PubMed ID:31335131 

Koch M, Pandi A, Borkowski O, Batista AC, and Faulon JL*. Custom-made transcriptional biosensors for metabolic engineering. Curr Opin Biotechnol. 2019 Oct;59:78-84. DOI:10.1016/j.copbio.2019.02.016 | PubMed ID:30921678 

Koch M, Faulon JL, and Borkowski O*. Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster. Front Bioeng Biotechnol. 2018;6:182. DOI:10.3389/fbioe.2018.00182 | PubMed ID:30555825

Borkowski O, Bricio C, Murgiano M, Rothschild-Mancinelli B, Stan GB, and Ellis T. Cell-free prediction of protein expression costs for growing cells. Nat Commun. 2018 Apr 13;9(1):1457. DOI:10.1038/s41467-018-03970-x | PubMed ID:29654285 

Ceroni F, Boo A, Furini S, Gorochowski TE, Borkowski O, Ladak YN, Awan AR, Gilbert C, Stan GB*, and Ellis T*. Burden-driven feedback control of gene expression. Nat Methods. 2018 May;15(5):387-393. DOI:10.1038/nmeth.4635 | PubMed ID:29578536

Borkowski O, Ceroni F, Stan GB*, and Ellis T*. Overloaded and stressed: whole-cell considerations for bacterial synthetic biology. Curr Opin Microbiol. 2016 Oct;33:123-130. DOI:10.1016/j.mib.2016.07.009 | PubMed ID:27494248 

Borkowski O, Gilbert C, and Ellis T*. SYNTHETIC BIOLOGY. On the record with E. coli DNA. Science. 2016 Jul 29;353(6298):444-5. DOI:10.1126/science.aah4438 | PubMed ID:27471292

Borkowski O, Goelzer A, Schaffer M, Calabre M, Mäder U, Aymerich S, Jules M*, and Fromion V*. Translation elicits a growth rate-dependent, genome-wide, differential protein production in Bacillus subtilis. Mol Syst Biol. 2016 May 17;12(5):870. DOI:10.15252/msb.20156608 | PubMed ID:27193784 

Borkowski O, Drew E, Subsoontorn P. Hands-free control of heterologous gene expression in batch cultures (https://doi.org/10.1101/150375)

Synthetic Biology at the Hand of Cell-Free Systems (https://doi.org/10.1007/978-981-15-0081-7_16)
 

Advances and applications of cell-free systems for metabolic production (https://doi.org/10.1016/B978-0-12-821477-0.00008-8)

Nature Research Bioengineering Community: Active learning leads to highly efficient predictions in cell-free systems (https://bioengineeringcommunity.nature.com/users/382588-olivier-borkowski/posts/66375-active-learning-leads-to-highly-efficient-predictions-in-cell-free-systems)
 

EuSynBioS: Optimization of cell-free biosensors for synthetic biology (https://www.eusynbios.org/blog/2019/9/2/optimization-of-cell-free-biosensors-for-synthetic-biology)