Biodesign

Synthetic biology

Our lab has been involved in Synthetic Biology since its inception developing fundamental genetic technologies for precise and predictable control of gene expression, uniform design of gene expression networks, technologies for genome-scale manipulation and characterization of gene function; the design of host strains optimized for engineering for different applications; and foundational genetic and computational/data science technologies that support the creation of biofoundries. We are very interested in predictable engineering in complex contexts beyond the bioreactor. Such applications emphasize the need for predictive/predictable, actuarily trustworthy biological design technologies.  We have ongoing projects involving the engineering of microbes, microbial communities, and bacteriophage cocktails for applications in sustainable materials production and biomass utilization, agriculture, bioremediation, and human health. We are most interested in those applications that have existential implications for humans on earth- from solutions for antibiotic resistance to terraforming.

Selected Publications

Ashley L. Azadeh Sean Carim, Alexey E. Kazakov

Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins Journal Article

In: 2020.

BibTeX

Crystal Zhong Benjamin A. Adler, Hualan Liu

Systematic Discovery of Salmonella Phage-Host Interactions via High-Throughput Genome-Wide Screens Journal Article

In: bioRxiv, 2020.

BibTeX

Benjamin A. Adler Vivek K. Mutalik, Harneet S. Rishi

High-throughput mapping of the phage resistance landscape in E. coli Journal Article

In: 2020.

BibTeX

Egbert, R G; Rishi, H S; Adler, B A; McCormick, D M; Toro, E; Gill, R T; Arkin, A P

A versatile platform strain for high-fidelity multiplex genome editing Journal Article

In: Nucleic Acids Res., 47 (6), pp. 3244–3256, 2019.

Abstract | BibTeX

Price, M N; Zane, G M; Kuehl, J V; Melnyk, R A; Wall, J D; Deutschbauer, A M; Arkin, A P

Correction: Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics Journal Article

In: PLoS Genet., 15 (4), pp. e1008106, 2019.

Abstract | BibTeX

Tei, M; Perkins, M L; Hsia, J; Arcak, M; Arkin, A P

Đesigning Spatially Đistributed Gene Regulatory Networks Ŧo Elicit Contrasting Patterns Journal Article

In: 8 (1), pp. 119–126, 2019.

Abstract | BibTeX

Mutalik, V K; Novichkov, P S; Price, M N; Owens, T K; Callaghan, M; Carim, S; Deutschbauer, A M; Arkin, A P

Đual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria Journal Article

In: Nat Commun, 10 (1), pp. 308, 2019.

Abstract | BibTeX

Thompson, M G; Blake-Hedges, J M; Cruz-Morales, P; Barajas, J F; Curran, S C; Eiben, C B; Harris, N C; Benites, V T; Gin, J W; Sharpless, W A; Twigg, F F; Skyrud, W; Krishna, R N; Pereira, J H; Baidoo, E E K; Petzold, C J; Adams, P D; Arkin, A P; Deutschbauer, A M; Keasling, J D

Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism Journal Article

In: mBio, 10 (3), 2019.

Abstract | BibTeX

Price, M N; Ray, J; Iavarone, A T; Carlson, H K; Ryan, E M; Malmstrom, R R; Arkin, A P; Deutschbauer, A M

Oxidative Pathways of Đeoxyribose and Đeoxyribonate Catabolism Journal Article

In: mSystems, 4 (1), 2019.

Abstract | BibTeX

Venturelli, O S; Carr, A C; Fisher, G; Hsu, R H; Lau, R; Bowen, B P; Hromada, S; Northen, T; Arkin, A P

Đeciphering microbial interactions in synthetic human gut microbiome communities Journal Article

In: Mol. Syst. Biol., 14 (6), pp. e8157, 2018.

Abstract | BibTeX

Price, M N; Zane, G M; Kuehl, J V; Melnyk, R A; Wall, J D; Deutschbauer, A M; Arkin, A P

Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics Journal Article

In: PLoS Genet., 14 (1), pp. e1007147, 2018.

Abstract | BibTeX

Coradetti, S T; Pinel, D; Geiselman, G M; Ito, M; Mondo, S J; Reilly, M C; Cheng, Y F; Bauer, S; Grigoriev, I V; Gladden, J M; Simmons, B A; Brem, R B; Arkin, A P; Skerker, J M

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides Journal Article

In: Elife, 7 , 2018.

Abstract | BibTeX