The Systems and Synthetic Biology Group

We focus on designing microbes and microbial communities for clean energy and improved safeguards for the environment and human health.  We use systems biology approaches to gain a predictive understanding of complex biological systems and uncover foundational design rules that govern system behavior.  Synthetic biology enables rational genome-scale redesign of organisms/communities and construction of biological systems with desired traits for specific applications.  Multidisciplinary approaches that cover molecular biology, biochemistry, and “omics” are used to investigate microbes and microbial communities as they respond to perturbations, especially those relevant to emerging issues in bioenergy, bioremediation, and pathogenesis.

Recent Publications

Prokaryotic Genome Annotation
J. A. Kimbrel, B. M. Jeffrey, C. S. Ward
Microbial Systems Biology (2022) 193-214.

Bridging Hydrometallurgy and Biochemistry: A Protein-based Process for Recovery and Separation of Rare Earth Elements
Z. Dong, J. A. Mattocks, G. J.P. Deblonde, D. Hu, Y. Jiao, J. A Cotruvo, Park, D.M.
ACS Central Science (2021).

Janthinobacter additions reduce rotifer grazing of microalga Microchloropsis salina in biotically complex communities
C. S. Ward, K. Rolison, M. Li, S. Rozen, C. L. Fisher, T. W. Lane, M. P. Thelen, R. K. Stuart
Algal Research (2021). 58, 102400.

A biosorption-based approach for selective extraction of rare earth elements from coal byproducts
D. M. Park, A. Middleton, R. Smith, G. Deblonde, D. Laudal, N. Theaker, H. Hsu-Kim, Y. Jiao.
Separation and Purification Technology (2020) 241, 116726.

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
A. I. Garber, K. H. Nealson, A. Okamoto, S. M. McAllister, C. S. Chan, R. A. Barco, N. Merino
Frontiers in Microbiology (2020) 11, 37.

Metabolomic Analysis Reveals Contributions of Citric and Citramalic Acids to Rare Earth Bioleaching by a Paecilomyces fungus
V. Brisson, W.-Q. Zhuang, L. Avarez-Cohen
Frontiers in Microbiology (2020) 10, 3008.

Selective collection of iron-rich dust particles by natural Trichodesmium colonies
N. Kessler, R. Armoza-Zvuloni, S. Wang, S. Basu, P. K. Weber, R. K. Stuart, Y. Shaked
The ISME Journal (2020) 14, 91-103.

Encapsulin carrier proteins for enhanced expression of antimicrobial peptides
T-H. Lee, T. S. Carpenter, P. D'haeseleer, D. F. Savage, M. C. Yung
Biotechnology and Bioengineering (2020) 117, 603-613.

Microbe encapsulation for selective rare-earth recovery from electronic waste leachates
A. Brewer, A. Dohnalkova, V. Shutthanandan, L. Kovarik, E. Chang, A. M. Sawvel, H. E. Mason, D. Reed, C. Ye, W. F. Hynes, L. N. Lammers, D. M. ParkY. Jiao
Environmental Science and Technology (2019) 53, 13888-13897.

Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil
V. Brisson, J. E. Schmidt, T. R. Northen, J. P. Vogel, A. C. M. Gaudin
Scientific Reports (2019) 9, 15611.

Guanidine-riboswitch-regulated efflux transporters protect bacteria against ionic liquid toxicity
D. A. Higgins
, J. Gladden, J. A. Kimbrel, B. A. Simmons, S. W. Singer, M. P. Thelen
Journal of Bacteriology (2019) 201, e00069-19.

A combinatorial sensor design in Caulobacter crescentus for selective environmental uranium detection
D. M. Park, M. J. Taffet  
ACS Synthetic Biology (2019) 8, 807-817.