Complex webs of life integrate and drive processes that affect outcomes from the individual health of a human or plant to entire planetary mineral cycles. Our laboratory leverages quantitative measurements, precision genetics, and model-driven experimentation to predict, control, and design biological function in the context of these webs. We are especially interested in understanding and ameliorating the processes that are interlinked with the radical changes our planet is and will be experiencing as climate is forced, populations grow, and pressures are placed on the resources we use to survive. We are also interested in what it might take to establish ourselves on the next planet as humanity begins to consider long term crewed missions on the Moon and Mars. Building safe, sustainable biotechnologies for environmental stewardship, health, food, and materials based on well-informed systems-level bioengineering is our main goal.

Laboratory Values
Just as we recognize the critical importance and value of the diversity of life in the environments we study, we value a diversity of backgrounds, beliefs, and experiences in our laboratory. We appreciate the power that fostering diverse minds brings to our science and our understanding of our mission and impact.


The Department of Energy's Systems Biology Knowledgebase (KBase) is an ambitious program to disrupt the way we do biological systems science for prediction and engineering. It is an open-source, extensible platform that runs on DOE high-end infrastructure and supports collaborative, reproducible, reusable, and openly publishable analyses of organisms and their communities to predict and design their functions.
September 29, 2020/by Academic Web Pages


The Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Scientific Focus Area that we help lead is dedicated to developing a generalizable approach to predictive causal microbial ecology. We seek to molecularly dissect the dispersal, drift, and selective forces that shape the assembly and activity of microbial communities in complex spatially and temporally variable niches.
August 25, 2020/by Academic Web Pages


The Center for the Utilization of Biological Engineering in Space (CUBES) was created to develop generalizable approaches to support biomanufacturing for deep space exploration that realizes the inherent mass, power, and volume advantages of space biotechnology over traditional abiotic approaches.
August 23, 2020/by Academic Web Pages


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.
August 22, 2020/by Academic Web Pages

Paradis, Charles J; Miller, John I; Moon, Ji-Won; Spencer, Sarah J; Lui, Lauren M; Nostrand, Joy D Van; Ning, Daliang; Steen, Andrew D; McKay, Larry D; Arkin, Adam P; Zhou, Jizhong; Alm, Eric J; Hazen, Terry C

Sustained ability of a natural microbial community to remove nitrate from groundwater Journal Article

In: BioRxiv, 2021.

Abstract | Links

Lui, Lauren M; Nielsen, Torben N; Arkin, Adam P

A method for achieving complete microbial genomes and improving bins from metagenomics data. Journal Article

In: PLoS Computational Biology, vol. 17, no. 5, pp. e1008972, 2021.

Abstract | Links

Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I-Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T B K; Nielsen, Torben; Kirton, Edward; Faria, José P; Edirisinghe, Janaka N; Henry, Christopher S; Jungbluth, Sean P; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M; Arkin, Adam P; Tringe, Susannah G; Visel, Axel; IMG,; Woyke, Tanja; Mouncey, Nigel J; Ivanova, Natalia N; Kyrpides, Nikos C; Eloe-Fadrosh, Emiley A

A genomic catalog of Earth's microbiomes. Journal Article

In: Nature Biotechnology, vol. 39, no. 4, pp. 499-509, 2021, ISSN: 1087-0156.

Abstract | Links

All Publications

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