Lawrence Berkeley National Lab
Environmental Genomics & Systems Biology
SFA Technical Co-Manager
aparkin@lbl.gov
(510) 643-5678
Adam Arkin is an expert in the systems and synthetic biology of microbes. His role as the SFA Technical Co-Manager is to ensure the scientific basis of the mission goals, working with the Science Leads and Principal Investigators to develop coherent projects that address high-value problems, especially those of scale. He helps Principal Investigators and Project Scientists effectively plan and execute experiments addressing relevant themes.
The Arkin lab is specifically engaged in developing the metafunctional genomic methods to identify the most important microbes and their environmental correlates in the field to drive prioritizations for isolation and enrichment in the lab; developing new genetic, culturing, and computational methods for mapping genotype-to-phenotype in these laboratory systems; and developing the integrated mechanistic microbial modeling systems for predicting community dynamics under perturbations in the field and laboratory.
Relevant Publications
New Origins of Replication Expand Our Toolkit for Understanding and Engineering Microbial Systems - Microbiology studies benefit immensely from the ability to genetically manipulate the bacterial strain of interest. Transition from purely genomic studies to genetics-enabled molecular biology approaches, often relies on plasmids, or small circular DNA elements distinct from the chromosome. In developing plasmid-based systems, knowledge of the origin of replication (the point at which DNA replication begins) that works with the bacteria’s… More →
ENIGMA Undergraduates Debut Beta Data-Exploration App at CDSS Poster Session - Congratulations to our ENIGMA undergraduate researchers Lia Grace Shamir, Haaziq Kazi, Rohan Samir Panchal, Fion Wu, and Annie Gao, who presented at the Data Discovery Symposium at the Hearst Memorial Mining Building on Wednesday, December 10, 2025. During the poster session, the group presented to Computing, Data Science, and Society (CDSS) 198 students and mentors. Their work focused on creating… More →
Interactive tools for functional annotation of bacterial genomes - ###How to predict a protein’s function or a bacterium’s capabilities Predicting what a bacterium can do from its genome is a complex task that involves understanding the functions of its encoded proteins. While automated software for predicting protein function is widely used, it is prone to errors, with over 10% of automated annotations for bacterial enzymes and transporters being incorrect.… More →
New Tool Enables Overexpression Libraries for High-throughput Protein Characterization - The development of a high-throughput method by for determining the function of predicted proteins of unknown function marks a significant advancement in the field of microbial biology. By utilizing DNA barcode sequencing and auxotrophic strains of E. coli, ENIGMA Researchers at Lawrence Berkeley National Laboratory can now assign functions to many previously uncharacterized genes. This breakthrough enables more complete identification… More →