Persistence Control SFA

Understanding the genetic determinants of environmental persistence, from microbe to community to ecosystem.

The Persistence Control of Engineered Functions in Complex Soil Microbiomes Science Focus Area (PerCon SFA), led by Dr. Robert Egbert at Pacific Northwest National Laboratory (PNNL), explores the potential to specify and control environmental niche for synthetic microbiomes deployed in rhizospheres to ensure safe deployment of productive and resilient bioenergy crops. Preventing the complementation of niche restrictions in synthetic communities (SynComs) requires a fundamental understanding of the connection between genotype and phenotype (function) in an organism, within communities, and in the context of the environment.

Collaborative Development Object

Improved protein annotation using machine learning, multi-omics data integration, and structural prediction

• Snekmer: Recodes, kmerizes (short protein sequences), and vectorizes curated protein sequences for machine learning training set(s) that represent targeted functional annotation profiles or to generate de novo clusters of protein families. (Beta-only)

Additional Information

Meet the Members

SFA Manager: Brian Thrall¹
SFA Principal Investigators: Robert Egbert¹
KBase Contacts: Chris Henry^2,3, Janaka Edirisinghe^2,3
Lead Developers: William Nelson¹
Project Team Leads: Adam Deutschbauer⁴, Neeraj Kumar¹, Jason McDermott¹

Affiliations: ¹Pacific Northwest National Laboratory, ²Argonne National Laboratory, ³KBase, ⁴Lawrence Berkeley National Laboratory

Resources

• PerCon SFA GitHub Repository
• Peptide Fingerprinting Predicts Function using Protein Annotation Tool – Research Highlight