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)
Meet the Members
SFA Manager: Brian Thrall1
SFA Principal Investigators: Robert Egbert1
KBase Contacts: Chris Henry2,3, Janaka Edirisinghe2,3
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
- PerCon SFA GitHub Repository
- Peptide Fingerprinting Predicts Function using Protein Annotation Tool – Research Highlight