Robert G. Egbert

Conjugative serine recombinase engineering enables genome integration in transformation-resistant bacteria and bioproduction pathway prototyping

This paper introduces cSAGE, a conjugation-based genome engineering platform that enables site-specific integration in transformation-resistant bacteria, demonstrating its utility in bioproduction pathway prototyping.

Rational reduction of a sorghum SynCom that preserves growth promotion reveals flavonoid-mediated plant microbe interactions

The paper reduces a sorghum synthetic microbial community to identify a stable, growth-promoting variant that enhances flavonoid production and plant growth through dynamic gene expression and metabolomic changes.

RhizoGrid: Illuminating Spatial Rhizosphere Dynamics

RhizoGrid integrates 3D-printed pot structures with spatial measurements to explore root-microbe interactions in sorghum rhizosphere.

Single-Molecule Imaging Reveals Transcription-Driven Supercoiling in Unconstrained DNA

The paper shows that transcription by RNAP generates and confines supercoiling in unconstrained DNA through dynamic topological domains.

Snekmer Learn/Apply: A kmer-based vector similarity approach to proteinclassification suitable for metagenomic datasets

The paper introduces an extension to the Snekmer tool that uses kmer libraries to annotate protein sequences with functional annotations, showing improved sensitivity over HMMs in metagenomic datasets.

Efficient genetic code expansion tools enable in vivo study of lysine acetylation in non-model bacteria

This paper develops a genetic code expansion platform for in vivo study of lysine acetylation in non-model bacteria, demonstrating its use in a non-E. coli strain.

Reinforced CRISPR interference enables reliable multiplex gene repression in phylogenetically distant bacteria

This paper develops a CRISPRi platform for multiplex gene repression in diverse bacteria, demonstrating its effectiveness in multiple species.

A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus

The paper compares a reduced-genome Rhodopseudomonas strain to others, finding it retains core metabolic versatility but lacks genes for high-affinity transport and biodegradation.

Defined synthetic microbial communities colonize and benefit field-grown sorghum

This study demonstrates that a defined synthetic microbial community can enhance sorghum growth in both lab and field settings, despite losing diversity in native environments.

The SAGE genetic toolkit enables highly efficient, iterative site-specific genome engineering in bacteria

The paper introduces SAGE, a genome engineering system for bacteria that enables efficient, iterative integration of DNA constructs without requiring selection.

A versatile platform strain for high-fidelity multiplex genome editing

The paper introduces a new bacterial recombineering strain, BioDesignER, with improved efficiency and fidelity for genome editing and engineered function control.

Self-destructive altruism in a synthetic developmental program enables complex feedstock utilization

The paper engineers a synthetic developmental gene network in E. coli that couples stochastic differentiation with programmed cell death to enable cooperative cellulose utilization, but also observes cheater phenotypes and models evolutionary escape.