Jonathan J. Silberg

The paper demonstrates how to use orthogonal trans-splicing ribozymes to store and report on multiple plasmid-encoded traits in microbial communities using RNA barcoding.

The paper evaluates how toxin-based biocontainment systems affect horizontal gene transfer in a wastewater microbiome using orthogonal catalytic RNA to track plasmid host range and persistence.

This paper develops ROSEATE, a model predicting bacterial optimal growth temperatures using protein structural features from a single gene, showing high accuracy and phylogenetic generalizability.

The paper demonstrates how domain insertion can create sulfite reductases with ligand-dependent activity, showing enhanced cellular activity in response to an endocrine disruptor.

The paper improves an RNA barcoding technology for tracking gene transfer in microbiomes by enhancing signal strength and modularity.

The paper introduces Ribodesigner, a tool to design catalytic RNAs that selectively barcode specific taxonomic groups, demonstrating increased selectivity over broad host range designs.

The paper introduces BiCASP, a high-throughput platform for screening electroactive microbes, enabling rapid and reproducible analysis of extracellular electron transfer.

This study examines how changes in matric and osmotic potential affect the transcription of Variovorax beijingensis, finding distinct but overlapping gene expression responses to these water potential shifts.

The paper uses a synthetic ribozyme to detect phage-host interactions in microbial communities through 16S rRNA sequencing, identifying Aeromonadales as a novel host for phage P1.

The paper uses synthetic RNA to store and detect information in microbial communities through rRNA sequencing, revealing differences in information storage across variants.

The paper shows how fusing Fd fragments to nanobodies and antigens can regulate electron transfer, with fusion order affecting functionality.

The paper identifies synonymous mutations in the AAV Rep gene that enhance genome packaging efficiency by affecting Rep-DNA interactions.

This paper introduces a ribozyme-mediated gene-fragment complementation system to report DNA transfer in soil by detecting methyl halides produced through conjugation events.

This paper describes an interdisciplinary graduate training program that improved teamwork confidence, particularly among women in STEM fields.

This paper develops recombinase-memory biosensors to record analyte detection in DNA over long durations, demonstrating their use in wastewater isolates.

The paper demonstrates the use of methyl bromide as a synthetic signaling molecule in a model soil consortium to report on gene expression and environmental conditions.

The paper develops a living bioelectronic sensor using engineered E. coli to detect contaminants in real-time with high sensitivity.

This study demonstrates that gas-reporting biosensors can detect gene expression in environmental soil matrices with minimal perturbation by optimizing hydration and biosensor titer.

This study identifies key residues in MtrA that influence extracellular electron transfer by systematically inserting peptides and analyzing their impact on respiration efficiency.

The paper develops artificial soils to study how individual abiotic factors affect microbial growth and signaling, finding that soil texture, mineralogy, and pH have additive effects while organic matter behaves emergently.

This study uses homologous recombination to create ferredoxin chimeras, revealing how thermostability and midpoint potential are inherited differently.

The paper introduces a split methyl halide transferase (sMHT) AND gate that reports post-translational reactions by synthesizing an indicator gas, enabling monitoring of microbial interactions in complex environments.

This paper designs chemical-dependent protein switches to control intracellular electron transfer by integrating ligand-binding domains with ferredoxin proteins.