Joseph T. Wade

Footprint-seq: a simple method to quantitatively map in vitro protein-DNA interactions on a genome-wide scale at high spatial resolution

Footprint-seq quantitatively maps protein-DNA interactions in vitro with high resolution and sensitivity, demonstrating its effectiveness for bacterial systems.

A plasmid-encoded H-NS protein selectively binds its own plasmid

This study shows that HppXCROD2, an H-NS homologue from plasmid pCROD2, selectively binds its own plasmid rather than the host chromosome or other plasmids.

RhlR quorum-sensing receptor ligand sensitivity regulates the differential expression of phenazine genes in Pseudomonas aeruginosa

This study identifies key residues in RhlR that determine ligand specificity and shows how ligand-driven gene regulation affects phenazine gene expression in Pseudomonas aeruginosa.

Identification of PAM Requirements for the Vibrio cholerae type I-E CRISPR-Cas System

The paper quantifies the effectiveness of all possible trinucleotide sequences as PAMs for the V. cholerae type I-E CRISPR-Cas system, identifying 15 functional PAMs out of 64.

Phase separation of mycobacterial Rho factor is associated with acid stress

This study shows that mycobacterial Rho forms liquid-liquid phase separation condensates under acid stress, which may help cells tolerate stress by terminating transcription.

Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli

The paper maps DNA binding of 139 E. coli TFs using ChIP-Seq and trains BoltzNet, a neural network that predicts TF binding energy from DNA sequence, validated with biophysical experiments.

A bacterial regulatory uORF senses multiple classes of ribosome-targeting antibiotics

The paper identifies a bacterial uORF, toiL, that responds to multiple classes of ribosome-targeting antibiotics by altering RNA secondary structure and regulating gene expression.

A Cryptic Prophage Transcription Factor Drives Phenotypic Changes via Host Gene Regulation

This study identifies DicC, a cryptic prophage transcription factor in E. coli, and shows it regulates hundreds of host genes, influencing bacterial phenotypes independently of other prophage genes.

Diversification of the Rho transcription termination factor in bacteria

This study analyzes Rho factor diversity in bacterial genomes, finding that most bacteria have atypical Rho structures with novel features and potential functional roles.

Widespread divergent transcription from prokaryotic promoters

The paper shows that prokaryotic promoters often drive divergent transcription due to symmetric elements and reciprocal stimulation between transcription start sites.

The evolutionary impact of Intragenic FliA Promoters in Proteobacteria

The paper investigates intragenic FliA promoters in E. coli, showing most are active but not conserved, with one exception that constrains gene evolution.