Georgia Doing

TEAL-seq: Targeted Expression Analysis Sequencing

TEAL-seq enables sensitive, species-specific gene expression analysis in complex microbial communities using highly multiplexed probes and isothermal amplification.

E.PathDash, pathway activation analysis of publicly available pathogen gene expression data

E.PathDash provides a tool for analyzing gene expression data from pathogens, enabling rapid pathway activation analysis and reproducibility assessment across multiple studies.

CF-Seq, An Accessible Web Application for Rapid Re-Analysis of Cystic Fibrosis Pathogen RNA Sequencing Studies

CF-Seq provides a web tool for re-analyzing CF pathogen RNA-seq data, enabling efficient filtering, visualization, and hypothesis generation across multiple studies.

Compendium-wide analysis of P. aeruginosa core and accessory genes reveal more nuanced transcriptional patterns

The paper analyzes transcriptional patterns of core and accessory genes in P. aeruginosa strains using a transcriptome compendium, revealing stable core gene expression patterns across strains.

Generative neural networks separate common and specific transcriptional responses

This paper introduces SOPHIE, a method using generative neural networks to distinguish common from specific transcriptional responses across datasets.

Correcting for experiment-specific variability in expression compendia can remove underlying signals

The paper simulates gene expression compendia to show that technical variability masks biological signals, but correction methods help when few experiments are combined, while more experiments make detection easier without correction.

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

PathCORE-T identifies and visualizes globally co-occurring pathways across transcriptomic datasets by analyzing features from machine learning models.

Unsupervised extraction of stable expression signatures from public compendia with eADAGE

The paper introduces eADAGE, an ensemble method to extract stable expression signatures from public data, revealing a phosphate starvation response in Pseudomonas aeruginosa controlled by PhoB and requiring KinB.