Timothy J. Donohue

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in a Biological Nutrient Removal Plant Operated at Hamptons Road Sanitation District (HRSD) with High and Low Dissolved Oxygen Conditions

The paper analyzes metagenomes and metagenome-assembled genomes from microbial communities in a wastewater treatment plant under varying dissolved oxygen conditions to understand microbial adaptation to low-DO environments.

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in a Biological Nutrient Removal Plant Operated at Los Angeles County Sanitation District (LACSD) with High and Low Dissolved Oxygen Conditions

The paper analyzes metagenomes and MAGs from a wastewater treatment plant under varying DO conditions to study microbial adaptation to energy-efficient processes.

A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

The paper introduces MuRCiS, a CRISPRi-Seq method to identify gene combinations critical for virulence in L. pneumophila, finding that lpg2888 and lpg3000 have redundant roles in macrophages, while lpg3000 is essential in amoebae.

Rewiring the specificity of extra-cytoplasmic function sigma factors

The paper deciphers the DNA-specificity code of ECF σ factors to predict their regulons and reveals their varied regulatory roles in bacterial gene regulation.

Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome

The paper integrates metagenomic, metatranscriptomic, and thermodynamic analyses to predict and characterize the metabolic network of an anaerobic microbiome producing medium-chain fatty acids from renewable feedstock.