James Abbott

Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interaction

The paper evaluates sampling methods for root exudates and rhizosphere microbiota in barley, finding comparable microbiota and exudation patterns across approaches.

Regulatory Rewiring Drives Intraspecies Competition in Bacillus subtilis

This study shows that disrupting quorum-sensing pathways in Bacillus subtilis provides a competitive advantage by increasing growth rate, with such mutations found in ~16% of isolates.

Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants

The paper identifies Acinetobacter sp. as a dominant bacterium in tomato plant microbiota and shows its functional role in nutrient mobilization and stress adaptation, while decoupling its presence from antimicrobial resistance genes.

Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays

This paper introduces DecoDen, a method that learns shared chromatin landscapes and de-noises histone modification assays across multiple tissues.

BugBuilder - An Automated Microbial Genome Assembly andAnalysis Pipeline

BugBuilder automates microbial genome assembly and annotation, producing outputs for database submission or downstream finishing.