Justin P. Shaffer

The paper models microbial community assembly dynamics in Barrett's esophagus and esophageal adenocarcinoma, finding neutral dynamics in normal tissue and BE but not EAC, with H. pylori showing non-neutral behavior in BE non-cancer outcomes.

This paper introduces OGUs, a metagenome analysis method that uses sequence alignment hits to reference genomes for community analysis, showing better performance in predicting biological traits than taxonomic or 16S rRNA methods.

This paper expands the interpretability of human metabolomes by using food-based annotations, increasing the fraction of molecular features understood 7-fold.

The paper introduces a low-cost, high-accuracy method for generating long-range sequencing data using short-read NGS systems, enabling de novo genome assembly and haplotype phasing with minimal DNA input.