Erica Marie Hartmann

Benchmarking Microbiome Methods for Improved Metagenomic Sequencing of Lower Respiratory Tract Samples

The paper benchmarks microbiome methods to improve metagenomic sequencing of lower respiratory tract samples by optimizing DNA purification strategies.

Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes

This paper introduces METa assembly, a method to prepare functional metagenomic libraries from low biomass samples, enabling the discovery of novel antibiotic resistance genes.

Comparative Metagenomics of Soda Lakes and the Rumen Reveals Novel Microbial Lineages and Carbohydrate-active Enzyme Diversity

This study compares metagenomic data from soda lakes and the rumen to identify novel microbial lineages and carbohydrate-active enzyme diversity.

Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter?

The paper evaluates metagenomic analysis methods in simulated and real environmental data, finding that newer marker-based methods perform better at lower taxonomic levels.

A distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia

The paper examines alveolar T cell responses in SARS-CoV-2 pneumonia patients, finding that early interferon signaling and targeting of structural proteins correlate with better clinical outcomes.

A synthetic biology approach to assemble and reboot clinically-relevant Pseudomonas aeruginosa tailed phages

This paper develops a synthetic biology method to construct and reboot clinically-relevant Pseudomonas aeruginosa phages, demonstrating successful cloning, assembly, and rebooting in different bacterial strains.

Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper

GeneGrouper clusters gene clusters across taxa to identify functional or evolutionary patterns, revealing a novel pduN pseudogene in Salmonella enterica.