Brian C. DeFelice

The paper tracks lineage evolution and transmission of Bacteroides thetaiotaomicron across hosts and ecological scales using genomic barcoding and whole-genome sequencing.

This paper develops a method for direct electrochemical cortisol detection using a defect-engineered graphene interface and transition-resolved interrogation, achieving sensitive and selective detection in biological fluids.

The paper presents a multimodal perturbation atlas using CRISPR knockouts in A549 cells, combining microscopy, phase imaging, and scRNA-seq to assess phenotypic resolution.

The paper shows that modifying microbial community composition, specifically overexpressing bile acid metabolic genes in Lactobacillus strains, can alter bile acid pool size and composition in mice.

The paper uses a single-strain dropout screen in a defined microbial community to show how removing specific strains affects community composition and metabolic output.

This study uses phage-based manipulation to reveal ecological interactions in gut microbiomes by targeting Escherichia fergusonii and analyzing its role in community dynamics.

The paper shows that nutrient competition drives changes in gut microbiome composition under drug perturbations, with implications for predicting and mitigating drug side effects.

This study identifies lactic acid from gut microbes as a key factor improving Drosophila survival during starvation by enhancing oxidative phosphorylation.

This study shows how initial population size and resource competition shape gut microbial community coalescence, with dose-dependent effects persisting even after many generations.

The paper maps subcellular localization of human proteins and shows proteome remodeling during viral infection by combining organelle immuno-capture with mass spectrometry.

Rapid QC-MS provides an automated dashboard for real-time quality control of LC-MS/MS data, improving efficiency and accuracy in untargeted workflows.

This study characterizes transcriptomic and metabolomic profiles in human urine, identifying distinct cell type repertoires and metabolic signals compared to plasma.

This paper uses evolutionary genomics to identify host metabolic pathways critical for intracellular bacterial survival, validating them through in vitro assays and metabolomics.