E. Borenstein

A Manifold-Based Framework for Studying the Dynamics of the Vaginal Microbiome

This study uses a manifold-based framework to analyze 8,026 vaginal samples and identify progression routes from healthy to bacterial vaginosis (BV) states, revealing key taxa and health indicators.

Microbial dispersion in the human gut through the lens of fecal transplant

The paper identifies microbial dependencies during gut colonization using fecal microbiota transplant data and shows agreement with in-vitro findings and population patterns.

A data-driven approach for predicting the impact of drugs on the human microbiome

This paper develops a data-driven framework to predict drug-microbiome interactions and shows it accurately predicts in vitro and in vivo outcomes, linking drug properties to microbiome dysbiosis and adverse effects.

MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data

MIMOSA2 identifies microbiome-metabolite relationships by integrating genomic and metabolomic data with metabolic models.

Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome

Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies

The paper evaluates the limitations of correlation-based analysis in microbiome-metabolome studies and introduces a framework to quantify microbial contributions to metabolite variation.

Metabolic Model-Based Analysis of the Emergence of Bacterial Cross-Feeding through Extensive Gene Loss

This study uses a simulation framework to show that metabolic cross-feeding can emerge spontaneously through genome reductive evolution in microbial communities.

The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition

The paper characterizes the distribution of type VI secretion systems in human gut microbiomes and links their presence to community composition changes.