Andrew Freiburger

The ModelSEED Biochemistry Database, 2026 update: grading multi-source thermodynamics

The paper updates the ModelSEED Biochemistry Database with expanded compounds and reactions, integrating multi-source thermodynamic data and grading reaction reliability.

Diet outperforms microbial transplant to drive microbiome recovery post-antibiotics

This study shows that a regular chow diet, not microbial transplant, enables rapid gut microbiome recovery after antibiotics in mice, and that diet is essential for effective fecal microbiota transplant.

Mapping the soil microbiome functions shaping wetland methane emissions

The paper maps soil microbiome functions in wetlands to understand methane emissions by analyzing microbial communities and gene expression across spatial and temporal gradients.

ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction

ModelSEED v2 improves genome-scale metabolic model reconstruction with enhanced energy metabolism and better pathway curation, leading to more accurate and comprehensive models.

Information- and Communication-Centric Approach in Cell Metabolism for Analyzing Behavior of Microbial Communities

The paper develops a community mutual information model to quantify information flow in microbial communities and demonstrates its application using simulated ecosystems.

A Molecular Communication model for cellular metabolism

The paper develops a molecular communication model integrating metabolic modeling and information theory to analyze how environmental perturbations affect cellular metabolism.

A microbial community growth model for dynamic phenotype predictions

This paper introduces CommPhitting, a dynamic model that predicts microbial community phenotype abundances and growth kinetics using experimental data and optimization.