V. Dubinkina

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC

The paper introduces StrainPGC and MIDAS v3 to accurately estimate intraspecific microbial gene content variation in metagenomic data, outperforming existing methods and revealing functional diversity in gut microbiomes.

Modeling bottlenecks, modularity, and context-dependency in behavioral control

This study uses a simple neural network model to explore how information bottlenecks affect behavioral control, showing that modular connectivity improves efficiency but increases context-dependency.

Complementary resource preferences spontaneously emerge in diauxic microbial communities

This study develops a model of diauxic microbial communities and finds that complementary resource preferences emerge spontaneously during community assembly.

Ecology-guided prediction of cross-feeding interactions in the human gut microbiome

The paper predicts hundreds of new cross-feeding interactions in the human gut microbiome using an ecology-based computational method called GutCP, supported by genome annotation evidence.

Evidence for a multi-level trophic organization of the human gut microbiome

The paper models the human gut microbiome as a multi-level trophic system, predicting four trophic levels and their metabolic interactions, which align with observed fecal metabolomes.

Multistability and regime shifts in microbial communities explained by competition for essential nutrients

This study explains multistability and regime shifts in microbial communities through a resource-explicit model and game-theoretical methods, showing that nutrient stoichiometry and supply balance influence stability and diversity.

Multiple stable states in microbial communities explained by the stable marriage problem

The paper introduces a model based on the stable marriage problem to predict and control transitions between stable states in microbial communities.