Germán Plata

Niche dimensionality drives microbial community structure

The paper infers microbial niche dimensionality from abundance data and shows it correlates with environmental complexity, competition, and biodiversity in human gut microbiomes.

Percolation and lifestyle transition in microbial metabolism

The paper identifies a percolation-like transition in bacterial metabolic networks that correlates with lifestyle differences between obligate symbionts and free-living generalists.

Designing host-associated microbiomes using the consumer/resource model

This paper introduces a generative model based on the consumer/resource framework to design host-associated microbiomes that correspond to desired host phenotypes and vice versa.

Functional optimization in distinct tissues and conditions constrains the rate of protein evolution

The paper shows that protein evolution rates are inversely related to functional optimality and expression levels across multiple organisms and tissues.

SMbiot: A Shared Latent Model for Microbiomes and their Hosts

SMbiot identifies low-dimensional latent variables that capture host-microbiome associations and predicts missing metadata or community compositions.

SiGMoiD: A super-statistical generative model for binary data

SiGMoiD is a generative model for binary data that infers constraints from data and handles large variable counts, enabling clustering and reduced dimensionality.