Valeria Souza

Running against the clock: describing microbial diversity in an extremely endangered microbial oasis in the Chihuahuan desert

The paper investigates microbial connectivity and diversity loss in the Cuatro Cienegas Basin, finding core microbial genera and declining diversity linked to groundwater overexploitation.

Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Cienegas Basin, Mexico

The paper evaluates virus-host prediction tools on a dataset of 1,046 pairs and applies the best-performing tools to a metagenomic dataset from the Cuatro Cienegas Basin, finding that alignment-free and alignment-based methods agree best when analyzing diverse viral communities.

MicNet Toolbox: visualizing and deconstructing a microbial network

The paper introduces MicNet Toolbox, a python tool for visualizing microbial communities and analyzing co-occurrence networks using UMAP, HDBSCAN, and an enhanced SparCC algorithm.

MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle

MEBS evaluates (meta)genomic datasets to infer metabolic capabilities, particularly for the sulfur cycle, using entropy-based scoring and Pfam domains.

A new multi-genomic approach for the study of biogeochemical cycles at global scale: the molecular reconstruction of the sulfur cycle

The paper introduces a method to analyze the sulfur cycle using genomic data, producing a sulfur score that classifies microorganisms and identifies key environments.