David Giron-Villalobos

Metabolite co-variation networks reveal keystone functions and an emergent pathogen state in the human urobiome.

This paper uses metabolomics co-variation networks to analyze urobiome-pathogen interactions, identifying keystone species and emergent pathogen states in a synthetic urobiome model.

Cross-study metagenomics analysis reveals distinct microbial signatures of urinary tract infections

The paper analyzes cross-study metagenomics data to identify microbial signatures associated with urinary tract infections and their genomic variation.

mb-PHENIX: Diffusion and Supervised Uniform Manifold Approximation for denoising microbiota data

mb-PHENIX denoises microbiota data by combining diffusion and supervised UMAP, improving differential abundance analysis in sparse and noisy count matrices.

Diffusion on PCA-UMAP manifold captures a well-balance of local, global, and continuum structures to denoise single-cell RNA sequencing data

The paper introduces sc-PHENIX, an imputation method for scRNA-seq data that addresses over-smoothing issues in diffusion-based approaches by using PCA-UMAP initialization.