Nicola Vitulo

Gempipe: a tool for drafting, curating and analyzing pan and multi-strain genome-scale metabolic models.

Gempipe improves multi-strain genome-scale metabolic model reconstruction by combining reference and reference-free methods, enhancing accuracy and enabling strain-specific metabolic analysis.

An improved reference of the grapevine genome supports reasserting the origin of the PN40024 highly-homozygous genotype

The paper improves the grapevine genome reference PN40024.v4 using long-read sequencing, enhancing continuity, haplotype resolution, and gene annotation.

MetaPhage: an automated pipeline for analyzing, annotating, and classifying bacteriophages in metagenomics sequencing data.

MetaPhage is a pipeline that automates the analysis, annotation, and classification of bacteriophages in metagenomics data, providing a comprehensive report and interactive visualization.

Assessment of statistical methods from single cell, bulk RNA-seq and metagenomics applied to microbiome data

The paper benchmarks statistical methods for microbiome data against RNA-seq methods, finding that univariate RNA-seq methods perform as well as microbiome-specific methods.