Rodolfo Brizola Toscan

PHI: A Galaxy-based workflow for reproducible prophage-host interaction analysis and standardized viral-genomics reporting

PHI is a Galaxy-based workflow that automates prophage-host interaction analysis and generates standardized reports, detecting 41 prophages across 14 hosts in a mock community.

Antimicrobial Resistance in Diverse Urban Microbiomes: Uncovering Patterns and Predictive Markers

This study analyzes AMR in urban microbiomes using metagenomic data, finding that AMR++ and Bowtie are effective for detecting AMR genes and that MGEs significantly impact resistome modeling.

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery

The paper simulates microbial communities to show sequencing depth and false positives significantly affect metagenome-assembled genome recovery accuracy.

CAMP: A modular metagenomics analysis system for integrated multi-step data exploration

CAMP provides a modular metagenomics analysis system that enables scalable, extensible workflows with integrated data visualization and reporting.

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

MuDoGeR simplifies genome recovery from metagenomes for non-experts, demonstrating effectiveness across various sample sizes.

Recovery of 447 Eukaryotic bins reveals major challenges for Eukaryote genome reconstruction from metagenomes.

The paper recovers 447 eukaryotic bins from metagenomes, highlighting challenges in genome reconstruction and the need for improved methods and reference genomes.

PredicTF: a tool to predict bacterial transcription factors in complex microbial communities.

PredicTF predicts bacterial transcription factors in microbial communities using genomic and metagenomic data from environmental isolates and anammox bioreactors.