Article

PathoFact 2.0: An Integrative Pipeline for Predicting Antimicrobial Resistance Genes, Virulence Factors, Toxins and Biosynthetic Gene Clusters in Metagenomes

2024-12-11

Abstract excerpt

<h4>Summary</h4> Antimicrobial resistance genes (ARGs) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections. PathoFact, a bioinformatics pipeline introduced in 2021, provides insights into ARGs, VFs, and bacterial toxins from metagenomic data. However, recent advancements in bioinformatics highlight the need for an updated version of PathoFact. We...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 72076693-dc86-5440-aef8-53a0d1120e15
DOI: 10.1101/2024.12.09.627531

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

PathoFact 2.0: An Integrative Pipeline for Predicting Antimicrobial Resistance Genes, Virulence Factors, Toxins and Biosynthetic Gene Clusters in MetagenomesDOI 10.1101/2024.12.09.627531Read

PathoFact: A pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic dataSemantic proximity Read

HyperVR–A hybrid prediction framework for virulence factors and antibiotic resistance genes in microbial dataSemantic proximity Read

Accessory genes define species-specific pathways to antibiotic resistanceSemantic proximity Read

An omics-based framework for assessing the health risk of antimicrobial resistance genesSemantic proximity Read

Shortest Unique Representative Hidden Markov Model (SurHMM) for Detecting Protein Toxins, Virulence Factors and Antibiotic Resistance GenesSemantic proximity Read

Predicting the secondary metabolic potential of microbiomes from marker genes using PSMPASemantic proximity Read

Sequencing methods to study the microbiome with antibiotic resistance genes in patients with pulmonary infectionsSemantic proximity Read

ARMOR (Antibiotic Resistance Modelling through Omics and Resistance-gene analysis)Semantic proximity Read

Phylogenomics, Epigenomics, Virulome, and Mobilome of Gram-negative Bacteria Co-resistant to Carbapenems and Polymyxins: A One-Health Systematic Review and Meta-analysesSemantic proximity Read

BIOTIA-DX RESISTANCE Achieved the Best Antimicrobial Resistance Phenotype Prediction Accuracy at CAMDA 2026Semantic proximity Read

A systematic analysis of machine learning pipelines for robust antimicrobial resistance predictionSemantic proximity Read

The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communitiesSemantic proximity Read