Antônio Pedro Camargo

The paper analyzes CRISPR spacers from metagenomic data to reveal patterns of CRISPR targeting across Earth's biomes, identifying selection pressures and non-host phage interactions.

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

The paper analyzes the gut virome in mother-infant pairs to identify factors influencing its development and persistence, finding that delivery mode and breastmilk shape the infant virome and that viral diversity is linked to food allergies.

The paper identifies conjugative megaplasmids in the human gut microbiome that can disseminate prophage genomes across bacterial lineages, explaining their wide distribution.

The paper identifies millions of new protein families from global metagenomic data, expanding the known repertoire of protein families and revealing potential novel functions.

The paper presents a global virome atlas, UHGV, and identifies genomic factors influencing phage-host interactions.

The paper identifies Jug phages as prevalent in human and animal gut microbiomes, showing high transcription activity and potential ecological significance.

The paper compares sequence search tools for detecting CRISPR spacer-target interactions and finds significant differences in their performance.

The paper uses protein structure prediction to analyze dark matter proteins in Orthornavirae, identifying new domains and highlighting the prevalence of disordered regions.

Gaia enables context-aware protein sequence search in microbial genomes by integrating sequence, structure, and genomic context information, improving annotation of functionally related genes.

The Open MetaGenomic (OMG) corpus combines 3.1T base pairs and 3.3B protein coding sequences in mixed amino-acid and nucleotide format to pretrain the genomic language model gLM2.

The paper predicts stop codon reassignment in bacteriophage genomes to improve functional annotation, showing significant increases in gene length and coding density.

geNomad identifies and annotates mobile genetic elements in sequencing data, discovering millions of new viruses and plasmids in public metagenomes.

The paper investigates how plant-associated microbiomes in nutrient-poor Brazilian campos rupestres substrates contribute to nutrient cycling, revealing novel microbial populations and mechanisms for phosphorus and nitrogen turnover.

The paper expands the global RNA virome by five-fold, identifying new clades of RNA bacteriophages and revealing novel virus-host interactions.

CheckV estimates completeness of metagenome-assembled viral contigs against GenBank plus 76,262 metagenome-derived complete genomes and trims host flanks; 86.9% of IMG/VR contigs were low-quality.

RNAsamba predicts RNA coding potential using a deep-learning model that analyzes whole sequences and ORFs, outperforming existing methods across multiple organisms.