Luis Pedro Coelho

The paper compares ARG detection pipelines and finds large discrepancies in reported ARG counts and composition across different habitats.

The paper uses long-read metagenomic sequencing to analyze urban soil samples, revealing novel microbial lineages and extensive functional diversity.

The paper uses long-read metagenomics to analyze pet dog gut microbiomes, generating high-quality MAGs and identifying antimicrobial resistance elements in a Shanghai cohort.

AEMB improves metagenomic binning efficiency by reducing computational demands while maintaining binning accuracy.

The paper quantifies discoverable bacterial and archaeal diversity in metagenomes, finding many novel phyla and genera hidden in current data.

The paper constructs a global microbial small ORFs catalogue and identifies a tool for annotating small proteins in microbial genomes.

The paper quantifies plankton community structure globally, revealing inverted biomass pyramids dominated by gelatinous organisms and predicting future shifts in oceanic carbon cycles.

SemiBin2 improves metagenomic binning by using self-supervised learning, outperforming previous methods in both short- and long-read sequencing.

metaMIC identifies and corrects misassemblies in metagenomic assemblies, improving downstream scaffolding and binning results.

SemiBin improves metagenomic binning by integrating reference genomes with semi-supervised deep learning, producing higher-quality bins with greater taxonomic diversity in simulated and real datasets.

GUNC detects and quantifies chimerism in prokaryotic genomes by analyzing contig lineage homogeneity, improving genome quality.

EXPERT uses transfer learning to improve microbial source tracking, showing better efficiency and accuracy in tracking gut microbiome changes in infants and colorectal cancer patients.

MACREL identifies high-quality antimicrobial peptide candidates from genomes and metagenomes using a novel set of peptide features and classifiers.

The paper analyzes pan-genomes of 155 prokaryotic species to assess how environmental and phylogenetic factors influence strain diversity and pan-genome features.

NG-meta-profiler is a fast metagenome profiler using NGLess, offering reproducibility and customization over existing tools.