Riccardo Vicedomini

This study evaluates Sourmash's ability to profile microbial strains from long-read metagenomes, showing accurate gene content recovery and abundance estimation.

This study combines HiFi long-read and short-read sequencing to improve MAG recovery and binning accuracy in soil microbiomes.

MADRe improves strain-level metagenomic classification by combining assembly-driven database reduction with probabilistic read mapping, achieving higher precision and fewer false positives than existing tools.

Mapler evaluates Hi-Fi long read metagenome assemblies, providing metrics to assess quality and identify bottlenecks in genome reconstruction.

decOM improves microbial source tracking in ancient oral metagenomes by using k-mer matrices, outperforming existing methods in accuracy.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

The paper identifies 50 genes with copy number variation in Neandertal, Denisovan, and Early Sapiens genomes, suggesting dietary adaptations related to lipid and carbohydrate metabolism.

Strainberry uses long-read data to separate microbial strains in low-complexity metagenomes, achieving high accuracy and additional genomic material in real datasets.

ProfileView uses probabilistic models to classify protein sequences and resolve functional diversity across different families, outperforming existing methods.