Daniel M. Portik

The paper introduces MODIFI, a tool for detecting DNA modifications in metagenomes, and identifies ECE-host linkages in environmental and human samples.

This study improves metagenome-assembled genomes from human gut microbiota using long-read sequencing and novel assembly methods, yielding more high-quality MAGs and uncovering uncultured diversity.

The paper uses HiFi sequencing to identify hypermethylation outliers in a rare disease cohort, finding allele-specific loss of regulatory elements linked to disease.

The paper benchmarks taxonomic classification and profiling methods for long-read metagenomic datasets, finding long-read methods outperform short-read ones in precision and recall.

This paper compares short-read and long-read sequencing approaches for clinical microbiome analysis, finding that long-read methods offer higher taxonomic and functional resolution and better microbial genome recovery.

FrogCap provides a modular probe set for phylogenomics and population genetics in frogs, tested across multiple scales and showing improved probe design success.

SuperCRUNCH is a Python toolkit for assembling large phylogenetic datasets, efficiently generating supermatrices and population-level datasets from GenBank and other sequence sources.