Migun Shakya

The paper characterizes global untreated wastewater microbial diversity using 1,344 metagenomes, revealing uncharacterized microbes and creating a public database for future research.

This study evaluates the impact of sequencing technologies and bioinformatic protocols on SARS-CoV-2 variant calling and introduces standardized parameters to improve pipeline consistency.

The paper introduces iSKIM, a method to detect intrahost mutations in SARS-CoV-2 raw sequencing data, revealing early emergence of mutations associated with variants of concern.

The paper uses a machine-learning classifier to distinguish gene transfer agents from viral homologs in alphaproteobacterial genomes, finding that many prophage predictions are likely GTAs.

Hi-C contacts assign assembled contigs to the cell they came from: 50 near-complete genomes among 252 clusters from one human fecal sample, plus plasmid-host links.