Shiraz Ali Shah

The paper compares DNA preparation methods for virome sequencing, finding that T7 DNA polymerase treatment improves representation of both ssDNA and dsDNA viruses compared to MDA or xGen kit.

MAGinator quantifies strain-level abundance of metagenome-assembled genomes and infers their functional and phylogenetic profiles from shotgun metagenomics data.

The paper develops PHAMB, a method to bin viral genomes from bulk metagenomics data, and applies it to the HMP2 cohort to recover viral genomes and explore viral-host interactions.

The paper identifies 31 host genetic loci influencing gut microbiome composition through GWAS and suggests causal effects in inflammatory diseases.

CRISPRCasTyper is a tool that identifies and classifies CRISPR-Cas loci in prokaryotic sequences using machine learning, achieving high accuracy in subtyping and handling fragmented data.

The paper introduces a machine learning approach to identify and classify CRISPR-Cas systems by combining regression and classification models to improve protein cascade quality and subtype prediction.

The paper identifies 39 new Type III CRISPR-Cas associated gene families using comparative genomics and presents them in an online database.