Shiraz Ali Shah

T7 DNA polymerase treatment improves quantitative sequencing of both double-stranded and single-stranded DNA viruses

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 enables strain-level quantification of de novo MAGs

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

Genome binning of viral entities from bulk 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.

Large-scale association analyses identify host factors influencing human gut microbiome composition

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

CRISPRCasTyper: An automated tool for the identification, annotation and classification of CRISPR-Cas loci

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.

CRISPRCasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems

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.

Conserved accessory proteins encoded with archaeal and bacterial Type III CRISPR-Cas gene cassettes that may specifically modulate, complement or extend interference activity

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