Faramarz Valafar

Hybran combines reference-based and ab initio methods to annotate prokaryotic genomes, improving accuracy by leveraging conserved features and filling gaps with predictions.

The paper evaluates syntenic block detection methods and their impact on rearrangement phylogeny using Mycobacterium tuberculosis genomes, finding that method choice affects results, especially in low-support branches.

The paper identifies rare alternative resistance markers in M. tuberculosis using gene-wise genome-wide association, uncovering novel associations with second-line injectable drug resistance.

The paper updates functional annotations for Mycobacterium tuberculosis genes using literature curation and structural modeling, identifying resistance, metabolic, and virulence genes.

The paper identifies Illumina sequencing biases in M. tuberculosis genomes across seven workflows, revealing blind spots and proposing strategies to mitigate them.

PBHoover and CigarRoller improve haploid variant calling on Pacific Biosciences data, enabling sensitive detection of subpopulations in clinical isolates.

This study analyzes 14 novel mutations in M. tuberculosis KatG using structural models to identify how they restrict access channels to the catalytic heme, potentially causing isoniazid resistance.

The paper assembles a high-quality H37Ra genome using SMRT sequencing, revealing fewer variants than previously thought and challenging prior conclusions about virulence in Mycobacterium tuberculosis.